PR-validation.yml

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: |
          pwd
          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