Merge pull request #2 from Sage-Bionetworks/simplify-output-binding

bump synapse client to 1.6.2.dev; modify CWL output binding

.gitignore

@@ -1 +1,2 @@
 datastore
+*.synapseConfig

Dockerfile

@@ -9,7 +9,7 @@ FROM ubuntu:16.04
 LABEL base.image="ubuntu:16.04"
 LABEL version="1"
 LABEL software="synapseclient"
-LABEL software.version="1.6.1"
+LABEL software.version="1.6.2.dev"
 LABEL description="Programmatic interface to Synapse services for Python"
 LABEL website="https://github.com/Sage-Bionetworks/synapsePythonClient"
 LABEL documentation="https://github.com/Sage-Bionetworks/synapsePythonClient"
@@ -20,8 +20,9 @@ LABEL tags="General"
 MAINTAINER James Eddy <[email protected]>
 
 # set version here to minimize need for edits below
-ENV VERSION=1.6.1
+# ENV VERSION=v1.6.2
 ENV BRANCH=develop
+ENV VERSION=6ba6a3ebde81fe8ed4d0c231ab42c613aa03334f
 
 # set up packages
 USER root
@@ -33,9 +34,9 @@ RUN apt-get update && \
 
 RUN git clone -b ${BRANCH} git://github.com/Sage-Bionetworks/synapsePythonClient.git && \
     cd synapsePythonClient && \
-    #git checkout v${VERSION} && \
+    git checkout ${VERSION} && \
     python setup.py develop
-    
+
 COPY bin/parse_config.py /usr/local/bin/
 COPY bin/synapse_get /usr/local/bin/
 RUN chmod a+x /usr/local/bin/synapse_get

Dockstore.cwl

@@ -17,8 +17,7 @@ dct:creator:
 
 requirements:
 - class: DockerRequirement
-  #dockerPull: quay.io/jaeddy/dockstore-tool-synapse-get:1.6.1--1
-  dockerPull: thomasvyu/synget
+  dockerPull: quay.io/jaeddy/dockstore-tool-synapse-get:1.6.2.dev--1
 
 inputs:
   config_file:
@@ -45,6 +44,6 @@ outputs:
       type: array
       items: File
     outputBinding:
-      glob: $(inputs.output_filename)
+      glob: "synapse_files/*"
 
 baseCommand: ["bash", "/usr/local/bin/synapse_get"]

bin/synapse_get

@@ -1,6 +1,7 @@
 #!/usr/bin/env bash
 set -euf -o pipefail
 
+# parse inputs and build command args
 CMD_ARGS=('synapse' 'get')
 while getopts "c:i:q:h" ARG; do
     case "$ARG" in
@@ -15,9 +16,17 @@ shift $(($OPTIND - 1))
 
 # parse credentials from config file
 CREDENTIALS=($(python /usr/local/bin/parse_config.py ${CONFIG}))
-# get file from Synapse
+
+# create temp folder to store files; add to command args
+SYN_DIR="synapse_files"
+mkdir $SYN_DIR
+CMD_ARGS=("${CMD_ARGS[@]}" '--downloadLocation' $SYN_DIR)
+
+# log in to Synapse
 synapse login -u ${CREDENTIALS[0]} -p ${CREDENTIALS[1]} --rememberMe
 
+# get file from Synapse
 COMMAND=$( IFS=' '; echo "${CMD_ARGS[*]}" );
 echo $COMMAND
-eval $COMMAND
+eval $COMMAND
+echo "Downloaded files: $(find ${SYN_DIR} -mindepth 1 -maxdepth 1)"

test.json → test_id.cwl.json

@@ -3,8 +3,5 @@
         "class": "File",
         "path": "test.synapseConfig"
     },
-    "synapse_id": "syn8556063",
-    "output_filename": [
-        "test.txt"
-    ]
+    "synapse_id": "syn8556063"
 }

test.query.json → test_query.cwl.json

@@ -3,9 +3,5 @@
         "class": "File",
         "path": "test.synapseConfig"
     },
-    "query": "select id from file where parentId == 'syn8507134'",
-    "output_filename": [
-        "test.txt",
-        "testingquery.txt"
-    ]
+    "query": "select id from file where parentId == 'syn8507134'"
 }