java-commands-integration-tests.yml

name: Run integration tests for java loading commands

on: [push, pull_request]

jobs:
  build:
    runs-on: ubuntu-latest
    steps:
      - name: 'Checkout Code'
        uses: actions/checkout@v4
        with:
          path: ./cbioportal-core
      - name: 'Get the cbioportal db version from pom.xml'
          run: |
            CBIO_DB_VERSION=$(python -c "import xml.etree.ElementTree as ET; tree = ET.parse('pom.xml'); root = tree.getroot(); ns = {'ns': 'http://maven.apache.org/POM/4.0.0'}; print(root.find('.//ns:cbioportal.version', ns).text)")
            echo "$CBIO_DB_VERSION=$CBIO_DB_VERSION" | tee -a $GITHUB_ENV
      - name: 'Download cgds.sql with cbioportal db schema of the given version'
          run: |
            curl -o cgds.sql https://raw.githubusercontent.com/cBioPortal/cbioportal/${{ env.CBIO_DB_VERSION }}/src/main/resources/db-scripts/cgds.sql
      - name: 'Prepare cbiportal db container'
        run: |
          docker run -p 3306:3306 \
            -v $(pwd)/src/test/resources/seed_mini.sql:/docker-entrypoint-initdb.d/seed.sql:ro \
            -v $(pwd)/cgds.sql:/docker-entrypoint-initdb.d/cgds.sql:ro \
            -e MYSQL_ROOT_PASSWORD=root \
            -e MYSQL_USER=cbio_user \
            -e MYSQL_PASSWORD=somepassword \
            -e MYSQL_DATABASE=cgds_test \
            mysql:5.7
      - name: 'Prepare cbiportal db container'
        mvn clean test -Dtest="**/integrationTest/**/*"
      - name: Set up JDK 21
          uses: actions/setup-java@v3
          with:
            java-version: '21'
            distribution: 'temurin'
            cache: maven
      - name: Run integration tests
        run: mvn test -Dtest="**/integrationTest/**/*"