Skip to content

Only allow SOMATIC or GERMLINE values for SV_Status column #317

Only allow SOMATIC or GERMLINE values for SV_Status column

Only allow SOMATIC or GERMLINE values for SV_Status column #317

Workflow file for this run

# 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]