WIP SAML2 config and tests #343
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 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.url=.*|spring.datasource.url=jdbc:mysql://cbioportal-database:3306/cbioportal?useSSL=false|' | \ | |
| sed 's|spring.datasource.username=.*|spring.datasource.username=cbio_user|' | \ | |
| sed 's|spring.datasource.password=.*|spring.datasource.password=somepassword|' \ | |
| > application.properties && \ | |
| echo "db.user=cbio_user" >> application.properties && \ | |
| echo "db.password=somepassword" >> application.properties && \ | |
| echo "db.connection_string=jdbc:mysql://cbioportal-database:3306/cbioportal?useSSL=false" >> application.properties && \ | |
| echo "db.driver=com.mysql.jdbc.Driver" >> 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: | | |
| export DOCKER_IMAGE_CBIOPORTAL=cbioportal/cbioportal:demo-rfc72-squash && 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 |