integration-test.yml

name: integration test

on: workflow_dispatch

jobs:
  # phase 1
  list:
    env:
      s3_bucket: s3://czbiohub-pipelines/utilities/
    runs-on: ubuntu-latest

    outputs:
      component_matrix: ${{ steps.set_matrix.outputs.components }}
      workflow_matrix: ${{ steps.set_matrix.outputs.workflows }}
      cache_key: ${{ steps.cache.outputs.cache_key }}

    steps:
    - uses: actions/checkout@v3
      with:
        submodules: true

    - uses: viash-io/viash-actions/setup@v3

    - uses: viash-io/viash-actions/project/sync-and-cache-s3@v3
      id: cache
      with:
        s3_bucket: $s3_bucket
        dest_path: resources_test
        cache_key_prefix: resources_test__

    - name: Remove target folder from .gitignore
      run: |
        # allow publishing the target folder
        sed -i '/^\/target\/$/d' .gitignore
        rm .gitmodules

    - uses: viash-io/viash-actions/ns-build@v3
      with:
        config_mod: .functionality.version := 'integration_build'
        parallel: true

    - name: Deploy to target branch
      uses: peaceiris/actions-gh-pages@v3
      with:
        github_token: ${{ secrets.GITHUB_TOKEN }}
        publish_dir: .
        publish_branch: integration_build
        exclude_assets: ''

    - id: ns_list_components
      uses: viash-io/viash-actions/ns-list@v3
      with:
        platform: docker
        src: src
        format: json

    - id: ns_list_workflows
      uses: viash-io/viash-actions/ns-list@v3
      with:
        src: workflows
        format: json

    - id: set_matrix
      run: |
        echo "components=$(jq -c '[ .[] | 
          { 
            "name": (.functionality.namespace + "/" + .functionality.name),
            "config": .info.config,
            "dir": .info.config | capture("^(?<dir>.*\/)").dir
          }
        ]' ${{ steps.ns_list_components.outputs.output_file }} )" >> $GITHUB_OUTPUT

        echo "workflows=$(jq -c '[ .[] | . as $config | (.functionality.test_resources // [])[] | select(.type == "nextflow_script", .entrypoint) |
          { 
            "name": ($config.functionality.namespace + "/" + $config.functionality.name),
            "main_script": (($config.info.config | capture("^(?<dir>.*\/)").dir) + "/" + .path),
            "entry": .entrypoint
          }
        ]' ${{ steps.ns_list_workflows.outputs.output_file }} )" >> $GITHUB_OUTPUT

  # phase 2
  build:
    needs: list

    runs-on: ubuntu-latest

    strategy:
      fail-fast: false
      matrix:
        component: ${{ fromJson(needs.list.outputs.component_matrix) }}

    steps:
    - uses: actions/checkout@v3
      with:
        submodules: true

    - uses: viash-io/viash-actions/setup@v3

    - name: Build container
      uses: viash-io/viash-actions/ns-build@v3
      with:
        config_mod: .functionality.version := 'integration_build'
        setup: build
        src: ${{ matrix.component.dir }}
        
    - name: Login to container registry
      uses: docker/login-action@v2
      with:
        # registry: ghcr.io
        username: ${{ secrets.DOCKER_HUB_USER }}
        password: ${{ secrets.DOCKER_HUB_PAT }}

    - name: Push container
      uses: viash-io/viash-actions/ns-build@v3
      with:
        config_mod: .functionality.version := 'integration_build'
        platform: docker
        src: ${{ matrix.component.dir }}
        setup: push

  ###################################
  # phase 3
  integration_test:
    needs: [ build, list ]
    if: "${{ needs.list.outputs.workflow_matrix != '[]' }}"

    runs-on: ubuntu-latest

    strategy:
      fail-fast: false
      matrix:
        component: ${{ fromJson(needs.list.outputs.workflow_matrix) }}

    steps:
    - uses: actions/checkout@v3
      with:
        submodules: true

    - uses: viash-io/viash-actions/setup@v3

    - uses: nf-core/setup-nextflow@v1.2.0

    # build target dir
    # use containers from integration_build branch, hopefully these are available
    - name: Build target dir
      uses: viash-io/viash-actions/ns-build@v3
      with:
        config_mod: ".functionality.version := 'integration_build'"
        parallel: true

    # use cache
    - name: Cache resources data
      uses: actions/cache@v3
      timeout-minutes: 5
      with:
        path: resources_test
        key: ${{ needs.list.outputs.cache_key }}
        fail-on-cache-miss: true

    - name: Run integration test
      timeout-minutes: 45
      run: |
        # todo: replace with viash test command
        export NXF_VER=22.04.5
        nextflow run . \
          -main-script "${{ matrix.component.main_script }}" \
          -entry "${{ matrix.component.entry }}" \
          -profile docker,mount_temp,no_publish \
          -c workflows/utils/labels_ci.config