build

[GEN-2332] Add workflow to build genome nexus annotator #1144

Workflow file for this run

	name: build

	on:
	push:
	branches: [main, develop]
	paths-ignore:
	- '**.md' # All Markdown files
	- '/docs/' # Documentation directory

	pull_request:
	types: [opened, reopened, labeled, synchronize]
	paths-ignore:
	- '**.md' # All Markdown files
	- '/docs/' # Documentation directory

	release:
	types: [created]

	workflow_dispatch:

	env:
	REGISTRY: ghcr.io
	IMAGE_NAME: ${{ github.repository }}
	TEST_PROJECT_SYNID: syn7208886 # synapse_id of the test synapse project
	TEST_SEQ_DATE: Jul-2022 # SEQ_DATE to use for test pipeline. Should match the one used in nf-genie.

	jobs:

	determine-changes:
	if: >-
	(
	(
	contains(github.event.pull_request.labels.*.name, 'run_integration_tests') &&
	github.event.pull_request.state == 'open'
	) \|\|
	(
	github.event_name == 'push' &&
	(github.ref_name == 'main' \|\| github.ref_name == 'develop')
	) \|\|
	(
	github.event_name == 'release'
	)
	)
	runs-on: ubuntu-latest
	outputs:
	non-test-changes: ${{ steps.get-changes.outputs.non-test-changes }}
	steps:
	- name: Checkout Code
	uses: actions/checkout@v3
	with:
	fetch-depth: 0

	- name: Determine Changes
	id: get-changes
	run: \|
	if [ "${{ github.event_name }}" == "push" ]; then
	echo "Handling a push event..."
	ALL_CHANGED_FILES=$(git diff --name-only HEAD^ HEAD)
	elif [ "${{ github.event_name }}" == "pull_request" ]; then
	echo "Handling a pull request event..."
	git fetch origin ${{ github.base_ref }}
	ALL_CHANGED_FILES=$(git diff --name-only origin/${{ github.base_ref }} HEAD)
	fi
	echo "All Changed Files: $ALL_CHANGED_FILES"
	NON_TEST_CHANGES=$(echo "$ALL_CHANGED_FILES" \| grep -v '^tests/' \|\| true)
	echo "Non-Test Changes: $NON_TEST_CHANGES"
	echo "::set-output name=non-test-changes::$NON_TEST_CHANGES"

	test:
	runs-on: ubuntu-latest
	if: >-
	(
	(
	contains(github.event.pull_request.labels.*.name, 'run_integration_tests') &&
	github.event.pull_request.state == 'open'
	) \|\|
	(
	github.event_name == 'push' &&
	(github.ref_name == 'main' \|\| github.ref_name == 'develop')
	) \|\|
	(
	github.event_name == 'release'
	)
	)
	strategy:
	matrix:
	python-version: ['3.10', 3.11]
	# python-version: ['3.10', 3.11, 3.12]
	steps:
	- uses: actions/checkout@v4
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v5
	with:
	python-version: ${{ matrix.python-version }}
	- name: Install dependencies
	run: \|
	sudo apt-get install -y bedtools
	python -m pip install --upgrade pip
	pip install pytest pytest-cov
	pip install .
	if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
	- name: Test with pytest
	run: \|
	pytest tests/ --cov=genie --cov=genie_registry --cov-report=html
	- name: Upload pytest test results
	uses: actions/upload-artifact@v4
	with:
	name: pytest-results-${{ matrix.python-version }}
	path: htmlcov
	# Use always() to always run this step to publish test results when there are test failures
	if: ${{ always() }}


	lint:
	runs-on: ubuntu-latest
	if: >-
	(
	(
	contains(github.event.pull_request.labels.*.name, 'run_integration_tests') &&
	github.event.pull_request.state == 'open'
	) \|\|
	(
	github.event_name == 'push' &&
	(github.ref_name == 'main' \|\| github.ref_name == 'develop')
	) \|\|
	(
	github.event_name == 'release'
	)
	)
	steps:
	- uses: actions/checkout@v4
	- uses: psf/black@stable
	with:
	version: "~=23.12"

	build-container:
	needs: [test, lint]
	if: >-
	(
	(
	contains(github.event.pull_request.labels.*.name, 'run_integration_tests') &&
	github.event.pull_request.state == 'open'
	) \|\|
	(
	github.event_name == 'push' &&
	(github.ref_name == 'main' \|\| github.ref_name == 'develop')
	) \|\|
	(
	github.event_name == 'release'
	)
	)
	runs-on: ubuntu-latest
	permissions:
	contents: read
	packages: write

	steps:
	- name: Checkout repository
	uses: actions/checkout@v4

	- name: Setup Docker buildx
	uses: docker/setup-buildx-action@v3

	- name: Log into registry ${{ env.REGISTRY }}
	uses: docker/login-action@v3
	with:
	registry: ${{ env.REGISTRY }}
	username: ${{ github.actor }}
	password: ${{ secrets.GITHUB_TOKEN }}

	- name: Extract Docker metadata
	id: meta
	uses: docker/metadata-action@v5
	with:
	images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}

	- name: Format tags as registry refs
	id: registry_refs
	env:
	TAGS: ${{ steps.meta.outputs.json }}
	run: \|
	echo "tags=$(echo $TAGS \| jq -r '.tags[] \| "type=registry,ref=\(.)_cache"')" >> $GITHUB_OUTPUT

	- name: Build and push Docker image
	id: build-and-push
	uses: docker/build-push-action@v5
	if: github.event_name != 'pull_request'
	with:
	context: .
	push: true
	provenance: false
	tags: ${{ steps.meta.outputs.tags }}
	labels: ${{ steps.meta.outputs.labels }}
	cache-from: ${{ steps.registry_refs.outputs.tags }},mode=max
	cache-to: ${{ steps.registry_refs.outputs.tags }},mode=max

	integration-tests:
	# Only runs for the following conditions:
	# - if github label "run_integration_tests"
	# - for commits during when pull request is open OR when it's a push into main or develop branches
	needs: [determine-changes, lint, test, build-container]
	runs-on: ubuntu-latest
	if: >-
	needs.determine-changes.outputs.non-test-changes &&
	(
	(
	contains(github.event.pull_request.labels.*.name, 'run_integration_tests') &&
	github.event.pull_request.state == 'open'
	) \|\|
	(
	github.event_name == 'push' &&
	(github.ref_name == 'main' \|\| github.ref_name == 'develop')
	) \|\|
	(
	github.event_name == 'release'
	)
	)
	steps:
	- name: Checkout repository
	uses: actions/checkout@v4

	- name: Extract Branch Name
	run: \|
	if [ "$GITHUB_HEAD_REF" != "" ]; then
	echo "BRANCH_NAME=$GITHUB_HEAD_REF" >> $GITHUB_ENV
	else
	echo "BRANCH_NAME=${GITHUB_REF#refs/heads/}" >> $GITHUB_ENV
	fi

	- name: Pull Public Docker Image from GHCR
	run: \|
	docker pull ghcr.io/sage-bionetworks/genie:${{ env.BRANCH_NAME }}

	- name: Start Docker Container
	run: \|
	docker run -d --name genie-container \
	-e SYNAPSE_AUTH_TOKEN="${{ secrets.SYNAPSE_AUTH_TOKEN }}" \
	ghcr.io/sage-bionetworks/genie:${{ env.BRANCH_NAME }} \
	sh -c "while true; do sleep 1; done"

	- name: Run validation in test pipeline
	run: \|
	docker exec genie-container \
	python3 /root/Genie/bin/input_to_database.py \
	mutation \
	--project_id ${{ env.TEST_PROJECT_SYNID }} \
	--onlyValidate \
	--genie_annotation_pkg /root/annotation-tools

	- name: Run processing on mutation data in test pipeline
	run: \|
	docker exec genie-container \
	python3 /root/Genie/bin/input_to_database.py mutation \
	--project_id ${{ env.TEST_PROJECT_SYNID }} \
	--genie_annotation_pkg /root/annotation-tools \
	--createNewMafDatabase

	- name: Run processing on non-mutation data in test pipeline
	run: \|
	docker exec genie-container \
	python3 /root/Genie/bin/input_to_database.py main \
	--project_id ${{ env.TEST_PROJECT_SYNID }}

	- name: Run consortium release in test pipeline
	run: \|
	docker exec genie-container \
	python3 /root/Genie/bin/database_to_staging.py ${{ env.TEST_SEQ_DATE }} ../cbioportal TEST --test

	- name: Run public release in test pipeline
	run: \|
	docker exec genie-container \
	python3 /root/Genie/bin/consortium_to_public.py ${{ env.TEST_SEQ_DATE }} ../cbioportal TEST --test

	- name: Stop and Remove Docker Container
	run: docker stop genie-container && docker rm genie-container

	deploy:
	needs: [test, lint, build-container]
	runs-on: ubuntu-latest
	if: github.event_name == 'release'
	permissions:
	id-token: write
	steps:
	- uses: actions/checkout@v4
	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: '3.x'
	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install setuptools wheel build
	- name: Build distributions
	run: python -m build
	- name: Publish to pypi
	uses: pypa/gh-action-pypi-publish@release/v1

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

[GEN-2332] Add workflow to build genome nexus annotator #1144

Workflow file

[GEN-2332] Add workflow to build genome nexus annotator #1144

Uh oh!

Workflow file for this run