Support for HCA data_use_restriction (#6131) #15762
Workflow file for this run
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| name: 'CI' | |
| on: | |
| pull_request: | |
| push: | |
| branches: [ 'develop', 'prod' ] | |
| jobs: | |
| test: | |
| runs-on: 'ubuntu-22.04' | |
| timeout-minutes: 45 | |
| steps: | |
| - uses: 'actions/checkout@v3' | |
| - run: 'cat environment.boot >> "$GITHUB_ENV"' | |
| - uses: 'actions/setup-python@v4.3.0' | |
| with: | |
| python-version: '${{ env.azul_python_version }}' | |
| cache: 'pip' | |
| cache-dependency-path: 'requirements.dev.txt' | |
| - name: 'Run unit tests and other checks' | |
| run: | | |
| source environment | |
| _link dev | |
| _refresh | |
| make virtualenv | |
| source .venv/bin/activate | |
| make requirements | |
| make environment.boot | |
| # FIXME: The default Azul registry is hosted privately on ECR, so we'd | |
| # have to provide credentials to use it. For now, it's | |
| # sufficient to pull 3rd party images directly from their | |
| # upstream registry, accepting the risk that a 3rd party image | |
| # is compromised. GitHub Actions have limited access to our | |
| # infrastructure (the token scope is limited). The worst that | |
| # could happen is that the token itself is revealed or that the | |
| # action falsely reports a passing build. | |
| # https://github.com/DataBiosphere/azul/issues/5188 | |
| # | |
| export azul_docker_registry="" | |
| # Hack: The use of chrgp compensates for a quirk of Docker. The | |
| # PyCharm image used by make format sets up a user called `developer` | |
| # and assigns it UID 1000. Actions is running as UID 1001. An | |
| # alternative would be to pass --user to `docker run` and bind-mount | |
| # an /etc/passwd that maps that to `developer`. We also need write | |
| # permissions for the group | |
| # | |
| chmod -R g+w . && sudo chgrp -R 1000 . && make format && sudo chgrp -R $(id -g) . | |
| make -C lambdas openapi | |
| make -C .github | |
| make anvil_schema | |
| make check_clean | |
| make pep8 | |
| AZUL_DEBUG=0 GITHUB_TOKEN=${{ secrets.GITHUB_TOKEN }} make test | |
| make check_clean | |
| coverage xml | |
| - uses: 'actions/upload-artifact@v3' | |
| with: | |
| name: 'coverage-file' | |
| path: 'coverage.xml' | |
| codecov: | |
| needs: 'test' | |
| runs-on: 'ubuntu-22.04' | |
| steps: | |
| - uses: 'actions/checkout@v3' | |
| - run: 'cat environment.boot >> "$GITHUB_ENV"' | |
| - uses: 'actions/setup-python@v4.3.0' | |
| with: | |
| python-version: '${{ env.azul_python_version }}' | |
| cache: 'pip' | |
| cache-dependency-path: 'requirements.dev.txt' | |
| - uses: 'actions/download-artifact@v3' | |
| with: | |
| name: 'coverage-file' | |
| - uses: 'codecov/codecov-action@v3' | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| files: 'coverage.xml' | |
| fail_ci_if_error: true | |
| coveralls: | |
| needs: 'test' | |
| runs-on: 'ubuntu-22.04' | |
| steps: | |
| - uses: 'actions/checkout@v3' | |
| - run: 'cat environment.boot >> "$GITHUB_ENV"' | |
| - uses: 'actions/setup-python@v4.3.0' | |
| with: | |
| python-version: '${{ env.azul_python_version }}' | |
| cache: 'pip' | |
| cache-dependency-path: 'requirements.dev.txt' | |
| - uses: 'actions/download-artifact@v3' | |
| with: | |
| name: 'coverage-file' | |
| - uses: 'coverallsapp/github-action@v2' | |
| with: | |
| github-token: ${{ secrets.COVERALLS_REPO_TOKEN }} | |
| codeql: | |
| runs-on: 'ubuntu-22.04' | |
| permissions: | |
| actions: 'read' | |
| contents: 'read' | |
| security-events: 'write' | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| language: [ 'python', 'javascript' ] | |
| steps: | |
| - uses: 'actions/checkout@v3' | |
| - run: 'cat environment.boot >> "$GITHUB_ENV"' | |
| - uses: 'actions/setup-python@v4.3.0' | |
| with: | |
| python-version: '${{ env.azul_python_version }}' | |
| cache: 'pip' | |
| cache-dependency-path: 'requirements.dev.txt' | |
| - uses: 'github/codeql-action/init@v2' | |
| with: | |
| languages: '${{ matrix.language }}' | |
| setup-python-dependencies: false | |
| config-file: './.github/codeql/codeql-config.yml' | |
| queries: 'security-and-quality' | |
| - uses: 'github/codeql-action/analyze@v2' | |
| with: | |
| category: '/language:${{matrix.language}}' |