Merge branch 'main' into task5-workflow #30
Workflow file for this run
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| # This workflow will install Python dependencies, run tests and lint with a single version of Python | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: Mapper Test | |
| on: | |
| push: | |
| branches: [task5-workflow] | |
| pull_request: | |
| branches: [task5-workflow] | |
| jobs: | |
| run_mapper: | |
| runs-on: ubuntu-latest | |
| name: Run Tests | |
| steps: | |
| - uses: actions/checkout@v2 | |
| name: Checkout out mapper repository | |
| - uses: actions/checkout@v2 | |
| name: Checkout test repository | |
| with: | |
| path: tests | |
| repository: "ccb-hms/ontology-mapper-tests" | |
| token: ${{ secrets.MAPPER_TESTING }} | |
| fetch-depth: 0 # otherwise, there would be errors pushing refs to the destination repository. | |
| - name: Set up Python 3.9 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.9 | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install flake8 pytest | |
| if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
| - name: Run mapper on UK Biobank source terms | |
| run: | | |
| python3 text2term.py -s $source_path -t $target_path -min 0 -o "./tests/mapper-outputs/ukb-efo/${GITHUB_SHA}.csv" | |
| env: | |
| source_path: ./tests/data/ukb-efo/terms.txt | |
| # https://github.com/EBISPOT/efo/releases/tag/v2019-03-18 | |
| # 2019-03-18 EFO 2.106, as referenced by: | |
| # https://github.com/EBISPOT/EFO-UKB-mappings/blob/master/ISMB_Mapping_UK_Biobank_to_EFO.pdf | |
| # page 2, footnote 9 | |
| target_path: ./tests/data/ukb-efo/efo-v2019-03-18.owl | |
| - name: Setup summary spreadsheet row | |
| run: | | |
| if grep -q "," <<< "${{ github.event.head_commit.message }}" | |
| then | |
| MSG='"${{ github.event.head_commit.message }}"' | |
| else | |
| MSG='${{ github.event.head_commit.message }}' | |
| fi | |
| echo -n "${GITHUB_REF},${GITHUB_SHA},${MSG},ukb-efo/${GITHUB_SHA}.csv," >> $summary_path | |
| working-directory: tests | |
| env: | |
| summary_path: summary.csv | |
| - name: Run coverage__one_error script | |
| run: | | |
| python3 $script_path | |
| working-directory: tests/compare-scripts | |
| env: | |
| script_path: coverage_one_error.py | |
| - name: Commit changes to tests repo | |
| run: | | |
| git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com" | |
| git config --local user.name "github-actions[bot]" | |
| git add mapper-outputs/* | |
| git add summary.csv | |
| git commit -m "Add files" | |
| working-directory: tests | |
| - name: Push changes | |
| uses: ad-m/github-push-action@master | |
| with: | |
| repository: "ccb-hms/ontology-mapper-tests" | |
| github_token: ${{ secrets.MAPPER_TESTING }} | |
| directory: "tests" |