Fix alteration count services #6215
Workflow file for this run
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name: Integration tests | |
on: [push, pull_request] | |
jobs: | |
build: | |
name: Integration tests | |
runs-on: ubuntu-latest | |
env: | |
PORTAL_SOURCE_DIR: /home/runner/work/cbioportal/cbioportal/cbioportal | |
PORTAL_COMPOSE_DIR: /home/runner/work/cbioportal/cbioportal/cbioportal-docker-compose | |
PORTAL_INFO_DIR: /home/runner/work/cbioportal/cbioportal/portalInfo | |
steps: | |
- name: 'Checkout cbioportal repo' | |
uses: actions/checkout@v4 | |
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: 'Copy application.properties' | |
working-directory: ./cbioportal | |
run: | | |
cp src/main/resources/application.properties.EXAMPLE src/main/resources/application.properties | |
- name: 'Build cbioportal' | |
working-directory: ./cbioportal | |
run: | | |
mvn -DskipTests clean install | |
- name: 'Checkout cbioportal-docker-compose repo' | |
uses: actions/checkout@master | |
with: | |
repository: cbioportal/cbioportal-docker-compose | |
ref: demo-rfc72 | |
path: ./cbioportal-docker-compose | |
- name: 'Initialize cbioportal-docker-compose' | |
working-directory: ./cbioportal-docker-compose | |
run: | | |
cd ./data && ./init.sh && rm -rf ./studies/* && cd ../config && \ | |
cat $PORTAL_SOURCE_DIR/src/main/resources/application.properties | \ | |
sed 's|spring.datasource.mysql.url=.*|spring.datasource.mysql.url=jdbc:mysql://cbioportal-database:3306/cbioportal?useSSL=false|' | \ | |
sed 's|spring.datasource.mysql.username=.*|spring.datasource.mysql.username=cbio_user|' | \ | |
sed 's|spring.datasource.mysql.password=.*|spring.datasource.mysql.password=somepassword|' \ | |
> application.properties | |
- name: 'Copy cgds.sql file into Docker Compose' | |
run: cp ./cbioportal/src/main/resources/db-scripts/cgds.sql ./cbioportal-docker-compose/data/. | |
- name: 'Dump Properties' | |
working-directory: ./cbioportal-docker-compose | |
run: cat config/application.properties | |
- name: 'Start cbioportal-docker-compose' | |
working-directory: ./cbioportal-docker-compose | |
run: | | |
docker-compose -f docker-compose.yml -f $PORTAL_SOURCE_DIR/test/integration/docker-compose-localbuild.yml up -d | |
- name: 'Wait for cbioportal to initialize ...' | |
id: startup | |
uses: nev7n/wait_for_response@v1 | |
with: | |
url: 'http://localhost:8080/api/health' | |
responseCode: 200 | |
timeout: 900000 | |
interval: 30000 | |
- name: Log cBioPortal Service | |
if: ${{ failure() && steps.startup.conclusion == 'failure' }} | |
working-directory: ./cbioportal-docker-compose | |
run: docker-compose logs cbioportal | |
- name: 'TEST - Validate and load study_es_0' | |
if: steps.startup.conclusion == 'success' | |
working-directory: ./cbioportal-docker-compose | |
run: | | |
$PORTAL_SOURCE_DIR/test/integration/test_load_study.sh | |
- name: 'TEST - Add OncoKB annotations to study' | |
if: steps.startup.conclusion == 'success' | |
working-directory: ./cbioportal-docker-compose | |
run: | | |
$PORTAL_SOURCE_DIR/test/integration/test_integration_test_oncokb_import.sh | |
- name: 'TEST - Update OncoKB annotations' | |
if: steps.startup.conclusion == 'success' | |
working-directory: ./cbioportal-docker-compose | |
run: | | |
$PORTAL_SOURCE_DIR/test/integration/test_update_oncokb.sh |