Validate Entity Stable ID #334
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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@v2 | |
| with: | |
| path: ./cbioportal | |
| - name: 'Install python requirements' | |
| working-directory: ./cbioportal | |
| run: | | |
| sudo apt-get install python3-setuptools && \ | |
| pip3 install -U wheel && \ | |
| pip3 install -r ./requirements.txt | |
| - name: 'Set up JDK 11' | |
| uses: actions/setup-java@v1 | |
| with: | |
| java-version: 11 | |
| - name: 'Cache Maven packages' | |
| uses: actions/cache@v1 | |
| with: | |
| path: ~/.m2 | |
| key: ${{ runner.os }}-m2-${{ hashFiles('**/pom.xml') }} | |
| restore-keys: ${{ runner.os }}-m2 | |
| - 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 | |
| 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/portal/target/portal/WEB-INF/classes/portal.properties | \ | |
| sed 's/db.host=.*/db.host=cbioportal-database:3306/g' | \ | |
| sed 's|db.connection_string=.*|db.connection_string=jdbc:mysql://cbioportal-database:3306/|g' \ | |
| > portal.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: 'TEST - Validate and load study_es_0' | |
| if: steps.startup.conclusion == 'success' | |
| working-directory: ./cbioportal-docker-compose | |
| run: | | |
| $PORTAL_SOURCE_DIR/test/integration/test_load_study.sh | |
| - name: 'TEST - Add OncoKB annotations to study' | |
| if: steps.startup.conclusion == 'success' | |
| working-directory: ./cbioportal | |
| run: | | |
| export PYTHONPATH=$PORTAL_SOURCE_DIR/core/src/main/scripts && \ | |
| $PORTAL_SOURCE_DIR/test/integration/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 |