FE-349 data clean up for hca ingest manifest.py #51
Workflow file for this run
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| name: PR Validation for Main | |
| on: | |
| pull_request: | |
| branches: | |
| - main | |
| concurrency: | |
| group: ${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| pr-validation: | |
| name: PR Validation | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: google-github-actions/[email protected] | |
| with: | |
| project_id: ${{ secrets.DEV_PROJECT_ID }} | |
| service_account_key: ${{ secrets.GCP_TEST_KEY }} | |
| export_default_credentials: true | |
| fetch-depth: 0 | |
| - name: Set up Python 3.9 for dataflow tests | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.9.16 | |
| - name: Install Poetry | |
| uses: snok/install-poetry@v1 | |
| with: | |
| version: 1.8 | |
| - name: Restore cache dependencies | |
| uses: actions/cache@v2 | |
| env: | |
| cache-name: cache-poetry-v2 | |
| with: | |
| path: ~/.cache/pypoetry | |
| # key uses pyproject.toml hash, so it's unique to each version of pyproject.toml | |
| key: ${{ runner.os }}-build-${{ env.cache-name }}-${{ hashFiles('./orchestration/pyproject.toml') }} | |
| # restore-keys: | | |
| # ${{ runner.os }}-build-${{ env.cache-name }}- | |
| # ${{ runner.os }}-build- | |
| # ${{ runner.os }}- | |
| # - name: Clear Poetry Artifacts (if necessary) | |
| # run: | | |
| # if [ -d ~/.cache/pypoetry/artifacts ]; then | |
| # echo "Clearing Poetry artifacts..." | |
| # rm -rf ~/.cache/pypoetry/artifacts | |
| # fi | |
| - name: Install dependencies | |
| run: poetry install | |
| working-directory: ${{ github.workspace }}/orchestration | |
| - uses: olafurpg/setup-scala@v10 | |
| with: | |
| java-version: [email protected] | |
| - name: Check Scala formatting | |
| run: sbt scalafmtCheckAll | |
| - name: Scala Compile | |
| run: sbt Compile/compile Test/compile IntegrationTest/compile | |
| - name: Scala Test | |
| run: sbt "set ThisBuild/coverageEnabled := true" test IntegrationTest/test coverageAggregate | |
| - name: Publish Scala Test coverage | |
| uses: codecov/codecov-action@v1 | |
| # We are skipping the E2E tests during PR validation until we refactor to test against TDR prod | |
| # See FE-203 and FE-204 for complete details | |
| # See the e2e README for instructions to run the tests locally (orchestration/hca_orchestration/tests/e2e/README.md) | |
| # - name: Run E2E test suite | |
| # run: poetry run pytest -v -m e2e | |
| # working-directory: ${{ github.workspace }}/orchestration |