Fix FHIR Conversion for Specimen in Lab Info (#2858) #865
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| name: Test message-parser Container | |
| on: | |
| pull_request: | |
| branches: | |
| - "**" | |
| paths: | |
| - containers/message-parser/** | |
| - containers/dibbs/** | |
| - containers/fhir-converter/** | |
| merge_group: | |
| types: | |
| - checks_requested | |
| push: | |
| branches: | |
| - main | |
| paths-ignore: | |
| - pyproject.toml | |
| workflow_dispatch: | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| env: | |
| TEST_RUNNER_PYTHON_VERSION: 3.11 | |
| CONTAINER: message-parser | |
| jobs: | |
| python-linting: | |
| uses: ./.github/workflows/linting-python.yaml | |
| with: | |
| python_runner_version: 3.11 # must be hardcoded; cannot pass in from env | |
| unit-test-python-containers: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Setup python ${{env.TEST_RUNNER_PYTHON_VERSION}} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{env.TEST_RUNNER_PYTHON_VERSION}} | |
| cache: pip | |
| - name: Install pytest and pytest-cov | |
| run: pip install pytest pytest-cov | |
| - name: Install dependencies | |
| working-directory: ./containers/${{env.CONTAINER}} | |
| run: | | |
| commit_hash=$(git rev-parse HEAD) | |
| find ./ -name requirements.txt -exec sed -i -e "s/phdi@main/phdi@${commit_hash}/g" {} \; | |
| pip install -r requirements.txt | |
| if [ -f dev-requirements.txt ]; then | |
| pip install -r dev-requirements.txt | |
| fi | |
| - name: Run unit tests for container with coverage | |
| working-directory: ./containers/${{env.CONTAINER}} | |
| run: | | |
| python -m pytest --cov-report xml --cov=. -m "not integration" tests/ | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| flags: ${{ env.CONTAINER }} | |
| integration-test-python-containers: | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 30 | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Setup python ${{env.TEST_RUNNER_PYTHON_VERSION}} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{env.TEST_RUNNER_PYTHON_VERSION}} | |
| cache: pip | |
| - name: Install pytest | |
| run: pip install pytest | |
| - name: Install dependencies | |
| working-directory: ./containers/${{env.CONTAINER}} | |
| # When running as a PR check, instead of importing the SDK from @main, | |
| # import it from the current commit. (Need to do this for all containers) | |
| run: | | |
| if [[ $GITHUB_REF != "refs/heads/main" ]]; then | |
| commit_hash=$(git rev-parse HEAD) | |
| find ./ -name requirements.txt -exec sed -i -e "s/phdi@main/phdi@${commit_hash}/g" {} \; | |
| fi | |
| pip install -r requirements.txt | |
| if [ -f dev-requirements.txt ]; then | |
| pip install -r dev-requirements.txt | |
| fi | |
| - name: Install Docker Compose | |
| run: | | |
| sudo curl -L "https://github.com/docker/compose/releases/download/1.29.2/docker-compose-$(uname -s)-$(uname -m)" -o /usr/local/bin/docker-compose | |
| sudo chmod +x /usr/local/bin/docker-compose | |
| - name: Run integration tests for containers | |
| working-directory: ./containers/${{env.CONTAINER}}/tests/integration | |
| run: | | |
| python -m pytest -m "integration" | |
| build-container: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v2 | |
| - name: Build ${{ env.CONTAINER }} Container | |
| uses: docker/build-push-action@v3 | |
| with: | |
| context: ./containers/${{ env.CONTAINER }} | |
| push: false | |
| cache-from: type=gha | |
| cache-to: type=gha,mode=max |