OncoKB annotator container #98
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| name: Test builds | |
| on: | |
| push: | |
| branches: [develop] | |
| pull_request: | |
| branches: [develop] | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| env: | |
| JFROG_REGISTRY: mskcc.jfrog.io | |
| JFROG_CONTAINER_REPO: mskcc.jfrog.io/omicswf-docker-dev-local/mskcc-omics-workflows | |
| GHCR_CONTAINER_REPO: ghcr.io/mskcc-omics-workflows/ | |
| jobs: | |
| dockerfile-changes: | |
| name: dockerfile-changes | |
| runs-on: ubuntu-latest | |
| permissions: | |
| pull-requests: read | |
| outputs: | |
| # Expose matched filters as job 'docker-images' output variable | |
| docker-images: ${{ steps.filter.outputs.changes }} | |
| steps: | |
| - name: Dump GitHub context | |
| env: | |
| GITHUB_CONTEXT: ${{ toJson(github) }} | |
| run: echo "$GITHUB_CONTEXT" | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 2 | |
| - name: debug | |
| run: git log --pretty=format:'%h' -n 2 | |
| - name: Create tags.yml to grab changes | |
| id: get_tags | |
| run: | | |
| for i in $(find containers -name "Dockerfile" -not -path "containers/testapp/0.0.2/*") | |
| do | |
| path=$(dirname $i) | |
| tag=$(echo $path | cut -f 2- -d/) | |
| echo -e "$tag:\n $path/**" | |
| done > .github/tags.yml | |
| - name: Add to tags.yml to grab changes in testapp/0.0.2 and github action workflows | |
| id: add_testapp_002_tag | |
| run: | | |
| echo -e "testapp/0.0.2:\n - testapp/0.0.2/**\n - .github/workflows/**\n - .hadolint.yml" >> .github/tags.yml | |
| - name: debug | |
| run: cat .github/tags.yml | |
| - uses: mirpedrol/paths-filter@main | |
| id: filter | |
| with: | |
| base: "develop" | |
| filters: ".github/tags.yml" | |
| token: "" | |
| dockerfile-lint: | |
| runs-on: ubuntu-latest | |
| name: dockerfile-lint | |
| needs: [dockerfile-changes] | |
| if: needs.dockerfile-changes.outputs.docker-images != '[]' | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| tags: ["${{ fromJson(needs.dockerfile-changes.outputs.docker-images) }}"] | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Hadolint | |
| uses: hadolint/[email protected] | |
| with: | |
| dockerfile: containers/${{ matrix.tags }}/Dockerfile | |
| verbose: true | |
| docker-validate-build: | |
| runs-on: ubuntu-latest | |
| name: dockerfile-build | |
| needs: [dockerfile-changes] | |
| if: needs.dockerfile-changes.outputs.docker-images != '[]' | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| tags: ["${{ fromJson(needs.dockerfile-changes.outputs.docker-images) }}"] | |
| steps: | |
| # save docker files | |
| - name: Move /var/lib/docker/ | |
| if: ${{ !github.event.act }} | |
| run: sudo mv /var/lib/docker/ "${GITHUB_WORKSPACE}/docker" | |
| - name: Maximize build space | |
| if: ${{ !github.event.act }} | |
| uses: easimon/maximize-build-space@master | |
| with: | |
| build-mount-path: /var/lib/docker/ | |
| remove-dotnet: 'true' | |
| remove-android: 'true' | |
| remove-haskell: 'true' | |
| remove-codeql: 'true' | |
| - name: Restore /var/lib/docker/ | |
| if: ${{ !github.event.act }} | |
| run: | | |
| sudo rsync -aPq "${GITHUB_WORKSPACE}/docker/" /var/lib/docker | |
| sudo rm -rf "${GITHUB_WORKSPACE}/docker" | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 | |
| with: | |
| python-version: "3.12" | |
| - name: Get docker repo name | |
| id: docker_repo_name | |
| run: echo name=$( dirname "${{ matrix.tags }}" ) >> $GITHUB_OUTPUT | |
| - name: Get docker version | |
| id: docker_repo_version | |
| run: echo version=$( basename "${{ matrix.tags }}" ) >> $GITHUB_OUTPUT | |
| - name: Set up QEMU | |
| uses: docker/setup-qemu-action@v3 | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Login to JFrog | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ${{ env.JFROG_REGISTRY }} | |
| username: ${{ secrets.MSK_JFROG_USERNAME }} | |
| password: ${{ secrets.MSK_JFROG_TOKEN }} | |
| - name: Build Image for JFrog | |
| uses: docker/build-push-action@v5 | |
| with: | |
| context: containers/${{ matrix.tags }}/ | |
| file: containers/${{ matrix.tags }}/Dockerfile | |
| load: true | |
| tags: ${{ env.JFROG_CONTAINER_REPO }}/${{ steps.docker_repo_name.outputs.name}}:${{steps.docker_repo_version.outputs.version}} | |
| - name: Install pip | |
| run: python -m pip install --upgrade pip | |
| - name: Install python docker package | |
| run : pip install docker jsonschema | |
| - name: Validate image build metadata | |
| run: | | |
| python .github/workflows/scripts/validate_docker.py ${{ env.JFROG_CONTAINER_REPO }}/${{ steps.docker_repo_name.outputs.name}}:${{steps.docker_repo_version.outputs.version}} .github/workflows/scripts/jsonschema/docker_image.json | |
| - name: Test JFrog image build | |
| run: | | |
| docker run --rm ${{ env.JFROG_CONTAINER_REPO }}/${{ steps.docker_repo_name.outputs.name}}:${{steps.docker_repo_version.outputs.version}} | |
| - name: Push image build to JFrog registry | |
| uses: docker/build-push-action@v5 | |
| with: | |
| context: containers/${{ matrix.tags }}/ | |
| file: containers/${{ matrix.tags }}/Dockerfile | |
| tags: ${{ env.JFROG_CONTAINER_REPO }}/${{ steps.docker_repo_name.outputs.name}}:${{steps.docker_repo_version.outputs.version}} | |
| push: true | |
| confirm-pass: | |
| runs-on: ubuntu-latest | |
| needs: [ dockerfile-changes, docker-validate-build, dockerfile-lint ] | |
| if: always() | |
| steps: | |
| - name: All tests ok | |
| if: ${{ success() || !contains(needs.*.result, 'failure') }} | |
| run: exit 0 | |
| - name: One or more tests failed | |
| if: ${{ contains(needs.*.result, 'failure') }} | |
| run: exit 1 | |
| - name: debug-print | |
| if: always() | |
| run: | | |
| echo "toJSON(needs) = ${{ toJSON(needs) }}" | |
| echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" |