Automated LC-MS analysis and data extraction for high-throughput chemistry #1011

Workflow file for this run

.github/workflows/submission.yml at 7c66658

	# Runs process_dataset.py on all new and changed files.
	#
	# Submissions from forks only trigger the "validation" step to validate the new
	# data. After merging into a new branch in the parent repo, the workflow will
	# run again and trigger the "update" step to add reaction IDs, etc. in
	# preparation for merging into the "main" branch.

	name: Submission

	on: [pull_request, push]

	env:
	ORD_SCHEMA_TAG: v0.3.93

	jobs:
	count_reactions:
	if: >-
	github.event_name == 'pull_request' &&
	! github.event.pull_request.head.repo.fork
	runs-on: ubuntu-latest
	steps:
	- name: Checkout ord-data
	uses: actions/checkout@v2
	with:
	ref: ${{ github.event.pull_request.head.sha }}
	lfs: true
	if: github.event_name == 'pull_request'
	- name: Checkout ord-schema
	uses: actions/checkout@v2
	with:
	repository: Open-Reaction-Database/ord-schema
	ref: ${{ env.ORD_SCHEMA_TAG }}
	path: ord-schema
	- uses: actions/setup-python@v4
	with:
	python-version: '3.11'
	- name: Install ord_schema
	run: \|
	cd "${GITHUB_WORKSPACE}/ord-schema"
	python -m pip install --upgrade pip
	python -m pip install wheel
	python -m pip install .
	- name: Update reactions badge
	run: \|
	cd "${GITHUB_WORKSPACE}"
	python ord-schema/badges/reactions.py --root=data --output=badges/reactions.svg
	git add badges/reactions.svg
	git config user.name github-actions
	git config user.email github-actions@github.com
	# Fail gracefully if there is nothing to commit.
	git commit -a -m "Update badges" \|\| (( $? == 1 ))
	git push "https://${GITHUB_ACTOR}:${GITHUB_TOKEN}@github.com/${GITHUB_REPOSITORY}.git" "HEAD:${GITHUB_HEAD_REF}"

	check_file_types:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v2
	- name: Add upstream for comparisons to HEAD
	run: \|
	cd "${GITHUB_WORKSPACE}"
	git remote add upstream \
	"https://github.com/Open-Reaction-Database/${GITHUB_REPOSITORY##*/}.git"
	echo "Current branch: $(git rev-parse --abbrev-ref HEAD)"
	git fetch --no-tags --prune --depth=1 upstream \
	+refs/heads/:refs/remotes/upstream/
	- name: Check changed files (PR from fork)
	run: \|
	cd "${GITHUB_WORKSPACE}"
	git diff --name-only upstream/main > changed_files.txt
	grep -vE '\.pb(txt)?(.gz)?$' changed_files.txt && \
	echo "Error: submissions should only contain (gzipped) .pbtxt or .pb files" && \
	exit 1 \|\| true
	if: >-
	github.event_name == 'pull_request' &&
	github.event.pull_request.head.repo.fork

	check_target_branch:
	runs-on: ubuntu-latest
	steps:
	- name: Check target branch
	run: \|
	echo "Target branch: ${GITHUB_BASE_REF}"
	test "${GITHUB_BASE_REF}" != "main"
	if: >-
	github.event_name == 'pull_request' &&
	github.event.pull_request.head.repo.fork

	process_submission:
	runs-on: ubuntu-latest
	steps:
	- name: Checkout ord-data
	uses: actions/checkout@v2
	with:
	lfs: true
	if: github.event_name == 'push'
	- name: Checkout ord-data
	uses: actions/checkout@v2
	with:
	ref: ${{ github.event.pull_request.head.sha }}
	lfs: true
	if: github.event_name == 'pull_request'
	- name: Add upstream for comparisons to HEAD
	run: \|
	cd "${GITHUB_WORKSPACE}"
	git remote add upstream \
	"https://github.com/Open-Reaction-Database/${GITHUB_REPOSITORY##*/}.git"
	echo "Current branch: $(git rev-parse --abbrev-ref HEAD)"
	git fetch --no-tags --prune --depth=1 upstream \
	+refs/heads/:refs/remotes/upstream/
	- name: Checkout ord-schema
	uses: actions/checkout@v2
	with:
	repository: Open-Reaction-Database/ord-schema
	ref: ${{ env.ORD_SCHEMA_TAG }}
	path: ord-schema
	- name: Identify changed files
	# NOTE(kearnes): This sets the NUM_CHANGED_FILES variable.
	run: \|
	cd "${GITHUB_WORKSPACE}"
	git diff --name-status upstream/main > changed_files.txt
	echo "Found $(wc -l < changed_files.txt \| tr -d ' ') changed files"
	cat changed_files.txt
	# Use `\|\| (( $? == 1 ))` in case no lines match (exit code is nonzero).
	grep -E "\.pb(txt)?(.gz)?$" changed_files.txt > changed_data_files.txt \|\| (( $? == 1 ))
	# Use LOCAL_NUM_CHANGED since ::set-env values are not available immediately.
	LOCAL_NUM_CHANGED="$(wc -l < changed_data_files.txt \| tr -d ' ')"
	echo "NUM_CHANGED_FILES=${LOCAL_NUM_CHANGED}" >> $GITHUB_ENV
	echo "Found ${LOCAL_NUM_CHANGED} changed dataset files"
	cat changed_data_files.txt
	- uses: actions/setup-python@v4
	with:
	python-version: '3.11'
	if: env.NUM_CHANGED_FILES != '0'
	- name: Install ord_schema
	run: \|
	cd "${GITHUB_WORKSPACE}/ord-schema"
	python -m pip install --upgrade pip
	python -m pip install wheel
	python -m pip install .
	if: env.NUM_CHANGED_FILES != '0'
	- name: Validate submission
	run: \|
	cd "${GITHUB_WORKSPACE}"
	python ./ord-schema/ord_schema/scripts/process_dataset.py \
	--input_file=changed_data_files.txt \
	--base=upstream/main
	if: >-
	env.NUM_CHANGED_FILES != '0' &&
	! (github.event_name == 'pull_request' &&
	! github.event.pull_request.head.repo.fork)
	- name: Update submission
	run: \|
	cd "${GITHUB_WORKSPACE}"
	python ./ord-schema/ord_schema/scripts/process_dataset.py \
	--input_file=changed_data_files.txt \
	--update \
	--cleanup \
	--base=upstream/main \
	--issue=${{ github.event.number }} \
	--token=${{ secrets.GITHUB_TOKEN }}
	git config user.name github-actions
	git config user.email github-actions@github.com
	# Fail gracefully if there is nothing to commit.
	git commit -a -m "Update submission" \|\| (( $? == 1 ))
	git push "https://${GITHUB_ACTOR}:${GITHUB_TOKEN}@github.com/${GITHUB_REPOSITORY}.git" "HEAD:${GITHUB_HEAD_REF}"
	if: >-
	env.NUM_CHANGED_FILES != '0' &&
	github.event_name == 'pull_request' &&
	! github.event.pull_request.head.repo.fork

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Automated LC-MS analysis and data extraction for high-throughput chemistry #1011

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Automated LC-MS analysis and data extraction for high-throughput chemistry #1011

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Workflow file for this run