get mutation data from genomic event table instead of mutation table … #4195
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| 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 |