Merge pull request #394 from ens-lgil/feature/gwas_cohorts #203
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| name: Django CI | |
| on: | |
| push: | |
| branches: | |
| - master | |
| pull_request: | |
| types: [opened, edited, reopened] | |
| env: | |
| DEBUG: False | |
| ALLOWED_HOSTS: 'localhost' | |
| PGS_LIVE_SITE: 'False' | |
| PGS_CURATION_SITE: 'True' | |
| DATABASE_NAME: 'db_test' | |
| DATABASE_USER: 'postgres' | |
| DATABASE_PASSWORD: 'postgres' | |
| DATABASE_HOST: 'localhost' | |
| DATABASE_PORT: 5432 | |
| DATABASE_PORT_LOCAL: 5432 | |
| DATABASE_NAME_2: 'db_test_benchmark' | |
| DATABASE_USER_2: 'postgres' | |
| DATABASE_PASSWORD_2: 'postgres' | |
| DATABASE_HOST_2: 'localhost' | |
| DATABASE_PORT_2: 5432 | |
| DATABASE_PORT_LOCAL_2: 5432 | |
| DATABASE_NAME_TRACKER: 'db_test_curation_tracker' | |
| DATABASE_USER_TRACKER: 'postgres' | |
| DATABASE_PASSWORD_TRACKER: 'postgres' | |
| DATABASE_HOST_TRACKER: 'localhost' | |
| DATABASE_PORT_TRACKER: 5432 | |
| DATABASE_PORT_LOCAL_TRACKER: 5432 | |
| REST_URL_ROOT: 'http://127.0.0.1/rest/' | |
| ELASTICSEARCH_URL_ROOT: 'http://localhost:9200' | |
| SECRET_KEY: 1234 | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| services: | |
| postgres: | |
| image: postgres:12 | |
| env: | |
| POSTGRES_USER: postgres | |
| POSTGRES_PASSWORD: postgres | |
| POSTGRES_DB: db_test | |
| ports: | |
| - 5432:5432 | |
| # needed because the postgres container does not provide a healthcheck | |
| options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: "3.11" | |
| - name: Install Python dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -r requirements.txt | |
| pip install -r requirements_local.txt | |
| pip install requests | |
| pip install xlrd openpyxl numpy | |
| - name: Install Elasticsearch | |
| run: | | |
| curl https://artifacts.elastic.co/downloads/elasticsearch/elasticsearch-7.15.0-amd64.deb -o elasticsearch.deb | |
| sudo dpkg -i --force-confnew elasticsearch.deb | |
| sudo chown -R elasticsearch:elasticsearch /etc/default/elasticsearch | |
| sudo service elasticsearch start | |
| - name: Run migrations | |
| run: python manage.py migrate | |
| - name: Run Tests | |
| run: python manage.py test catalog/tests curation/tests rest_api/tests |