integration-test.yml

name: Integration tests
on: [push, pull_request]
jobs:
  build:
    name: Integration tests
    runs-on: ubuntu-latest
    env: 
      PORTAL_SOURCE_DIR: /home/runner/work/cbioportal/cbioportal/cbioportal
      PORTAL_COMPOSE_DIR: /home/runner/work/cbioportal/cbioportal/cbioportal-docker-compose
      PORTAL_INFO_DIR: /home/runner/work/cbioportal/cbioportal/portalInfo
    steps:
      - name: 'Checkout cbioportal repo'
        uses: actions/checkout@v2
        with:
          path: ./cbioportal
      - name: 'Install python requirements'
        working-directory: ./cbioportal
        run: |
          sudo apt-get install python3-setuptools && \
          pip3 install -U wheel && \
          pip3 install -r ./requirements.txt
      - name: 'Set up JDK 11'
        uses: actions/setup-java@v1
        with:
          java-version: 11
      - name: 'Cache Maven packages'
        uses: actions/cache@v1
        with:
          path: ~/.m2
          key: ${{ runner.os }}-m2-${{ hashFiles('**/pom.xml') }}
          restore-keys: ${{ runner.os }}-m2
      - name: 'Build cbioportal'
        working-directory: ./cbioportal
        run: |
          mvn -DskipTests clean install
      - name: 'Checkout cbioportal-docker-compose repo'
        uses: actions/checkout@master
        with:
          repository: cbioportal/cbioportal-docker-compose
          path: ./cbioportal-docker-compose
      - name: 'Initialize cbioportal-docker-compose'
        working-directory: ./cbioportal-docker-compose
        run: |
          cd ./data && ./init.sh && rm -rf ./studies/* && cd ../config && \
          cat $PORTAL_SOURCE_DIR/portal/target/portal/WEB-INF/classes/portal.properties | \
              sed 's/db.host=.*/db.host=cbioportal-database:3306/g' | \
              sed 's|db.connection_string=.*|db.connection_string=jdbc:mysql://cbioportal-database:3306/|g' \
              > portal.properties
      - name: 'Start cbioportal-docker-compose'
        working-directory: ./cbioportal-docker-compose
        run: |
          docker-compose -f docker-compose.yml -f $PORTAL_SOURCE_DIR/test/integration/docker-compose-localbuild.yml up -d
      - name: 'Wait for cbioportal to initialize ...'
        id: startup
        uses: nev7n/wait_for_response@v1
        with:
          url: 'http://localhost:8080/api/health'
          responseCode: 200
          timeout: 900000
          interval: 30000
      - name: 'TEST - Validate and load study_es_0'
        if: steps.startup.conclusion == 'success'
        working-directory: ./cbioportal-docker-compose
        run: |
          $PORTAL_SOURCE_DIR/test/integration/test_load_study.sh
      - name: 'TEST - Add OncoKB annotations to study'
        if: steps.startup.conclusion == 'success'
        working-directory: ./cbioportal
        run: |
          export PYTHONPATH=$PORTAL_SOURCE_DIR/core/src/main/scripts && \
          $PORTAL_SOURCE_DIR/test/integration/integration_test_oncokb_import.sh
      - name: 'TEST - Update OncoKB annotations'
        if: steps.startup.conclusion == 'success'
        working-directory: ./cbioportal-docker-compose
        run: |
          $PORTAL_SOURCE_DIR/test/integration/test_update_oncokb.sh