FE-349 add data clean up to hca ingest manifest.py #39
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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@v4 | |
| - uses: google-github-actions/setup-gcloud@v2 | |
| 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@v5 | |
| with: | |
| python-version: 3.9.16 | |
| - name: Install Poetry | |
| uses: snok/install-poetry@v1 | |
| with: | |
| version: 1.1.9 | |
| - name: Restore cache dependencies | |
| uses: actions/cache@v4 | |
| env: | |
| cache-name: cache-poetry-v4 | |
| with: | |
| path: ~/.cache/pypoetry | |
| 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: 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 |