fix: add time to meds and procedures #2999
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: Test orchestration Container | |
| on: | |
| pull_request: | |
| branches: | |
| - "**" | |
| 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: orchestration | |
| jobs: | |
| orchestration-python-linting: # This job is the same as the python-linting job in linting-python.yaml but does not run if using linting-python.yaml | |
| 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 dependencies | |
| run: | | |
| pip install -U pip | |
| pip install ruff==0.4.3 | |
| - name: Run linter (ruff) | |
| run: | | |
| ruff check --output-format=github . | |
| - name: Run formatter (ruff) | |
| run: | | |
| ruff format --check | |
| orchestration-unit-test-python: | |
| runs-on: ubuntu-latest | |
| services: | |
| test-db: | |
| image: postgres:13-alpine3.16 | |
| env: | |
| POSTGRES_PASSWORD: pw | |
| POSTGRES_DB: testdb | |
| POSTGRES_USER: postgres | |
| # Set health checks to wait until postgres has started | |
| options: >- | |
| --health-cmd pg_isready | |
| --health-interval 10s | |
| --health-timeout 5s | |
| --health-retries 5 | |
| --name testdb | |
| ports: | |
| - 5432:5432 | |
| 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 }} | |
| orchestration-integration-test-python: | |
| 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@${commit_hash}/g" {} \; | |
| fi | |
| pip install -r requirements.txt | |
| if [ -f dev-requirements.txt ]; then | |
| pip install -r dev-requirements.txt | |
| fi | |
| - name: Run integration tests for containers | |
| env: | |
| MPI_DBNAME: testdb | |
| MPI_PASSWORD: pw | |
| MPI_DB_TYPE: postgres | |
| MPI_HOST: localhost | |
| MPI_USER: postgres | |
| MPI_PORT: 5432 | |
| working-directory: ./containers/${{env.CONTAINER}}/tests/integration | |
| run: | | |
| python -m pytest -m "integration" | |
| build-orchestration-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 | |
| build-args: | | |
| "INGESTION_URL=${{secrets.INGESTION_URL}}" | |
| "MESSAGE_PARSER_URL=${{secrets.MESSAGE_PARSER_URL}}" | |
| "SMARTY_AUTH_ID=${{secrets.SMARTY_AUTH_ID}}" | |
| "SMARTY_AUTH_TOKEN=${{secrets.SMARTY_AUTH_TOKEN}}" |