user_geneset_tests.yml

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