+
+
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
deleted file mode 100644
index 86dd0b42..00000000
--- a/CODE_OF_CONDUCT.md
+++ /dev/null
@@ -1,3 +0,0 @@
-# Contributor Covenant Code of Conduct
-
-We subscribe to [Sage Bionetwork's Code of Conduct](https://sagebionetworks.org/code-of-conduct/), which is adapted from the [Contributor Covenant](https://www.contributor-covenant.org/).
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
deleted file mode 100644
index d13c99d5..00000000
--- a/CONTRIBUTING.md
+++ /dev/null
@@ -1,166 +0,0 @@
-
-## Contributing
-
-We welcome all contributions! Please head to [issues](https://github.com/Sage-Bionetworks/Genie/issues) to either file any bugs/feature requests or find a task you want to assist with. Make sure to assign yourself the task if you decide to work on it.
-
-## Coding Style
-
-This package uses `flake8` - it's settings are described in [setup.cfg](setup.cfg). The code in this package is also automatically formatted by `black` for consistency.
-
-## The Development Life Cycle
-
-### Fork and clone this repository
-
-1. See the [Github docs](https://help.github.com/articles/fork-a-repo/) for how to make a copy (a fork) of a repository to your own Github account.
-1. Then, [clone the repository](https://help.github.com/articles/cloning-a-repository/) to your local machine so you can begin making changes.
-1. Add this repository as an [upstream remote](https://help.github.com/en/articles/configuring-a-remote-for-a-fork) on your local git repository so that you are able to fetch the latest commits.
-1. On your local machine make sure you have the latest version of the `develop` branch:
-
- ```
- git checkout develop
- git pull upstream develop
- ```
-
-### Install development dependencies
-
-This will install all the dependencies of the package including the active branch of `Genie`. We highly recommend that you leverage some form of python version management like [pyenv](https://github.com/pyenv/pyenv) or [anaconda](https://www.anaconda.com/products/individual). There are two ways you can install the dependencies for this package.
-
-#### pip
-This is the more traditional way of installing dependencies. Follow instructions [here](https://pip.pypa.io/en/stable/installation/) to learn how to install pip.
-
-```
-pip install -r requirements-dev.txt
-pip install -r requirements.txt
-```
-
-#### pipenv
-`pipenv` is a Python package manager. Learn more about [pipenv](https://pipenv.pypa.io/en/latest/) and how to install it.
-
-```
-# Coming soon
-```
-
-### Developing
-
-The GENIE project follows the standard [git flow](https://www.atlassian.com/git/tutorials/comparing-workflows/gitflow-workflow) development strategy.
-> To ensure the most fluid development, try not to push to your `develop` or `main` branch.
-
-1. (Assuming you have followed all 4 steps above in the "fork and clone this repository" section). Navigate to your cloned repository on your computer/server.
-1. Make sure your `develop` branch is up to date with the `Sage-Bionetworks/Genie` `develop` branch.
-
- ```
- cd {your-github-username}/Genie
- git checkout develop
- git pull upstream develop
- ```
-
-1. Create a feature branch which off the `develop` branch. If there is a GitHub/JIRA issue that you are addressing, name the branch after the issue with some more detail (like `{GH|JIRA}-123-add-some-new-feature`).
-
- ```
- git checkout develop
- git checkout -b JIRA-123-new-feature
- ```
-
-1. At this point, you have only created the branch locally, you need to push this to your fork on GitHub.
-
- ```
- git push --set-upstream origin JIRA-123-new-feature
- ```
-
- You should now be able to see the branch on GitHub. Make commits as you deem necessary. It helps to provide useful commit messages - a commit message saying 'Update' is a lot less helpful than saying 'Remove X parameter because it was unused'.
-
- ```
- git commit changed_file.txt -m "Remove X parameter because it was unused"
- git push
- ```
-
-1. (Make sure you have follow instructions in "Install development dependencies") Once you have made your additions or changes, make sure you write tests and run the test suite. More information on testing below.
-
- ```
- pytest ./test
- ```
-
-1. (Make sure you have follow instructions in "Install development dependencies") Make sure to run the auto python code formatter, black.
-
- ```
- black ./
- ```
-
-1. Once you have completed all the steps above, in Github, create a pull request from the feature branch of your fork to the `develop` branch of Sage-Bionetworks/Genie.
-
-> *A code maintainer must review and accept your pull request.* A code review ideally happens with both the contributor and the reviewer present, but is not strictly required for contributing. This can be performed remotely (e.g., Zoom, Hangout, or other video or phone conference).
-
-This package uses [semantic versioning](https://semver.org/) for releasing new versions. The version should be updated on the `develop` branch as changes are reviewed and merged in by a code maintainer. The version for the package is maintained in the [genie/__init__.py](genie/__init__.py) file. A github release should also occur every time `develop` is pushed into `main` and it should match the version for the package.
-
-### Testing
-
-#### Running test pipeline
-
-Make sure to run each of the [pipeline steps here](README.md#developing-locally) on the test pipeline and verify that your pipeline runs as expected. This is __not__ automatically run by Github Actions and have to be manually run.
-
-#### Running tests
-
-##### Tests in Python
-
-This package uses [`pytest`](https://pytest.org/en/latest/) to run tests. The test code is located in the [tests](./tests) subdirectory.
-
-Here's how to run the test suite:
-
-```shell
-pytest -vs tests/
-```
-
-Tests in Python are also run automatically by Github Actions on any pull request and are required to pass before merging.
-
-##### Tests in R
-
-This package uses [`testthat`](https://testthat.r-lib.org/) to run tests in R. The test code is located in the [testthat](./R/tests/testthat) subdirectory.
-
-Here's how to run the test suite:
-
-```shell
-Rscript -e "testthat::test_dir('R/tests/testthat/')"
-```
-
-#### Test Development
-
-Please add tests for new code. These might include unit tests (to test specific functionality of code that was added to support fixing the bug or feature), integration tests (to test that the feature is usable - e.g., it should have complete the expected behavior as reported in the feature request or bug report), or both.
-
-##### Mock Testing
-
-It is recommended to use the following style (see example below) for mock testing across this package:
-
-```python
-from unittest.mock import patch
-...
-patch.object(MODULE_NAME, "FUNCTION_TO_MOCK_NAME".return_value=SOME_RETURN_VALUE)
-```
-
-### Release Procedure (For Package Maintainers)
-
-Follow gitflow best practices as linked above.
-
-1. Always merge all new features into `develop` branch first (unless it is a documentation, readme, or github action patch into `main`)
-1. After initial features are ready in the `develop` branch, create a `release-X.X` branch (do not need to push this branch to remote) to prepare for the release.
- 1. update the `__version__` parameter in `genie/__init__.py`
-1. Merge `release-X.X` branch into `main` - Not by pull request!
-1. Create release tag (`v...`) and a brief message
-1. Push tag and change(s) from `main`
-1. Create a new release on the repo. Include release notes. Also include any known bugs for each release here. Wait for the CI/CD to finish.
-1. Merge `main` back into `develop`
-1. Push `develop`
-
-### Modifying Docker
-
-Follow this section when modifying the [Dockerfile](https://github.com/Sage-Bionetworks/Genie/blob/main/Dockerfile):
-
-1. Have your synapse authentication token handy
-1. ```docker build -f Dockerfile -t .```
-1. ```docker run --rm -it -e SYNAPSE_AUTH_TOKEN=$YOUR_SYNAPSE_TOKEN ```
-1. Run [test code](README.md#developing-locally) relevant to the dockerfile changes to make sure changes are present and working
-1. Once changes are tested, follow [genie contributing guidelines](#developing) for adding it to the repo
-1. Once deployed to main, make sure docker image was successfully deployed remotely (our docker image gets automatically deployed) [here](https://hub.docker.com/repository/docker/sagebionetworks/genie/builds)
-
-#### Dockerhub
-
-This repository does not use github actions to push docker images. By adding the `sagebiodockerhub` github user as an Admin to this GitHub repository, we can configure an automated build in DockerHub. You can view the builds [here](https://hub.docker.com/repository/docker/sagebionetworks/genie/builds). To get admin access to the DockerHub repository, ask Sage IT to be added to the `genieadmin` DockerHub team.
diff --git a/Dockerfile b/Dockerfile
deleted file mode 100644
index 3d9638f1..00000000
--- a/Dockerfile
+++ /dev/null
@@ -1,89 +0,0 @@
-FROM ubuntu:focal-20220113
-ENV DEBIAN_FRONTEND=noninteractive
-
-# Must install this because gpg not installed
-RUN apt-get update && \
- apt-get install -y --no-install-recommends \
- software-properties-common \
- dirmngr \
- wget && \
- apt-get clean && \
- rm -rf /var/lib/apt/lists/*
-
-#RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
-SHELL ["/bin/bash", "-o", "pipefail", "-c"]
-RUN wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
-RUN add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
-
-# General sys dependencies
-RUN apt-get update && apt-get install -y --allow-unauthenticated --no-install-recommends \
- bedtools \
- dos2unix \
- python3 \
- python3-pip \
- python3-dev \
- git \
- r-base \
- r-base-dev \
- cmake \
- curl \
- # synapser client dependencies
- dpkg-dev \
- zlib1g-dev \
- libssl-dev \
- libffi-dev \
- libcurl4-openssl-dev \
- # VariantAnnotation dependency
- libxml2-dev \
- # Supports data guide creation
- texlive \
- texinfo \
- # texlive-generic-recommended \
- texlive-latex-extra \
- # genome nexus
- openjdk-11-jre \
- # This is for reticulate
- python3.8-venv && \
- apt-get clean && \
- rm -rf /var/lib/apt/lists/*
-
-#install pandoc 1.19.2.1 (dashboard use)
-# RUN wget https://github.com/jgm/pandoc/releases/download/1.19.2.1/pandoc-1.19.2.1-1-amd64.deb
-# RUN dpkg -i pandoc-1.19.2.1-1-amd64.deb
-RUN wget https://github.com/jgm/pandoc/releases/download/3.0.1/pandoc-3.0.1-1-amd64.deb
-RUN dpkg -i pandoc-3.0.1-1-amd64.deb
-
-
-
-# Only copy most recent changes in code are always installed
-# Do not build from local computer
-WORKDIR /root/Genie
-# Copy install packages first, because R installation takes
-# a long time and unless there are changes to the actual
-# R packages used. So the only files copied over are
-# renv/ renv.lock and the installation R script
-COPY R/install_packages.R R/install_packages.R
-COPY renv/ renv/
-COPY renv.lock renv.lock
-RUN Rscript R/install_packages.R
-
-ENV CRYPTOGRAPHY_DONT_BUILD_RUST=true
-COPY . .
-RUN echo "source('renv/activate.R')" >> .Rprofile
-
-# TODO Must include R/ and templates/ within the
-# genie/ directory to use MANIFEST.in
-# For now, install using develop parameter so that
-# the package is called from the directory
-RUN pip3 install --no-cache-dir -r requirements.txt
-RUN python3 setup.py develop
-# RUN pip3 install --no-cache-dir .
-
-WORKDIR /root/
-# Must move this git clone to after the install of Genie,
-# because must update cbioportal
-RUN git clone https://github.com/cBioPortal/cbioportal.git -b v5.3.19
-RUN git clone https://github.com/Sage-Bionetworks/annotation-tools.git -b 0.0.5
-
-
-WORKDIR /root/Genie
diff --git a/LICENSE b/LICENSE
deleted file mode 100644
index 4c4bc201..00000000
--- a/LICENSE
+++ /dev/null
@@ -1,21 +0,0 @@
-MIT License
-
-Copyright (c) 2018 Sage Bionetworks
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
diff --git a/MANIFEST.in b/MANIFEST.in
deleted file mode 100644
index 29c2bd75..00000000
--- a/MANIFEST.in
+++ /dev/null
@@ -1,4 +0,0 @@
-# This file currently doesn't do anything because
-# R/ and templates/ isn't within the genie/ directory
-graft R/
-graft templates/
diff --git a/R/MAFinBED.R b/R/MAFinBED.R
deleted file mode 100644
index 7f8b39a3..00000000
--- a/R/MAFinBED.R
+++ /dev/null
@@ -1,186 +0,0 @@
-library(argparse)
-parser <- ArgumentParser()
-parser$add_argument("filepath", help = "Filepath to write variants")
-parser$add_argument("--testing", action = "store_true", help = "Use testing files")
-args <- parser$parse_args()
-testing <- args$testing
-filepath <- args$filepath
-
-
-# libraries
-library(synapser)
-#pyExec("syn.table_query_timeout=50000")
-library(VariantAnnotation)
-
-# args = commandArgs(trailingOnly=TRUE)
-# if (length(args) != 2) {
-# stop("Must supply a boolean value and a filepath to write variants not in bed")
-# }
-# SAGE login
-synLogin()
-#testing = as.logical(args[1])
-if (testing) {
- databaseSynIdMappingId = 'syn11600968'
-} else {
- databaseSynIdMappingId = 'syn10967259'
-}
-databaseSynIdMapping = synTableQuery(sprintf('select * from %s', databaseSynIdMappingId),
- includeRowIdAndRowVersion = F)
-databaseSynIdMappingDf = synapser::as.data.frame(databaseSynIdMapping)
-patientSynId = databaseSynIdMappingDf$Id[databaseSynIdMappingDf$Database == "patient"]
-sampleSynId = databaseSynIdMappingDf$Id[databaseSynIdMappingDf$Database == "sample"]
-bedSynId = databaseSynIdMappingDf$Id[databaseSynIdMappingDf$Database == "bed"]
-mafSynId = databaseSynIdMappingDf$Id[databaseSynIdMappingDf$Database == "vcf2maf"]
-assayInfoSynId = databaseSynIdMappingDf$Id[databaseSynIdMappingDf$Database == "assayinfo"]
-centerMappingSynId = databaseSynIdMappingDf$Id[databaseSynIdMappingDf$Database == "centerMapping"]
-
-centerMapping = synTableQuery(sprintf('select * from %s where release is true',
- centerMappingSynId),
- includeRowIdAndRowVersion = F)
-centerMappingDf = synapser::as.data.frame(centerMapping)
-process_centers = paste(centerMappingDf$center, collapse="','")
-# read aggregated clinical data from tables
-patient = synTableQuery(sprintf("SELECT * FROM %s where CENTER in ('%s')",
- patientSynId, process_centers),
- includeRowIdAndRowVersion = F)
-sample = synTableQuery(sprintf("SELECT * FROM %s where CENTER in ('%s')",
- sampleSynId, process_centers),
- includeRowIdAndRowVersion = F)
-
-patientData = synapser::as.data.frame(patient)
-sampleData = synapser::as.data.frame(sample)
-sampleData$AGE_AT_SEQ_REPORT_NUMERICAL <- NULL
-patientData$BIRTH_YEAR_NUMERICAL <- NULL
-patientData$CENTER <- NULL
-genieClinData <- merge.data.frame(patientData,
- sampleData,
- by = "PATIENT_ID")
-
-#EXCLUDE PHS-TRISEQ-V1 SAMPLES
-# genieClinData <- genieClinData[genieClinData$SEQ_ASSAY_ID != "PHS-TRISEQ-V1",]
-
-# read aggregated BED file data
-genieBed = synTableQuery(sprintf("SELECT * FROM %s where CENTER in ('%s')",
- bedSynId, process_centers),
- includeRowIdAndRowVersion = F)
-genieBedData = synapser::as.data.frame(genieBed)
-
-#Pad the bed file with the assay information
-assayInfo = synTableQuery(sprintf("SELECT * FROM %s where CENTER in ('%s')",
- assayInfoSynId, process_centers),
- includeRowIdAndRowVersion = F)
-assayInfoData = synapser::as.data.frame(assayInfo)
-for (seq_assay in unique(genieBedData$SEQ_ASSAY_ID)) {
- if (any(assayInfoData$SEQ_ASSAY_ID == seq_assay)) {
- genepadding = assayInfoData$gene_padding[assayInfoData$SEQ_ASSAY_ID == seq_assay]
- } else {
- genepadding = 10
- }
- starts = genieBedData$Start_Position[genieBedData$SEQ_ASSAY_ID == seq_assay]
- ends = genieBedData$End_Position[genieBedData$SEQ_ASSAY_ID == seq_assay]
- genieBedData$Start_Position[genieBedData$SEQ_ASSAY_ID == seq_assay] = starts - genepadding
- genieBedData$End_Position[genieBedData$SEQ_ASSAY_ID == seq_assay] = ends + genepadding
-}
-# read aggregated MAF file
-# FILTERED OUT COMMON VARIANTS HERE
-#genieMut = synTableQuery(sprintf('SELECT * FROM %s where FILTER <> "common_variant"', mafSynId))
-genieMut = synTableQuery(sprintf("SELECT * FROM %s where Center in ('%s') and Annotation_Status = 'SUCCESS'",
- mafSynId, process_centers))
-genieMutData = synapser::as.data.frame(genieMut)
-#Only use samples that exist in the clinical sample data pool
-genieMutData <- genieMutData[genieMutData$Tumor_Sample_Barcode %in% genieClinData$SAMPLE_ID,]
-print(nrow(genieMutData))
-
-
-originalCols = colnames(genieMutData)
-# records with count data that preclude a VAF estimate - set VAF to 100% (1/1, alt/depth) genieMutData$t_depth <- as.numeric(genieMutData$t_depth)
-genieMutData$t_depth <- as.numeric(genieMutData$t_depth)
-noVAF.idx = which((genieMutData$t_depth == 0) | is.na(genieMutData$t_depth))
-#keeps the order if factors exist
-#genieMutData$t_alt_count_num = as.numeric(levels(genieMutData$t_alt_count))[genieMutData$t_alt_count]
-genieMutData$t_alt_count_num = as.numeric(genieMutData$t_alt_count)
-genieMutData$t_alt_count_num[noVAF.idx] = 1
-genieMutData$t_depth_new = genieMutData$t_depth
-genieMutData$t_depth_new[noVAF.idx] = 1
-
-#genieMutData$t_depth_new[is.na(genieMutData$t_alt_count_num)] = 1
-#genieMutData$t_alt_count_num[is.na(genieMutData$t_alt_count_num)] = 1
-# get VRanges for all variants called in the MAF
-genieMutData$t_alt_count_num[is.na(genieMutData$Tumor_Seq_Allele2)] = NA
-
-mafVR = VRanges(seqnames = Rle(paste0("chr",genieMutData$Chromosome)),
- ranges = IRanges(start = genieMutData$Start_Position,
- end = genieMutData$End_Position),
- ref = genieMutData$Reference_Allele,
- # alt = genieMutData$Tumor_Seq_Allele2,
- altDepth = genieMutData$t_alt_count_num,
- # totalDepth = genieMutData$t_depth_new,
- sampleNames = genieMutData$Tumor_Sample_Barcode)
-seqlevels(mafVR) = sort(seqlevels(mafVR))
-
-# get GRanges for each bed
-bedGR = split(genieBedData, factor(genieBedData$SEQ_ASSAY_ID))
-bedGR = lapply(bedGR, function(x) {
- GR = GRanges(seqnames = Rle(paste0("chr",x$Chromosome)),
- ranges = IRanges(start = x$Start_Position, end = x$End_Position))
- seqlevels(GR) = sort(seqlevels(GR))
- return(GR)
-})
-
-# all inclusive list of samples should be from the clinical data file
-# therefore factor levels for Tumor_Sample_Barcode in the MAF should be set to that of SAMPLE_ID of clinical data table
-# check that no samples are listed in the MAF that are not listed in the clinical data file
-# reversing the order of the inputs would tell you which samples are submitted that have no entries (no mutations) in the MAF
-#if (length(setdiff(levels(genieMutData$Tumor_Sample_Barcode),levels(genieClinData$SAMPLE_ID)))==0) {
-# genieMutData$Tumor_Sample_Barcode = factor(genieMutData$Tumor_Sample_Barcode, levels=levels(genieClinData$SAMPLE_ID))
-#}
-
-# add factor to MAF and set to FALSE, forcing the variant to bed match for TRUE below to clear filter
-oldInBed = as.logical(genieMutData$inBED)
-genieMutData$inBED = FALSE
-# collect some stats in panStats and set inBED to TRUE if variant is in corresponding BED
-seq_assays = unique(genieClinData$SEQ_ASSAY_ID[!is.na(genieClinData$SEQ_ASSAY_ID)])
-panStats = data.frame()
-for (panelName in seq_assays) {
- print(panelName)
- samples.idx = which(genieClinData$SEQ_ASSAY_ID == panelName)
- panStats[panelName,"samples"] = length(samples.idx)
- samples.idx = which(genieMutData$Tumor_Sample_Barcode %in% genieClinData$SAMPLE_ID[samples.idx])
- panStats[panelName,"samples with calls"] = length(unique(genieMutData$Tumor_Sample_Barcode[samples.idx]))
- panStats[panelName,"variants calls"] = length(samples.idx)
- panStats[panelName,"unique variants calls"] = length(unique(mafVR[samples.idx]))
- if (length(samples.idx) > 0 && !is.null(bedGR[[panelName]])) {
- genieMutData$inBED[samples.idx] = mafVR[samples.idx] %over% bedGR[[panelName]]
- }
- panStats[panelName,"variants called out of BED"] = length(samples.idx[!genieMutData$inBED[samples.idx]])
- panStats[panelName,"unique variants called out of BED"] = length(unique(mafVR[samples.idx[!genieMutData$inBED[samples.idx]]]))
-}
-genieMutData$t_depth_new <- NULL
-genieMutData$t_alt_count_num <- NULL
-# Commented out below because of PFLM-4975
-#Compare old inBED with new inBED column
-#If there are differences, update only the diffs
-# updateMutData = genieMutData[genieMutData$inBED != oldInBed,]
-# if (nrow(updateMutData) > 0) {
-# #write.csv(updateMutData[c("ROW_ID","ROW_VERSION","inBED")],"update_inbed.csv",row.names = F)
-# #Need to chunk the upload
-
-# #it is an amazon problem, where amazon kills the connection while reading the csv from s3.
-# chunk = 100000
-# rows = 0
-# while (rows*chunk < nrow(updateMutData)) {
-# if ((rows + 1)* chunk > nrow(updateMutData)) {
-# to_update = updateMutData[((rows*chunk)+1):nrow(updateMutData),c("ROW_ID","ROW_VERSION","inBED")]
-# } else{
-# to_update = updateMutData[((rows*chunk)+1):((rows+1)*chunk),c("ROW_ID","ROW_VERSION","inBED")]
-# }
-# synStore(Table(mafSynId, to_update))
-# rows = rows+1
-# }
-# #synStore(Table(mafSynId, updateMutData[c("ROW_ID","ROW_VERSION","inBED")]))
-# #synStore(Table(mafSynId, "update_inbed.csv"))
-# }
-updateMutData = genieMutData[genieMutData$inBED == FALSE,
- c('Chromosome', 'Start_Position', 'End_Position',
- 'Reference_Allele', 'Tumor_Seq_Allele2', 'Tumor_Sample_Barcode', 'Center')]
-write.csv(updateMutData,filepath,row.names = F)
diff --git a/R/dashboard_markdown_generator.R b/R/dashboard_markdown_generator.R
deleted file mode 100644
index b3f2a488..00000000
--- a/R/dashboard_markdown_generator.R
+++ /dev/null
@@ -1,62 +0,0 @@
-#suppressPackageStartupMessages(library(synapserutils))
-suppressPackageStartupMessages(library(argparse))
-parser <- ArgumentParser()
-parser$add_argument("release",
- help = "Release version (ie. 5.3-consortium)")
-parser$add_argument("--template_path",
- help = "Path to dashboardTemplate.Rmd",
- default="dashboardTemplate.Rmd")
-parser$add_argument("--staging",
- action = "store_true",
- help = "Use staging files")
-parser$add_argument("--testing",
- action = "store_true",
- help = "Use testing files")
-
-args <- parser$parse_args()
-release <- args$release
-template_path <- args$template_path
-suppressPackageStartupMessages(library(synapser))
-suppressPackageStartupMessages(library(rmarkdown))
-
-synLogin()
-
-if (args$staging) {
- database_synid_mappingid = 'syn12094210'
-} else if (args$testing) {
- database_synid_mappingid = 'syn11600968'
-} else{
- database_synid_mappingid = 'syn10967259'
-}
-
-# For testing only
-# database_synid_mappingid = 'syn10967259'
-# genie_user=NULL
-# genie_pass=NULL
-# release = "9.3-consortium"
-# template_path = "genie/dashboardTemplate.Rmd"
-#
-
-
-rmarkdown_path = sprintf('%s.Rmd', release)
-file.copy(template_path, rmarkdown_path, overwrite = T)
-rmarkdown::render(rmarkdown_path,
- params = list("database_synid_mappingid" = database_synid_mappingid,
- "release" = release))
-# Obtain release folder
-database_synid_mapping = synTableQuery(sprintf('select * from %s',
- database_synid_mappingid))
-database_synid_mappingdf = as.data.frame(database_synid_mapping)
-release_folder_fileview_synid = database_synid_mappingdf$Id[
- database_synid_mappingdf$Database == "releaseFolder"
-]
-release_folder = synTableQuery(sprintf("select id from %s where name = '%s'",
- release_folder_fileview_synid, release))
-release_folder_synid = release_folder$asDataFrame()$id
-#Store the html file.
-html_path = sprintf('%s.html', release)
-release_html_ent = synStore(File(html_path,
- parentId = release_folder_synid))
-synStore(Wiki(markdown = sprintf("${preview?entityId=%s}",
- release_html_ent$properties$id),
- owner = release_folder_synid))
diff --git a/R/dashboard_template_functions.R b/R/dashboard_template_functions.R
deleted file mode 100644
index 0fe44323..00000000
--- a/R/dashboard_template_functions.R
+++ /dev/null
@@ -1,41 +0,0 @@
-# ---------------------------------------------------------------------------
-# Title: dashboard_template_functions.R
-# Description: This script contains helper functions used in
-# templates/dashboardTemplate.Rmd
-# ---------------------------------------------------------------------------
-
-#' This function gets the database to synapse id mapping table,
-#' maps the provided database_name to its synapse id and returns it
-#'
-#' @param database_name (str) database name in database
-#' to synapse id mapping table
-#' @param database_synid_mappingid (str) synapse id of the database
-#' to synapse id mapping table
-#'
-#' @return (str) synapse id of the mapped database name
-get_syn_id_from_mapped_database <- function(database_name, database_synid_mappingid){
- database_synid_mapping = synTableQuery(sprintf('select * from %s',
- database_synid_mappingid))
- database_synid_mappingdf = as.data.frame(database_synid_mapping)
- table_synid = database_synid_mappingdf$Id[database_synid_mappingdf$Database == database_name]
- return(table_synid)
-}
-
-#' This function creates a table of failed annotation counts by grouped columns
-#' @param maf_data (data.frame) input maf data frame
-#' @param group_by_cols (str vector) list of columns to create counts by
-#' @param counts_col_name (str) name to give to the counts column
-#'
-#' @return (data.frame) counts table
-get_failed_annotation_table_counts <- function(maf_data, group_by_cols, counts_col_name){
- table_counts <- table(maf_data[maf_data$Annotation_Status == "FAILED", group_by_cols])
-
- if (nrow(table_counts) == 0){
- counts_table <- data.frame(matrix(ncol = length(group_by_cols) + 1, nrow = 0))
- } else{
- counts_table <- as.data.frame(table_counts)
- }
- colnames(counts_table) <- c(group_by_cols, counts_col_name)
- counts_table <- counts_table[do.call(order, counts_table[group_by_cols]), ]
- return(counts_table)
-}
\ No newline at end of file
diff --git a/R/install_packages.R b/R/install_packages.R
deleted file mode 100644
index 33d1a2c1..00000000
--- a/R/install_packages.R
+++ /dev/null
@@ -1,11 +0,0 @@
-source("renv/activate.R")
-renv::restore()
-library(synapser)
-library(dplyr)
-library(argparse)
-library(UpSetR)
-library(rmarkdown)
-library(testthat)
-library(VariantAnnotation)
-library(xtable)
-library(ggpubr)
diff --git a/R/mergeCheck.R b/R/mergeCheck.R
deleted file mode 100644
index cbecb283..00000000
--- a/R/mergeCheck.R
+++ /dev/null
@@ -1,107 +0,0 @@
-# Do not use scientific notation
-options(scipen=999)
-library(argparse)
-parser <- ArgumentParser()
-parser$add_argument("--testing",
- action = "store_true",
- help = "Use testing files")
-args <- parser$parse_args()
-testing <- args$testing
-
-library(synapser)
-library(VariantAnnotation)
-
-get_working_dir <- function() {
- cmdArgs <- commandArgs(trailingOnly = FALSE)
- needle <- "--file="
- match <- grep(needle, cmdArgs)
- if (length(match) > 0) {
- # Rscript
- return(dirname(normalizePath(sub(needle, "", cmdArgs[match]))))
- } else {
- # 'source'd via R console
- return("./")
- }
-}
-working_dir = get_working_dir()
-source(file.path(working_dir, "mergecheck_functions.R"))
-# Run quick unit test to make sure that the function hasn't be changed
-source(file.path(working_dir, "test_flag_variants.R"))
-
-# login to synapse
-synLogin()
-# limits
-variant_limit = 100000
-tbl_size_limit = 500
-
-#testing = as.logical(args[1])
-if (testing) {
- databaseSynIdMappingId = 'syn11600968'
-} else {
- databaseSynIdMappingId = 'syn10967259'
-}
-databaseSynIdMapping = synTableQuery(sprintf('select * from %s', databaseSynIdMappingId),
- includeRowIdAndRowVersion = F)
-databaseSynIdMappingDf = synapser::as.data.frame(databaseSynIdMapping)
-sampleSynId = databaseSynIdMappingDf$Id[databaseSynIdMappingDf$Database == "sample"]
-mutationsInCisSynId =
- databaseSynIdMappingDf$Id[databaseSynIdMappingDf$Database == "mutationsInCis"]
-mafSynId = databaseSynIdMappingDf$Id[databaseSynIdMappingDf$Database == "vcf2maf"]
-
-centersTable = synTableQuery(sprintf('select distinct CENTER from %s', sampleSynId),
- includeRowIdAndRowVersion = F)
-centers = synapser::as.data.frame(centersTable)
-centers = centers$CENTER
-
-centerMappingSynId = databaseSynIdMappingDf$Id[databaseSynIdMappingDf$Database == "centerMapping"]
-centerMapping = synTableQuery(sprintf('select * from %s where release is true',
- centerMappingSynId),
- includeRowIdAndRowVersion = F)
-centerMappingDf = synapser::as.data.frame(centerMapping)
-centerMappingDf$mutationInCisFilter = as.character(centerMappingDf$mutationInCisFilter)
-# Have this here for now until the annotations are changed in the center mapping folder
-centerMappingDf$mutationInCisFilter[centerMappingDf$mutationInCisFilter == "TRUE"] = "ON"
-centerMappingDf$mutationInCisFilter[centerMappingDf$mutationInCisFilter == "FALSE"] = "OFF"
-
-# ON - Filter is on: TOSS SAMPLES
-# OFF - Filter is off: KEEP SAMPLES
-# FLAG - Filter is on, but don't toss samples: FLAG BUT KEEP SAMPLES
-
-for (center in centers) {
- print(center)
- # read aggregated clinical data
- clin_query_string = sprintf("select SAMPLE_ID from %s where CENTER = '%s'",
- sampleSynId, center)
- genieClinTable = synTableQuery(clin_query_string, includeRowIdAndRowVersion = F)
- genieClinData = synapser::as.data.frame(genieClinTable)
- maf_query_string = sprintf("select Tumor_Sample_Barcode, count(Tumor_Sample_Barcode) from %s where Center = '%s' group by Tumor_Sample_Barcode",
- mafSynId, center)
- mafSampleCountTable = synTableQuery(maf_query_string, includeRowIdAndRowVersion = F)
- mafSampleCount = synapser::as.data.frame(mafSampleCountTable)
- mafSampleCount =
- mafSampleCount[mafSampleCount$Tumor_Sample_Barcode %in% genieClinData$SAMPLE_ID,]
- total = 0
- splitBySamples = c()
- samplesToQuery = c()
- for (sample in mafSampleCount$Tumor_Sample_Barcode) {
- total = total + mafSampleCount[mafSampleCount$Tumor_Sample_Barcode == sample, "COUNT(Tumor_Sample_Barcode)"]
- samplesToQuery = c(sample,samplesToQuery)
- if (total > variant_limit || sample == mafSampleCount$Tumor_Sample_Barcode[nrow(mafSampleCount)]) {
- splitBySamples = c(splitBySamples, paste(samplesToQuery,collapse = "','"))
- total = 0
- samplesToQuery = c()
- }
- }
- for (querySamples in splitBySamples) {
- samplesToRun = unlist(strsplit(querySamples, "','"))
- # read aggregated MAF file
- genieMutTable = synTableQuery(sprintf("SELECT Center,Tumor_Sample_Barcode,Hugo_Symbol,HGVSp_Short,Variant_Classification,Chromosome,Start_Position,Reference_Allele,Tumor_Seq_Allele2,t_depth,t_alt_count,End_Position,Protein_position FROM %s where Tumor_Sample_Barcode in ('%s') and inBED is true and Annotation_Status = 'SUCCESS'",
- mafSynId, querySamples),
- includeRowIdAndRowVersion = F)
- #genieMutTable = synTableQuery(sprintf("SELECT Center,Tumor_Sample_Barcode,Hugo_Symbol,HGVSp_Short,Variant_Classification,Chromosome,Start_Position,Reference_Allele,Tumor_Seq_Allele2,t_depth,t_alt_count,End_Position,Protein_position FROM %s where Tumor_Sample_Barcode in ('%s')", mafSynId, querySamples),includeRowIdAndRowVersion=F)
-
- genieMutData = synapser::as.data.frame(genieMutTable)
- flag_variants_to_merge(genieMutData, genieClinData, samplesToRun, upload = TRUE)
- #write.csv(rbind(annotated_df[is.na(annotated_df$Flag),],new_rows), "Missing_variant_annotation.csv", row.names=F)
- }#FOR LOOP END FOR QUERY SAMPLES
-}
diff --git a/R/mergecheck_functions.R b/R/mergecheck_functions.R
deleted file mode 100644
index cdb681d2..00000000
--- a/R/mergecheck_functions.R
+++ /dev/null
@@ -1,175 +0,0 @@
-# Update mutation in cis table
-uploadToTable <- function(tbl, databaseSynId, subSetSamples, centerMappingDf) {
- # Old samples
- # filterCenters = centerMappingDf$center[centerMappingDf$mutationInCisFilter == TRUE]
- keepCenters = centerMappingDf$center[centerMappingDf$mutationInCisFilter == "OFF"]
- flagCenters = centerMappingDf$center[centerMappingDf$mutationInCisFilter == "FLAG"]
- query_string = sprintf("SELECT * FROM %s where Tumor_Sample_Barcode in ('%s')",
- databaseSynId,
- subSetSamples)
- annotated <- synapser::synTableQuery(query_string)
- annotated_df <- synapser::as.data.frame(annotated)
- annotated_df$HGVSp_Short[is.na(annotated_df$HGVSp_Short)] <- ""
- samples = paste(annotated_df$Tumor_Sample_Barcode,
- "Sp:", annotated_df$HGVSp_Short,
- "str:", annotated_df$Start_Position,
- "ref:", annotated_df$Reference_Allele,
- "tumor:", annotated_df$Tumor_Seq_Allele2)
- # New samples
- #tbl$HGVSp_Short[is.na(tbl$HGVSp_Short)] <- ""
- #This has to be done because HGVSp_Short is a factor
- nodup_tbl <- tbl[!duplicated(tbl),]
- hgvsp = as.character(nodup_tbl$HGVSp_Short)
- hgvsp[is.na(hgvsp)] <- ""
- new_samples = paste(nodup_tbl$Tumor_Sample_Barcode,
- "Sp:", hgvsp,
- "str:", nodup_tbl$Start_Position,
- "ref:", nodup_tbl$Reference_Allele,
- "tumor:", nodup_tbl$Tumor_Seq_Allele2)
- #Any data that is not the current output but in the database will be changed to FIXED
- if (nrow(annotated_df) > 0 ) {
- # FLAG variants first
- if (any(annotated_df$Center %in% flagCenters)) {
- annotated_df$Flag[annotated_df$Center %in% flagCenters] = "FLAG"
- }
- if (any(annotated_df$Flag[!samples %in% new_samples] == "TOSS")) {
- annotated_df$Flag[!samples %in% new_samples][
- annotated_df$Flag[!samples %in% new_samples] == "TOSS"] = "FIXED"
- }
- if (any(annotated_df$Center %in% keepCenters)) {
- annotated_df$Flag[annotated_df$Center %in% keepCenters] = "KEEP"
- }
- synapser::synStore(Table(databaseSynId, annotated_df))
- }
-
- #Append any new data
- new_rows = nodup_tbl[!new_samples %in% samples,]
- #Even when nodup_tbl is empty, it can be subsetted, causing one NA row to be uploaded.
- if (nrow(new_rows) > 0 && nrow(nodup_tbl) > 0) {
- #By default everything is labelled TOSS unless the default filter is FALSE
- #NOTE: If a center is set from default filter TRUE -> FALSE then switches back,
- # This center's mutationInCis KEEP data will have to be erased.
- # And processing will have to be run again after mutationsInCis is run on this center
- # Due to the centers mutationInCis input file.
- new_rows$Flag = "TOSS"
- new_rows$Flag[new_rows$Center %in% keepCenters] = "KEEP"
- new_rows$Flag[new_rows$Center %in% flagCenters] = "FLAG"
- tableToAppend <- synapser::Table(databaseSynId, new_rows)
- synapser::synStore(tableToAppend)
- }
-}
-
-# Flag variants to merge
-flag_variants_to_merge <- function(genieMutData, genieClinData, samplesToRun, upload = TRUE) {
-
- genieMutData <- data.frame( lapply( genieMutData , factor ))
- # Create factors for clinical data
-
- SAMPLE_ID = genieClinData$SAMPLE_ID[genieClinData$SAMPLE_ID %in% samplesToRun]
- genieClinData = data.frame(SAMPLE_ID)
- genieClinData <- data.frame( lapply( genieClinData , factor ))
- # all inclusive list of samples should be from the clinical data file
- # therefore factor levels for Tumor_Sample_Barcode in the MAF should be set to that of SAMPLE_ID of clinical data table
- # check that no samples are listed in the MAF that are not listed in the clinical data file
- # reversing the order of the inputs would tell you which samples are submitted that have no entries (no mutations) in the MAF
- if (length(setdiff(levels(genieMutData$Tumor_Sample_Barcode),
- levels(genieClinData$SAMPLE_ID))) == 0) {
- genieMutData$Tumor_Sample_Barcode = factor(genieMutData$Tumor_Sample_Barcode,
- levels = levels(genieClinData$SAMPLE_ID))
- }
-
- # records with count data that preclude a VAF estimate - set VAF to 100% (1/1, alt/depth)
- # genieMutData$t_depth <- as.numeric(genieMutData$t_depth) DONT DO THIS LINE...
- genieMutData$t_depth <- as.numeric(levels(genieMutData$t_depth))[genieMutData$t_depth]
- noVAF.idx = which((genieMutData$t_depth == 0) | is.na(genieMutData$t_depth))
- genieMutData$t_alt_count_num =
- as.numeric(levels(genieMutData$t_alt_count))[genieMutData$t_alt_count]
- #if (length(noVAF.idx) > 0) {
- genieMutData$t_alt_count_num[noVAF.idx] = 1
- genieMutData$t_depth[noVAF.idx] = 1
- #}
- genieMutData$Start_Position <- as.numeric(as.character(genieMutData$Start_Position))
- genieMutData$End_Position <- as.numeric(as.character(genieMutData$End_Position))
- genieMutData$Tumor_Seq_Allele2 <- as.character(genieMutData$Tumor_Seq_Allele2)
- #invalid class âVRangesâ object: if 'alt' is 'NA', then 'altDepth' should be 'NA'
- genieMutData$t_alt_count_num[is.na(genieMutData$Tumor_Seq_Allele2)] <- NA
-
- # get VRanges for all variants called in the MAF
- mafVR = VRanges(seqnames = Rle(paste0("chr",genieMutData$Chromosome)),
- ranges = IRanges(start = genieMutData$Start_Position,
- end = genieMutData$End_Position),
- ref = genieMutData$Reference_Allele,
- # alt = genieMutData$Tumor_Seq_Allele2,
- altDepth = genieMutData$t_alt_count_num,
- totalDepth = genieMutData$t_depth,
- sampleNames = genieMutData$Tumor_Sample_Barcode)
- seqlevels(mafVR) = sort(seqlevels(mafVR))
-
- # precompute
- vaf = altDepth(mafVR)/totalDepth(mafVR)
- ord = order(mafVR)
-
- # start with empty table
- tbl = genieMutData[1, c("Center","Tumor_Sample_Barcode","Hugo_Symbol",
- "HGVSp_Short","Variant_Classification","Chromosome",
- "Start_Position","Reference_Allele","Tumor_Seq_Allele2",
- "t_alt_count_num","t_depth")]
- tbl = tbl[-1,]
-
- # check for potential variants that may need to be evaluated for merge (cis/trans)
- genieMutData$Tumor_Sample_Barcode <- as.character(genieMutData$Tumor_Sample_Barcode)
- #genieClinData$SAMPLE_ID <- as.character(genieClinData$SAMPLE_ID)
- t = Sys.time()
- samplesRun = c()
- for (i in 1:length(samplesToRun)) {
-
- # get sample indices (in order from pre sort above)
- idx = ord[which(genieMutData$Tumor_Sample_Barcode[ord] == samplesToRun[i])]
- samplesRun = c(samplesRun, samplesToRun[i])
- # get length of idx
- l = length(idx)
-
- # if sample has more than one variant
- if (l > 1) {
- # get differences in BPs of variant sites
- dBP = distance(mafVR[idx[1:(l - 1)]], mafVR[idx[2:(l)]])
- # get difference in VAFs of variants
- dVAF = abs(diff(vaf[idx]))
-
- # potential matches - criteria of difference in BPs between of > 0 & < 6 bps difference, < 5% VAF difference
- pm = which((dBP > 0) & (dBP < 6) & (dVAF < .05))
- for (m in pm) {
- # calc difference in codon number
- codonDiff = abs(diff(as.numeric(sapply(strsplit(as.character(genieMutData$Protein_position[c(idx[m],idx[m + 1])]),split = "/"),"[",1))))
- if (is.na(codonDiff) | (codonDiff == 1)) {
- tbl = rbind(tbl,genieMutData[c(idx[m],idx[m + 1]),
- c("Center","Tumor_Sample_Barcode","Hugo_Symbol",
- "HGVSp_Short","Variant_Classification","Chromosome",
- "Start_Position","Reference_Allele",
- "Tumor_Seq_Allele2","t_alt_count_num","t_depth")])
- }
- }
- }
- if (upload) {
- # time ticker per 100 cases
- if ((i %% 100) == 0) {
- print(i)
- t[2] = Sys.time()
- print(t[2] - t[1])
- t[1] = t[2]
- }
- #HAve to keep track of how far it is in the chunk
- if (nrow(tbl) > tbl_size_limit || i == length(samplesToRun)) {
- uploadToTable(tbl, mutationsInCisSynId, paste(samplesRun, collapse = "','"), centerMappingDf)
- tbl = genieMutData[1,c("Center","Tumor_Sample_Barcode","Hugo_Symbol",
- "HGVSp_Short","Variant_Classification","Chromosome",
- "Start_Position","Reference_Allele","Tumor_Seq_Allele2",
- "t_alt_count_num","t_depth")]
- tbl = tbl[-1,]
- samplesRun = c()
- }
- } else {
- return(tbl)
- }
- }
-}
diff --git a/R/test_flag_variants.R b/R/test_flag_variants.R
deleted file mode 100644
index 556a4191..00000000
--- a/R/test_flag_variants.R
+++ /dev/null
@@ -1,95 +0,0 @@
-get_working_dir <- function() {
- cmdArgs <- commandArgs(trailingOnly = FALSE)
- needle <- "--file="
- match <- grep(needle, cmdArgs)
- if (length(match) > 0) {
- # Rscript
- return(dirname(normalizePath(sub(needle, "", cmdArgs[match]))))
- } else {
- # 'source'd via R console
- return("./")
- }
-}
-working_dir = get_working_dir()
-source(file.path(working_dir, "mergecheck_functions.R"))
-library(testthat)
-library(VariantAnnotation)
-genieMutData = matrix(nrow = 2, ncol = 13)
-colnames(genieMutData) = c("Chromosome", "Hugo_Symbol", "Start_Position", "End_Position", "Reference_Allele",
- "Tumor_Seq_Allele2", "t_depth", 't_alt_count', "Tumor_Sample_Barcode",
- "Protein_position", "HGVSp_Short", "Variant_Classification", "Center")
-
-
-genieMutData[,'Chromosome'] = c("1", "1")
-genieMutData[,'Start_Position'] = c("1", "3")
-genieMutData[,'End_Position'] = c("1", "3")
-genieMutData[,'Reference_Allele'] = c("A", "C")
-genieMutData[,'Tumor_Seq_Allele2'] = c("T", "G")
-genieMutData[,'t_alt_count'] = c(1, 2)
-genieMutData[,'t_depth'] = c(100, 100)
-genieMutData[,'Tumor_Sample_Barcode'] = c("SAGE1", "SAGE1")
-genieMutData[,'Protein_position'] = c("3/4", "4/4")
-genieMutData[,'Hugo_Symbol'] = c("ROS1", "ROS1")
-genieMutData[,'Center'] = c("SAGE", "SAGE")
-
-genieMutData = as.data.frame(genieMutData, stringsAsFactors = F)
-genieClinData = data.frame(SAMPLE_ID = c("SAGE1"),
- stringsAsFactors = F)
-
-test_that("Mutations are flagged, same starts and ends", {
- tbl = flag_variants_to_merge(genieMutData, genieClinData, c("SAGE1"), upload=F)
- expected = genieMutData[, c("Center", "Tumor_Sample_Barcode", "Hugo_Symbol",
- "Variant_Classification", "Chromosome", "Start_Position",
- "Reference_Allele", "Tumor_Seq_Allele2","t_depth",
- "HGVSp_Short")]
- expected$t_alt_count_num = c(1, 2)
- # Change everything to factors or else its difficult to validate is absurd
- # This is ok because we don't do anything with factors after the function is ran
- expected <- data.frame( lapply( expected , factor ))
- tbl <- data.frame( lapply( tbl , factor ))
- expect_equal(tbl, expected[,colnames(tbl)])
-})
-
-genieMutData$Start_Position[2] = "15"
-genieMutData$End_Position[2] = "15"
-test_that("Mutations are not flagged", {
- tbl = flag_variants_to_merge(genieMutData, genieClinData, c("SAGE1"), upload=F)
- expect_equal(nrow(tbl), 0)
- expect_equal(colnames(tbl), c("Center", "Tumor_Sample_Barcode", "Hugo_Symbol", "HGVSp_Short",
- "Variant_Classification", "Chromosome", "Start_Position",
- "Reference_Allele", "Tumor_Seq_Allele2", "t_alt_count_num", "t_depth"))
-
-})
-
-genieMutData$Start_Position = c("1", "10")
-genieMutData$End_Position = c("5", "12")
-test_that("Mutations are flagged, different starts and ends", {
- tbl = flag_variants_to_merge(genieMutData, genieClinData, c("SAGE1"), upload=F)
- expected = genieMutData[, c("Center", "Tumor_Sample_Barcode", "Hugo_Symbol",
- "Variant_Classification", "Chromosome", "Start_Position",
- "Reference_Allele", "Tumor_Seq_Allele2","t_depth",
- "HGVSp_Short")]
- expected$t_alt_count_num = c(1, 2)
- # Change everything to factors or else its difficult to validate is absurd
- # This is ok because we don't do anything with factors after the function is ran
- expected <- data.frame( lapply( expected , factor ))
- tbl <- data.frame( lapply( tbl , factor ))
- expect_equal(tbl, expected[,colnames(tbl)])
-})
-
-
-genieMutData$Start_Position = c("1", "10")
-genieMutData$End_Position = c("5", "12")
-test_that("Mutations not flagged, different starts and ends", {
- tbl = flag_variants_to_merge(genieMutData, genieClinData, c("SAGE1"), upload=F)
- expected = genieMutData[, c("Center", "Tumor_Sample_Barcode", "Hugo_Symbol",
- "Variant_Classification", "Chromosome", "Start_Position",
- "Reference_Allele", "Tumor_Seq_Allele2","t_depth",
- "HGVSp_Short")]
- expected$t_alt_count_num = c(1, 2)
- # Change everything to factors or else its difficult to validate is absurd
- # This is ok because we don't do anything with factors after the function is ran
- expected <- data.frame( lapply( expected , factor ))
- tbl <- data.frame( lapply( tbl , factor ))
- expect_equal(tbl, expected[,colnames(tbl)])
-})
diff --git a/R/tests/testthat/test_dashboard_template_functions.R b/R/tests/testthat/test_dashboard_template_functions.R
deleted file mode 100644
index ceb6aa6e..00000000
--- a/R/tests/testthat/test_dashboard_template_functions.R
+++ /dev/null
@@ -1,69 +0,0 @@
-# tests for dashboard_template_functions.R
-
-source("../../dashboard_template_functions.R")
-
-library(synapser)
-library(testthat)
-
-sample_counts_table <- function() {
- data <- data.frame(
- Center = factor(c("GOLD","SAGE", "TEST"),
- levels = c("GOLD", "SAGE", "TEST")),
- Counts = c(1, 2, 1)
- )
- return(data)
-}
-
-empty_counts_table <- function() {
- data <- data.frame(
- Center = logical(),
- Counts = logical()
- )
- return(data)
-}
-
-sample_maf_table <- function() {
- data <- data.frame(
- Center = c("TEST", "TEST", "SAGE", "SAGE", "GOLD", "BRONZE"),
- Tumor_Sample_Barcode = c("SAGE1", "SAGE2", "SAGE3", "SAGE4", "SAGE5", "SAGE6"),
- Annotation_Status = c("SUCCESS", "FAILED", "FAILED", "FAILED", "FAILED", "SUCCESS")
- )
- return(data)
-}
-
-sample_maf_table_no_failed_annotations <- function() {
- data <- data.frame(
- Center = c("TEST", "SAGE", "GOLD"),
- Tumor_Sample_Barcode = c("SAGE1", "SAGE2", "SAGE3"),
- Annotation_Status = c("SUCCESS", "SUCCESS", "SUCCESS")
- )
- return(data)
-}
-
-
-test_that("get_syn_id_from_mapped_database_gets_correct_value", {
- synLogin()
- result <- get_syn_id_from_mapped_database(
- database_name = "main",
- database_synid_mappingid = "syn11600968"
- )
- expect_equal(result, "syn7208886")
-})
-
-
-test_that("get_failed_annotation_table_counts_returns_expected_output", {
- result <- get_failed_annotation_table_counts(
- maf_data=sample_maf_table(),
- group_by_cols="Center",
- counts_col_name="Counts")
- expect_equal(result, sample_counts_table())
-})
-
-test_that("get_failed_annotation_table_counts_returns_empty_table_with_no_failed_annotations", {
- result <- get_failed_annotation_table_counts(
- maf_data=sample_maf_table_no_failed_annotations(),
- group_by_cols="Center",
- counts_col_name="Counts")
- expect_equal(result, empty_counts_table())
-})
-
diff --git a/README.md b/README.md
deleted file mode 100644
index 555bb925..00000000
--- a/README.md
+++ /dev/null
@@ -1,136 +0,0 @@
-
-
-# AACR Project GENIE
-
-[](https://pypi.org/project/aacrgenie)
-[](https://hub.docker.com/r/sagebionetworks/genie)
-[](https://github.com/Sage-Bionetworks/Genie)
-
-
-## Introduction
-
-This repository documents code used to gather, QC, standardize, and analyze data uploaded by institutes participating in AACR's Project GENIE (Genomics, Evidence, Neoplasia, Information, Exchange).
-
-## Dependencies
-
-This package contains both R, Python and cli tools. These are tools or packages you will need, to be able to reproduce these results:
-- Python >=3.8 or <3.10
- - `pip install -r requirements.txt`
-- [bedtools](https://bedtools.readthedocs.io/en/latest/content/installation.html)
-- R 4.2.2
- - `renv::install()`
- - Follow instructions [here](https://r-docs.synapse.org/#note-for-windows-and-mac-users) to install synapser
-- [Java > 8](https://www.java.com/en/download/)
- - For mac users, it seems to work better to run `brew install java`
-- [wget](https://www.gnu.org/software/wget/)
- - For mac users, have to run `brew install wget`
-
-## File Validator
-
-One of the features of the `aacrgenie` package is that is provides a local validation tool that GENIE data contributors and install and use to validate their files locally prior to uploading to Synapse.
-
-```
-pip install aacrgenie
-genie -v
-```
-
-This will install all the necessary components for you to run the validator locally on all of your files, including the Synapse client. Please view the help to see how to run to validator.
-
-```
-genie validate -h
-genie validate data_clinical_supp_SAGE.txt SAGE
-```
-
-
-## Contributing
-
-Please view [contributing guide](CONTRIBUTING.md) to learn how to contribute to the GENIE package.
-
-
-# Sage Bionetworks Only
-
-## Developing locally
-
-These are instructions on how you would develop and test the pipeline locally.
-
-1. Make sure you have read through the [GENIE Onboarding Docs](https://sagebionetworks.jira.com/wiki/spaces/APGD/pages/2163344270/Onboarding) and have access to all of the required repositories, resources and synapse projects for Main GENIE.
-1. Be sure you are invited to the Synapse GENIE Admin team.
-1. Make sure you are a Synapse certified user: [Certified User - Synapse User Account Types](https://help.synapse.org/docs/Synapse-User-Account-Types.2007072795.html#SynapseUserAccountTypes-CertifiedUser)
-1. Clone this repo and install the package locally.
-
- ```
- pip install -e .
- pip install -r requirements.txt
- pip install -r requirements-dev.txt
- ```
-
- If you are having trouble with the above, try installing via `pipenv`
-
- 1. Specify a python version that is supported by this repo:
- ```pipenv --python ```
-
- 1. [pipenv install from requirements file](https://docs.pipenv.org/en/latest/advanced.html#importing-from-requirements-txt)
-
- 1. Activate your `pipenv`:
- ```pipenv shell```
-
-1. Configure the Synapse client to authenticate to Synapse.
- 1. Create a Synapse [Personal Access token (PAT)](https://help.synapse.org/docs/Managing-Your-Account.2055405596.html#ManagingYourAccount-PersonalAccessTokens).
- 1. Add a `~/.synapseConfig` file
- ```
- [authentication]
- authtoken =
- ```
- 1. OR set an environmental variable
- ```
- export SYNAPSE_AUTH_TOKEN=
- ```
- 1. Confirm you can log in your terminal.
- ```shell
- synapse login
- ```
-
-1. Run the different pipelines on the test project. The `--project_id syn7208886` points to the test project.
-
- 1. Validate all the files **excluding vcf files**:
-
- ```
- python bin/input_to_database.py main --project_id syn7208886 --onlyValidate
- ```
-
- 1. Validate **all** the files:
-
- ```
- python bin/input_to_database.py mutation --project_id syn7208886 --onlyValidate --genie_annotation_pkg ../annotation-tools
- ```
-
- 1. Process all the files aside from the mutation (maf, vcf) files. The mutation processing was split because it takes at least 2 days to process all the production mutation data. Ideally, there is a parameter to exclude or include file types to process/validate, but that is not implemented.
-
- ```
- python bin/input_to_database.py main --project_id syn7208886 --deleteOld
- ```
-
- 1. Process the mutation data. Be sure to clone this repo: https://github.com/Sage-Bionetworks/annotation-tools and `git checkout` the version of the repo pinned to the [Dockerfile](https://github.com/Sage-Bionetworks/Genie/blob/main/Dockerfile). This repo houses the code that re-annotates the mutation data with genome nexus. The `--createNewMafDatabase` will create a new mutation tables in the test project. This flag is necessary for production data for two main reasons:
- * During processing of mutation data, the data is appended to the data, so without creating an empty table, there will be duplicated data uploaded.
- * By design, Synapse Tables were meant to be appended to. When a Synapse Tables is updated, it takes time to index the table and return results. This can cause problems for the pipeline when trying to query the mutation table. It is actually faster to create an entire new table than updating or deleting all rows and appending new rows when dealing with millions of rows.
- * If you run this more than once on the same day, you'll run into an issue with overwriting the narrow maf table as it already exists. Be sure to rename the current narrow maf database under `Tables` in the test synapse project and try again.
-
- ```
- python bin/input_to_database.py mutation --project_id syn7208886 --deleteOld --genie_annotation_pkg ../annotation-tools --createNewMafDatabase
- ```
-
- 1. Create a consortium release. Be sure to add the `--test` parameter. Be sure to clone the cbioportal repo: https://github.com/cBioPortal/cbioportal and `git checkout` the version of the repo pinned to the [Dockerfile](https://github.com/Sage-Bionetworks/Genie/blob/main/Dockerfile)
-
- ```
- python bin/database_to_staging.py Jan-2017 ../cbioportal TEST --test
- ```
-
- 1. Create a public release. Be sure to add the `--test` parameter. Be sure to clone the cbioportal repo: https://github.com/cBioPortal/cbioportal and `git checkout` the version of the repo pinned to the [Dockerfile](https://github.com/Sage-Bionetworks/Genie/blob/main/Dockerfile)
-
- ```
- python bin/consortium_to_public.py Jan-2017 ../cbioportal TEST --test
- ```
-
-## Production
-
-The production pipeline is run on Nextflow Tower and the Nextflow workflow is captured in [nf-genie](https://github.com/Sage-Bionetworks-Workflows/nf-genie). It is wise to create an ec2 via the Sage Bionetworks service catalog to work with the production data, because there is limited PHI in GENIE.
diff --git a/assets/_mkdocstrings.css b/assets/_mkdocstrings.css
new file mode 100644
index 00000000..85449ec7
--- /dev/null
+++ b/assets/_mkdocstrings.css
@@ -0,0 +1,119 @@
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+ border-radius: .1rem;
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+ padding: 0 .3em;
+ font-weight: bold;
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+
+code.doc-symbol-attribute {
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+code.doc-symbol-attribute::after {
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+
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+ color: inherit;
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Qa(e,t){document.body.append(e);let{width:r}=ce(e);e.style.setProperty("--md-tooltip-width",`${r}px`),e.remove();let o=cr(t),n=typeof o!="undefined"?De(o):I({x:0,y:0}),i=S(et(t),kt(t)).pipe(K());return z([i,n]).pipe(m(([a,s])=>{let{x:p,y:c}=Ue(t),l=ce(t),f=t.closest("table");return f&&t.parentElement&&(p+=f.offsetLeft+t.parentElement.offsetLeft,c+=f.offsetTop+t.parentElement.offsetTop),{active:a,offset:{x:p-s.x+l.width/2-r/2,y:c-s.y+l.height+8}}}))}function Vn(e){let t=e.title;if(!t.length)return M;let r=`__tooltip_${qa++}`,o=Pt(r,"inline"),n=P(".md-typeset",o);return n.innerHTML=t,C(()=>{let i=new g;return i.subscribe({next({offset:a}){o.style.setProperty("--md-tooltip-x",`${a.x}px`),o.style.setProperty("--md-tooltip-y",`${a.y}px`)},complete(){o.style.removeProperty("--md-tooltip-x"),o.style.removeProperty("--md-tooltip-y")}}),S(i.pipe(v(({active:a})=>a)),i.pipe(_e(250),v(({active:a})=>!a))).subscribe({next({active:a}){a?(e.insertAdjacentElement("afterend",o),e.setAttribute("aria-describedby",r),e.removeAttribute("title")):(o.remove(),e.removeAttribute("aria-describedby"),e.setAttribute("title",t))},complete(){o.remove(),e.removeAttribute("aria-describedby"),e.setAttribute("title",t)}}),i.pipe(Le(16,me)).subscribe(({active:a})=>{o.classList.toggle("md-tooltip--active",a)}),i.pipe(ct(125,me),v(()=>!!e.offsetParent),m(()=>e.offsetParent.getBoundingClientRect()),m(({x:a})=>a)).subscribe({next(a){a?o.style.setProperty("--md-tooltip-0",`${-a}px`):o.style.removeProperty("--md-tooltip-0")},complete(){o.style.removeProperty("--md-tooltip-0")}}),Qa(o,e).pipe(E(a=>i.next(a)),L(()=>i.complete()),m(a=>R({ref:e},a)))}).pipe(Qe(se))}function Ka({viewport$:e}){if(!G("header.autohide"))return I(!1);let t=e.pipe(m(({offset:{y:n}})=>n),Ye(2,1),m(([n,i])=>[nMath.abs(i-n.y)>100),m(([,[n]])=>n),K()),o=Ve("search");return z([e,o]).pipe(m(([{offset:n},i])=>n.y>400&&!i),K(),b(n=>n?r:I(!1)),Q(!1))}function Nn(e,t){return C(()=>z([ge(e),Ka(t)])).pipe(m(([{height:r},o])=>({height:r,hidden:o})),K((r,o)=>r.height===o.height&&r.hidden===o.hidden),B(1))}function zn(e,{header$:t,main$:r}){return C(()=>{let o=new g,n=o.pipe(X(),ne(!0));o.pipe(Z("active"),We(t)).subscribe(([{active:a},{hidden:s}])=>{e.classList.toggle("md-header--shadow",a&&!s),e.hidden=s});let i=ue($("[title]",e)).pipe(v(()=>G("content.tooltips")),oe(a=>Vn(a)));return r.subscribe(o),t.pipe(U(n),m(a=>R({ref:e},a)),Pe(i.pipe(U(n))))})}function Ya(e,{viewport$:t,header$:r}){return mr(e,{viewport$:t,header$:r}).pipe(m(({offset:{y:o}})=>{let{height:n}=ce(e);return{active:o>=n}}),Z("active"))}function qn(e,t){return C(()=>{let r=new g;r.subscribe({next({active:n}){e.classList.toggle("md-header__title--active",n)},complete(){e.classList.remove("md-header__title--active")}});let o=fe(".md-content h1");return typeof o=="undefined"?M:Ya(o,t).pipe(E(n=>r.next(n)),L(()=>r.complete()),m(n=>R({ref:e},n)))})}function Qn(e,{viewport$:t,header$:r}){let o=r.pipe(m(({height:i})=>i),K()),n=o.pipe(b(()=>ge(e).pipe(m(({height:i})=>({top:e.offsetTop,bottom:e.offsetTop+i})),Z("bottom"))));return z([o,n,t]).pipe(m(([i,{top:a,bottom:s},{offset:{y:p},size:{height:c}}])=>(c=Math.max(0,c-Math.max(0,a-p,i)-Math.max(0,c+p-s)),{offset:a-i,height:c,active:a-i<=p})),K((i,a)=>i.offset===a.offset&&i.height===a.height&&i.active===a.active))}function Ba(e){let t=__md_get("__palette")||{index:e.findIndex(o=>matchMedia(o.getAttribute("data-md-color-media")).matches)},r=Math.max(0,Math.min(t.index,e.length-1));return I(...e).pipe(oe(o=>d(o,"change").pipe(m(()=>o))),Q(e[r]),m(o=>({index:e.indexOf(o),color:{media:o.getAttribute("data-md-color-media"),scheme:o.getAttribute("data-md-color-scheme"),primary:o.getAttribute("data-md-color-primary"),accent:o.getAttribute("data-md-color-accent")}})),B(1))}function Kn(e){let t=$("input",e),r=x("meta",{name:"theme-color"});document.head.appendChild(r);let o=x("meta",{name:"color-scheme"});document.head.appendChild(o);let n=$t("(prefers-color-scheme: light)");return C(()=>{let i=new g;return i.subscribe(a=>{if(document.body.setAttribute("data-md-color-switching",""),a.color.media==="(prefers-color-scheme)"){let s=matchMedia("(prefers-color-scheme: light)"),p=document.querySelector(s.matches?"[data-md-color-media='(prefers-color-scheme: light)']":"[data-md-color-media='(prefers-color-scheme: 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c.pipe(ee(t)).subscribe({next([{height:l},{height:f}]){i.style.height=`${l-2*a}px`,e.style.top=`${f}px`},complete(){i.style.height="",e.style.top=""}}),c.pipe(Ae()).subscribe(()=>{for(let l of $(".md-nav__link--active[href]",e)){if(!l.clientHeight)continue;let f=l.closest(".md-sidebar__scrollwrap");if(typeof f!="undefined"){let u=l.offsetTop-f.offsetTop,{height:h}=ce(f);f.scrollTo({top:u-h/2})}}}),ue($("label[tabindex]",e)).pipe(oe(l=>d(l,"click").pipe(be(se),m(()=>l),U(p)))).subscribe(l=>{let f=P(`[id="${l.htmlFor}"]`);P(`[aria-labelledby="${l.id}"]`).setAttribute("aria-expanded",`${f.checked}`)}),as(e,r).pipe(E(l=>s.next(l)),L(()=>s.complete()),m(l=>R({ref:e},l)))})}function fi(e,t){if(typeof t!="undefined"){let r=`https://api.github.com/repos/${e}/${t}`;return Ct(Ne(`${r}/releases/latest`).pipe(ve(()=>M),m(o=>({version:o.tag_name})),Be({})),Ne(r).pipe(ve(()=>M),m(o=>({stars:o.stargazers_count,forks:o.forks_count})),Be({}))).pipe(m(([o,n])=>R(R({},o),n)))}else{let r=`https://api.github.com/users/${e}`;return Ne(r).pipe(m(o=>({repositories:o.public_repos})),Be({}))}}function ui(e,t){let r=`https://${e}/api/v4/projects/${encodeURIComponent(t)}`;return Ne(r).pipe(ve(()=>M),m(({star_count:o,forks_count:n})=>({stars:o,forks:n})),Be({}))}function di(e){let t=e.match(/^.+github\.com\/([^/]+)\/?([^/]+)?/i);if(t){let[,r,o]=t;return fi(r,o)}if(t=e.match(/^.+?([^/]*gitlab[^/]+)\/(.+?)\/?$/i),t){let[,r,o]=t;return ui(r,o)}return M}var ss;function cs(e){return ss||(ss=C(()=>{let t=__md_get("__source",sessionStorage);if(t)return I(t);if(ae("consent").length){let o=__md_get("__consent");if(!(o&&o.github))return M}return di(e.href).pipe(E(o=>__md_set("__source",o,sessionStorage)))}).pipe(ve(()=>M),v(t=>Object.keys(t).length>0),m(t=>({facts:t})),B(1)))}function hi(e){let t=P(":scope > :last-child",e);return C(()=>{let r=new g;return 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n=t.pipe(m(({offset:{y:a}})=>a),Ye(2,1),m(([a,s])=>a>s&&s>0),K()),i=r.pipe(m(({active:a})=>a));return z([i,n]).pipe(m(([a,s])=>!(a&&s)),K(),U(o.pipe(Ce(1))),ne(!0),st({delay:250}),m(a=>({hidden:a})))}function gi(e,{viewport$:t,header$:r,main$:o,target$:n}){let i=new g,a=i.pipe(X(),ne(!0));return i.subscribe({next({hidden:s}){e.hidden=s,s?(e.setAttribute("tabindex","-1"),e.blur()):e.removeAttribute("tabindex")},complete(){e.style.top="",e.hidden=!0,e.removeAttribute("tabindex")}}),r.pipe(U(a),Z("height")).subscribe(({height:s})=>{e.style.top=`${s+16}px`}),d(e,"click").subscribe(s=>{s.preventDefault(),window.scrollTo({top:0})}),ms(e,{viewport$:t,main$:o,target$:n}).pipe(E(s=>i.next(s)),L(()=>i.complete()),m(s=>R({ref:e},s)))}function xi({document$:e,viewport$:t}){e.pipe(b(()=>$(".md-ellipsis")),oe(r=>tt(r).pipe(U(e.pipe(Ce(1))),v(o=>o),m(()=>r),Te(1))),v(r=>r.offsetWidth{let o=r.innerText,n=r.closest("a")||r;return n.title=o,lt(n,{viewport$:t}).pipe(U(e.pipe(Ce(1))),L(()=>n.removeAttribute("title")))})).subscribe(),e.pipe(b(()=>$(".md-status")),oe(r=>lt(r,{viewport$:t}))).subscribe()}function yi({document$:e,tablet$:t}){e.pipe(b(()=>$(".md-toggle--indeterminate")),E(r=>{r.indeterminate=!0,r.checked=!1}),oe(r=>d(r,"change").pipe(Dr(()=>r.classList.contains("md-toggle--indeterminate")),m(()=>r))),ee(t)).subscribe(([r,o])=>{r.classList.remove("md-toggle--indeterminate"),o&&(r.checked=!1)})}function fs(){return/(iPad|iPhone|iPod)/.test(navigator.userAgent)}function Ei({document$:e}){e.pipe(b(()=>$("[data-md-scrollfix]")),E(t=>t.removeAttribute("data-md-scrollfix")),v(fs),oe(t=>d(t,"touchstart").pipe(m(()=>t)))).subscribe(t=>{let r=t.scrollTop;r===0?t.scrollTop=1:r+t.offsetHeight===t.scrollHeight&&(t.scrollTop=r-1)})}function wi({viewport$:e,tablet$:t}){z([Ve("search"),t]).pipe(m(([r,o])=>r&&!o),b(r=>I(r).pipe(Ge(r?400:100))),ee(e)).subscribe(([r,{offset:{y:o}}])=>{if(r)document.body.setAttribute("data-md-scrolllock",""),document.body.style.top=`-${o}px`;else{let n=-1*parseInt(document.body.style.top,10);document.body.removeAttribute("data-md-scrolllock"),document.body.style.top="",n&&window.scrollTo(0,n)}})}Object.entries||(Object.entries=function(e){let t=[];for(let r of Object.keys(e))t.push([r,e[r]]);return t});Object.values||(Object.values=function(e){let t=[];for(let r of Object.keys(e))t.push(e[r]);return t});typeof Element!="undefined"&&(Element.prototype.scrollTo||(Element.prototype.scrollTo=function(e,t){typeof e=="object"?(this.scrollLeft=e.left,this.scrollTop=e.top):(this.scrollLeft=e,this.scrollTop=t)}),Element.prototype.replaceWith||(Element.prototype.replaceWith=function(...e){let t=this.parentNode;if(t){e.length===0&&t.removeChild(this);for(let r=e.length-1;r>=0;r--){let o=e[r];typeof o=="string"?o=document.createTextNode(o):o.parentNode&&o.parentNode.removeChild(o),r?t.insertBefore(this.previousSibling,o):t.replaceChild(o,this)}}}));function us(){return location.protocol==="file:"?wt(`${new URL("search/search_index.js",Xr.base)}`).pipe(m(()=>__index),B(1)):Ne(new URL("search/search_index.json",Xr.base))}document.documentElement.classList.remove("no-js");document.documentElement.classList.add("js");var ot=Yo(),jt=nn(),Ot=cn(jt),Zr=on(),Oe=bn(),hr=$t("(min-width: 960px)"),Si=$t("(min-width: 1220px)"),Oi=pn(),Xr=ye(),Mi=document.forms.namedItem("search")?us():Ke,eo=new g;Bn({alert$:eo});var to=new g;G("navigation.instant")&&Zn({location$:jt,viewport$:Oe,progress$:to}).subscribe(ot);var Ti;((Ti=Xr.version)==null?void 0:Ti.provider)==="mike"&&ii({document$:ot});S(jt,Ot).pipe(Ge(125)).subscribe(()=>{Je("drawer",!1),Je("search",!1)});Zr.pipe(v(({mode:e})=>e==="global")).subscribe(e=>{switch(e.type){case"p":case",":let t=fe("link[rel=prev]");typeof t!="undefined"&&pt(t);break;case"n":case".":let r=fe("link[rel=next]");typeof r!="undefined"&&pt(r);break;case"Enter":let o=Re();o instanceof HTMLLabelElement&&o.click()}});xi({viewport$:Oe,document$:ot});yi({document$:ot,tablet$:hr});Ei({document$:ot});wi({viewport$:Oe,tablet$:hr});var rt=Nn(Se("header"),{viewport$:Oe}),Ft=ot.pipe(m(()=>Se("main")),b(e=>Qn(e,{viewport$:Oe,header$:rt})),B(1)),ds=S(...ae("consent").map(e=>xn(e,{target$:Ot})),...ae("dialog").map(e=>Dn(e,{alert$:eo})),...ae("header").map(e=>zn(e,{viewport$:Oe,header$:rt,main$:Ft})),...ae("palette").map(e=>Kn(e)),...ae("progress").map(e=>Yn(e,{progress$:to})),...ae("search").map(e=>li(e,{index$:Mi,keyboard$:Zr})),...ae("source").map(e=>hi(e))),hs=C(()=>S(...ae("announce").map(e=>gn(e)),...ae("content").map(e=>Un(e,{viewport$:Oe,target$:Ot,print$:Oi})),...ae("content").map(e=>G("search.highlight")?mi(e,{index$:Mi,location$:jt}):M),...ae("header-title").map(e=>qn(e,{viewport$:Oe,header$:rt})),...ae("sidebar").map(e=>e.getAttribute("data-md-type")==="navigation"?Nr(Si,()=>Jr(e,{viewport$:Oe,header$:rt,main$:Ft})):Nr(hr,()=>Jr(e,{viewport$:Oe,header$:rt,main$:Ft}))),...ae("tabs").map(e=>bi(e,{viewport$:Oe,header$:rt})),...ae("toc").map(e=>vi(e,{viewport$:Oe,header$:rt,main$:Ft,target$:Ot})),...ae("top").map(e=>gi(e,{viewport$:Oe,header$:rt,main$:Ft,target$:Ot})))),Li=ot.pipe(b(()=>hs),Pe(ds),B(1));Li.subscribe();window.document$=ot;window.location$=jt;window.target$=Ot;window.keyboard$=Zr;window.viewport$=Oe;window.tablet$=hr;window.screen$=Si;window.print$=Oi;window.alert$=eo;window.progress$=to;window.component$=Li;})();
+//# sourceMappingURL=bundle.ebd0bdb7.min.js.map
+
diff --git a/assets/javascripts/bundle.ebd0bdb7.min.js.map b/assets/javascripts/bundle.ebd0bdb7.min.js.map
new file mode 100644
index 00000000..cec23df7
--- /dev/null
+++ b/assets/javascripts/bundle.ebd0bdb7.min.js.map
@@ -0,0 +1,7 @@
+{
+ "version": 3,
+ "sources": ["node_modules/focus-visible/dist/focus-visible.js", "node_modules/clipboard/dist/clipboard.js", "node_modules/escape-html/index.js", "src/templates/assets/javascripts/bundle.ts", "node_modules/rxjs/node_modules/tslib/tslib.es6.js", "node_modules/rxjs/src/internal/util/isFunction.ts", "node_modules/rxjs/src/internal/util/createErrorClass.ts", "node_modules/rxjs/src/internal/util/UnsubscriptionError.ts", "node_modules/rxjs/src/internal/util/arrRemove.ts", "node_modules/rxjs/src/internal/Subscription.ts", "node_modules/rxjs/src/internal/config.ts", "node_modules/rxjs/src/internal/scheduler/timeoutProvider.ts", "node_modules/rxjs/src/internal/util/reportUnhandledError.ts", "node_modules/rxjs/src/internal/util/noop.ts", "node_modules/rxjs/src/internal/NotificationFactories.ts", "node_modules/rxjs/src/internal/util/errorContext.ts", "node_modules/rxjs/src/internal/Subscriber.ts", "node_modules/rxjs/src/internal/symbol/observable.ts", "node_modules/rxjs/src/internal/util/identity.ts", "node_modules/rxjs/src/internal/util/pipe.ts", "node_modules/rxjs/src/internal/Observable.ts", "node_modules/rxjs/src/internal/util/lift.ts", "node_modules/rxjs/src/internal/operators/OperatorSubscriber.ts", "node_modules/rxjs/src/internal/scheduler/animationFrameProvider.ts", "node_modules/rxjs/src/internal/util/ObjectUnsubscribedError.ts", "node_modules/rxjs/src/internal/Subject.ts", "node_modules/rxjs/src/internal/BehaviorSubject.ts", "node_modules/rxjs/src/internal/scheduler/dateTimestampProvider.ts", "node_modules/rxjs/src/internal/ReplaySubject.ts", "node_modules/rxjs/src/internal/scheduler/Action.ts", "node_modules/rxjs/src/internal/scheduler/intervalProvider.ts", "node_modules/rxjs/src/internal/scheduler/AsyncAction.ts", "node_modules/rxjs/src/internal/Scheduler.ts", "node_modules/rxjs/src/internal/scheduler/AsyncScheduler.ts", "node_modules/rxjs/src/internal/scheduler/async.ts", "node_modules/rxjs/src/internal/scheduler/QueueAction.ts", "node_modules/rxjs/src/internal/scheduler/QueueScheduler.ts", "node_modules/rxjs/src/internal/scheduler/queue.ts", "node_modules/rxjs/src/internal/scheduler/AnimationFrameAction.ts", "node_modules/rxjs/src/internal/scheduler/AnimationFrameScheduler.ts", "node_modules/rxjs/src/internal/scheduler/animationFrame.ts", "node_modules/rxjs/src/internal/observable/empty.ts", "node_modules/rxjs/src/internal/util/isScheduler.ts", "node_modules/rxjs/src/internal/util/args.ts", "node_modules/rxjs/src/internal/util/isArrayLike.ts", "node_modules/rxjs/src/internal/util/isPromise.ts", "node_modules/rxjs/src/internal/util/isInteropObservable.ts", "node_modules/rxjs/src/internal/util/isAsyncIterable.ts", "node_modules/rxjs/src/internal/util/throwUnobservableError.ts", "node_modules/rxjs/src/internal/symbol/iterator.ts", "node_modules/rxjs/src/internal/util/isIterable.ts", "node_modules/rxjs/src/internal/util/isReadableStreamLike.ts", "node_modules/rxjs/src/internal/observable/innerFrom.ts", "node_modules/rxjs/src/internal/util/executeSchedule.ts", "node_modules/rxjs/src/internal/operators/observeOn.ts", "node_modules/rxjs/src/internal/operators/subscribeOn.ts", "node_modules/rxjs/src/internal/scheduled/scheduleObservable.ts", "node_modules/rxjs/src/internal/scheduled/schedulePromise.ts", "node_modules/rxjs/src/internal/scheduled/scheduleArray.ts", "node_modules/rxjs/src/internal/scheduled/scheduleIterable.ts", "node_modules/rxjs/src/internal/scheduled/scheduleAsyncIterable.ts", "node_modules/rxjs/src/internal/scheduled/scheduleReadableStreamLike.ts", "node_modules/rxjs/src/internal/scheduled/scheduled.ts", "node_modules/rxjs/src/internal/observable/from.ts", "node_modules/rxjs/src/internal/observable/of.ts", "node_modules/rxjs/src/internal/observable/throwError.ts", "node_modules/rxjs/src/internal/util/EmptyError.ts", "node_modules/rxjs/src/internal/util/isDate.ts", "node_modules/rxjs/src/internal/operators/map.ts", "node_modules/rxjs/src/internal/util/mapOneOrManyArgs.ts", "node_modules/rxjs/src/internal/util/argsArgArrayOrObject.ts", "node_modules/rxjs/src/internal/util/createObject.ts", "node_modules/rxjs/src/internal/observable/combineLatest.ts", "node_modules/rxjs/src/internal/operators/mergeInternals.ts", "node_modules/rxjs/src/internal/operators/mergeMap.ts", "node_modules/rxjs/src/internal/operators/mergeAll.ts", "node_modules/rxjs/src/internal/operators/concatAll.ts", "node_modules/rxjs/src/internal/observable/concat.ts", "node_modules/rxjs/src/internal/observable/defer.ts", "node_modules/rxjs/src/internal/observable/fromEvent.ts", "node_modules/rxjs/src/internal/observable/fromEventPattern.ts", "node_modules/rxjs/src/internal/observable/timer.ts", "node_modules/rxjs/src/internal/observable/merge.ts", "node_modules/rxjs/src/internal/observable/never.ts", "node_modules/rxjs/src/internal/util/argsOrArgArray.ts", "node_modules/rxjs/src/internal/operators/filter.ts", "node_modules/rxjs/src/internal/observable/zip.ts", "node_modules/rxjs/src/internal/operators/audit.ts", "node_modules/rxjs/src/internal/operators/auditTime.ts", "node_modules/rxjs/src/internal/operators/bufferCount.ts", "node_modules/rxjs/src/internal/operators/catchError.ts", "node_modules/rxjs/src/internal/operators/scanInternals.ts", "node_modules/rxjs/src/internal/operators/combineLatest.ts", "node_modules/rxjs/src/internal/operators/combineLatestWith.ts", "node_modules/rxjs/src/internal/operators/debounce.ts", "node_modules/rxjs/src/internal/operators/debounceTime.ts", "node_modules/rxjs/src/internal/operators/defaultIfEmpty.ts", "node_modules/rxjs/src/internal/operators/take.ts", "node_modules/rxjs/src/internal/operators/ignoreElements.ts", "node_modules/rxjs/src/internal/operators/mapTo.ts", "node_modules/rxjs/src/internal/operators/delayWhen.ts", "node_modules/rxjs/src/internal/operators/delay.ts", "node_modules/rxjs/src/internal/operators/distinctUntilChanged.ts", "node_modules/rxjs/src/internal/operators/distinctUntilKeyChanged.ts", "node_modules/rxjs/src/internal/operators/throwIfEmpty.ts", "node_modules/rxjs/src/internal/operators/endWith.ts", "node_modules/rxjs/src/internal/operators/finalize.ts", "node_modules/rxjs/src/internal/operators/first.ts", "node_modules/rxjs/src/internal/operators/takeLast.ts", "node_modules/rxjs/src/internal/operators/merge.ts", "node_modules/rxjs/src/internal/operators/mergeWith.ts", "node_modules/rxjs/src/internal/operators/repeat.ts", "node_modules/rxjs/src/internal/operators/scan.ts", "node_modules/rxjs/src/internal/operators/share.ts", "node_modules/rxjs/src/internal/operators/shareReplay.ts", "node_modules/rxjs/src/internal/operators/skip.ts", "node_modules/rxjs/src/internal/operators/skipUntil.ts", "node_modules/rxjs/src/internal/operators/startWith.ts", "node_modules/rxjs/src/internal/operators/switchMap.ts", "node_modules/rxjs/src/internal/operators/takeUntil.ts", "node_modules/rxjs/src/internal/operators/takeWhile.ts", "node_modules/rxjs/src/internal/operators/tap.ts", "node_modules/rxjs/src/internal/operators/throttle.ts", "node_modules/rxjs/src/internal/operators/throttleTime.ts", "node_modules/rxjs/src/internal/operators/withLatestFrom.ts", "node_modules/rxjs/src/internal/operators/zip.ts", "node_modules/rxjs/src/internal/operators/zipWith.ts", "src/templates/assets/javascripts/browser/document/index.ts", "src/templates/assets/javascripts/browser/element/_/index.ts", "src/templates/assets/javascripts/browser/element/focus/index.ts", "src/templates/assets/javascripts/browser/element/hover/index.ts", "src/templates/assets/javascripts/utilities/h/index.ts", "src/templates/assets/javascripts/utilities/round/index.ts", "src/templates/assets/javascripts/browser/script/index.ts", "src/templates/assets/javascripts/browser/element/size/_/index.ts", "src/templates/assets/javascripts/browser/element/size/content/index.ts", "src/templates/assets/javascripts/browser/element/offset/_/index.ts", "src/templates/assets/javascripts/browser/element/offset/content/index.ts", "src/templates/assets/javascripts/browser/element/visibility/index.ts", "src/templates/assets/javascripts/browser/toggle/index.ts", "src/templates/assets/javascripts/browser/keyboard/index.ts", "src/templates/assets/javascripts/browser/location/_/index.ts", "src/templates/assets/javascripts/browser/location/hash/index.ts", "src/templates/assets/javascripts/browser/media/index.ts", "src/templates/assets/javascripts/browser/request/index.ts", "src/templates/assets/javascripts/browser/viewport/offset/index.ts", "src/templates/assets/javascripts/browser/viewport/size/index.ts", "src/templates/assets/javascripts/browser/viewport/_/index.ts", "src/templates/assets/javascripts/browser/viewport/at/index.ts", "src/templates/assets/javascripts/browser/worker/index.ts", "src/templates/assets/javascripts/_/index.ts", "src/templates/assets/javascripts/components/_/index.ts", "src/templates/assets/javascripts/components/announce/index.ts", "src/templates/assets/javascripts/components/consent/index.ts", "src/templates/assets/javascripts/templates/tooltip/index.tsx", "src/templates/assets/javascripts/templates/annotation/index.tsx", "src/templates/assets/javascripts/templates/clipboard/index.tsx", "src/templates/assets/javascripts/templates/search/index.tsx", "src/templates/assets/javascripts/templates/source/index.tsx", "src/templates/assets/javascripts/templates/tabbed/index.tsx", "src/templates/assets/javascripts/templates/table/index.tsx", "src/templates/assets/javascripts/templates/version/index.tsx", "src/templates/assets/javascripts/components/tooltip2/index.ts", "src/templates/assets/javascripts/components/content/annotation/_/index.ts", "src/templates/assets/javascripts/components/content/annotation/list/index.ts", "src/templates/assets/javascripts/components/content/annotation/block/index.ts", "src/templates/assets/javascripts/components/content/code/_/index.ts", "src/templates/assets/javascripts/components/content/details/index.ts", "src/templates/assets/javascripts/components/content/mermaid/index.css", "src/templates/assets/javascripts/components/content/mermaid/index.ts", "src/templates/assets/javascripts/components/content/table/index.ts", "src/templates/assets/javascripts/components/content/tabs/index.ts", "src/templates/assets/javascripts/components/content/_/index.ts", "src/templates/assets/javascripts/components/dialog/index.ts", "src/templates/assets/javascripts/components/tooltip/index.ts", "src/templates/assets/javascripts/components/header/_/index.ts", "src/templates/assets/javascripts/components/header/title/index.ts", "src/templates/assets/javascripts/components/main/index.ts", "src/templates/assets/javascripts/components/palette/index.ts", "src/templates/assets/javascripts/components/progress/index.ts", "src/templates/assets/javascripts/integrations/clipboard/index.ts", "src/templates/assets/javascripts/integrations/sitemap/index.ts", "src/templates/assets/javascripts/integrations/instant/index.ts", "src/templates/assets/javascripts/integrations/search/highlighter/index.ts", "src/templates/assets/javascripts/integrations/search/worker/message/index.ts", "src/templates/assets/javascripts/integrations/search/worker/_/index.ts", "src/templates/assets/javascripts/integrations/version/index.ts", "src/templates/assets/javascripts/components/search/query/index.ts", "src/templates/assets/javascripts/components/search/result/index.ts", "src/templates/assets/javascripts/components/search/share/index.ts", "src/templates/assets/javascripts/components/search/suggest/index.ts", "src/templates/assets/javascripts/components/search/_/index.ts", "src/templates/assets/javascripts/components/search/highlight/index.ts", "src/templates/assets/javascripts/components/sidebar/index.ts", "src/templates/assets/javascripts/components/source/facts/github/index.ts", "src/templates/assets/javascripts/components/source/facts/gitlab/index.ts", "src/templates/assets/javascripts/components/source/facts/_/index.ts", "src/templates/assets/javascripts/components/source/_/index.ts", "src/templates/assets/javascripts/components/tabs/index.ts", "src/templates/assets/javascripts/components/toc/index.ts", "src/templates/assets/javascripts/components/top/index.ts", "src/templates/assets/javascripts/patches/ellipsis/index.ts", "src/templates/assets/javascripts/patches/indeterminate/index.ts", "src/templates/assets/javascripts/patches/scrollfix/index.ts", "src/templates/assets/javascripts/patches/scrolllock/index.ts", "src/templates/assets/javascripts/polyfills/index.ts"],
+ "sourcesContent": ["(function (global, factory) {\n typeof exports === 'object' && typeof module !== 'undefined' ? factory() :\n typeof define === 'function' && define.amd ? define(factory) :\n (factory());\n}(this, (function () { 'use strict';\n\n /**\n * Applies the :focus-visible polyfill at the given scope.\n * A scope in this case is either the top-level Document or a Shadow Root.\n *\n * @param {(Document|ShadowRoot)} scope\n * @see https://github.com/WICG/focus-visible\n */\n function applyFocusVisiblePolyfill(scope) {\n var hadKeyboardEvent = true;\n var hadFocusVisibleRecently = false;\n var hadFocusVisibleRecentlyTimeout = null;\n\n var inputTypesAllowlist = {\n text: true,\n search: true,\n url: true,\n tel: true,\n email: true,\n password: true,\n number: true,\n date: true,\n month: true,\n week: true,\n time: true,\n datetime: true,\n 'datetime-local': true\n };\n\n /**\n * Helper function for legacy browsers and iframes which sometimes focus\n * elements like document, body, and non-interactive SVG.\n * @param {Element} el\n */\n function isValidFocusTarget(el) {\n if (\n el &&\n el !== document &&\n el.nodeName !== 'HTML' &&\n el.nodeName !== 'BODY' &&\n 'classList' in el &&\n 'contains' in el.classList\n ) {\n return true;\n }\n return false;\n }\n\n /**\n * Computes whether the given element should automatically trigger the\n * `focus-visible` class being added, i.e. whether it should always match\n * `:focus-visible` when focused.\n * @param {Element} el\n * @return {boolean}\n */\n function focusTriggersKeyboardModality(el) {\n var type = el.type;\n var tagName = el.tagName;\n\n if (tagName === 'INPUT' && inputTypesAllowlist[type] && !el.readOnly) {\n return true;\n }\n\n if (tagName === 'TEXTAREA' && !el.readOnly) {\n return true;\n }\n\n if (el.isContentEditable) {\n return true;\n }\n\n return false;\n }\n\n /**\n * Add the `focus-visible` class to the given element if it was not added by\n * the author.\n * @param {Element} el\n */\n function addFocusVisibleClass(el) {\n if (el.classList.contains('focus-visible')) {\n return;\n }\n el.classList.add('focus-visible');\n el.setAttribute('data-focus-visible-added', '');\n }\n\n /**\n * Remove the `focus-visible` class from the given element if it was not\n * originally added by the author.\n * @param {Element} el\n */\n function removeFocusVisibleClass(el) {\n if (!el.hasAttribute('data-focus-visible-added')) {\n return;\n }\n el.classList.remove('focus-visible');\n el.removeAttribute('data-focus-visible-added');\n }\n\n /**\n * If the most recent user interaction was via the keyboard;\n * and the key press did not include a meta, alt/option, or control key;\n * then the modality is keyboard. Otherwise, the modality is not keyboard.\n * Apply `focus-visible` to any current active element and keep track\n * of our keyboard modality state with `hadKeyboardEvent`.\n * @param {KeyboardEvent} e\n */\n function onKeyDown(e) {\n if (e.metaKey || e.altKey || e.ctrlKey) {\n return;\n }\n\n if (isValidFocusTarget(scope.activeElement)) {\n addFocusVisibleClass(scope.activeElement);\n }\n\n hadKeyboardEvent = true;\n }\n\n /**\n * If at any point a user clicks with a pointing device, ensure that we change\n * the modality away from keyboard.\n * This avoids the situation where a user presses a key on an already focused\n * element, and then clicks on a different element, focusing it with a\n * pointing device, while we still think we're in keyboard modality.\n * @param {Event} e\n */\n function onPointerDown(e) {\n hadKeyboardEvent = false;\n }\n\n /**\n * On `focus`, add the `focus-visible` class to the target if:\n * - the target received focus as a result of keyboard navigation, or\n * - the event target is an element that will likely require interaction\n * via the keyboard (e.g. a text box)\n * @param {Event} e\n */\n function onFocus(e) {\n // Prevent IE from focusing the document or HTML element.\n if (!isValidFocusTarget(e.target)) {\n return;\n }\n\n if (hadKeyboardEvent || focusTriggersKeyboardModality(e.target)) {\n addFocusVisibleClass(e.target);\n }\n }\n\n /**\n * On `blur`, remove the `focus-visible` class from the target.\n * @param {Event} e\n */\n function onBlur(e) {\n if (!isValidFocusTarget(e.target)) {\n return;\n }\n\n if (\n e.target.classList.contains('focus-visible') ||\n e.target.hasAttribute('data-focus-visible-added')\n ) {\n // To detect a tab/window switch, we look for a blur event followed\n // rapidly by a visibility change.\n // If we don't see a visibility change within 100ms, it's probably a\n // regular focus change.\n hadFocusVisibleRecently = true;\n window.clearTimeout(hadFocusVisibleRecentlyTimeout);\n hadFocusVisibleRecentlyTimeout = window.setTimeout(function() {\n hadFocusVisibleRecently = false;\n }, 100);\n removeFocusVisibleClass(e.target);\n }\n }\n\n /**\n * If the user changes tabs, keep track of whether or not the previously\n * focused element had .focus-visible.\n * @param {Event} e\n */\n function onVisibilityChange(e) {\n if (document.visibilityState === 'hidden') {\n // If the tab becomes active again, the browser will handle calling focus\n // on the element (Safari actually calls it twice).\n // If this tab change caused a blur on an element with focus-visible,\n // re-apply the class when the user switches back to the tab.\n if (hadFocusVisibleRecently) {\n hadKeyboardEvent = true;\n }\n addInitialPointerMoveListeners();\n }\n }\n\n /**\n * Add a group of listeners to detect usage of any pointing devices.\n * These listeners will be added when the polyfill first loads, and anytime\n * the window is blurred, so that they are active when the window regains\n * focus.\n */\n function addInitialPointerMoveListeners() {\n document.addEventListener('mousemove', onInitialPointerMove);\n document.addEventListener('mousedown', onInitialPointerMove);\n document.addEventListener('mouseup', onInitialPointerMove);\n document.addEventListener('pointermove', onInitialPointerMove);\n document.addEventListener('pointerdown', onInitialPointerMove);\n document.addEventListener('pointerup', onInitialPointerMove);\n document.addEventListener('touchmove', onInitialPointerMove);\n document.addEventListener('touchstart', onInitialPointerMove);\n document.addEventListener('touchend', onInitialPointerMove);\n }\n\n function removeInitialPointerMoveListeners() {\n document.removeEventListener('mousemove', onInitialPointerMove);\n document.removeEventListener('mousedown', onInitialPointerMove);\n document.removeEventListener('mouseup', onInitialPointerMove);\n document.removeEventListener('pointermove', onInitialPointerMove);\n document.removeEventListener('pointerdown', onInitialPointerMove);\n document.removeEventListener('pointerup', onInitialPointerMove);\n document.removeEventListener('touchmove', onInitialPointerMove);\n document.removeEventListener('touchstart', onInitialPointerMove);\n document.removeEventListener('touchend', onInitialPointerMove);\n }\n\n /**\n * When the polfyill first loads, assume the user is in keyboard modality.\n * If any event is received from a pointing device (e.g. mouse, pointer,\n * touch), turn off keyboard modality.\n * This accounts for situations where focus enters the page from the URL bar.\n * @param {Event} e\n */\n function onInitialPointerMove(e) {\n // Work around a Safari quirk that fires a mousemove on whenever the\n // window blurs, even if you're tabbing out of the page. \u00AF\\_(\u30C4)_/\u00AF\n if (e.target.nodeName && e.target.nodeName.toLowerCase() === 'html') {\n return;\n }\n\n hadKeyboardEvent = false;\n removeInitialPointerMoveListeners();\n }\n\n // For some kinds of state, we are interested in changes at the global scope\n // only. For example, global pointer input, global key presses and global\n // visibility change should affect the state at every scope:\n document.addEventListener('keydown', onKeyDown, true);\n document.addEventListener('mousedown', onPointerDown, true);\n document.addEventListener('pointerdown', onPointerDown, true);\n document.addEventListener('touchstart', onPointerDown, true);\n document.addEventListener('visibilitychange', onVisibilityChange, true);\n\n addInitialPointerMoveListeners();\n\n // For focus and blur, we specifically care about state changes in the local\n // scope. This is because focus / blur events that originate from within a\n // shadow root are not re-dispatched from the host element if it was already\n // the active element in its own scope:\n scope.addEventListener('focus', onFocus, true);\n scope.addEventListener('blur', onBlur, true);\n\n // We detect that a node is a ShadowRoot by ensuring that it is a\n // DocumentFragment and also has a host property. This check covers native\n // implementation and polyfill implementation transparently. If we only cared\n // about the native implementation, we could just check if the scope was\n // an instance of a ShadowRoot.\n if (scope.nodeType === Node.DOCUMENT_FRAGMENT_NODE && scope.host) {\n // Since a ShadowRoot is a special kind of DocumentFragment, it does not\n // have a root element to add a class to. So, we add this attribute to the\n // host element instead:\n scope.host.setAttribute('data-js-focus-visible', '');\n } else if (scope.nodeType === Node.DOCUMENT_NODE) {\n document.documentElement.classList.add('js-focus-visible');\n document.documentElement.setAttribute('data-js-focus-visible', '');\n }\n }\n\n // It is important to wrap all references to global window and document in\n // these checks to support server-side rendering use cases\n // @see https://github.com/WICG/focus-visible/issues/199\n if (typeof window !== 'undefined' && typeof document !== 'undefined') {\n // Make the polyfill helper globally available. This can be used as a signal\n // to interested libraries that wish to coordinate with the polyfill for e.g.,\n // applying the polyfill to a shadow root:\n window.applyFocusVisiblePolyfill = applyFocusVisiblePolyfill;\n\n // Notify interested libraries of the polyfill's presence, in case the\n // polyfill was loaded lazily:\n var event;\n\n try {\n event = new CustomEvent('focus-visible-polyfill-ready');\n } catch (error) {\n // IE11 does not support using CustomEvent as a constructor directly:\n event = document.createEvent('CustomEvent');\n event.initCustomEvent('focus-visible-polyfill-ready', false, false, {});\n }\n\n window.dispatchEvent(event);\n }\n\n if (typeof document !== 'undefined') {\n // Apply the polyfill to the global document, so that no JavaScript\n // coordination is required to use the polyfill in the top-level document:\n applyFocusVisiblePolyfill(document);\n }\n\n})));\n", "/*!\n * clipboard.js v2.0.11\n * https://clipboardjs.com/\n *\n * Licensed MIT \u00A9 Zeno Rocha\n */\n(function webpackUniversalModuleDefinition(root, factory) {\n\tif(typeof exports === 'object' && typeof module === 'object')\n\t\tmodule.exports = factory();\n\telse if(typeof define === 'function' && define.amd)\n\t\tdefine([], factory);\n\telse if(typeof exports === 'object')\n\t\texports[\"ClipboardJS\"] = factory();\n\telse\n\t\troot[\"ClipboardJS\"] = factory();\n})(this, function() {\nreturn /******/ (function() { // webpackBootstrap\n/******/ \tvar __webpack_modules__ = ({\n\n/***/ 686:\n/***/ (function(__unused_webpack_module, __webpack_exports__, __webpack_require__) {\n\n\"use strict\";\n\n// EXPORTS\n__webpack_require__.d(__webpack_exports__, {\n \"default\": function() { return /* binding */ clipboard; }\n});\n\n// EXTERNAL MODULE: ./node_modules/tiny-emitter/index.js\nvar tiny_emitter = __webpack_require__(279);\nvar tiny_emitter_default = /*#__PURE__*/__webpack_require__.n(tiny_emitter);\n// EXTERNAL MODULE: ./node_modules/good-listener/src/listen.js\nvar listen = __webpack_require__(370);\nvar listen_default = /*#__PURE__*/__webpack_require__.n(listen);\n// EXTERNAL MODULE: ./node_modules/select/src/select.js\nvar src_select = __webpack_require__(817);\nvar select_default = /*#__PURE__*/__webpack_require__.n(src_select);\n;// CONCATENATED MODULE: ./src/common/command.js\n/**\n * Executes a given operation type.\n * @param {String} type\n * @return {Boolean}\n */\nfunction command(type) {\n try {\n return document.execCommand(type);\n } catch (err) {\n return false;\n }\n}\n;// CONCATENATED MODULE: ./src/actions/cut.js\n\n\n/**\n * Cut action wrapper.\n * @param {String|HTMLElement} target\n * @return {String}\n */\n\nvar ClipboardActionCut = function ClipboardActionCut(target) {\n var selectedText = select_default()(target);\n command('cut');\n return selectedText;\n};\n\n/* harmony default export */ var actions_cut = (ClipboardActionCut);\n;// CONCATENATED MODULE: ./src/common/create-fake-element.js\n/**\n * Creates a fake textarea element with a value.\n * @param {String} value\n * @return {HTMLElement}\n */\nfunction createFakeElement(value) {\n var isRTL = document.documentElement.getAttribute('dir') === 'rtl';\n var fakeElement = document.createElement('textarea'); // Prevent zooming on iOS\n\n fakeElement.style.fontSize = '12pt'; // Reset box model\n\n fakeElement.style.border = '0';\n fakeElement.style.padding = '0';\n fakeElement.style.margin = '0'; // Move element out of screen horizontally\n\n fakeElement.style.position = 'absolute';\n fakeElement.style[isRTL ? 'right' : 'left'] = '-9999px'; // Move element to the same position vertically\n\n var yPosition = window.pageYOffset || document.documentElement.scrollTop;\n fakeElement.style.top = \"\".concat(yPosition, \"px\");\n fakeElement.setAttribute('readonly', '');\n fakeElement.value = value;\n return fakeElement;\n}\n;// CONCATENATED MODULE: ./src/actions/copy.js\n\n\n\n/**\n * Create fake copy action wrapper using a fake element.\n * @param {String} target\n * @param {Object} options\n * @return {String}\n */\n\nvar fakeCopyAction = function fakeCopyAction(value, options) {\n var fakeElement = createFakeElement(value);\n options.container.appendChild(fakeElement);\n var selectedText = select_default()(fakeElement);\n command('copy');\n fakeElement.remove();\n return selectedText;\n};\n/**\n * Copy action wrapper.\n * @param {String|HTMLElement} target\n * @param {Object} options\n * @return {String}\n */\n\n\nvar ClipboardActionCopy = function ClipboardActionCopy(target) {\n var options = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {\n container: document.body\n };\n var selectedText = '';\n\n if (typeof target === 'string') {\n selectedText = fakeCopyAction(target, options);\n } else if (target instanceof HTMLInputElement && !['text', 'search', 'url', 'tel', 'password'].includes(target === null || target === void 0 ? void 0 : target.type)) {\n // If input type doesn't support `setSelectionRange`. Simulate it. https://developer.mozilla.org/en-US/docs/Web/API/HTMLInputElement/setSelectionRange\n selectedText = fakeCopyAction(target.value, options);\n } else {\n selectedText = select_default()(target);\n command('copy');\n }\n\n return selectedText;\n};\n\n/* harmony default export */ var actions_copy = (ClipboardActionCopy);\n;// CONCATENATED MODULE: ./src/actions/default.js\nfunction _typeof(obj) { \"@babel/helpers - typeof\"; if (typeof Symbol === \"function\" && typeof Symbol.iterator === \"symbol\") { _typeof = function _typeof(obj) { return typeof obj; }; } else { _typeof = function _typeof(obj) { return obj && typeof Symbol === \"function\" && obj.constructor === Symbol && obj !== Symbol.prototype ? \"symbol\" : typeof obj; }; } return _typeof(obj); }\n\n\n\n/**\n * Inner function which performs selection from either `text` or `target`\n * properties and then executes copy or cut operations.\n * @param {Object} options\n */\n\nvar ClipboardActionDefault = function ClipboardActionDefault() {\n var options = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : {};\n // Defines base properties passed from constructor.\n var _options$action = options.action,\n action = _options$action === void 0 ? 'copy' : _options$action,\n container = options.container,\n target = options.target,\n text = options.text; // Sets the `action` to be performed which can be either 'copy' or 'cut'.\n\n if (action !== 'copy' && action !== 'cut') {\n throw new Error('Invalid \"action\" value, use either \"copy\" or \"cut\"');\n } // Sets the `target` property using an element that will be have its content copied.\n\n\n if (target !== undefined) {\n if (target && _typeof(target) === 'object' && target.nodeType === 1) {\n if (action === 'copy' && target.hasAttribute('disabled')) {\n throw new Error('Invalid \"target\" attribute. Please use \"readonly\" instead of \"disabled\" attribute');\n }\n\n if (action === 'cut' && (target.hasAttribute('readonly') || target.hasAttribute('disabled'))) {\n throw new Error('Invalid \"target\" attribute. You can\\'t cut text from elements with \"readonly\" or \"disabled\" attributes');\n }\n } else {\n throw new Error('Invalid \"target\" value, use a valid Element');\n }\n } // Define selection strategy based on `text` property.\n\n\n if (text) {\n return actions_copy(text, {\n container: container\n });\n } // Defines which selection strategy based on `target` property.\n\n\n if (target) {\n return action === 'cut' ? actions_cut(target) : actions_copy(target, {\n container: container\n });\n }\n};\n\n/* harmony default export */ var actions_default = (ClipboardActionDefault);\n;// CONCATENATED MODULE: ./src/clipboard.js\nfunction clipboard_typeof(obj) { \"@babel/helpers - typeof\"; if (typeof Symbol === \"function\" && typeof Symbol.iterator === \"symbol\") { clipboard_typeof = function _typeof(obj) { return typeof obj; }; } else { clipboard_typeof = function _typeof(obj) { return obj && typeof Symbol === \"function\" && obj.constructor === Symbol && obj !== Symbol.prototype ? \"symbol\" : typeof obj; }; } return clipboard_typeof(obj); }\n\nfunction _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError(\"Cannot call a class as a function\"); } }\n\nfunction _defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if (\"value\" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } }\n\nfunction _createClass(Constructor, protoProps, staticProps) { if (protoProps) _defineProperties(Constructor.prototype, protoProps); if (staticProps) _defineProperties(Constructor, staticProps); return Constructor; }\n\nfunction _inherits(subClass, superClass) { if (typeof superClass !== \"function\" && superClass !== null) { throw new TypeError(\"Super expression must either be null or a function\"); } subClass.prototype = Object.create(superClass && superClass.prototype, { constructor: { value: subClass, writable: true, configurable: true } }); if (superClass) _setPrototypeOf(subClass, superClass); }\n\nfunction _setPrototypeOf(o, p) { _setPrototypeOf = Object.setPrototypeOf || function _setPrototypeOf(o, p) { o.__proto__ = p; return o; }; return _setPrototypeOf(o, p); }\n\nfunction _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = _getPrototypeOf(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = _getPrototypeOf(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return _possibleConstructorReturn(this, result); }; }\n\nfunction _possibleConstructorReturn(self, call) { if (call && (clipboard_typeof(call) === \"object\" || typeof call === \"function\")) { return call; } return _assertThisInitialized(self); }\n\nfunction _assertThisInitialized(self) { if (self === void 0) { throw new ReferenceError(\"this hasn't been initialised - super() hasn't been called\"); } return self; }\n\nfunction _isNativeReflectConstruct() { if (typeof Reflect === \"undefined\" || !Reflect.construct) return false; if (Reflect.construct.sham) return false; if (typeof Proxy === \"function\") return true; try { Date.prototype.toString.call(Reflect.construct(Date, [], function () {})); return true; } catch (e) { return false; } }\n\nfunction _getPrototypeOf(o) { _getPrototypeOf = Object.setPrototypeOf ? Object.getPrototypeOf : function _getPrototypeOf(o) { return o.__proto__ || Object.getPrototypeOf(o); }; return _getPrototypeOf(o); }\n\n\n\n\n\n\n/**\n * Helper function to retrieve attribute value.\n * @param {String} suffix\n * @param {Element} element\n */\n\nfunction getAttributeValue(suffix, element) {\n var attribute = \"data-clipboard-\".concat(suffix);\n\n if (!element.hasAttribute(attribute)) {\n return;\n }\n\n return element.getAttribute(attribute);\n}\n/**\n * Base class which takes one or more elements, adds event listeners to them,\n * and instantiates a new `ClipboardAction` on each click.\n */\n\n\nvar Clipboard = /*#__PURE__*/function (_Emitter) {\n _inherits(Clipboard, _Emitter);\n\n var _super = _createSuper(Clipboard);\n\n /**\n * @param {String|HTMLElement|HTMLCollection|NodeList} trigger\n * @param {Object} options\n */\n function Clipboard(trigger, options) {\n var _this;\n\n _classCallCheck(this, Clipboard);\n\n _this = _super.call(this);\n\n _this.resolveOptions(options);\n\n _this.listenClick(trigger);\n\n return _this;\n }\n /**\n * Defines if attributes would be resolved using internal setter functions\n * or custom functions that were passed in the constructor.\n * @param {Object} options\n */\n\n\n _createClass(Clipboard, [{\n key: \"resolveOptions\",\n value: function resolveOptions() {\n var options = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : {};\n this.action = typeof options.action === 'function' ? options.action : this.defaultAction;\n this.target = typeof options.target === 'function' ? options.target : this.defaultTarget;\n this.text = typeof options.text === 'function' ? options.text : this.defaultText;\n this.container = clipboard_typeof(options.container) === 'object' ? options.container : document.body;\n }\n /**\n * Adds a click event listener to the passed trigger.\n * @param {String|HTMLElement|HTMLCollection|NodeList} trigger\n */\n\n }, {\n key: \"listenClick\",\n value: function listenClick(trigger) {\n var _this2 = this;\n\n this.listener = listen_default()(trigger, 'click', function (e) {\n return _this2.onClick(e);\n });\n }\n /**\n * Defines a new `ClipboardAction` on each click event.\n * @param {Event} e\n */\n\n }, {\n key: \"onClick\",\n value: function onClick(e) {\n var trigger = e.delegateTarget || e.currentTarget;\n var action = this.action(trigger) || 'copy';\n var text = actions_default({\n action: action,\n container: this.container,\n target: this.target(trigger),\n text: this.text(trigger)\n }); // Fires an event based on the copy operation result.\n\n this.emit(text ? 'success' : 'error', {\n action: action,\n text: text,\n trigger: trigger,\n clearSelection: function clearSelection() {\n if (trigger) {\n trigger.focus();\n }\n\n window.getSelection().removeAllRanges();\n }\n });\n }\n /**\n * Default `action` lookup function.\n * @param {Element} trigger\n */\n\n }, {\n key: \"defaultAction\",\n value: function defaultAction(trigger) {\n return getAttributeValue('action', trigger);\n }\n /**\n * Default `target` lookup function.\n * @param {Element} trigger\n */\n\n }, {\n key: \"defaultTarget\",\n value: function defaultTarget(trigger) {\n var selector = getAttributeValue('target', trigger);\n\n if (selector) {\n return document.querySelector(selector);\n }\n }\n /**\n * Allow fire programmatically a copy action\n * @param {String|HTMLElement} target\n * @param {Object} options\n * @returns Text copied.\n */\n\n }, {\n key: \"defaultText\",\n\n /**\n * Default `text` lookup function.\n * @param {Element} trigger\n */\n value: function defaultText(trigger) {\n return getAttributeValue('text', trigger);\n }\n /**\n * Destroy lifecycle.\n */\n\n }, {\n key: \"destroy\",\n value: function destroy() {\n this.listener.destroy();\n }\n }], [{\n key: \"copy\",\n value: function copy(target) {\n var options = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {\n container: document.body\n };\n return actions_copy(target, options);\n }\n /**\n * Allow fire programmatically a cut action\n * @param {String|HTMLElement} target\n * @returns Text cutted.\n */\n\n }, {\n key: \"cut\",\n value: function cut(target) {\n return actions_cut(target);\n }\n /**\n * Returns the support of the given action, or all actions if no action is\n * given.\n * @param {String} [action]\n */\n\n }, {\n key: \"isSupported\",\n value: function isSupported() {\n var action = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : ['copy', 'cut'];\n var actions = typeof action === 'string' ? [action] : action;\n var support = !!document.queryCommandSupported;\n actions.forEach(function (action) {\n support = support && !!document.queryCommandSupported(action);\n });\n return support;\n }\n }]);\n\n return Clipboard;\n}((tiny_emitter_default()));\n\n/* harmony default export */ var clipboard = (Clipboard);\n\n/***/ }),\n\n/***/ 828:\n/***/ (function(module) {\n\nvar DOCUMENT_NODE_TYPE = 9;\n\n/**\n * A polyfill for Element.matches()\n */\nif (typeof Element !== 'undefined' && !Element.prototype.matches) {\n var proto = Element.prototype;\n\n proto.matches = proto.matchesSelector ||\n proto.mozMatchesSelector ||\n proto.msMatchesSelector ||\n proto.oMatchesSelector ||\n proto.webkitMatchesSelector;\n}\n\n/**\n * Finds the closest parent that matches a selector.\n *\n * @param {Element} element\n * @param {String} selector\n * @return {Function}\n */\nfunction closest (element, selector) {\n while (element && element.nodeType !== DOCUMENT_NODE_TYPE) {\n if (typeof element.matches === 'function' &&\n element.matches(selector)) {\n return element;\n }\n element = element.parentNode;\n }\n}\n\nmodule.exports = closest;\n\n\n/***/ }),\n\n/***/ 438:\n/***/ (function(module, __unused_webpack_exports, __webpack_require__) {\n\nvar closest = __webpack_require__(828);\n\n/**\n * Delegates event to a selector.\n *\n * @param {Element} element\n * @param {String} selector\n * @param {String} type\n * @param {Function} callback\n * @param {Boolean} useCapture\n * @return {Object}\n */\nfunction _delegate(element, selector, type, callback, useCapture) {\n var listenerFn = listener.apply(this, arguments);\n\n element.addEventListener(type, listenerFn, useCapture);\n\n return {\n destroy: function() {\n element.removeEventListener(type, listenerFn, useCapture);\n }\n }\n}\n\n/**\n * Delegates event to a selector.\n *\n * @param {Element|String|Array} [elements]\n * @param {String} selector\n * @param {String} type\n * @param {Function} callback\n * @param {Boolean} useCapture\n * @return {Object}\n */\nfunction delegate(elements, selector, type, callback, useCapture) {\n // Handle the regular Element usage\n if (typeof elements.addEventListener === 'function') {\n return _delegate.apply(null, arguments);\n }\n\n // Handle Element-less usage, it defaults to global delegation\n if (typeof type === 'function') {\n // Use `document` as the first parameter, then apply arguments\n // This is a short way to .unshift `arguments` without running into deoptimizations\n return _delegate.bind(null, document).apply(null, arguments);\n }\n\n // Handle Selector-based usage\n if (typeof elements === 'string') {\n elements = document.querySelectorAll(elements);\n }\n\n // Handle Array-like based usage\n return Array.prototype.map.call(elements, function (element) {\n return _delegate(element, selector, type, callback, useCapture);\n });\n}\n\n/**\n * Finds closest match and invokes callback.\n *\n * @param {Element} element\n * @param {String} selector\n * @param {String} type\n * @param {Function} callback\n * @return {Function}\n */\nfunction listener(element, selector, type, callback) {\n return function(e) {\n e.delegateTarget = closest(e.target, selector);\n\n if (e.delegateTarget) {\n callback.call(element, e);\n }\n }\n}\n\nmodule.exports = delegate;\n\n\n/***/ }),\n\n/***/ 879:\n/***/ (function(__unused_webpack_module, exports) {\n\n/**\n * Check if argument is a HTML element.\n *\n * @param {Object} value\n * @return {Boolean}\n */\nexports.node = function(value) {\n return value !== undefined\n && value instanceof HTMLElement\n && value.nodeType === 1;\n};\n\n/**\n * Check if argument is a list of HTML elements.\n *\n * @param {Object} value\n * @return {Boolean}\n */\nexports.nodeList = function(value) {\n var type = Object.prototype.toString.call(value);\n\n return value !== undefined\n && (type === '[object NodeList]' || type === '[object HTMLCollection]')\n && ('length' in value)\n && (value.length === 0 || exports.node(value[0]));\n};\n\n/**\n * Check if argument is a string.\n *\n * @param {Object} value\n * @return {Boolean}\n */\nexports.string = function(value) {\n return typeof value === 'string'\n || value instanceof String;\n};\n\n/**\n * Check if argument is a function.\n *\n * @param {Object} value\n * @return {Boolean}\n */\nexports.fn = function(value) {\n var type = Object.prototype.toString.call(value);\n\n return type === '[object Function]';\n};\n\n\n/***/ }),\n\n/***/ 370:\n/***/ (function(module, __unused_webpack_exports, __webpack_require__) {\n\nvar is = __webpack_require__(879);\nvar delegate = __webpack_require__(438);\n\n/**\n * Validates all params and calls the right\n * listener function based on its target type.\n *\n * @param {String|HTMLElement|HTMLCollection|NodeList} target\n * @param {String} type\n * @param {Function} callback\n * @return {Object}\n */\nfunction listen(target, type, callback) {\n if (!target && !type && !callback) {\n throw new Error('Missing required arguments');\n }\n\n if (!is.string(type)) {\n throw new TypeError('Second argument must be a String');\n }\n\n if (!is.fn(callback)) {\n throw new TypeError('Third argument must be a Function');\n }\n\n if (is.node(target)) {\n return listenNode(target, type, callback);\n }\n else if (is.nodeList(target)) {\n return listenNodeList(target, type, callback);\n }\n else if (is.string(target)) {\n return listenSelector(target, type, callback);\n }\n else {\n throw new TypeError('First argument must be a String, HTMLElement, HTMLCollection, or NodeList');\n }\n}\n\n/**\n * Adds an event listener to a HTML element\n * and returns a remove listener function.\n *\n * @param {HTMLElement} node\n * @param {String} type\n * @param {Function} callback\n * @return {Object}\n */\nfunction listenNode(node, type, callback) {\n node.addEventListener(type, callback);\n\n return {\n destroy: function() {\n node.removeEventListener(type, callback);\n }\n }\n}\n\n/**\n * Add an event listener to a list of HTML elements\n * and returns a remove listener function.\n *\n * @param {NodeList|HTMLCollection} nodeList\n * @param {String} type\n * @param {Function} callback\n * @return {Object}\n */\nfunction listenNodeList(nodeList, type, callback) {\n Array.prototype.forEach.call(nodeList, function(node) {\n node.addEventListener(type, callback);\n });\n\n return {\n destroy: function() {\n Array.prototype.forEach.call(nodeList, function(node) {\n node.removeEventListener(type, callback);\n });\n }\n }\n}\n\n/**\n * Add an event listener to a selector\n * and returns a remove listener function.\n *\n * @param {String} selector\n * @param {String} type\n * @param {Function} callback\n * @return {Object}\n */\nfunction listenSelector(selector, type, callback) {\n return delegate(document.body, selector, type, callback);\n}\n\nmodule.exports = listen;\n\n\n/***/ }),\n\n/***/ 817:\n/***/ (function(module) {\n\nfunction select(element) {\n var selectedText;\n\n if (element.nodeName === 'SELECT') {\n element.focus();\n\n selectedText = element.value;\n }\n else if (element.nodeName === 'INPUT' || element.nodeName === 'TEXTAREA') {\n var isReadOnly = element.hasAttribute('readonly');\n\n if (!isReadOnly) {\n element.setAttribute('readonly', '');\n }\n\n element.select();\n element.setSelectionRange(0, element.value.length);\n\n if (!isReadOnly) {\n element.removeAttribute('readonly');\n }\n\n selectedText = element.value;\n }\n else {\n if (element.hasAttribute('contenteditable')) {\n element.focus();\n }\n\n var selection = window.getSelection();\n var range = document.createRange();\n\n range.selectNodeContents(element);\n selection.removeAllRanges();\n selection.addRange(range);\n\n selectedText = selection.toString();\n }\n\n return selectedText;\n}\n\nmodule.exports = select;\n\n\n/***/ }),\n\n/***/ 279:\n/***/ (function(module) {\n\nfunction E () {\n // Keep this empty so it's easier to inherit from\n // (via https://github.com/lipsmack from https://github.com/scottcorgan/tiny-emitter/issues/3)\n}\n\nE.prototype = {\n on: function (name, callback, ctx) {\n var e = this.e || (this.e = {});\n\n (e[name] || (e[name] = [])).push({\n fn: callback,\n ctx: ctx\n });\n\n return this;\n },\n\n once: function (name, callback, ctx) {\n var self = this;\n function listener () {\n self.off(name, listener);\n callback.apply(ctx, arguments);\n };\n\n listener._ = callback\n return this.on(name, listener, ctx);\n },\n\n emit: function (name) {\n var data = [].slice.call(arguments, 1);\n var evtArr = ((this.e || (this.e = {}))[name] || []).slice();\n var i = 0;\n var len = evtArr.length;\n\n for (i; i < len; i++) {\n evtArr[i].fn.apply(evtArr[i].ctx, data);\n }\n\n return this;\n },\n\n off: function (name, callback) {\n var e = this.e || (this.e = {});\n var evts = e[name];\n var liveEvents = [];\n\n if (evts && callback) {\n for (var i = 0, len = evts.length; i < len; i++) {\n if (evts[i].fn !== callback && evts[i].fn._ !== callback)\n liveEvents.push(evts[i]);\n }\n }\n\n // Remove event from queue to prevent memory leak\n // Suggested by https://github.com/lazd\n // Ref: https://github.com/scottcorgan/tiny-emitter/commit/c6ebfaa9bc973b33d110a84a307742b7cf94c953#commitcomment-5024910\n\n (liveEvents.length)\n ? e[name] = liveEvents\n : delete e[name];\n\n return this;\n }\n};\n\nmodule.exports = E;\nmodule.exports.TinyEmitter = E;\n\n\n/***/ })\n\n/******/ \t});\n/************************************************************************/\n/******/ \t// The module cache\n/******/ \tvar __webpack_module_cache__ = {};\n/******/ \t\n/******/ \t// The require function\n/******/ \tfunction __webpack_require__(moduleId) {\n/******/ \t\t// Check if module is in cache\n/******/ \t\tif(__webpack_module_cache__[moduleId]) {\n/******/ \t\t\treturn __webpack_module_cache__[moduleId].exports;\n/******/ \t\t}\n/******/ \t\t// Create a new module (and put it into the cache)\n/******/ \t\tvar module = __webpack_module_cache__[moduleId] = {\n/******/ \t\t\t// no module.id needed\n/******/ \t\t\t// no module.loaded needed\n/******/ \t\t\texports: {}\n/******/ \t\t};\n/******/ \t\n/******/ \t\t// Execute the module function\n/******/ \t\t__webpack_modules__[moduleId](module, module.exports, __webpack_require__);\n/******/ \t\n/******/ \t\t// Return the exports of the module\n/******/ \t\treturn module.exports;\n/******/ \t}\n/******/ \t\n/************************************************************************/\n/******/ \t/* webpack/runtime/compat get default export */\n/******/ \t!function() {\n/******/ \t\t// getDefaultExport function for compatibility with non-harmony modules\n/******/ \t\t__webpack_require__.n = function(module) {\n/******/ \t\t\tvar getter = module && module.__esModule ?\n/******/ \t\t\t\tfunction() { return module['default']; } :\n/******/ \t\t\t\tfunction() { return module; };\n/******/ \t\t\t__webpack_require__.d(getter, { a: getter });\n/******/ \t\t\treturn getter;\n/******/ \t\t};\n/******/ \t}();\n/******/ \t\n/******/ \t/* webpack/runtime/define property getters */\n/******/ \t!function() {\n/******/ \t\t// define getter functions for harmony exports\n/******/ \t\t__webpack_require__.d = function(exports, definition) {\n/******/ \t\t\tfor(var key in definition) {\n/******/ \t\t\t\tif(__webpack_require__.o(definition, key) && !__webpack_require__.o(exports, key)) {\n/******/ \t\t\t\t\tObject.defineProperty(exports, key, { enumerable: true, get: definition[key] });\n/******/ \t\t\t\t}\n/******/ \t\t\t}\n/******/ \t\t};\n/******/ \t}();\n/******/ \t\n/******/ \t/* webpack/runtime/hasOwnProperty shorthand */\n/******/ \t!function() {\n/******/ \t\t__webpack_require__.o = function(obj, prop) { return Object.prototype.hasOwnProperty.call(obj, prop); }\n/******/ \t}();\n/******/ \t\n/************************************************************************/\n/******/ \t// module exports must be returned from runtime so entry inlining is disabled\n/******/ \t// startup\n/******/ \t// Load entry module and return exports\n/******/ \treturn __webpack_require__(686);\n/******/ })()\n.default;\n});", "/*!\n * escape-html\n * Copyright(c) 2012-2013 TJ Holowaychuk\n * Copyright(c) 2015 Andreas Lubbe\n * Copyright(c) 2015 Tiancheng \"Timothy\" Gu\n * MIT Licensed\n */\n\n'use strict';\n\n/**\n * Module variables.\n * @private\n */\n\nvar matchHtmlRegExp = /[\"'&<>]/;\n\n/**\n * Module exports.\n * @public\n */\n\nmodule.exports = escapeHtml;\n\n/**\n * Escape special characters in the given string of html.\n *\n * @param {string} string The string to escape for inserting into HTML\n * @return {string}\n * @public\n */\n\nfunction escapeHtml(string) {\n var str = '' + string;\n var match = matchHtmlRegExp.exec(str);\n\n if (!match) {\n return str;\n }\n\n var escape;\n var html = '';\n var index = 0;\n var lastIndex = 0;\n\n for (index = match.index; index < str.length; index++) {\n switch (str.charCodeAt(index)) {\n case 34: // \"\n escape = '"';\n break;\n case 38: // &\n escape = '&';\n break;\n case 39: // '\n escape = ''';\n break;\n case 60: // <\n escape = '<';\n break;\n case 62: // >\n escape = '>';\n break;\n default:\n continue;\n }\n\n if (lastIndex !== index) {\n html += str.substring(lastIndex, index);\n }\n\n lastIndex = index + 1;\n html += escape;\n }\n\n return lastIndex !== index\n ? html + str.substring(lastIndex, index)\n : html;\n}\n", "/*\n * Copyright (c) 2016-2024 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport \"focus-visible\"\n\nimport {\n EMPTY,\n NEVER,\n Observable,\n Subject,\n defer,\n delay,\n filter,\n map,\n merge,\n mergeWith,\n shareReplay,\n switchMap\n} from \"rxjs\"\n\nimport { configuration, feature } from \"./_\"\nimport {\n at,\n getActiveElement,\n getOptionalElement,\n requestJSON,\n setLocation,\n setToggle,\n watchDocument,\n watchKeyboard,\n watchLocation,\n watchLocationTarget,\n watchMedia,\n watchPrint,\n watchScript,\n watchViewport\n} from \"./browser\"\nimport {\n getComponentElement,\n getComponentElements,\n mountAnnounce,\n mountBackToTop,\n mountConsent,\n mountContent,\n mountDialog,\n mountHeader,\n mountHeaderTitle,\n mountPalette,\n mountProgress,\n mountSearch,\n mountSearchHiglight,\n mountSidebar,\n mountSource,\n mountTableOfContents,\n mountTabs,\n watchHeader,\n watchMain\n} from \"./components\"\nimport {\n SearchIndex,\n setupClipboardJS,\n setupInstantNavigation,\n setupVersionSelector\n} from \"./integrations\"\nimport {\n patchEllipsis,\n patchIndeterminate,\n patchScrollfix,\n patchScrolllock\n} from \"./patches\"\nimport \"./polyfills\"\n\n/* ----------------------------------------------------------------------------\n * Functions - @todo refactor\n * ------------------------------------------------------------------------- */\n\n/**\n * Fetch search index\n *\n * @returns Search index observable\n */\nfunction fetchSearchIndex(): Observable {\n if (location.protocol === \"file:\") {\n return watchScript(\n `${new URL(\"search/search_index.js\", config.base)}`\n )\n .pipe(\n // @ts-ignore - @todo fix typings\n map(() => __index),\n shareReplay(1)\n )\n } else {\n return requestJSON(\n new URL(\"search/search_index.json\", config.base)\n )\n }\n}\n\n/* ----------------------------------------------------------------------------\n * Application\n * ------------------------------------------------------------------------- */\n\n/* Yay, JavaScript is available */\ndocument.documentElement.classList.remove(\"no-js\")\ndocument.documentElement.classList.add(\"js\")\n\n/* Set up navigation observables and subjects */\nconst document$ = watchDocument()\nconst location$ = watchLocation()\nconst target$ = watchLocationTarget(location$)\nconst keyboard$ = watchKeyboard()\n\n/* Set up media observables */\nconst viewport$ = watchViewport()\nconst tablet$ = watchMedia(\"(min-width: 960px)\")\nconst screen$ = watchMedia(\"(min-width: 1220px)\")\nconst print$ = watchPrint()\n\n/* Retrieve search index, if search is enabled */\nconst config = configuration()\nconst index$ = document.forms.namedItem(\"search\")\n ? fetchSearchIndex()\n : NEVER\n\n/* Set up Clipboard.js integration */\nconst alert$ = new Subject()\nsetupClipboardJS({ alert$ })\n\n/* Set up progress indicator */\nconst progress$ = new Subject()\n\n/* Set up instant navigation, if enabled */\nif (feature(\"navigation.instant\"))\n setupInstantNavigation({ location$, viewport$, progress$ })\n .subscribe(document$)\n\n/* Set up version selector */\nif (config.version?.provider === \"mike\")\n setupVersionSelector({ document$ })\n\n/* Always close drawer and search on navigation */\nmerge(location$, target$)\n .pipe(\n delay(125)\n )\n .subscribe(() => {\n setToggle(\"drawer\", false)\n setToggle(\"search\", false)\n })\n\n/* Set up global keyboard handlers */\nkeyboard$\n .pipe(\n filter(({ mode }) => mode === \"global\")\n )\n .subscribe(key => {\n switch (key.type) {\n\n /* Go to previous page */\n case \"p\":\n case \",\":\n const prev = getOptionalElement(\"link[rel=prev]\")\n if (typeof prev !== \"undefined\")\n setLocation(prev)\n break\n\n /* Go to next page */\n case \"n\":\n case \".\":\n const next = getOptionalElement(\"link[rel=next]\")\n if (typeof next !== \"undefined\")\n setLocation(next)\n break\n\n /* Expand navigation, see https://bit.ly/3ZjG5io */\n case \"Enter\":\n const active = getActiveElement()\n if (active instanceof HTMLLabelElement)\n active.click()\n }\n })\n\n/* Set up patches */\npatchEllipsis({ viewport$, document$ })\npatchIndeterminate({ document$, tablet$ })\npatchScrollfix({ document$ })\npatchScrolllock({ viewport$, tablet$ })\n\n/* Set up header and main area observable */\nconst header$ = watchHeader(getComponentElement(\"header\"), { viewport$ })\nconst main$ = document$\n .pipe(\n map(() => getComponentElement(\"main\")),\n switchMap(el => watchMain(el, { viewport$, header$ })),\n shareReplay(1)\n )\n\n/* Set up control component observables */\nconst control$ = merge(\n\n /* Consent */\n ...getComponentElements(\"consent\")\n .map(el => mountConsent(el, { target$ })),\n\n /* Dialog */\n ...getComponentElements(\"dialog\")\n .map(el => mountDialog(el, { alert$ })),\n\n /* Header */\n ...getComponentElements(\"header\")\n .map(el => mountHeader(el, { viewport$, header$, main$ })),\n\n /* Color palette */\n ...getComponentElements(\"palette\")\n .map(el => mountPalette(el)),\n\n /* Progress bar */\n ...getComponentElements(\"progress\")\n .map(el => mountProgress(el, { progress$ })),\n\n /* Search */\n ...getComponentElements(\"search\")\n .map(el => mountSearch(el, { index$, keyboard$ })),\n\n /* Repository information */\n ...getComponentElements(\"source\")\n .map(el => mountSource(el))\n)\n\n/* Set up content component observables */\nconst content$ = defer(() => merge(\n\n /* Announcement bar */\n ...getComponentElements(\"announce\")\n .map(el => mountAnnounce(el)),\n\n /* Content */\n ...getComponentElements(\"content\")\n .map(el => mountContent(el, { viewport$, target$, print$ })),\n\n /* Search highlighting */\n ...getComponentElements(\"content\")\n .map(el => feature(\"search.highlight\")\n ? mountSearchHiglight(el, { index$, location$ })\n : EMPTY\n ),\n\n /* Header title */\n ...getComponentElements(\"header-title\")\n .map(el => mountHeaderTitle(el, { viewport$, header$ })),\n\n /* Sidebar */\n ...getComponentElements(\"sidebar\")\n .map(el => el.getAttribute(\"data-md-type\") === \"navigation\"\n ? at(screen$, () => mountSidebar(el, { viewport$, header$, main$ }))\n : at(tablet$, () => mountSidebar(el, { viewport$, header$, main$ }))\n ),\n\n /* Navigation tabs */\n ...getComponentElements(\"tabs\")\n .map(el => mountTabs(el, { viewport$, header$ })),\n\n /* Table of contents */\n ...getComponentElements(\"toc\")\n .map(el => mountTableOfContents(el, {\n viewport$, header$, main$, target$\n })),\n\n /* Back-to-top button */\n ...getComponentElements(\"top\")\n .map(el => mountBackToTop(el, { viewport$, header$, main$, target$ }))\n))\n\n/* Set up component observables */\nconst component$ = document$\n .pipe(\n switchMap(() => content$),\n mergeWith(control$),\n shareReplay(1)\n )\n\n/* Subscribe to all components */\ncomponent$.subscribe()\n\n/* ----------------------------------------------------------------------------\n * Exports\n * ------------------------------------------------------------------------- */\n\nwindow.document$ = document$ /* Document observable */\nwindow.location$ = location$ /* Location subject */\nwindow.target$ = target$ /* Location target observable */\nwindow.keyboard$ = keyboard$ /* Keyboard observable */\nwindow.viewport$ = viewport$ /* Viewport observable */\nwindow.tablet$ = tablet$ /* Media tablet observable */\nwindow.screen$ = screen$ /* Media screen observable */\nwindow.print$ = print$ /* Media print observable */\nwindow.alert$ = alert$ /* Alert subject */\nwindow.progress$ = progress$ /* Progress indicator subject */\nwindow.component$ = component$ /* Component observable */\n", "/*! *****************************************************************************\r\nCopyright (c) Microsoft Corporation.\r\n\r\nPermission to use, copy, modify, and/or distribute this software for any\r\npurpose with or without fee is hereby granted.\r\n\r\nTHE SOFTWARE IS PROVIDED \"AS IS\" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH\r\nREGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY\r\nAND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT,\r\nINDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM\r\nLOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR\r\nOTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR\r\nPERFORMANCE OF THIS SOFTWARE.\r\n***************************************************************************** */\r\n/* global Reflect, Promise */\r\n\r\nvar extendStatics = function(d, b) {\r\n extendStatics = Object.setPrototypeOf ||\r\n ({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||\r\n function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };\r\n return extendStatics(d, b);\r\n};\r\n\r\nexport function __extends(d, b) {\r\n if (typeof b !== \"function\" && b !== null)\r\n throw new TypeError(\"Class extends value \" + String(b) + \" is not a constructor or null\");\r\n extendStatics(d, b);\r\n function __() { this.constructor = d; }\r\n d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());\r\n}\r\n\r\nexport var __assign = function() {\r\n __assign = Object.assign || function __assign(t) {\r\n for (var s, i = 1, n = arguments.length; i < n; i++) {\r\n s = arguments[i];\r\n for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p)) t[p] = s[p];\r\n }\r\n return t;\r\n }\r\n return __assign.apply(this, arguments);\r\n}\r\n\r\nexport function __rest(s, e) {\r\n var t = {};\r\n for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p) && e.indexOf(p) < 0)\r\n t[p] = s[p];\r\n if (s != null && typeof Object.getOwnPropertySymbols === \"function\")\r\n for (var i = 0, p = Object.getOwnPropertySymbols(s); i < p.length; i++) {\r\n if (e.indexOf(p[i]) < 0 && Object.prototype.propertyIsEnumerable.call(s, p[i]))\r\n t[p[i]] = s[p[i]];\r\n }\r\n return t;\r\n}\r\n\r\nexport function __decorate(decorators, target, key, desc) {\r\n var c = arguments.length, r = c < 3 ? target : desc === null ? desc = Object.getOwnPropertyDescriptor(target, key) : desc, d;\r\n if (typeof Reflect === \"object\" && typeof Reflect.decorate === \"function\") r = Reflect.decorate(decorators, target, key, desc);\r\n else for (var i = decorators.length - 1; i >= 0; i--) if (d = decorators[i]) r = (c < 3 ? d(r) : c > 3 ? d(target, key, r) : d(target, key)) || r;\r\n return c > 3 && r && Object.defineProperty(target, key, r), r;\r\n}\r\n\r\nexport function __param(paramIndex, decorator) {\r\n return function (target, key) { decorator(target, key, paramIndex); }\r\n}\r\n\r\nexport function __metadata(metadataKey, metadataValue) {\r\n if (typeof Reflect === \"object\" && typeof Reflect.metadata === \"function\") return Reflect.metadata(metadataKey, metadataValue);\r\n}\r\n\r\nexport function __awaiter(thisArg, _arguments, P, generator) {\r\n function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }\r\n return new (P || (P = Promise))(function (resolve, reject) {\r\n function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }\r\n function rejected(value) { try { step(generator[\"throw\"](value)); } catch (e) { reject(e); } }\r\n function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }\r\n step((generator = generator.apply(thisArg, _arguments || [])).next());\r\n });\r\n}\r\n\r\nexport function __generator(thisArg, body) {\r\n var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;\r\n return g = { next: verb(0), \"throw\": verb(1), \"return\": verb(2) }, typeof Symbol === \"function\" && (g[Symbol.iterator] = function() { return this; }), g;\r\n function verb(n) { return function (v) { return step([n, v]); }; }\r\n function step(op) {\r\n if (f) throw new TypeError(\"Generator is already executing.\");\r\n while (_) try {\r\n if (f = 1, y && (t = op[0] & 2 ? y[\"return\"] : op[0] ? y[\"throw\"] || ((t = y[\"return\"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;\r\n if (y = 0, t) op = [op[0] & 2, t.value];\r\n switch (op[0]) {\r\n case 0: case 1: t = op; break;\r\n case 4: _.label++; return { value: op[1], done: false };\r\n case 5: _.label++; y = op[1]; op = [0]; continue;\r\n case 7: op = _.ops.pop(); _.trys.pop(); continue;\r\n default:\r\n if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }\r\n if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }\r\n if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }\r\n if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }\r\n if (t[2]) _.ops.pop();\r\n _.trys.pop(); continue;\r\n }\r\n op = body.call(thisArg, _);\r\n } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }\r\n if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };\r\n }\r\n}\r\n\r\nexport var __createBinding = Object.create ? (function(o, m, k, k2) {\r\n if (k2 === undefined) k2 = k;\r\n Object.defineProperty(o, k2, { enumerable: true, get: function() { return m[k]; } });\r\n}) : (function(o, m, k, k2) {\r\n if (k2 === undefined) k2 = k;\r\n o[k2] = m[k];\r\n});\r\n\r\nexport function __exportStar(m, o) {\r\n for (var p in m) if (p !== \"default\" && !Object.prototype.hasOwnProperty.call(o, p)) __createBinding(o, m, p);\r\n}\r\n\r\nexport function __values(o) {\r\n var s = typeof Symbol === \"function\" && Symbol.iterator, m = s && o[s], i = 0;\r\n if (m) return m.call(o);\r\n if (o && typeof o.length === \"number\") return {\r\n next: function () {\r\n if (o && i >= o.length) o = void 0;\r\n return { value: o && o[i++], done: !o };\r\n }\r\n };\r\n throw new TypeError(s ? \"Object is not iterable.\" : \"Symbol.iterator is not defined.\");\r\n}\r\n\r\nexport function __read(o, n) {\r\n var m = typeof Symbol === \"function\" && o[Symbol.iterator];\r\n if (!m) return o;\r\n var i = m.call(o), r, ar = [], e;\r\n try {\r\n while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);\r\n }\r\n catch (error) { e = { error: error }; }\r\n finally {\r\n try {\r\n if (r && !r.done && (m = i[\"return\"])) m.call(i);\r\n }\r\n finally { if (e) throw e.error; }\r\n }\r\n return ar;\r\n}\r\n\r\n/** @deprecated */\r\nexport function __spread() {\r\n for (var ar = [], i = 0; i < arguments.length; i++)\r\n ar = ar.concat(__read(arguments[i]));\r\n return ar;\r\n}\r\n\r\n/** @deprecated */\r\nexport function __spreadArrays() {\r\n for (var s = 0, i = 0, il = arguments.length; i < il; i++) s += arguments[i].length;\r\n for (var r = Array(s), k = 0, i = 0; i < il; i++)\r\n for (var a = arguments[i], j = 0, jl = a.length; j < jl; j++, k++)\r\n r[k] = a[j];\r\n return r;\r\n}\r\n\r\nexport function __spreadArray(to, from, pack) {\r\n if (pack || arguments.length === 2) for (var i = 0, l = from.length, ar; i < l; i++) {\r\n if (ar || !(i in from)) {\r\n if (!ar) ar = Array.prototype.slice.call(from, 0, i);\r\n ar[i] = from[i];\r\n }\r\n }\r\n return to.concat(ar || Array.prototype.slice.call(from));\r\n}\r\n\r\nexport function __await(v) {\r\n return this instanceof __await ? (this.v = v, this) : new __await(v);\r\n}\r\n\r\nexport function __asyncGenerator(thisArg, _arguments, generator) {\r\n if (!Symbol.asyncIterator) throw new TypeError(\"Symbol.asyncIterator is not defined.\");\r\n var g = generator.apply(thisArg, _arguments || []), i, q = [];\r\n return i = {}, verb(\"next\"), verb(\"throw\"), verb(\"return\"), i[Symbol.asyncIterator] = function () { return this; }, i;\r\n function verb(n) { if (g[n]) i[n] = function (v) { return new Promise(function (a, b) { q.push([n, v, a, b]) > 1 || resume(n, v); }); }; }\r\n function resume(n, v) { try { step(g[n](v)); } catch (e) { settle(q[0][3], e); } }\r\n function step(r) { r.value instanceof __await ? Promise.resolve(r.value.v).then(fulfill, reject) : settle(q[0][2], r); }\r\n function fulfill(value) { resume(\"next\", value); }\r\n function reject(value) { resume(\"throw\", value); }\r\n function settle(f, v) { if (f(v), q.shift(), q.length) resume(q[0][0], q[0][1]); }\r\n}\r\n\r\nexport function __asyncDelegator(o) {\r\n var i, p;\r\n return i = {}, verb(\"next\"), verb(\"throw\", function (e) { throw e; }), verb(\"return\"), i[Symbol.iterator] = function () { return this; }, i;\r\n function verb(n, f) { i[n] = o[n] ? function (v) { return (p = !p) ? { value: __await(o[n](v)), done: n === \"return\" } : f ? f(v) : v; } : f; }\r\n}\r\n\r\nexport function __asyncValues(o) {\r\n if (!Symbol.asyncIterator) throw new TypeError(\"Symbol.asyncIterator is not defined.\");\r\n var m = o[Symbol.asyncIterator], i;\r\n return m ? m.call(o) : (o = typeof __values === \"function\" ? __values(o) : o[Symbol.iterator](), i = {}, verb(\"next\"), verb(\"throw\"), verb(\"return\"), i[Symbol.asyncIterator] = function () { return this; }, i);\r\n function verb(n) { i[n] = o[n] && function (v) { return new Promise(function (resolve, reject) { v = o[n](v), settle(resolve, reject, v.done, v.value); }); }; }\r\n function settle(resolve, reject, d, v) { Promise.resolve(v).then(function(v) { resolve({ value: v, done: d }); }, reject); }\r\n}\r\n\r\nexport function __makeTemplateObject(cooked, raw) {\r\n if (Object.defineProperty) { Object.defineProperty(cooked, \"raw\", { value: raw }); } else { cooked.raw = raw; }\r\n return cooked;\r\n};\r\n\r\nvar __setModuleDefault = Object.create ? (function(o, v) {\r\n Object.defineProperty(o, \"default\", { enumerable: true, value: v });\r\n}) : function(o, v) {\r\n o[\"default\"] = v;\r\n};\r\n\r\nexport function __importStar(mod) {\r\n if (mod && mod.__esModule) return mod;\r\n var result = {};\r\n if (mod != null) for (var k in mod) if (k !== \"default\" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);\r\n __setModuleDefault(result, mod);\r\n return result;\r\n}\r\n\r\nexport function __importDefault(mod) {\r\n return (mod && mod.__esModule) ? mod : { default: mod };\r\n}\r\n\r\nexport function __classPrivateFieldGet(receiver, state, kind, f) {\r\n if (kind === \"a\" && !f) throw new TypeError(\"Private accessor was defined without a getter\");\r\n if (typeof state === \"function\" ? receiver !== state || !f : !state.has(receiver)) throw new TypeError(\"Cannot read private member from an object whose class did not declare it\");\r\n return kind === \"m\" ? f : kind === \"a\" ? f.call(receiver) : f ? f.value : state.get(receiver);\r\n}\r\n\r\nexport function __classPrivateFieldSet(receiver, state, value, kind, f) {\r\n if (kind === \"m\") throw new TypeError(\"Private method is not writable\");\r\n if (kind === \"a\" && !f) throw new TypeError(\"Private accessor was defined without a setter\");\r\n if (typeof state === \"function\" ? receiver !== state || !f : !state.has(receiver)) throw new TypeError(\"Cannot write private member to an object whose class did not declare it\");\r\n return (kind === \"a\" ? f.call(receiver, value) : f ? f.value = value : state.set(receiver, value)), value;\r\n}\r\n", "/**\n * Returns true if the object is a function.\n * @param value The value to check\n */\nexport function isFunction(value: any): value is (...args: any[]) => any {\n return typeof value === 'function';\n}\n", "/**\n * Used to create Error subclasses until the community moves away from ES5.\n *\n * This is because compiling from TypeScript down to ES5 has issues with subclassing Errors\n * as well as other built-in types: https://github.com/Microsoft/TypeScript/issues/12123\n *\n * @param createImpl A factory function to create the actual constructor implementation. The returned\n * function should be a named function that calls `_super` internally.\n */\nexport function createErrorClass(createImpl: (_super: any) => any): T {\n const _super = (instance: any) => {\n Error.call(instance);\n instance.stack = new Error().stack;\n };\n\n const ctorFunc = createImpl(_super);\n ctorFunc.prototype = Object.create(Error.prototype);\n ctorFunc.prototype.constructor = ctorFunc;\n return ctorFunc;\n}\n", "import { createErrorClass } from './createErrorClass';\n\nexport interface UnsubscriptionError extends Error {\n readonly errors: any[];\n}\n\nexport interface UnsubscriptionErrorCtor {\n /**\n * @deprecated Internal implementation detail. Do not construct error instances.\n * Cannot be tagged as internal: https://github.com/ReactiveX/rxjs/issues/6269\n */\n new (errors: any[]): UnsubscriptionError;\n}\n\n/**\n * An error thrown when one or more errors have occurred during the\n * `unsubscribe` of a {@link Subscription}.\n */\nexport const UnsubscriptionError: UnsubscriptionErrorCtor = createErrorClass(\n (_super) =>\n function UnsubscriptionErrorImpl(this: any, errors: (Error | string)[]) {\n _super(this);\n this.message = errors\n ? `${errors.length} errors occurred during unsubscription:\n${errors.map((err, i) => `${i + 1}) ${err.toString()}`).join('\\n ')}`\n : '';\n this.name = 'UnsubscriptionError';\n this.errors = errors;\n }\n);\n", "/**\n * Removes an item from an array, mutating it.\n * @param arr The array to remove the item from\n * @param item The item to remove\n */\nexport function arrRemove(arr: T[] | undefined | null, item: T) {\n if (arr) {\n const index = arr.indexOf(item);\n 0 <= index && arr.splice(index, 1);\n }\n}\n", "import { isFunction } from './util/isFunction';\nimport { UnsubscriptionError } from './util/UnsubscriptionError';\nimport { SubscriptionLike, TeardownLogic, Unsubscribable } from './types';\nimport { arrRemove } from './util/arrRemove';\n\n/**\n * Represents a disposable resource, such as the execution of an Observable. A\n * Subscription has one important method, `unsubscribe`, that takes no argument\n * and just disposes the resource held by the subscription.\n *\n * Additionally, subscriptions may be grouped together through the `add()`\n * method, which will attach a child Subscription to the current Subscription.\n * When a Subscription is unsubscribed, all its children (and its grandchildren)\n * will be unsubscribed as well.\n *\n * @class Subscription\n */\nexport class Subscription implements SubscriptionLike {\n /** @nocollapse */\n public static EMPTY = (() => {\n const empty = new Subscription();\n empty.closed = true;\n return empty;\n })();\n\n /**\n * A flag to indicate whether this Subscription has already been unsubscribed.\n */\n public closed = false;\n\n private _parentage: Subscription[] | Subscription | null = null;\n\n /**\n * The list of registered finalizers to execute upon unsubscription. Adding and removing from this\n * list occurs in the {@link #add} and {@link #remove} methods.\n */\n private _finalizers: Exclude[] | null = null;\n\n /**\n * @param initialTeardown A function executed first as part of the finalization\n * process that is kicked off when {@link #unsubscribe} is called.\n */\n constructor(private initialTeardown?: () => void) {}\n\n /**\n * Disposes the resources held by the subscription. May, for instance, cancel\n * an ongoing Observable execution or cancel any other type of work that\n * started when the Subscription was created.\n * @return {void}\n */\n unsubscribe(): void {\n let errors: any[] | undefined;\n\n if (!this.closed) {\n this.closed = true;\n\n // Remove this from it's parents.\n const { _parentage } = this;\n if (_parentage) {\n this._parentage = null;\n if (Array.isArray(_parentage)) {\n for (const parent of _parentage) {\n parent.remove(this);\n }\n } else {\n _parentage.remove(this);\n }\n }\n\n const { initialTeardown: initialFinalizer } = this;\n if (isFunction(initialFinalizer)) {\n try {\n initialFinalizer();\n } catch (e) {\n errors = e instanceof UnsubscriptionError ? e.errors : [e];\n }\n }\n\n const { _finalizers } = this;\n if (_finalizers) {\n this._finalizers = null;\n for (const finalizer of _finalizers) {\n try {\n execFinalizer(finalizer);\n } catch (err) {\n errors = errors ?? [];\n if (err instanceof UnsubscriptionError) {\n errors = [...errors, ...err.errors];\n } else {\n errors.push(err);\n }\n }\n }\n }\n\n if (errors) {\n throw new UnsubscriptionError(errors);\n }\n }\n }\n\n /**\n * Adds a finalizer to this subscription, so that finalization will be unsubscribed/called\n * when this subscription is unsubscribed. If this subscription is already {@link #closed},\n * because it has already been unsubscribed, then whatever finalizer is passed to it\n * will automatically be executed (unless the finalizer itself is also a closed subscription).\n *\n * Closed Subscriptions cannot be added as finalizers to any subscription. Adding a closed\n * subscription to a any subscription will result in no operation. (A noop).\n *\n * Adding a subscription to itself, or adding `null` or `undefined` will not perform any\n * operation at all. (A noop).\n *\n * `Subscription` instances that are added to this instance will automatically remove themselves\n * if they are unsubscribed. Functions and {@link Unsubscribable} objects that you wish to remove\n * will need to be removed manually with {@link #remove}\n *\n * @param teardown The finalization logic to add to this subscription.\n */\n add(teardown: TeardownLogic): void {\n // Only add the finalizer if it's not undefined\n // and don't add a subscription to itself.\n if (teardown && teardown !== this) {\n if (this.closed) {\n // If this subscription is already closed,\n // execute whatever finalizer is handed to it automatically.\n execFinalizer(teardown);\n } else {\n if (teardown instanceof Subscription) {\n // We don't add closed subscriptions, and we don't add the same subscription\n // twice. Subscription unsubscribe is idempotent.\n if (teardown.closed || teardown._hasParent(this)) {\n return;\n }\n teardown._addParent(this);\n }\n (this._finalizers = this._finalizers ?? []).push(teardown);\n }\n }\n }\n\n /**\n * Checks to see if a this subscription already has a particular parent.\n * This will signal that this subscription has already been added to the parent in question.\n * @param parent the parent to check for\n */\n private _hasParent(parent: Subscription) {\n const { _parentage } = this;\n return _parentage === parent || (Array.isArray(_parentage) && _parentage.includes(parent));\n }\n\n /**\n * Adds a parent to this subscription so it can be removed from the parent if it\n * unsubscribes on it's own.\n *\n * NOTE: THIS ASSUMES THAT {@link _hasParent} HAS ALREADY BEEN CHECKED.\n * @param parent The parent subscription to add\n */\n private _addParent(parent: Subscription) {\n const { _parentage } = this;\n this._parentage = Array.isArray(_parentage) ? (_parentage.push(parent), _parentage) : _parentage ? [_parentage, parent] : parent;\n }\n\n /**\n * Called on a child when it is removed via {@link #remove}.\n * @param parent The parent to remove\n */\n private _removeParent(parent: Subscription) {\n const { _parentage } = this;\n if (_parentage === parent) {\n this._parentage = null;\n } else if (Array.isArray(_parentage)) {\n arrRemove(_parentage, parent);\n }\n }\n\n /**\n * Removes a finalizer from this subscription that was previously added with the {@link #add} method.\n *\n * Note that `Subscription` instances, when unsubscribed, will automatically remove themselves\n * from every other `Subscription` they have been added to. This means that using the `remove` method\n * is not a common thing and should be used thoughtfully.\n *\n * If you add the same finalizer instance of a function or an unsubscribable object to a `Subscription` instance\n * more than once, you will need to call `remove` the same number of times to remove all instances.\n *\n * All finalizer instances are removed to free up memory upon unsubscription.\n *\n * @param teardown The finalizer to remove from this subscription\n */\n remove(teardown: Exclude): void {\n const { _finalizers } = this;\n _finalizers && arrRemove(_finalizers, teardown);\n\n if (teardown instanceof Subscription) {\n teardown._removeParent(this);\n }\n }\n}\n\nexport const EMPTY_SUBSCRIPTION = Subscription.EMPTY;\n\nexport function isSubscription(value: any): value is Subscription {\n return (\n value instanceof Subscription ||\n (value && 'closed' in value && isFunction(value.remove) && isFunction(value.add) && isFunction(value.unsubscribe))\n );\n}\n\nfunction execFinalizer(finalizer: Unsubscribable | (() => void)) {\n if (isFunction(finalizer)) {\n finalizer();\n } else {\n finalizer.unsubscribe();\n }\n}\n", "import { Subscriber } from './Subscriber';\nimport { ObservableNotification } from './types';\n\n/**\n * The {@link GlobalConfig} object for RxJS. It is used to configure things\n * like how to react on unhandled errors.\n */\nexport const config: GlobalConfig = {\n onUnhandledError: null,\n onStoppedNotification: null,\n Promise: undefined,\n useDeprecatedSynchronousErrorHandling: false,\n useDeprecatedNextContext: false,\n};\n\n/**\n * The global configuration object for RxJS, used to configure things\n * like how to react on unhandled errors. Accessible via {@link config}\n * object.\n */\nexport interface GlobalConfig {\n /**\n * A registration point for unhandled errors from RxJS. These are errors that\n * cannot were not handled by consuming code in the usual subscription path. For\n * example, if you have this configured, and you subscribe to an observable without\n * providing an error handler, errors from that subscription will end up here. This\n * will _always_ be called asynchronously on another job in the runtime. This is because\n * we do not want errors thrown in this user-configured handler to interfere with the\n * behavior of the library.\n */\n onUnhandledError: ((err: any) => void) | null;\n\n /**\n * A registration point for notifications that cannot be sent to subscribers because they\n * have completed, errored or have been explicitly unsubscribed. By default, next, complete\n * and error notifications sent to stopped subscribers are noops. However, sometimes callers\n * might want a different behavior. For example, with sources that attempt to report errors\n * to stopped subscribers, a caller can configure RxJS to throw an unhandled error instead.\n * This will _always_ be called asynchronously on another job in the runtime. This is because\n * we do not want errors thrown in this user-configured handler to interfere with the\n * behavior of the library.\n */\n onStoppedNotification: ((notification: ObservableNotification, subscriber: Subscriber) => void) | null;\n\n /**\n * The promise constructor used by default for {@link Observable#toPromise toPromise} and {@link Observable#forEach forEach}\n * methods.\n *\n * @deprecated As of version 8, RxJS will no longer support this sort of injection of a\n * Promise constructor. If you need a Promise implementation other than native promises,\n * please polyfill/patch Promise as you see appropriate. Will be removed in v8.\n */\n Promise?: PromiseConstructorLike;\n\n /**\n * If true, turns on synchronous error rethrowing, which is a deprecated behavior\n * in v6 and higher. This behavior enables bad patterns like wrapping a subscribe\n * call in a try/catch block. It also enables producer interference, a nasty bug\n * where a multicast can be broken for all observers by a downstream consumer with\n * an unhandled error. DO NOT USE THIS FLAG UNLESS IT'S NEEDED TO BUY TIME\n * FOR MIGRATION REASONS.\n *\n * @deprecated As of version 8, RxJS will no longer support synchronous throwing\n * of unhandled errors. All errors will be thrown on a separate call stack to prevent bad\n * behaviors described above. Will be removed in v8.\n */\n useDeprecatedSynchronousErrorHandling: boolean;\n\n /**\n * If true, enables an as-of-yet undocumented feature from v5: The ability to access\n * `unsubscribe()` via `this` context in `next` functions created in observers passed\n * to `subscribe`.\n *\n * This is being removed because the performance was severely problematic, and it could also cause\n * issues when types other than POJOs are passed to subscribe as subscribers, as they will likely have\n * their `this` context overwritten.\n *\n * @deprecated As of version 8, RxJS will no longer support altering the\n * context of next functions provided as part of an observer to Subscribe. Instead,\n * you will have access to a subscription or a signal or token that will allow you to do things like\n * unsubscribe and test closed status. Will be removed in v8.\n */\n useDeprecatedNextContext: boolean;\n}\n", "import type { TimerHandle } from './timerHandle';\ntype SetTimeoutFunction = (handler: () => void, timeout?: number, ...args: any[]) => TimerHandle;\ntype ClearTimeoutFunction = (handle: TimerHandle) => void;\n\ninterface TimeoutProvider {\n setTimeout: SetTimeoutFunction;\n clearTimeout: ClearTimeoutFunction;\n delegate:\n | {\n setTimeout: SetTimeoutFunction;\n clearTimeout: ClearTimeoutFunction;\n }\n | undefined;\n}\n\nexport const timeoutProvider: TimeoutProvider = {\n // When accessing the delegate, use the variable rather than `this` so that\n // the functions can be called without being bound to the provider.\n setTimeout(handler: () => void, timeout?: number, ...args) {\n const { delegate } = timeoutProvider;\n if (delegate?.setTimeout) {\n return delegate.setTimeout(handler, timeout, ...args);\n }\n return setTimeout(handler, timeout, ...args);\n },\n clearTimeout(handle) {\n const { delegate } = timeoutProvider;\n return (delegate?.clearTimeout || clearTimeout)(handle as any);\n },\n delegate: undefined,\n};\n", "import { config } from '../config';\nimport { timeoutProvider } from '../scheduler/timeoutProvider';\n\n/**\n * Handles an error on another job either with the user-configured {@link onUnhandledError},\n * or by throwing it on that new job so it can be picked up by `window.onerror`, `process.on('error')`, etc.\n *\n * This should be called whenever there is an error that is out-of-band with the subscription\n * or when an error hits a terminal boundary of the subscription and no error handler was provided.\n *\n * @param err the error to report\n */\nexport function reportUnhandledError(err: any) {\n timeoutProvider.setTimeout(() => {\n const { onUnhandledError } = config;\n if (onUnhandledError) {\n // Execute the user-configured error handler.\n onUnhandledError(err);\n } else {\n // Throw so it is picked up by the runtime's uncaught error mechanism.\n throw err;\n }\n });\n}\n", "/* tslint:disable:no-empty */\nexport function noop() { }\n", "import { CompleteNotification, NextNotification, ErrorNotification } from './types';\n\n/**\n * A completion object optimized for memory use and created to be the\n * same \"shape\" as other notifications in v8.\n * @internal\n */\nexport const COMPLETE_NOTIFICATION = (() => createNotification('C', undefined, undefined) as CompleteNotification)();\n\n/**\n * Internal use only. Creates an optimized error notification that is the same \"shape\"\n * as other notifications.\n * @internal\n */\nexport function errorNotification(error: any): ErrorNotification {\n return createNotification('E', undefined, error) as any;\n}\n\n/**\n * Internal use only. Creates an optimized next notification that is the same \"shape\"\n * as other notifications.\n * @internal\n */\nexport function nextNotification(value: T) {\n return createNotification('N', value, undefined) as NextNotification;\n}\n\n/**\n * Ensures that all notifications created internally have the same \"shape\" in v8.\n *\n * TODO: This is only exported to support a crazy legacy test in `groupBy`.\n * @internal\n */\nexport function createNotification(kind: 'N' | 'E' | 'C', value: any, error: any) {\n return {\n kind,\n value,\n error,\n };\n}\n", "import { config } from '../config';\n\nlet context: { errorThrown: boolean; error: any } | null = null;\n\n/**\n * Handles dealing with errors for super-gross mode. Creates a context, in which\n * any synchronously thrown errors will be passed to {@link captureError}. Which\n * will record the error such that it will be rethrown after the call back is complete.\n * TODO: Remove in v8\n * @param cb An immediately executed function.\n */\nexport function errorContext(cb: () => void) {\n if (config.useDeprecatedSynchronousErrorHandling) {\n const isRoot = !context;\n if (isRoot) {\n context = { errorThrown: false, error: null };\n }\n cb();\n if (isRoot) {\n const { errorThrown, error } = context!;\n context = null;\n if (errorThrown) {\n throw error;\n }\n }\n } else {\n // This is the general non-deprecated path for everyone that\n // isn't crazy enough to use super-gross mode (useDeprecatedSynchronousErrorHandling)\n cb();\n }\n}\n\n/**\n * Captures errors only in super-gross mode.\n * @param err the error to capture\n */\nexport function captureError(err: any) {\n if (config.useDeprecatedSynchronousErrorHandling && context) {\n context.errorThrown = true;\n context.error = err;\n }\n}\n", "import { isFunction } from './util/isFunction';\nimport { Observer, ObservableNotification } from './types';\nimport { isSubscription, Subscription } from './Subscription';\nimport { config } from './config';\nimport { reportUnhandledError } from './util/reportUnhandledError';\nimport { noop } from './util/noop';\nimport { nextNotification, errorNotification, COMPLETE_NOTIFICATION } from './NotificationFactories';\nimport { timeoutProvider } from './scheduler/timeoutProvider';\nimport { captureError } from './util/errorContext';\n\n/**\n * Implements the {@link Observer} interface and extends the\n * {@link Subscription} class. While the {@link Observer} is the public API for\n * consuming the values of an {@link Observable}, all Observers get converted to\n * a Subscriber, in order to provide Subscription-like capabilities such as\n * `unsubscribe`. Subscriber is a common type in RxJS, and crucial for\n * implementing operators, but it is rarely used as a public API.\n *\n * @class Subscriber\n */\nexport class Subscriber extends Subscription implements Observer {\n /**\n * A static factory for a Subscriber, given a (potentially partial) definition\n * of an Observer.\n * @param next The `next` callback of an Observer.\n * @param error The `error` callback of an\n * Observer.\n * @param complete The `complete` callback of an\n * Observer.\n * @return A Subscriber wrapping the (partially defined)\n * Observer represented by the given arguments.\n * @nocollapse\n * @deprecated Do not use. Will be removed in v8. There is no replacement for this\n * method, and there is no reason to be creating instances of `Subscriber` directly.\n * If you have a specific use case, please file an issue.\n */\n static create(next?: (x?: T) => void, error?: (e?: any) => void, complete?: () => void): Subscriber {\n return new SafeSubscriber(next, error, complete);\n }\n\n /** @deprecated Internal implementation detail, do not use directly. Will be made internal in v8. */\n protected isStopped: boolean = false;\n /** @deprecated Internal implementation detail, do not use directly. Will be made internal in v8. */\n protected destination: Subscriber | Observer; // this `any` is the escape hatch to erase extra type param (e.g. R)\n\n /**\n * @deprecated Internal implementation detail, do not use directly. Will be made internal in v8.\n * There is no reason to directly create an instance of Subscriber. This type is exported for typings reasons.\n */\n constructor(destination?: Subscriber | Observer) {\n super();\n if (destination) {\n this.destination = destination;\n // Automatically chain subscriptions together here.\n // if destination is a Subscription, then it is a Subscriber.\n if (isSubscription(destination)) {\n destination.add(this);\n }\n } else {\n this.destination = EMPTY_OBSERVER;\n }\n }\n\n /**\n * The {@link Observer} callback to receive notifications of type `next` from\n * the Observable, with a value. The Observable may call this method 0 or more\n * times.\n * @param {T} [value] The `next` value.\n * @return {void}\n */\n next(value?: T): void {\n if (this.isStopped) {\n handleStoppedNotification(nextNotification(value), this);\n } else {\n this._next(value!);\n }\n }\n\n /**\n * The {@link Observer} callback to receive notifications of type `error` from\n * the Observable, with an attached `Error`. Notifies the Observer that\n * the Observable has experienced an error condition.\n * @param {any} [err] The `error` exception.\n * @return {void}\n */\n error(err?: any): void {\n if (this.isStopped) {\n handleStoppedNotification(errorNotification(err), this);\n } else {\n this.isStopped = true;\n this._error(err);\n }\n }\n\n /**\n * The {@link Observer} callback to receive a valueless notification of type\n * `complete` from the Observable. Notifies the Observer that the Observable\n * has finished sending push-based notifications.\n * @return {void}\n */\n complete(): void {\n if (this.isStopped) {\n handleStoppedNotification(COMPLETE_NOTIFICATION, this);\n } else {\n this.isStopped = true;\n this._complete();\n }\n }\n\n unsubscribe(): void {\n if (!this.closed) {\n this.isStopped = true;\n super.unsubscribe();\n this.destination = null!;\n }\n }\n\n protected _next(value: T): void {\n this.destination.next(value);\n }\n\n protected _error(err: any): void {\n try {\n this.destination.error(err);\n } finally {\n this.unsubscribe();\n }\n }\n\n protected _complete(): void {\n try {\n this.destination.complete();\n } finally {\n this.unsubscribe();\n }\n }\n}\n\n/**\n * This bind is captured here because we want to be able to have\n * compatibility with monoid libraries that tend to use a method named\n * `bind`. In particular, a library called Monio requires this.\n */\nconst _bind = Function.prototype.bind;\n\nfunction bind any>(fn: Fn, thisArg: any): Fn {\n return _bind.call(fn, thisArg);\n}\n\n/**\n * Internal optimization only, DO NOT EXPOSE.\n * @internal\n */\nclass ConsumerObserver implements Observer {\n constructor(private partialObserver: Partial>) {}\n\n next(value: T): void {\n const { partialObserver } = this;\n if (partialObserver.next) {\n try {\n partialObserver.next(value);\n } catch (error) {\n handleUnhandledError(error);\n }\n }\n }\n\n error(err: any): void {\n const { partialObserver } = this;\n if (partialObserver.error) {\n try {\n partialObserver.error(err);\n } catch (error) {\n handleUnhandledError(error);\n }\n } else {\n handleUnhandledError(err);\n }\n }\n\n complete(): void {\n const { partialObserver } = this;\n if (partialObserver.complete) {\n try {\n partialObserver.complete();\n } catch (error) {\n handleUnhandledError(error);\n }\n }\n }\n}\n\nexport class SafeSubscriber extends Subscriber {\n constructor(\n observerOrNext?: Partial> | ((value: T) => void) | null,\n error?: ((e?: any) => void) | null,\n complete?: (() => void) | null\n ) {\n super();\n\n let partialObserver: Partial>;\n if (isFunction(observerOrNext) || !observerOrNext) {\n // The first argument is a function, not an observer. The next\n // two arguments *could* be observers, or they could be empty.\n partialObserver = {\n next: (observerOrNext ?? undefined) as (((value: T) => void) | undefined),\n error: error ?? undefined,\n complete: complete ?? undefined,\n };\n } else {\n // The first argument is a partial observer.\n let context: any;\n if (this && config.useDeprecatedNextContext) {\n // This is a deprecated path that made `this.unsubscribe()` available in\n // next handler functions passed to subscribe. This only exists behind a flag\n // now, as it is *very* slow.\n context = Object.create(observerOrNext);\n context.unsubscribe = () => this.unsubscribe();\n partialObserver = {\n next: observerOrNext.next && bind(observerOrNext.next, context),\n error: observerOrNext.error && bind(observerOrNext.error, context),\n complete: observerOrNext.complete && bind(observerOrNext.complete, context),\n };\n } else {\n // The \"normal\" path. Just use the partial observer directly.\n partialObserver = observerOrNext;\n }\n }\n\n // Wrap the partial observer to ensure it's a full observer, and\n // make sure proper error handling is accounted for.\n this.destination = new ConsumerObserver(partialObserver);\n }\n}\n\nfunction handleUnhandledError(error: any) {\n if (config.useDeprecatedSynchronousErrorHandling) {\n captureError(error);\n } else {\n // Ideal path, we report this as an unhandled error,\n // which is thrown on a new call stack.\n reportUnhandledError(error);\n }\n}\n\n/**\n * An error handler used when no error handler was supplied\n * to the SafeSubscriber -- meaning no error handler was supplied\n * do the `subscribe` call on our observable.\n * @param err The error to handle\n */\nfunction defaultErrorHandler(err: any) {\n throw err;\n}\n\n/**\n * A handler for notifications that cannot be sent to a stopped subscriber.\n * @param notification The notification being sent\n * @param subscriber The stopped subscriber\n */\nfunction handleStoppedNotification(notification: ObservableNotification, subscriber: Subscriber) {\n const { onStoppedNotification } = config;\n onStoppedNotification && timeoutProvider.setTimeout(() => onStoppedNotification(notification, subscriber));\n}\n\n/**\n * The observer used as a stub for subscriptions where the user did not\n * pass any arguments to `subscribe`. Comes with the default error handling\n * behavior.\n */\nexport const EMPTY_OBSERVER: Readonly> & { closed: true } = {\n closed: true,\n next: noop,\n error: defaultErrorHandler,\n complete: noop,\n};\n", "/**\n * Symbol.observable or a string \"@@observable\". Used for interop\n *\n * @deprecated We will no longer be exporting this symbol in upcoming versions of RxJS.\n * Instead polyfill and use Symbol.observable directly *or* use https://www.npmjs.com/package/symbol-observable\n */\nexport const observable: string | symbol = (() => (typeof Symbol === 'function' && Symbol.observable) || '@@observable')();\n", "/**\n * This function takes one parameter and just returns it. Simply put,\n * this is like `(x: T): T => x`.\n *\n * ## Examples\n *\n * This is useful in some cases when using things like `mergeMap`\n *\n * ```ts\n * import { interval, take, map, range, mergeMap, identity } from 'rxjs';\n *\n * const source$ = interval(1000).pipe(take(5));\n *\n * const result$ = source$.pipe(\n * map(i => range(i)),\n * mergeMap(identity) // same as mergeMap(x => x)\n * );\n *\n * result$.subscribe({\n * next: console.log\n * });\n * ```\n *\n * Or when you want to selectively apply an operator\n *\n * ```ts\n * import { interval, take, identity } from 'rxjs';\n *\n * const shouldLimit = () => Math.random() < 0.5;\n *\n * const source$ = interval(1000);\n *\n * const result$ = source$.pipe(shouldLimit() ? take(5) : identity);\n *\n * result$.subscribe({\n * next: console.log\n * });\n * ```\n *\n * @param x Any value that is returned by this function\n * @returns The value passed as the first parameter to this function\n */\nexport function identity(x: T): T {\n return x;\n}\n", "import { identity } from './identity';\nimport { UnaryFunction } from '../types';\n\nexport function pipe(): typeof identity;\nexport function pipe(fn1: UnaryFunction): UnaryFunction;\nexport function pipe(fn1: UnaryFunction, fn2: UnaryFunction): UnaryFunction;\nexport function pipe(fn1: UnaryFunction, fn2: UnaryFunction, fn3: UnaryFunction): UnaryFunction;\nexport function pipe(\n fn1: UnaryFunction,\n fn2: UnaryFunction,\n fn3: UnaryFunction,\n fn4: UnaryFunction\n): UnaryFunction;\nexport function pipe(\n fn1: UnaryFunction,\n fn2: UnaryFunction,\n fn3: UnaryFunction,\n fn4: UnaryFunction,\n fn5: UnaryFunction\n): UnaryFunction;\nexport function pipe(\n fn1: UnaryFunction,\n fn2: UnaryFunction,\n fn3: UnaryFunction,\n fn4: UnaryFunction,\n fn5: UnaryFunction,\n fn6: UnaryFunction\n): UnaryFunction;\nexport function pipe(\n fn1: UnaryFunction,\n fn2: UnaryFunction,\n fn3: UnaryFunction,\n fn4: UnaryFunction,\n fn5: UnaryFunction,\n fn6: UnaryFunction,\n fn7: UnaryFunction\n): UnaryFunction;\nexport function pipe(\n fn1: UnaryFunction,\n fn2: UnaryFunction,\n fn3: UnaryFunction,\n fn4: UnaryFunction,\n fn5: UnaryFunction,\n fn6: UnaryFunction,\n fn7: UnaryFunction,\n fn8: UnaryFunction\n): UnaryFunction;\nexport function pipe(\n fn1: UnaryFunction,\n fn2: UnaryFunction,\n fn3: UnaryFunction,\n fn4: UnaryFunction,\n fn5: UnaryFunction,\n fn6: UnaryFunction,\n fn7: UnaryFunction,\n fn8: UnaryFunction,\n fn9: UnaryFunction\n): UnaryFunction;\nexport function pipe(\n fn1: UnaryFunction,\n fn2: UnaryFunction,\n fn3: UnaryFunction,\n fn4: UnaryFunction,\n fn5: UnaryFunction,\n fn6: UnaryFunction,\n fn7: UnaryFunction,\n fn8: UnaryFunction,\n fn9: UnaryFunction,\n ...fns: UnaryFunction[]\n): UnaryFunction;\n\n/**\n * pipe() can be called on one or more functions, each of which can take one argument (\"UnaryFunction\")\n * and uses it to return a value.\n * It returns a function that takes one argument, passes it to the first UnaryFunction, and then\n * passes the result to the next one, passes that result to the next one, and so on. \n */\nexport function pipe(...fns: Array>): UnaryFunction {\n return pipeFromArray(fns);\n}\n\n/** @internal */\nexport function pipeFromArray(fns: Array>): UnaryFunction {\n if (fns.length === 0) {\n return identity as UnaryFunction;\n }\n\n if (fns.length === 1) {\n return fns[0];\n }\n\n return function piped(input: T): R {\n return fns.reduce((prev: any, fn: UnaryFunction) => fn(prev), input as any);\n };\n}\n", "import { Operator } from './Operator';\nimport { SafeSubscriber, Subscriber } from './Subscriber';\nimport { isSubscription, Subscription } from './Subscription';\nimport { TeardownLogic, OperatorFunction, Subscribable, Observer } from './types';\nimport { observable as Symbol_observable } from './symbol/observable';\nimport { pipeFromArray } from './util/pipe';\nimport { config } from './config';\nimport { isFunction } from './util/isFunction';\nimport { errorContext } from './util/errorContext';\n\n/**\n * A representation of any set of values over any amount of time. This is the most basic building block\n * of RxJS.\n *\n * @class Observable\n */\nexport class Observable implements Subscribable {\n /**\n * @deprecated Internal implementation detail, do not use directly. Will be made internal in v8.\n */\n source: Observable | undefined;\n\n /**\n * @deprecated Internal implementation detail, do not use directly. Will be made internal in v8.\n */\n operator: Operator | undefined;\n\n /**\n * @constructor\n * @param {Function} subscribe the function that is called when the Observable is\n * initially subscribed to. This function is given a Subscriber, to which new values\n * can be `next`ed, or an `error` method can be called to raise an error, or\n * `complete` can be called to notify of a successful completion.\n */\n constructor(subscribe?: (this: Observable, subscriber: Subscriber) => TeardownLogic) {\n if (subscribe) {\n this._subscribe = subscribe;\n }\n }\n\n // HACK: Since TypeScript inherits static properties too, we have to\n // fight against TypeScript here so Subject can have a different static create signature\n /**\n * Creates a new Observable by calling the Observable constructor\n * @owner Observable\n * @method create\n * @param {Function} subscribe? the subscriber function to be passed to the Observable constructor\n * @return {Observable} a new observable\n * @nocollapse\n * @deprecated Use `new Observable()` instead. Will be removed in v8.\n */\n static create: (...args: any[]) => any = (subscribe?: (subscriber: Subscriber) => TeardownLogic) => {\n return new Observable(subscribe);\n };\n\n /**\n * Creates a new Observable, with this Observable instance as the source, and the passed\n * operator defined as the new observable's operator.\n * @method lift\n * @param operator the operator defining the operation to take on the observable\n * @return a new observable with the Operator applied\n * @deprecated Internal implementation detail, do not use directly. Will be made internal in v8.\n * If you have implemented an operator using `lift`, it is recommended that you create an\n * operator by simply returning `new Observable()` directly. See \"Creating new operators from\n * scratch\" section here: https://rxjs.dev/guide/operators\n */\n lift(operator?: Operator): Observable {\n const observable = new Observable();\n observable.source = this;\n observable.operator = operator;\n return observable;\n }\n\n subscribe(observerOrNext?: Partial> | ((value: T) => void)): Subscription;\n /** @deprecated Instead of passing separate callback arguments, use an observer argument. Signatures taking separate callback arguments will be removed in v8. Details: https://rxjs.dev/deprecations/subscribe-arguments */\n subscribe(next?: ((value: T) => void) | null, error?: ((error: any) => void) | null, complete?: (() => void) | null): Subscription;\n /**\n * Invokes an execution of an Observable and registers Observer handlers for notifications it will emit.\n *\n * Use it when you have all these Observables, but still nothing is happening.\n *\n * `subscribe` is not a regular operator, but a method that calls Observable's internal `subscribe` function. It\n * might be for example a function that you passed to Observable's constructor, but most of the time it is\n * a library implementation, which defines what will be emitted by an Observable, and when it be will emitted. This means\n * that calling `subscribe` is actually the moment when Observable starts its work, not when it is created, as it is often\n * the thought.\n *\n * Apart from starting the execution of an Observable, this method allows you to listen for values\n * that an Observable emits, as well as for when it completes or errors. You can achieve this in two\n * of the following ways.\n *\n * The first way is creating an object that implements {@link Observer} interface. It should have methods\n * defined by that interface, but note that it should be just a regular JavaScript object, which you can create\n * yourself in any way you want (ES6 class, classic function constructor, object literal etc.). In particular, do\n * not attempt to use any RxJS implementation details to create Observers - you don't need them. Remember also\n * that your object does not have to implement all methods. If you find yourself creating a method that doesn't\n * do anything, you can simply omit it. Note however, if the `error` method is not provided and an error happens,\n * it will be thrown asynchronously. Errors thrown asynchronously cannot be caught using `try`/`catch`. Instead,\n * use the {@link onUnhandledError} configuration option or use a runtime handler (like `window.onerror` or\n * `process.on('error)`) to be notified of unhandled errors. Because of this, it's recommended that you provide\n * an `error` method to avoid missing thrown errors.\n *\n * The second way is to give up on Observer object altogether and simply provide callback functions in place of its methods.\n * This means you can provide three functions as arguments to `subscribe`, where the first function is equivalent\n * of a `next` method, the second of an `error` method and the third of a `complete` method. Just as in case of an Observer,\n * if you do not need to listen for something, you can omit a function by passing `undefined` or `null`,\n * since `subscribe` recognizes these functions by where they were placed in function call. When it comes\n * to the `error` function, as with an Observer, if not provided, errors emitted by an Observable will be thrown asynchronously.\n *\n * You can, however, subscribe with no parameters at all. This may be the case where you're not interested in terminal events\n * and you also handled emissions internally by using operators (e.g. using `tap`).\n *\n * Whichever style of calling `subscribe` you use, in both cases it returns a Subscription object.\n * This object allows you to call `unsubscribe` on it, which in turn will stop the work that an Observable does and will clean\n * up all resources that an Observable used. Note that cancelling a subscription will not call `complete` callback\n * provided to `subscribe` function, which is reserved for a regular completion signal that comes from an Observable.\n *\n * Remember that callbacks provided to `subscribe` are not guaranteed to be called asynchronously.\n * It is an Observable itself that decides when these functions will be called. For example {@link of}\n * by default emits all its values synchronously. Always check documentation for how given Observable\n * will behave when subscribed and if its default behavior can be modified with a `scheduler`.\n *\n * #### Examples\n *\n * Subscribe with an {@link guide/observer Observer}\n *\n * ```ts\n * import { of } from 'rxjs';\n *\n * const sumObserver = {\n * sum: 0,\n * next(value) {\n * console.log('Adding: ' + value);\n * this.sum = this.sum + value;\n * },\n * error() {\n * // We actually could just remove this method,\n * // since we do not really care about errors right now.\n * },\n * complete() {\n * console.log('Sum equals: ' + this.sum);\n * }\n * };\n *\n * of(1, 2, 3) // Synchronously emits 1, 2, 3 and then completes.\n * .subscribe(sumObserver);\n *\n * // Logs:\n * // 'Adding: 1'\n * // 'Adding: 2'\n * // 'Adding: 3'\n * // 'Sum equals: 6'\n * ```\n *\n * Subscribe with functions ({@link deprecations/subscribe-arguments deprecated})\n *\n * ```ts\n * import { of } from 'rxjs'\n *\n * let sum = 0;\n *\n * of(1, 2, 3).subscribe(\n * value => {\n * console.log('Adding: ' + value);\n * sum = sum + value;\n * },\n * undefined,\n * () => console.log('Sum equals: ' + sum)\n * );\n *\n * // Logs:\n * // 'Adding: 1'\n * // 'Adding: 2'\n * // 'Adding: 3'\n * // 'Sum equals: 6'\n * ```\n *\n * Cancel a subscription\n *\n * ```ts\n * import { interval } from 'rxjs';\n *\n * const subscription = interval(1000).subscribe({\n * next(num) {\n * console.log(num)\n * },\n * complete() {\n * // Will not be called, even when cancelling subscription.\n * console.log('completed!');\n * }\n * });\n *\n * setTimeout(() => {\n * subscription.unsubscribe();\n * console.log('unsubscribed!');\n * }, 2500);\n *\n * // Logs:\n * // 0 after 1s\n * // 1 after 2s\n * // 'unsubscribed!' after 2.5s\n * ```\n *\n * @param {Observer|Function} observerOrNext (optional) Either an observer with methods to be called,\n * or the first of three possible handlers, which is the handler for each value emitted from the subscribed\n * Observable.\n * @param {Function} error (optional) A handler for a terminal event resulting from an error. If no error handler is provided,\n * the error will be thrown asynchronously as unhandled.\n * @param {Function} complete (optional) A handler for a terminal event resulting from successful completion.\n * @return {Subscription} a subscription reference to the registered handlers\n * @method subscribe\n */\n subscribe(\n observerOrNext?: Partial> | ((value: T) => void) | null,\n error?: ((error: any) => void) | null,\n complete?: (() => void) | null\n ): Subscription {\n const subscriber = isSubscriber(observerOrNext) ? observerOrNext : new SafeSubscriber(observerOrNext, error, complete);\n\n errorContext(() => {\n const { operator, source } = this;\n subscriber.add(\n operator\n ? // We're dealing with a subscription in the\n // operator chain to one of our lifted operators.\n operator.call(subscriber, source)\n : source\n ? // If `source` has a value, but `operator` does not, something that\n // had intimate knowledge of our API, like our `Subject`, must have\n // set it. We're going to just call `_subscribe` directly.\n this._subscribe(subscriber)\n : // In all other cases, we're likely wrapping a user-provided initializer\n // function, so we need to catch errors and handle them appropriately.\n this._trySubscribe(subscriber)\n );\n });\n\n return subscriber;\n }\n\n /** @internal */\n protected _trySubscribe(sink: Subscriber): TeardownLogic {\n try {\n return this._subscribe(sink);\n } catch (err) {\n // We don't need to return anything in this case,\n // because it's just going to try to `add()` to a subscription\n // above.\n sink.error(err);\n }\n }\n\n /**\n * Used as a NON-CANCELLABLE means of subscribing to an observable, for use with\n * APIs that expect promises, like `async/await`. You cannot unsubscribe from this.\n *\n * **WARNING**: Only use this with observables you *know* will complete. If the source\n * observable does not complete, you will end up with a promise that is hung up, and\n * potentially all of the state of an async function hanging out in memory. To avoid\n * this situation, look into adding something like {@link timeout}, {@link take},\n * {@link takeWhile}, or {@link takeUntil} amongst others.\n *\n * #### Example\n *\n * ```ts\n * import { interval, take } from 'rxjs';\n *\n * const source$ = interval(1000).pipe(take(4));\n *\n * async function getTotal() {\n * let total = 0;\n *\n * await source$.forEach(value => {\n * total += value;\n * console.log('observable -> ' + value);\n * });\n *\n * return total;\n * }\n *\n * getTotal().then(\n * total => console.log('Total: ' + total)\n * );\n *\n * // Expected:\n * // 'observable -> 0'\n * // 'observable -> 1'\n * // 'observable -> 2'\n * // 'observable -> 3'\n * // 'Total: 6'\n * ```\n *\n * @param next a handler for each value emitted by the observable\n * @return a promise that either resolves on observable completion or\n * rejects with the handled error\n */\n forEach(next: (value: T) => void): Promise;\n\n /**\n * @param next a handler for each value emitted by the observable\n * @param promiseCtor a constructor function used to instantiate the Promise\n * @return a promise that either resolves on observable completion or\n * rejects with the handled error\n * @deprecated Passing a Promise constructor will no longer be available\n * in upcoming versions of RxJS. This is because it adds weight to the library, for very\n * little benefit. If you need this functionality, it is recommended that you either\n * polyfill Promise, or you create an adapter to convert the returned native promise\n * to whatever promise implementation you wanted. Will be removed in v8.\n */\n forEach(next: (value: T) => void, promiseCtor: PromiseConstructorLike): Promise;\n\n forEach(next: (value: T) => void, promiseCtor?: PromiseConstructorLike): Promise {\n promiseCtor = getPromiseCtor(promiseCtor);\n\n return new promiseCtor((resolve, reject) => {\n const subscriber = new SafeSubscriber({\n next: (value) => {\n try {\n next(value);\n } catch (err) {\n reject(err);\n subscriber.unsubscribe();\n }\n },\n error: reject,\n complete: resolve,\n });\n this.subscribe(subscriber);\n }) as Promise;\n }\n\n /** @internal */\n protected _subscribe(subscriber: Subscriber): TeardownLogic {\n return this.source?.subscribe(subscriber);\n }\n\n /**\n * An interop point defined by the es7-observable spec https://github.com/zenparsing/es-observable\n * @method Symbol.observable\n * @return {Observable} this instance of the observable\n */\n [Symbol_observable]() {\n return this;\n }\n\n /* tslint:disable:max-line-length */\n pipe(): Observable;\n pipe(op1: OperatorFunction): Observable;\n pipe(op1: OperatorFunction, op2: OperatorFunction): Observable;\n pipe(op1: OperatorFunction, op2: OperatorFunction, op3: OperatorFunction): Observable;\n pipe(\n op1: OperatorFunction,\n op2: OperatorFunction,\n op3: OperatorFunction,\n op4: OperatorFunction\n ): Observable;\n pipe(\n op1: OperatorFunction,\n op2: OperatorFunction,\n op3: OperatorFunction,\n op4: OperatorFunction,\n op5: OperatorFunction\n ): Observable;\n pipe(\n op1: OperatorFunction,\n op2: OperatorFunction,\n op3: OperatorFunction,\n op4: OperatorFunction,\n op5: OperatorFunction,\n op6: OperatorFunction\n ): Observable;\n pipe(\n op1: OperatorFunction,\n op2: OperatorFunction,\n op3: OperatorFunction,\n op4: OperatorFunction,\n op5: OperatorFunction,\n op6: OperatorFunction,\n op7: OperatorFunction\n ): Observable;\n pipe(\n op1: OperatorFunction,\n op2: OperatorFunction,\n op3: OperatorFunction,\n op4: OperatorFunction,\n op5: OperatorFunction,\n op6: OperatorFunction,\n op7: OperatorFunction,\n op8: OperatorFunction\n ): Observable;\n pipe(\n op1: OperatorFunction,\n op2: OperatorFunction,\n op3: OperatorFunction,\n op4: OperatorFunction,\n op5: OperatorFunction,\n op6: OperatorFunction,\n op7: OperatorFunction,\n op8: OperatorFunction,\n op9: OperatorFunction\n ): Observable;\n pipe(\n op1: OperatorFunction,\n op2: OperatorFunction,\n op3: OperatorFunction,\n op4: OperatorFunction,\n op5: OperatorFunction,\n op6: OperatorFunction,\n op7: OperatorFunction,\n op8: OperatorFunction,\n op9: OperatorFunction,\n ...operations: OperatorFunction[]\n ): Observable;\n /* tslint:enable:max-line-length */\n\n /**\n * Used to stitch together functional operators into a chain.\n * @method pipe\n * @return {Observable} the Observable result of all of the operators having\n * been called in the order they were passed in.\n *\n * ## Example\n *\n * ```ts\n * import { interval, filter, map, scan } from 'rxjs';\n *\n * interval(1000)\n * .pipe(\n * filter(x => x % 2 === 0),\n * map(x => x + x),\n * scan((acc, x) => acc + x)\n * )\n * .subscribe(x => console.log(x));\n * ```\n */\n pipe(...operations: OperatorFunction[]): Observable {\n return pipeFromArray(operations)(this);\n }\n\n /* tslint:disable:max-line-length */\n /** @deprecated Replaced with {@link firstValueFrom} and {@link lastValueFrom}. Will be removed in v8. Details: https://rxjs.dev/deprecations/to-promise */\n toPromise(): Promise