main-build-and-deploy.yml

name: Main branch Build and Deployment
on:
  pull_request:
    types: [closed]
    branches:
      - main
jobs:
  on-merge-and-deploy:
    name: Skip on unmerged or 'no-deploy' PRs
    if: github.event.pull_request.merged == true && !contains(github.event.pull_request.labels.*.name, 'no-deploy')
    runs-on: ubuntu-22.04
    steps:
    - name: Confirm execution
      shell: bash
      run: |
        echo "PR merge detected and deployment wanted."
  pipeline-deploy-aws-infra:
    name: Deploy/update AWS infrastructure for pipeline
    needs: [on-merge-and-deploy]
    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-deploy
        aws-region: us-east-1
    - name: CDK validations (resource assertions and cdk diff)
      run: make validate
    - name: cdk deploy
      run: cdk deploy PaviPipelineCdkStack --require-approval never
  pipeline-seq-retrieval-build-and-push-docker-image:
    needs: [on-merge-and-deploy, pipeline-deploy-aws-infra]
    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: Store release tag in env
      shell: bash
      run: |
        echo "tagname=$(git describe --tags)" >> $GITHUB_ENV
    # 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}}-build-image-pipeline-seq-retrieval
        aws-region: us-east-1
    - name: Amazon ECR login
      id: login-ecr
      uses: aws-actions/amazon-ecr-login@v2
    - name: Build and push container image
      uses: docker/build-push-action@v5
      with:
        context: ./pipeline/seq_retrieval/
        push: true
        tags: |
          ${{ steps.login-ecr.outputs.registry }}/agr_pavi/pipeline_seq_retrieval:${{ env.tagname }}
          ${{ steps.login-ecr.outputs.registry }}/agr_pavi/pipeline_seq_retrieval:${{ github.event.pull_request.base.ref }}
        platforms: linux/amd64
  pipeline-alignment-build-and-push-docker-image:
    needs: [on-merge-and-deploy, pipeline-deploy-aws-infra]
    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: Store release tag in env
      shell: bash
      run: |
        echo "tagname=$(git describe --tags)" >> $GITHUB_ENV
    # 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}}-build-image-pipeline-seq-retrieval
        aws-region: us-east-1
    - name: Amazon ECR login
      id: login-ecr
      uses: aws-actions/amazon-ecr-login@v2
    - name: Build and push container image
      uses: docker/build-push-action@v5
      with:
        context: ./pipeline/alignment/
        push: true
        tags: |
          ${{ steps.login-ecr.outputs.registry }}/agr_pavi/pipeline_alignment:${{ env.tagname }}
          ${{ steps.login-ecr.outputs.registry }}/agr_pavi/pipeline_alignment:${{ github.event.pull_request.base.ref }}
        platforms: linux/amd64