Run integration tests for java loading commands #7

	name: Run integration tests for java loading commands

	on: [push, pull_request]

	jobs:
	build:
	runs-on: ubuntu-latest
	steps:
	- name: 'Checkout Code'
	uses: actions/checkout@v4
	with:
	path: ./cbioportal-core

	- name: 'Get the cbioportal db version from pom.xml'
	working-directory: ./cbioportal-core
	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'
	working-directory: ./cbioportal-core
	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'
	working-directory: ./cbioportal-core
	run: \|
	docker run -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: 'Run database-dependent tests'
	working-directory: ./cbioportal-core
	run: mvn test -Dtest="/integrationTest//*"

	- name: Set up JDK 21
	uses: actions/setup-java@v3
	with:
	java-version: '21'
	distribution: 'temurin'
	cache: maven

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