WIP: don't simply toss extensions #1033
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| name: CI | |
| on: | |
| pull_request: | |
| push: | |
| branches: | |
| - main | |
| paths-ignore: | |
| - 'docs/**' | |
| - '*.md' | |
| # The goal here is to cancel older workflows when a PR is updated (because it's pointless work) | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.head_ref || github.ref_name }} | |
| cancel-in-progress: true | |
| jobs: | |
| unittest: | |
| name: unit tests | |
| runs-on: ubuntu-22.04 | |
| strategy: | |
| matrix: | |
| # Don't go crazy with the Python versions as the test suite is a beast. | |
| # Just test the minimum version we support. | |
| python-version: ["3.10"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install .[tests] | |
| - name: Check out MS tool | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: microsoft/Tools-for-Health-Data-Anonymization | |
| path: mstool | |
| - name: Build MS tool | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install dotnet6 | |
| dotnet publish \ | |
| --runtime=linux-x64 \ | |
| --configuration=Release \ | |
| -p:PublishSingleFile=true \ | |
| --output=$HOME/.local/bin \ | |
| mstool/FHIR/src/Microsoft.Health.Fhir.Anonymizer.R4.CommandLineTool | |
| - name: Test with pytest | |
| run: | | |
| python -m pytest --cov=cumulus_etl --cov-report=xml | |
| - name: Log missing coverage | |
| run: | | |
| coverage report -m --skip-covered | |
| - name: Check coverage report | |
| if: github.ref != 'refs/heads/main' | |
| uses: orgoro/[email protected] | |
| with: | |
| coverageFile: coverage.xml | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| thresholdAll: .98 | |
| thresholdNew: 1 | |
| thresholdModified: 1 | |
| nlp-regression: | |
| runs-on: ubuntu-latest | |
| env: | |
| UMLS_API_KEY: ${{ secrets.UMLS_API_KEY }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install Docker | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Build ETL image | |
| uses: docker/build-push-action@v6 | |
| with: | |
| load: true # just build, no push | |
| tags: smartonfhir/cumulus-etl:latest | |
| build-args: | | |
| LOCAL_VERSION=${{ github.sha }} | |
| - name: Download NLP images | |
| run: | | |
| # Just start the specific services we need, to conserve CI disk space | |
| docker compose up -d --quiet-pull cnlpt-negation ctakes-covid | |
| - name: Run NLP | |
| run: | | |
| export DATADIR=$(realpath tests/data/nlp-regression) | |
| # Run the NLP task | |
| docker compose run --rm \ | |
| --volume $DATADIR:/in \ | |
| cumulus-etl \ | |
| /in/input \ | |
| /in/run-output \ | |
| /in/phi \ | |
| --export-group nlp-test \ | |
| --export-timestamp 2024-08-29 \ | |
| --output-format=ndjson \ | |
| --task covid_symptom__nlp_results | |
| # Compare results | |
| export OUTDIR=$DATADIR/run-output/covid_symptom__nlp_results | |
| sudo chown -R $(id -u) $OUTDIR | |
| sed -i 's/"generated_on": "[^"]*", //g' $OUTDIR/*.ndjson | |
| diff -upr $DATADIR/expected-output $OUTDIR | |
| echo "All Good!" | |
| lint: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install linters | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install .[dev] | |
| - name: Run ruff | |
| run: ruff check --output-format=github . |