add pattern for normalized_id #96
Workflow file for this run
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| name: checks | |
| on: [push, pull_request] | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| env: | |
| AWS_ACCESS_KEY_ID: ${{ secrets.DUMMY_AWS_ACCESS_KEY_ID }} | |
| AWS_SECRET_ACCESS_KEY: ${{ secrets.DUMMY_AWS_SECRET_ACCESS_KEY }} | |
| AWS_DEFAULT_REGION: us-east-2 | |
| AWS_DEFAULT_OUTPUT: text | |
| DISEASE_NORM_DB_URL: ${{ matrix.db_url }} | |
| DISEASE_TEST: true | |
| strategy: | |
| matrix: | |
| db_url: ["http://localhost:8002", "postgres://postgres:postgres@localhost:5432/disease_normalizer_test"] | |
| python-version: ['3.8', '3.9', '3.10', '3.11'] | |
| services: | |
| postgres: | |
| image: postgres:14 | |
| env: | |
| POSTGRES_USER: 'postgres' | |
| POSTGRES_DB: 'disease_normalizer_test' | |
| POSTGRES_PASSWORD: 'postgres' | |
| ports: | |
| - 5432:5432 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Build local DynamoDB | |
| if: ${{ env.DISEASE_NORM_DB_URL == 'http://localhost:8002' }} | |
| run: | | |
| chmod +x ./tests/scripts/dynamodb_run.sh | |
| ./tests/scripts/dynamodb_run.sh | |
| - name: Install DynamoDB dependencies | |
| if: ${{ env.DISEASE_NORM_DB_URL == 'http://localhost:8002' }} | |
| run: python3 -m pip install ".[etl,test]" | |
| - name: Install PG dependencies | |
| if: ${{ env.DISEASE_NORM_DB_URL != 'http://localhost:8002' }} | |
| run: python3 -m pip install ".[pg,etl,test]" | |
| - name: Run tests | |
| run: python3 -m pytest tests/ | |
| lint: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.8', '3.9', '3.10', '3.11'] | |
| env: | |
| AWS_ACCESS_KEY_ID: ${{ secrets.DUMMY_AWS_ACCESS_KEY_ID }} | |
| AWS_SECRET_ACCESS_KEY: ${{ secrets.DUMMY_AWS_SECRET_ACCESS_KEY }} | |
| AWS_DEFAULT_REGION: us-east-2 | |
| AWS_DEFAULT_OUTPUT: text | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Setup Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: python3 -m pip install ".[dev]" | |
| - name: flake8 check | |
| run: flake8 disease/ tests/ setup.py | |
| - name: black check | |
| run: black --check disease/ tests/ setup.py | |
| - name: isort check | |
| run: isort --profile black --check disease/ tests/ setup.py |