Updated username in CODEOWNERS to valid team name #516

Workflow file for this run

.github/workflows/PR-validation.yml at 7bfef97

	name: PR validation
	on:
	pull_request:
	types: [synchronize, opened, reopened, edited, labeled, unlabeled]
	branches:
	- main
	concurrency:
	group: ${{ github.workflow }}-${{ github.event.pull_request.number }}
	cancel-in-progress: true
	jobs:
	container-build-context:
	name: define container image build context variables
	runs-on: ubuntu-22.04
	outputs:
	tagname: ${{ steps.store_tagname.outputs.tagname }}
	steps:
	- name: Store image tag in env
	id: store_tagname
	shell: bash
	run: \|
	echo "tagname=PR-${{ github.event.pull_request.number }}-validation" >> $GITHUB_OUTPUT
	pipeline-seq-retrieval-update-dependency-lock-files:
	name: pipeline/seq_retrieval update and upload dependency lock file
	runs-on: ubuntu-22.04
	defaults:
	run:
	shell: bash
	working-directory: ./pipeline/seq_retrieval/
	steps:
	- uses: actions/setup-python@v5
	with:
	python-version: '3.12'
	- name: Check out repository code
	uses: actions/checkout@v4
	with:
	fetch-depth: 0
	sparse-checkout: \|
	pipeline/seq_retrieval/
	- name: Update lock files
	if: ${{ !contains(github.event.pull_request.labels.*.name, 'no-deps-lock-updates') }}
	shell: bash
	run: \|
	make pip-tools update-deps-lock update-test-deps-lock
	- name: Upload updated (main) lock file as artifact
	uses: actions/upload-artifact@v4
	with:
	name: pipeline_seq_retrieval_deps_lock
	path: pipeline/seq_retrieval/requirements.txt
	if-no-files-found: error
	- name: Upload updated (test) lock file as artifact
	uses: actions/upload-artifact@v4
	with:
	name: pipeline_seq_retrieval_tests_deps_lock
	path: pipeline/seq_retrieval/tests/requirements.txt
	if-no-files-found: error
	api-update-dependency-lock-files:
	name: api update and upload dependency lock file
	runs-on: ubuntu-22.04
	defaults:
	run:
	shell: bash
	working-directory: ./api/
	steps:
	- uses: actions/setup-python@v5
	with:
	python-version: '3.12'
	- name: Check out repository code
	uses: actions/checkout@v4
	with:
	fetch-depth: 0
	sparse-checkout: \|
	api/
	- name: Update lock files
	if: ${{ !contains(github.event.pull_request.labels.*.name, 'no-deps-lock-updates') }}
	shell: bash
	run: \|
	make pip-tools update-deps-lock update-test-deps-lock
	- name: Upload updated (main) lock file as artifact
	uses: actions/upload-artifact@v4
	with:
	name: api_deps_lock
	path: api/requirements.txt
	if-no-files-found: error
	- name: Upload updated (test) lock file as artifact
	uses: actions/upload-artifact@v4
	with:
	name: api_tests_deps_lock
	path: api/tests/requirements.txt
	if-no-files-found: error
	webui-update-dependency-lock-files:
	name: webui update and upload dependency lock file
	runs-on: ubuntu-22.04
	defaults:
	run:
	shell: bash
	working-directory: ./webui/
	steps:
	- uses: actions/setup-node@v4
	with:
	node-version: "20"
	- name: Check out repository code
	uses: actions/checkout@v4
	with:
	fetch-depth: 0
	sparse-checkout: \|
	webui/
	- name: Update lock files
	if: ${{ !contains(github.event.pull_request.labels.*.name, 'no-deps-lock-updates') }}
	shell: bash
	run: \|
	make update-deps-lock
	- name: Upload updated lock file as artifact
	uses: actions/upload-artifact@v4
	with:
	name: webui_deps_lock
	path: webui/package-lock.json
	if-no-files-found: error
	shared-aws-infra-update-dependency-lock-files:
	name: shared_aws_infra update and upload dependency lock file
	runs-on: ubuntu-22.04
	defaults:
	run:
	shell: bash
	working-directory: ./shared_aws_infra/
	steps:
	- uses: actions/setup-python@v5
	with:
	python-version: '3.12'
	- name: Check out repository code
	uses: actions/checkout@v4
	with:
	fetch-depth: 0
	sparse-checkout: \|
	shared_aws_infra/
	- name: Update lock files
	if: ${{ !contains(github.event.pull_request.labels.*.name, 'no-deps-lock-updates') }}
	shell: bash
	run: \|
	make pip-tools update-deps-lock update-test-deps-lock
	- name: Upload updated (main) lock file as artifact
	uses: actions/upload-artifact@v4
	with:
	name: shared_aws_infra_deps_lock
	path: shared_aws_infra/requirements.txt
	if-no-files-found: error
	- name: Upload updated (test) lock file as artifact
	uses: actions/upload-artifact@v4
	with:
	name: shared_aws_infra_test_deps_lock
	path: shared_aws_infra/tests/requirements.txt
	if-no-files-found: error
	shared-aws-infra-code-checks:
	name: shared_aws_infra code checks
	needs:
	- shared-aws-infra-update-dependency-lock-files
	runs-on: ubuntu-22.04
	defaults:
	run:
	working-directory: ./shared_aws_infra
	steps:
	- name: Check out repository code
	uses: actions/checkout@v4
	with:
	fetch-depth: 0
	sparse-checkout: \|
	shared_aws_infra/
	- name: Download updated shared_aws_infra (main) dependencies lock file
	uses: actions/download-artifact@v4
	with:
	name: shared_aws_infra_deps_lock
	path: shared_aws_infra
	- name: Download updated shared_aws_infra (test) dependencies lock file
	uses: actions/download-artifact@v4
	with:
	name: shared_aws_infra_test_deps_lock
	path: shared_aws_infra/tests
	- name: Setup Python
	uses: actions/setup-python@v5
	with:
	python-version: "3.12"
	- name: Code typing test
	run: \|
	make run-type-checks
	- name: Code style test
	run: \|
	make run-style-checks
	- name: Unit tests
	run: make run-unit-tests
	shared-aws-infra-package-build:
	name: shared_aws_infra python package build
	needs:
	- shared-aws-infra-code-checks
	runs-on: ubuntu-22.04
	defaults:
	run:
	working-directory: ./shared_aws_infra
	steps:
	- name: Check out repository code
	uses: actions/checkout@v4
	with:
	fetch-depth: 0
	sparse-checkout: \|
	shared_aws_infra/
	- name: Download updated shared_aws_infra (main) dependencies lock file
	uses: actions/download-artifact@v4
	with:
	name: shared_aws_infra_deps_lock
	path: shared_aws_infra
	- name: Download updated shared_aws_infra (test) dependencies lock file
	uses: actions/download-artifact@v4
	with:
	name: shared_aws_infra_test_deps_lock
	path: shared_aws_infra/tests
	- name: Setup Python
	uses: actions/setup-python@v5
	with:
	python-version: "3.12"
	- name: Build package
	run: \|
	make clean build
	- name: Upload package as artifact
	uses: actions/upload-artifact@v4
	with:
	name: shared_aws_infra_package
	path: shared_aws_infra/dist/pavi_shared_aws_infra-0.0.0-py3-none-any.whl
	pipeline-aws-infra-update-dependency-lock-files:
	name: pipeline/aws_infra update and upload dependency lock file
	needs:
	- shared-aws-infra-package-build
	runs-on: ubuntu-22.04
	defaults:
	run:
	shell: bash
	working-directory: ./pipeline/aws_infra/
	steps:
	- uses: actions/setup-python@v5
	with:
	python-version: '3.12'
	- name: Check out repository code
	uses: actions/checkout@v4
	with:
	fetch-depth: 0
	sparse-checkout: \|
	pipeline/aws_infra/
	- name: Download shared AWS infra package
	uses: actions/download-artifact@v4
	with:
	name: shared_aws_infra_package
	path: /tmp/
	- name: Update lock files
	if: ${{ !contains(github.event.pull_request.labels.*.name, 'no-deps-lock-updates') }}
	shell: bash
	run: \|
	make pip-tools update-deps-lock update-test-deps-lock
	- name: Upload updated (main) lock file as artifact
	uses: actions/upload-artifact@v4
	with:
	name: pipeline_aws_infra_deps_lock
	path: pipeline/aws_infra/requirements.txt
	if-no-files-found: error
	- name: Upload updated (test) lock file as artifact
	uses: actions/upload-artifact@v4
	with:
	name: pipeline_aws_infra_tests_deps_lock
	path: pipeline/aws_infra/tests/requirements.txt
	if-no-files-found: error
	api-aws-infra-update-dependency-lock-files:
	name: api/aws_infra update and upload dependency lock file
	needs:
	- shared-aws-infra-package-build
	runs-on: ubuntu-22.04
	defaults:
	run:
	shell: bash
	working-directory: ./api/aws_infra/
	steps:
	- uses: actions/setup-python@v5
	with:
	python-version: '3.12'
	- name: Check out repository code
	uses: actions/checkout@v4
	with:
	fetch-depth: 0
	sparse-checkout: \|
	api/aws_infra/
	- name: Download shared AWS infra package
	uses: actions/download-artifact@v4
	with:
	name: shared_aws_infra_package
	path: /tmp/
	- name: Update lock files
	if: ${{ !contains(github.event.pull_request.labels.*.name, 'no-deps-lock-updates') }}
	shell: bash
	run: \|
	make pip-tools update-deps-lock update-test-deps-lock
	- name: Upload updated (main) lock file as artifact
	uses: actions/upload-artifact@v4
	with:
	name: api_aws_infra_deps_lock
	path: api/aws_infra/requirements.txt
	if-no-files-found: error
	- name: Upload updated (test) lock file as artifact
	uses: actions/upload-artifact@v4
	with:
	name: api_aws_infra_tests_deps_lock
	path: api/aws_infra/tests/requirements.txt
	if-no-files-found: error
	webui-aws-infra-update-dependency-lock-files:
	name: webui/aws_infra update and upload dependency lock file
	needs:
	- shared-aws-infra-package-build
	runs-on: ubuntu-22.04
	defaults:
	run:
	shell: bash
	working-directory: ./webui/aws_infra/
	steps:
	- uses: actions/setup-python@v5
	with:
	python-version: '3.12'
	- name: Check out repository code
	uses: actions/checkout@v4
	with:
	fetch-depth: 0
	sparse-checkout: \|
	webui/aws_infra/
	- name: Download shared AWS infra package
	uses: actions/download-artifact@v4
	with:
	name: shared_aws_infra_package
	path: /tmp/
	- name: Update lock files
	if: ${{ !contains(github.event.pull_request.labels.*.name, 'no-deps-lock-updates') }}
	shell: bash
	run: \|
	make pip-tools update-deps-lock update-test-deps-lock
	- name: Upload updated (main) lock file as artifact
	uses: actions/upload-artifact@v4
	with:
	name: webui_aws_infra_deps_lock
	path: webui/aws_infra/requirements.txt
	if-no-files-found: error
	- name: Upload updated (test) lock file as artifact
	uses: actions/upload-artifact@v4
	with:
	name: webui_aws_infra_tests_deps_lock
	path: webui/aws_infra/tests/requirements.txt
	if-no-files-found: error
	pipeline-seq-retrieval-container-image-build:
	name: pipeline/seq_retrieval container-image build
	needs:
	- container-build-context
	- pipeline-seq-retrieval-update-dependency-lock-files
	permissions:
	id-token: write # This is required for requesting the JWT for gaining permissions to assume the IAM role to perform AWS actions
	runs-on: ubuntu-22.04
	steps:
	- name: Check out repository code
	uses: actions/checkout@v4
	with:
	fetch-depth: 0
	sparse-checkout: \|
	pipeline/seq_retrieval/
	- name: Download updated seq_retrieval (main) dependencies lock file
	uses: actions/download-artifact@v4
	with:
	name: pipeline_seq_retrieval_deps_lock
	path: pipeline/seq_retrieval
	- name: Set up Docker Buildx
	uses: docker/setup-buildx-action@v3
	# This step will configure environment variables to be used by all steps
	# involving AWS interaction further down
	- name: AWS credentials configuration
	uses: aws-actions/configure-aws-credentials@v4
	with:
	role-to-assume: ${{ secrets.GH_ACTIONS_AWS_ROLE }}
	role-session-name: gh-actions-${{github.run_id}}.${{github.run_number}}.${{github.run_attempt}}-seq-retrieval-image-upload
	aws-region: us-east-1
	- name: Amazon ECR login
	id: login-ecr
	uses: aws-actions/amazon-ecr-login@v2
	- name: Build container image
	uses: docker/build-push-action@v5
	with:
	context: ./pipeline/seq_retrieval/
	push: false
	tags: agr_pavi/pipeline_seq_retrieval:latest
	outputs: type=docker,dest=/tmp/pavi_seq_retrieval_docker_image.tar
	- name: Upload image as artifact (share between jobs)
	uses: actions/upload-artifact@v4
	with:
	name: seq_retrieval_image
	path: /tmp/pavi_seq_retrieval_docker_image.tar
	- name: Load, tag and push image to registry
	run: \|
	docker load --input /tmp/pavi_seq_retrieval_docker_image.tar
	docker tag agr_pavi/pipeline_seq_retrieval:latest ${{ steps.login-ecr.outputs.registry }}/agr_pavi/pipeline_seq_retrieval:${{needs.container-build-context.outputs.tagname}}
	docker push ${{ steps.login-ecr.outputs.registry }}/agr_pavi/pipeline_seq_retrieval:${{needs.container-build-context.outputs.tagname}}
	pipeline-seq-retrieval-code-checks:
	name: pipeline/seq_retrieval code checks
	needs:
	- pipeline-seq-retrieval-update-dependency-lock-files
	runs-on: ubuntu-22.04
	defaults:
	run:
	shell: bash
	working-directory: ./pipeline/seq_retrieval/
	steps:
	- name: Check out repository code
	uses: actions/checkout@v4
	with:
	fetch-depth: 0
	sparse-checkout: \|
	pipeline/seq_retrieval/
	- name: Download updated seq_retrieval (main) dependencies lock file
	uses: actions/download-artifact@v4
	with:
	name: pipeline_seq_retrieval_deps_lock
	path: pipeline/seq_retrieval
	- name: Download updated seq_retrieval (test) dependencies lock file
	uses: actions/download-artifact@v4
	with:
	name: pipeline_seq_retrieval_tests_deps_lock
	path: pipeline/seq_retrieval/tests
	- uses: actions/setup-python@v5
	with:
	python-version: '3.12'
	- name: Code typing test
	run: \|
	make run-type-checks
	- name: Code style test
	run: \|
	make run-style-checks
	- name: Run unit tests
	run: \|
	make run-unit-tests
	pipeline-alignment-container-image-build:
	name: pipeline/alignment container-image build
	needs:
	- container-build-context
	permissions:
	id-token: write # This is required for requesting the JWT for gaining permissions to assume the IAM role to perform AWS actions
	runs-on: ubuntu-22.04
	steps:
	- name: Check out repository code
	uses: actions/checkout@v4
	with:
	fetch-depth: 0
	sparse-checkout: \|
	pipeline/alignment/
	- name: Set up Docker Buildx
	uses: docker/setup-buildx-action@v3
	# This step will configure environment variables to be used by all steps
	# involving AWS interaction further down
	- name: AWS credentials configuration
	uses: aws-actions/configure-aws-credentials@v4
	with:
	role-to-assume: ${{ secrets.GH_ACTIONS_AWS_ROLE }}
	role-session-name: gh-actions-${{github.run_id}}.${{github.run_number}}.${{github.run_attempt}}-alignment-image-upload
	aws-region: us-east-1
	- name: Amazon ECR login
	id: login-ecr
	uses: aws-actions/amazon-ecr-login@v2
	- name: Build container image
	uses: docker/build-push-action@v5
	with:
	context: ./pipeline/alignment/
	push: false
	tags: agr_pavi/pipeline_alignment:latest
	outputs: type=docker,dest=/tmp/pavi_alignment_docker_image.tar
	- name: Upload image as artifact (share between jobs)
	uses: actions/upload-artifact@v4
	with:
	name: alignment_image
	path: /tmp/pavi_alignment_docker_image.tar
	- name: Load, tag and push image to registry
	run: \|
	docker load --input /tmp/pavi_alignment_docker_image.tar
	docker tag agr_pavi/pipeline_alignment:latest ${{ steps.login-ecr.outputs.registry }}/agr_pavi/pipeline_alignment:${{needs.container-build-context.outputs.tagname}}
	docker push ${{ steps.login-ecr.outputs.registry }}/agr_pavi/pipeline_alignment:${{needs.container-build-context.outputs.tagname}}
	pipeline-alignment-unit-testing:
	name: pipeline/alignment unit testing
	needs:
	- pipeline-alignment-container-image-build
	runs-on: ubuntu-22.04
	defaults:
	run:
	shell: bash
	working-directory: ./pipeline/alignment/
	steps:
	- name: Check out repository code
	uses: actions/checkout@v4
	with:
	fetch-depth: 0
	sparse-checkout: \|
	pipeline/alignment/
	- name: Download alignment image artifact (from previous job)
	uses: actions/download-artifact@v4
	with:
	name: alignment_image
	path: /tmp
	- name: Load alignment Docker image
	run: \|
	docker load --input /tmp/pavi_alignment_docker_image.tar
	- name: Run unit test
	run: \|
	make run-unit-tests
	pipeline-workflow-integration-testing:
	name: pipeline/workflow integration testing
	needs:
	- container-build-context
	- pipeline-seq-retrieval-container-image-build
	- pipeline-alignment-container-image-build
	permissions:
	id-token: write # This is required for requesting the JWT for gaining permissions to assume the IAM role to perform AWS actions
	runs-on: ubuntu-22.04
	defaults:
	run:
	shell: bash
	working-directory: ./pipeline/workflow/
	steps:
	- name: Check out repository code
	uses: actions/checkout@v4
	with:
	fetch-depth: 0
	sparse-checkout: \|
	pipeline/workflow/
	tests/resources/
	- name: Download seq_retrieval image artifact (from previous job)
	uses: actions/download-artifact@v4
	with:
	name: seq_retrieval_image
	path: /tmp
	- name: Download alignment image artifact (from previous job)
	uses: actions/download-artifact@v4
	with:
	name: alignment_image
	path: /tmp
	- name: Load seq_retrieval Docker image
	run: \|
	docker load --input /tmp/pavi_seq_retrieval_docker_image.tar
	- name: Load alignment Docker image
	run: \|
	docker load --input /tmp/pavi_alignment_docker_image.tar
	- name: Run local integration test
	run: \|
	make run-integration-test-local
	# This step will configure environment variables to be used by all steps
	# involving AWS interaction further down
	- name: AWS credentials configuration
	uses: aws-actions/configure-aws-credentials@v4
	with:
	role-to-assume: ${{ secrets.GH_ACTIONS_AWS_ROLE }}
	role-session-name: gh-actions-${{github.run_id}}.${{github.run_number}}.${{github.run_attempt}}-workflow-aws-test
	aws-region: us-east-1
	- name: Run AWS integration test
	run: \|
	make run-integration-test-aws TAG_NAME=${{needs.container-build-context.outputs.tagname}}
	pipeline-aws-infra-code-checks:
	name: pipeline/aws_infra code checks
	needs:
	- pipeline-aws-infra-update-dependency-lock-files
	- shared-aws-infra-package-build
	permissions:
	id-token: write # This is required for requesting the JWT for gaining permissions to assume the IAM role to perform AWS actions
	runs-on: ubuntu-22.04
	defaults:
	run:
	working-directory: ./pipeline/aws_infra
	steps:
	- name: Check out repository code
	uses: actions/checkout@v4
	with:
	fetch-depth: 0
	sparse-checkout: \|
	pipeline/aws_infra/
	- name: Download updated pipeline/aws_infra (main) dependencies lock file
	uses: actions/download-artifact@v4
	with:
	name: pipeline_aws_infra_deps_lock
	path: pipeline/aws_infra
	- name: Download updated aws_infra (test) dependencies lock file
	uses: actions/download-artifact@v4
	with:
	name: pipeline_aws_infra_tests_deps_lock
	path: pipeline/aws_infra/tests
	- name: Download shared AWS infra package
	uses: actions/download-artifact@v4
	with:
	name: shared_aws_infra_package
	path: /tmp/
	- name: Setup Python
	uses: actions/setup-python@v5
	with:
	python-version: "3.12"
	- name: Code typing test
	run: \|
	make run-type-checks
	- name: Code style test
	run: \|
	make run-style-checks
	- name: Setup node.js (CDK requirement)
	uses: actions/setup-node@v4
	with:
	node-version: "18"
	- name: Install CDK CLI
	run: npm install -g aws-cdk
	- name: Install CDK stack dependencies
	run: pip install -r requirements.txt
	- name: AWS credentials configuration
	uses: aws-actions/configure-aws-credentials@v4
	with:
	role-to-assume: ${{secrets.GH_ACTIONS_AWS_ROLE}}
	role-session-name: gh-actions-${{github.run_id}}.${{github.run_number}}.${{github.run_attempt}}-cdk-test
	aws-region: us-east-1
	- name: Validate production CDK stack code
	run: make validate
	api-code-checks:
	name: API code checks
	needs:
	- api-update-dependency-lock-files
	runs-on: ubuntu-22.04
	defaults:
	run:
	shell: bash
	working-directory: ./api/
	steps:
	- name: Check out repository code
	uses: actions/checkout@v4
	with:
	fetch-depth: 0
	sparse-checkout: \|
	api/
	- name: Download updated api (main) dependencies lock file
	uses: actions/download-artifact@v4
	with:
	name: api_deps_lock
	path: api
	- name: Download updated api (test) dependencies lock file
	uses: actions/download-artifact@v4
	with:
	name: api_tests_deps_lock
	path: api/tests
	- uses: actions/setup-python@v5
	with:
	python-version: '3.12'
	- name: Code typing test
	run: \|
	make run-type-checks
	- name: Code style test
	run: \|
	make run-style-checks
	api-container-image-build:
	name: API container-image build
	needs:
	- api-update-dependency-lock-files
	runs-on: ubuntu-22.04
	steps:
	- name: Check out repository code
	uses: actions/checkout@v4
	with:
	fetch-depth: 0
	- name: Download updated api (main) dependencies lock file
	uses: actions/download-artifact@v4
	with:
	name: api_deps_lock
	path: api
	- name: Download updated api (test) dependencies lock file
	uses: actions/download-artifact@v4
	with:
	name: api_tests_deps_lock
	path: api/tests
	- name: Set up Docker Buildx
	uses: docker/setup-buildx-action@v3
	- name: Build container image
	uses: docker/build-push-action@v5
	with:
	context: ./
	file: api/Dockerfile
	push: false
	tags: agr_pavi/api:latest
	outputs: type=docker,dest=/tmp/pavi_api_docker_image.tar
	- name: Upload image as artifact (share between jobs)
	uses: actions/upload-artifact@v4
	with:
	name: api_image
	path: /tmp/pavi_api_docker_image.tar
	api-unit-integration-testing:
	name: API unit and integration testing
	needs:
	- api-update-dependency-lock-files
	- pipeline-seq-retrieval-container-image-build
	- pipeline-alignment-container-image-build
	runs-on: ubuntu-22.04
	defaults:
	run:
	shell: bash
	working-directory: ./api/
	steps:
	- name: Check out repository code
	uses: actions/checkout@v4
	with:
	fetch-depth: 0
	- name: Download updated api (main) dependencies lock file
	uses: actions/download-artifact@v4
	with:
	name: api_deps_lock
	path: api
	- name: Download updated api (test) dependencies lock file
	uses: actions/download-artifact@v4
	with:
	name: api_tests_deps_lock
	path: api/tests
	- name: Download seq_retrieval image artifact (from previous job)
	uses: actions/download-artifact@v4
	with:
	name: seq_retrieval_image
	path: /tmp
	- name: Download alignment image artifact (from previous job)
	uses: actions/download-artifact@v4
	with:
	name: alignment_image
	path: /tmp
	- name: Load seq_retrieval Docker image
	run: \|
	docker load --input /tmp/pavi_seq_retrieval_docker_image.tar
	- name: Load alignment Docker image
	run: \|
	docker load --input /tmp/pavi_alignment_docker_image.tar
	- uses: actions/setup-python@v5
	with:
	python-version: '3.12'
	- name: Run unit and integration tests
	run: \|
	make run-tests
	api-container-integration-testing:
	name: API container integration testing (AWS batch execution)
	needs:
	- container-build-context
	- pipeline-seq-retrieval-container-image-build
	- pipeline-alignment-container-image-build
	- api-container-image-build
	- api-update-dependency-lock-files
	permissions:
	id-token: write # This is required for requesting the JWT for gaining permissions to assume the IAM role to perform AWS actions
	runs-on: ubuntu-22.04
	defaults:
	run:
	shell: bash
	working-directory: ./api/
	steps:
	- name: Check out repository code
	uses: actions/checkout@v4
	with:
	fetch-depth: 0
	sparse-checkout: \|
	api/
	tests/resources/
	- name: Download updated api (main) dependencies lock file
	uses: actions/download-artifact@v4
	with:
	name: api_deps_lock
	path: api
	- name: Download updated api (test) dependencies lock file
	uses: actions/download-artifact@v4
	with:
	name: api_tests_deps_lock
	path: api/tests
	- name: Download API image artifact (from previous job)
	uses: actions/download-artifact@v4
	with:
	name: api_image
	path: /tmp
	- name: Load API Docker image
	run: \|
	docker load --input /tmp/pavi_api_docker_image.tar
	- uses: actions/setup-python@v5
	with:
	python-version: '3.12'
	# This step will configure environment variables to be used by all steps
	# involving AWS interaction further down
	- name: AWS credentials configuration
	uses: aws-actions/configure-aws-credentials@v4
	with:
	role-to-assume: ${{ secrets.GH_ACTIONS_AWS_ROLE }}
	role-session-name: gh-actions-${{github.run_id}}.${{github.run_number}}.${{github.run_attempt}}-api-aws-test
	aws-region: us-east-1
	- name: Run container integration test (AWS execution)
	run: \|
	make run-integration-test-container TAG_NAME=${{needs.container-build-context.outputs.tagname}}
	api-aws-infra-code-checks:
	name: api/aws_infra code checks
	needs:
	- api-aws-infra-update-dependency-lock-files
	- shared-aws-infra-package-build
	permissions:
	id-token: write # This is required for requesting the JWT for gaining permissions to assume the IAM role to perform AWS actions
	runs-on: ubuntu-22.04
	defaults:
	run:
	working-directory: ./api/aws_infra
	steps:
	- name: Check out repository code
	uses: actions/checkout@v4
	with:
	fetch-depth: 0
	sparse-checkout: \|
	api/aws_infra/
	- name: Download updated api/aws_infra (main) dependencies lock file
	uses: actions/download-artifact@v4
	with:
	name: api_aws_infra_deps_lock
	path: api/aws_infra
	- name: Download updated api/aws_infra (test) dependencies lock file
	uses: actions/download-artifact@v4
	with:
	name: api_aws_infra_tests_deps_lock
	path: api/aws_infra/tests
	- name: Download shared AWS infra package
	uses: actions/download-artifact@v4
	with:
	name: shared_aws_infra_package
	path: /tmp/
	- name: Setup Python
	uses: actions/setup-python@v5
	with:
	python-version: "3.12"
	- name: Code typing test
	run: \|
	make run-type-checks
	- name: Code style test
	run: \|
	make run-style-checks
	- name: Setup node.js (CDK requirement)
	uses: actions/setup-node@v4
	with:
	node-version: "18"
	- name: Install CDK CLI
	run: npm install -g aws-cdk
	- name: Install CDK stack dependencies
	run: pip install -r requirements.txt
	- name: AWS credentials configuration
	uses: aws-actions/configure-aws-credentials@v4
	with:
	role-to-assume: ${{secrets.GH_ACTIONS_AWS_ROLE}}
	role-session-name: gh-actions-${{github.run_id}}.${{github.run_number}}.${{github.run_attempt}}-cdk-test
	aws-region: us-east-1
	- name: Validate production CDK stack code
	run: make validate-all
	webui-aws-infra-code-checks:
	name: webui/aws_infra code checks
	needs:
	- webui-aws-infra-update-dependency-lock-files
	- shared-aws-infra-package-build
	permissions:
	id-token: write # This is required for requesting the JWT for gaining permissions to assume the IAM role to perform AWS actions
	runs-on: ubuntu-22.04
	defaults:
	run:
	working-directory: ./webui/aws_infra
	steps:
	- name: Check out repository code
	uses: actions/checkout@v4
	with:
	fetch-depth: 0
	sparse-checkout: \|
	webui/aws_infra/
	- name: Download updated webui/aws_infra (main) dependencies lock file
	uses: actions/download-artifact@v4
	with:
	name: webui_aws_infra_deps_lock
	path: webui/aws_infra
	- name: Download updated webui/aws_infra (test) dependencies lock file
	uses: actions/download-artifact@v4
	with:
	name: webui_aws_infra_tests_deps_lock
	path: webui/aws_infra/tests
	- name: Download shared AWS infra package
	uses: actions/download-artifact@v4
	with:
	name: shared_aws_infra_package
	path: /tmp/
	- name: Setup Python
	uses: actions/setup-python@v5
	with:
	python-version: "3.12"
	- name: Code typing test
	run: \|
	make run-type-checks
	- name: Code style test
	run: \|
	make run-style-checks
	- name: Setup node.js (CDK requirement)
	uses: actions/setup-node@v4
	with:
	node-version: "18"
	- name: Install CDK CLI
	run: npm install -g aws-cdk
	- name: Install CDK stack dependencies
	run: pip install -r requirements.txt
	- name: AWS credentials configuration
	uses: aws-actions/configure-aws-credentials@v4
	with:
	role-to-assume: ${{secrets.GH_ACTIONS_AWS_ROLE}}
	role-session-name: gh-actions-${{github.run_id}}.${{github.run_number}}.${{github.run_attempt}}-cdk-test
	aws-region: us-east-1
	- name: Validate production CDK stack code
	run: make validate-all
	webui-code-checks:
	name: webUI code checks
	needs:
	- webui-update-dependency-lock-files
	runs-on: ubuntu-22.04
	defaults:
	run:
	shell: bash
	working-directory: ./webui/
	steps:
	- name: Check out repository code
	uses: actions/checkout@v4
	with:
	fetch-depth: 0
	sparse-checkout: \|
	webui/
	- name: Download updated webui dependencies lock file
	uses: actions/download-artifact@v4
	with:
	name: webui_deps_lock
	path: webui
	- uses: actions/setup-node@v4
	with:
	node-version: "20"
	- name: Code typing test
	run: \|
	make run-type-checks
	- name: Code style test
	run: \|
	make run-style-checks
	webui-container-image-build:
	name: webUI container-image build
	needs:
	- webui-update-dependency-lock-files
	runs-on: ubuntu-22.04
	steps:
	- name: Check out repository code
	uses: actions/checkout@v4
	with:
	fetch-depth: 0
	- name: Download updated webui dependencies lock file
	uses: actions/download-artifact@v4
	with:
	name: webui_deps_lock
	path: webui
	- name: Set up Docker Buildx
	uses: docker/setup-buildx-action@v3
	- name: Build container image
	uses: docker/build-push-action@v5
	with:
	context: ./webui/
	file: webui/Dockerfile
	push: false
	tags: agr_pavi/webui:latest
	outputs: type=docker,dest=/tmp/pavi_webui_docker_image.tar
	commit-deps-lock-updates:
	#TODO: Moving the commit from before to after merge to prevent need for repetitive forced reruns of PR-validation.
	# * Convert this job into job that tars up all updated dependency files and uploads them as a single artifact.
	# * The new artifact should then be downloaded, unpacked and committed in the main-build-and-deploy workflow.
	# * PR validation should get an additional job that reports in the open PR if dependency files have been updated,
	# with a link to the updated files or summary report to enable inspection before merge (download and report git diff?).
	runs-on: ubuntu-22.04
	#Only commit updated lock files on successfull validation (to prevent PR cluttering)
	needs:
	- shared-aws-infra-update-dependency-lock-files
	- shared-aws-infra-package-build
	- api-aws-infra-update-dependency-lock-files
	- api-aws-infra-code-checks
	- pipeline-aws-infra-update-dependency-lock-files
	- pipeline-aws-infra-code-checks
	- webui-aws-infra-update-dependency-lock-files
	- webui-aws-infra-code-checks
	- api-update-dependency-lock-files
	- api-container-integration-testing
	- api-unit-integration-testing
	- api-code-checks
	- pipeline-seq-retrieval-update-dependency-lock-files
	- pipeline-seq-retrieval-code-checks
	- pipeline-workflow-integration-testing
	- webui-update-dependency-lock-files
	- webui-code-checks
	- webui-container-image-build
	permissions:
	contents: write
	steps:
	- uses: actions/checkout@v4
	with:
	ref: ${{ github.head_ref }}
	fetch-depth: 0
	- name: Download updated seq_retrieval (main) dependencies lock file
	uses: actions/download-artifact@v4
	with:
	name: pipeline_seq_retrieval_deps_lock
	path: pipeline/seq_retrieval
	- name: Download updated seq_retrieval (test) dependencies lock file
	uses: actions/download-artifact@v4
	with:
	name: pipeline_seq_retrieval_tests_deps_lock
	path: pipeline/seq_retrieval/tests
	- name: Download updated api (main) dependencies lock file
	uses: actions/download-artifact@v4
	with:
	name: api_deps_lock
	path: api
	- name: Download updated api (test) dependencies lock file
	uses: actions/download-artifact@v4
	with:
	name: api_tests_deps_lock
	path: api/tests
	- name: Download updated pipeline/aws_infra (main) dependencies lock file
	uses: actions/download-artifact@v4
	with:
	name: pipeline_aws_infra_deps_lock
	path: pipeline/aws_infra
	- name: Download updated pipeline/aws_infra (test) dependencies lock file
	uses: actions/download-artifact@v4
	with:
	name: pipeline_aws_infra_tests_deps_lock
	path: pipeline/aws_infra/tests
	- name: Download updated shared_aws_infra (main) dependencies lock file
	uses: actions/download-artifact@v4
	with:
	name: shared_aws_infra_deps_lock
	path: shared_aws_infra
	- name: Download updated shared_aws_infra (test) dependencies lock file
	uses: actions/download-artifact@v4
	with:
	name: shared_aws_infra_test_deps_lock
	path: shared_aws_infra/tests
	- name: Download updated api/aws_infra (main) dependencies lock file
	uses: actions/download-artifact@v4
	with:
	name: api_aws_infra_deps_lock
	path: api/aws_infra
	- name: Download updated api/aws_infra (test) dependencies lock file
	uses: actions/download-artifact@v4
	with:
	name: api_aws_infra_tests_deps_lock
	path: api/aws_infra/tests
	- name: Download updated webui/aws_infra (main) dependencies lock file
	uses: actions/download-artifact@v4
	with:
	name: webui_aws_infra_deps_lock
	path: webui/aws_infra
	- name: Download updated webui/aws_infra (test) dependencies lock file
	uses: actions/download-artifact@v4
	with:
	name: webui_aws_infra_tests_deps_lock
	path: webui/aws_infra/tests
	- name: Download updated webui dependencies lock file
	uses: actions/download-artifact@v4
	with:
	name: webui_deps_lock
	path: webui
	# Independent shared_aws_infra lock files commit required to pin hash representing the package
	# to be included in depending aws_infra components' lock files.
	- name: commit shared_aws_infra dependency lock file changes
	uses: stefanzweifel/git-auto-commit-action@v5
	with:
	commit_message: Auto-updated pavi_shared_aws_infra deps lock files
	file_pattern: 'shared_aws_infra/requirements.txt shared_aws_infra/tests/requirements.txt'
	disable_globbing: true
	# Build pavi_shared_aws_infra package (to ensure hash includes latest commit date)
	- name: Setup Python
	uses: actions/setup-python@v5
	with:
	python-version: "3.12"
	- name: Build and install the pavi_shared_aws_infra package
	working-directory: ./shared_aws_infra
	run: \|
	make clean build install
	- name: Update pavi_shared_aws_infra dependencies
	run: \|
	make -C api/aws_infra/ pip-tools update-deps-lock-shared-aws-infra-only update-test-deps-lock-shared-aws-infra-only
	make -C pipeline/aws_infra/ pip-tools update-deps-lock-shared-aws-infra-only update-test-deps-lock-shared-aws-infra-only
	make -C webui/aws_infra/ pip-tools update-deps-lock-shared-aws-infra-only update-test-deps-lock-shared-aws-infra-only
	- name: commit remaining dependency lock file changes
	uses: stefanzweifel/git-auto-commit-action@v5
	with:
	commit_message: Auto-updated deps lock files
	file_pattern: 'requirements.txt package-lock.json'
	disable_globbing: true

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