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Incremental data upload for mutations, case lists, patient and sample attributes #1

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Incremental data upload for mutations, case lists, patient and sample attributes

Incremental data upload for mutations, case lists, patient and sample attributes #1

Workflow file for this run

.github/workflows/java-commands-integration-tests.yml at 88c3736
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

Check failure on line 12 in .github/workflows/java-commands-integration-tests.yml

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You have an error in your yaml syntax on line 12
- 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 cbiportal db container'
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: 'Prepare cbiportal db container'
mvn clean test -Dtest="**/integrationTest/**/*"
- name: Set up JDK 21
uses: actions/setup-java@v3
with:
java-version: '21'
distribution: 'temurin'
cache: maven
- name: Run integration tests
run: mvn test -Dtest="**/integrationTest/**/*"