add missing inheritance mode to prioritized search #7637
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| name: Unit Tests | |
| # Run the test suite on pushes (incl. merges) to master and dev | |
| # Run the test suite when a PR is opened, pushed to, or reopened | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - dev | |
| paths-ignore: | |
| - 'vlm/**' | |
| - '.github/workflows/*vlm*.yaml' | |
| pull_request: | |
| types: [opened, synchronize, reopened] | |
| paths-ignore: | |
| - 'vlm/**' | |
| - '.github/workflows/*vlm*.yaml' | |
| jobs: | |
| python: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [3.11] | |
| services: | |
| # Label used to access the service container | |
| postgres: | |
| # Docker Hub image | |
| image: postgres | |
| # Provide the password for postgres | |
| env: | |
| POSTGRES_PASSWORD: "pgtest" | |
| # Set health checks to wait until postgres has started | |
| options: >- | |
| --health-cmd pg_isready | |
| --health-interval 10s | |
| --health-timeout 5s | |
| --health-retries 5 | |
| ports: | |
| # Maps tcp port 5432 on service container to the host | |
| - 5432:5432 | |
| clickhouse: | |
| image: bitnamilegacy/clickhouse:latest | |
| ports: | |
| - 9000:9000 # Native client interface | |
| volumes: | |
| - /var/tmp:/var/seqr/clickhouse-data | |
| - /tmp:/in-memory-dir | |
| options: >- | |
| --health-cmd "clickhouse-client --query 'SELECT 1'" | |
| --health-interval 10s | |
| --health-timeout 5s | |
| --health-retries 5 | |
| --name clickhouse | |
| env: | |
| CLICKHOUSE_USER: clickhouse_test | |
| CLICKHOUSE_PASSWORD: clickhouse_test | |
| ALLOW_EMPTY_PASSWORD: no | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Clickhouse Settings | |
| run: | | |
| cat <<EOF > test_config.xml | |
| <clickhouse> | |
| <users> | |
| <clickhouse_test> | |
| <named_collection_control>1</named_collection_control> | |
| </clickhouse_test> | |
| </users> | |
| </clickhouse> | |
| EOF | |
| docker cp ${{ github.workspace }}/test_config.xml clickhouse:/etc/clickhouse-server/users.d/users.xml | |
| docker exec clickhouse clickhouse-client --query "SYSTEM RELOAD USERS" | |
| docker exec clickhouse clickhouse-client --query "CREATE USER clickhouse_read_only IDENTIFIED WITH plaintext_password BY 'clickhouse_test'" | |
| docker exec clickhouse clickhouse-client --query "CREATE SETTINGS PROFILE clickhouse_settings SETTINGS flatten_nested=0, join_use_nulls=1, stop_refreshable_materialized_views_on_startup=1 TO clickhouse_test, clickhouse_read_only" | |
| docker exec clickhouse clickhouse-client --query "GRANT SELECT, SYSTEM VIEWS, dictGet ON *.* TO clickhouse_read_only" | |
| docker exec clickhouse clickhouse-client --query "CREATE NAMED COLLECTION seqr_postgres_named_collection AS user='postgres', password='pgtest', host='postgres', port='5432'" | |
| docker exec clickhouse clickhouse-client --query "SYSTEM RELOAD USERS" | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Use pip cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/.cache/pip | |
| key: pip-${{ hashFiles('**/requirements*.txt') }} | |
| restore-keys: | | |
| pip- | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip wheel | |
| pip install -r requirements.txt | |
| pip install -r requirements-dev.txt | |
| - name: Run coverage tests | |
| run: | | |
| export CLICKHOUSE_READER_USER=clickhouse_read_only | |
| export CLICKHOUSE_WRITER_USER=clickhouse_test | |
| export CLICKHOUSE_SERVICE_HOSTNAME=localhost | |
| coverage run --source="./matchmaker","./seqr","./reference_data","./panelapp","./clickhouse_search" --omit="*/migrations/*","*/apps.py","*/admin.py" manage.py test -p '*_tests.py' -v 2 reference_data seqr matchmaker panelapp clickhouse_search | |
| coverage report -m --fail-under=99 | |
| coverage report | (! grep [1-8][0-9]%) | |
| coverage report | (! grep 9[0-5]%) | |
| nodejs: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| node-version: [14] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Use Node.js ${{ matrix.node-version }} | |
| uses: actions/setup-node@v3 | |
| with: | |
| node-version: ${{ matrix.node-version }} | |
| cache: "npm" | |
| cache-dependency-path: ui/package-lock.json | |
| - run: npm install -g npm@7.24.2 | |
| - run: npm ci | |
| working-directory: ./ui | |
| - run: npm run lint | |
| working-directory: ./ui | |
| - run: npm test | |
| working-directory: ./ui |