KANBAN-535: First components of AWS stack #39
Workflow file for this run
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| name: PR validation | |
| on: | |
| pull_request: | |
| types: [synchronize, opened, reopened, edited] | |
| branches: | |
| - main | |
| jobs: | |
| pipeline-seq-retrieval-container-image-build: | |
| name: pipeline/seq_retrieval container-image build | |
| 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: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Build container image | |
| uses: docker/build-push-action@v5 | |
| with: | |
| context: ./pipeline/seq_retrieval/ | |
| push: false | |
| tags: agr_pavi/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 | |
| pipeline-seq-retrieval-python-typing-check: | |
| name: pipeline/seq_retrieval python typing check | |
| 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/ | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.12' | |
| - name: Check python typing | |
| run: | | |
| make run-python-type-check | |
| pipeline-seq-retrieval-python-style-check: | |
| name: pipeline/seq_retrieval python style check | |
| 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/ | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.12' | |
| - name: Check python style | |
| run: | | |
| make run-python-style-check | |
| pipeline-seq-retrieval-unit-tests: | |
| name: pipeline/seq_retrieval unit tests | |
| 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/ | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.12' | |
| - name: Run unit tests | |
| run: | | |
| make run-unit-tests | |
| pipeline-alignment-container-image-build: | |
| name: pipeline/alignment container-image build | |
| 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 | |
| - name: Build container image | |
| uses: docker/build-push-action@v5 | |
| with: | |
| context: ./pipeline/alignment/ | |
| push: false | |
| tags: agr_pavi/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 | |
| pipeline-workflow-integration-testing: | |
| name: pipeline/workflow integration testing | |
| needs: | |
| - pipeline-seq-retrieval-container-image-build | |
| - pipeline-alignment-container-image-build | |
| 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/ | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - 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 integration test | |
| run: | | |
| make run-integration-test | |
| pipeline-aws-infra-cdk-test: | |
| name: pipeline/aws_infra CDK test | |
| 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 | |
| - name: Setup node.js (CDK requirement) | |
| uses: actions/setup-node@v4 | |
| with: | |
| node-version: "18" | |
| - name: Install CDK | |
| run: npm install -g aws-cdk | |
| - name: Setup Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| - 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: cdk diff | |
| run: cdk diff |