fetch missing patient clinical data for the density plot (#11132) #5174
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| name: Core tests | |
| on: [push, pull_request] | |
| jobs: | |
| build: | |
| name: Setup and Test | |
| runs-on: ubuntu-latest | |
| services: | |
| mysql: | |
| image: mysql:5.7 | |
| env: | |
| MYSQL_ROOT_PASSWORD: root | |
| ports: | |
| - 3306 | |
| options: --health-cmd="mysqladmin ping" --health-interval=10s --health-timeout=5s --health-retries=10 | |
| steps: | |
| - name: 'Checkout cbioportal repo' | |
| uses: actions/checkout@v2 | |
| with: | |
| path: ./cbioportal | |
| - name: 'Set up JDK 21' | |
| uses: oracle-actions/setup-java@v1 | |
| with: | |
| website: oracle.com | |
| release: 21 | |
| - name: 'Cache Maven packages' | |
| uses: actions/cache@v1 | |
| with: | |
| path: ~/.m2 | |
| key: ${{ runner.os }}-m2-${{ hashFiles('**/pom.xml') }} | |
| restore-keys: ${{ runner.os }}-m2 | |
| - name: 'Setup mysql' | |
| run: | | |
| sudo systemctl start mysql && \ | |
| mysql --host=127.0.0.1 --port=3306 --user=root --password=root <<< 'SET GLOBAL local_infile=1' && \ | |
| mysql --host=127.0.0.1 --port=3306 --user=root --password=root <<< 'CREATE DATABASE cgds_test' && \ | |
| mysql --host=127.0.0.1 --port=3306 --user=root --password=root <<< "CREATE USER 'cbio_user'@'localhost' IDENTIFIED BY 'somepassword'" && \ | |
| mysql --host=127.0.0.1 --port=3306 --user=root --password=root <<< "GRANT ALL ON cgds_test.* TO 'cbio_user'@'localhost'" && \ | |
| mysql --host=127.0.0.1 --port=3306 --user=root --password=root <<< "flush privileges" | |
| - name: 'Copy maven settings' | |
| working-directory: ./cbioportal | |
| run: | | |
| mkdir -p ~/.m2 && \ | |
| cp .github/settings.xml ~/.m2 | |
| - name: 'Create application.properties' | |
| working-directory: ./cbioportal | |
| run: | | |
| cp src/main/resources/application.properties.EXAMPLE src/main/resources/application.properties | |
| - name: 'Build cBioPortal once without tests' | |
| working-directory: ./cbioportal | |
| run: | | |
| mvn -q -U -Ppublic -DskipTests clean install | |
| - name: 'Build cbioportal with tests' | |
| working-directory: ./cbioportal | |
| run: | | |
| mvn -q -U -Ppublic clean install | |
| - name: 'Run tests separately' | |
| working-directory: ./cbioportal | |
| run: | | |
| mvn -U -Ppublic test -Ddb.test.username=cbio_user -Ddb.test.password=somepassword | |
| - name: 'Run integration tests separately' | |
| working-directory: ./cbioportal | |
| run: | | |
| mvn -U -Ppublic integration-test -Ddb.test.username=cbio_user -Ddb.test.password=somepassword |