Validate test data in CI job #57
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| on: | |
| pull_request: | |
| branches: [ "master", "main" ] | |
| push: | |
| branches: [ "master", "main" ] | |
| jobs: | |
| check_data_models: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| data_model_file: [ | |
| 'PRIMED_phenotype_data_model.json', | |
| 'PRIMED_genotype_data_model.json', | |
| 'PRIMED_GSR_data_model.json' | |
| ] | |
| name: Check data model | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| - name: Setup R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: "4.2.3" | |
| - name: Install dependencies | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| cache-version: 1 | |
| packages: github::UW-GAC/AnvilDataModels, any::sessioninfo | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Check ${{ matrix.data_model_file }} file | |
| run: | | |
| AnvilDataModels::json_to_dm("${{ matrix.data_model_file }}") | |
| shell: Rscript {0} | |
| check_test_data: | |
| runs-on: ubuntu-latest | |
| name: Check test data | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| - name: Checkout primed-file-checks | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: UW-GAC/primed-file-checks | |
| path: primed-file-checks | |
| # Install Java to this VM. This Java version and distribution is compatible with Cromwell. | |
| # This is the same step as used by broadinstitute/cromwell/.github/set_up_cromwell_action. | |
| - name: Setup JDK | |
| uses: actions/setup-java@v3 | |
| with: | |
| distribution: temurin | |
| java-version: 11 | |
| # Get cromwell jar file | |
| - uses: robinraju/[email protected] | |
| with: | |
| repository: 'broadinstitute/cromwell' | |
| tag: '87' | |
| fileName: 'cromwell-87.jar' | |
| - name: Validate test data | |
| run: | | |
| java -jar cromwell-87.jar run primed-file-checks/validate_phenotype_model.wdl --inputs test_data/wdl_inputs_validate_phenotype_model.json | |
| shell: bash | |
| - name: Success! | |
| run: echo "Success!" |