Validator update: only allow SOMATIC or GERMLINE values for SV_Status column #318
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| # This workflow will build a Java project with Maven, and cache/restore any dependencies to improve the workflow execution time | |
| # For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-java-with-maven | |
| # This workflow uses actions that are not certified by GitHub. | |
| # They are provided by a third-party and are governed by | |
| # separate terms of service, privacy policy, and support | |
| # documentation. | |
| name: Java CI with Maven | |
| on: [push, pull_request] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - 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 cbioportal db container | |
| run: | | |
| docker run -d -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: Wait for cBioPortal database | |
| run: | | |
| until mysqladmin ping -h"127.0.0.1" -P"3306" --silent; do | |
| echo 'waiting for cBioPortal database' | |
| sleep 3 | |
| done | |
| - name: Set up JDK 21 | |
| uses: actions/setup-java@v3 | |
| with: | |
| java-version: '21' | |
| distribution: 'temurin' | |
| cache: maven | |
| - name: Build and run tests | |
| run: mvn -B integration-test --file pom.xml | |
| # Optional: Uploads the full dependency graph to GitHub to improve the quality of Dependabot alerts this repository can receive | |
| - name: Update dependency graph | |
| uses: advanced-security/[email protected] | |