Upgrade to biothings 1.0.x #647
Workflow file for this run
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| name: User Geneset Tests | |
| on: | |
| push: {} | |
| pull_request: | |
| branches: | |
| - master | |
| jobs: | |
| run_user_geneset_tests: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: [ "3.8", "3.9", "3.10", "3.11", "3.12" ] | |
| services: | |
| elasticsearch: | |
| image: docker.elastic.co/elasticsearch/elasticsearch:8.15.3 | |
| env: | |
| discovery.type : single-node | |
| xpack.security.enabled: false | |
| xpack.security.http.ssl.enabled: false | |
| xpack.security.transport.ssl.enabled: false | |
| options: >- | |
| --health-cmd "curl http://localhost:9200/_cluster/health" | |
| --health-interval 10s | |
| --health-timeout 5s | |
| --health-retries 10 | |
| ports: | |
| - 9200:9200 | |
| steps: | |
| - name: Create ES Index | |
| run: | | |
| sleep 60 | |
| curl -X PUT http://localhost:9200/user_genesets | |
| - name: Clone frontend repo | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: biothings/mygeneset.info-website | |
| path: mygeneset.info-website | |
| - name: Set up Node | |
| uses: actions/setup-node@v2 | |
| with: | |
| node-version: "16" | |
| - name: Install packages | |
| run: yarn install | |
| working-directory: mygeneset.info-website | |
| - name: Build app | |
| run: yarn build | |
| working-directory: mygeneset.info-website | |
| - name: Start Frontend | |
| run: | | |
| yarn serve & | |
| sleep 30 | |
| working-directory: mygeneset.info-website | |
| - name: Checkout MyGeneset source | |
| uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Upgrade pip | |
| run: pip install --upgrade pip | |
| - name: Install dependencies | |
| run: pip install -r requirements_web.txt | |
| - name: Get web config file | |
| run: wget https://gist.githubusercontent.com/ravila4/9f20d64f51fc23c10b1b70b679a7d3ab/raw/1199ab75b78cc71549fa73e6283810cf2c081682/config.py | |
| working-directory: src | |
| - name: Start API | |
| run: python index.py --webapp & | |
| working-directory: src | |
| env: | |
| ORCID_CLIENT_ID: ${{ secrets.ORCID_CLIENT_ID }} | |
| ORCID_CLIENT_SECRET: ${{ secrets.ORCID_CLIENT_SECRET }} | |
| - name: Install PyTest | |
| run: pip install pytest | |
| - name: Install Selenium | |
| run: pip install selenium | |
| - name: Install Selenium Wire | |
| run: pip install selenium-wire | |
| - name: Install Webdriver Manager | |
| run: pip install webdriver-manager | |
| - name: Install Blinker | |
| run: pip install blinker==1.7.0 | |
| - name: Install/Upgrade setuptools | |
| run: pip install --upgrade setuptools | |
| - name: Run App Tests | |
| run: pytest test_user_genesets.py | |
| working-directory: src/tests | |
| env: | |
| ORCID_USERNAME: ${{ secrets.ORCID_USERNAME }} | |
| ORCID_PASSWORD: ${{ secrets.ORCID_PASSWORD }} | |
| GITHUB_USERNAME: ${{ secrets.GIT_HUB_USERNAME }} | |
| GITHUB_PASSWORD: ${{ secrets.GIT_HUB_PASSWORD }} | |
| - name: Setup tmate debug session on failure | |
| if: ${{ failure() }} | |
| uses: mxschmitt/action-tmate@v3 |