diff --git a/.github/workflows/integration-test.yml b/.github/workflows/integration-test.yml index ff62d497749..08d2c2d44c9 100644 --- a/.github/workflows/integration-test.yml +++ b/.github/workflows/integration-test.yml @@ -42,8 +42,11 @@ jobs: 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.connection_string=.*|db.connection_string=jdbc:mysql://cbioportal-database:3306/cbioportal?useSSL=false|g' \ + cat $PORTAL_SOURCE_DIR/portal/target/classes/portal.properties | \ + sed 's|db.host=.*||' | \ + sed 's|db.portal_db_name=.*||' | \ + sed 's|db.use_ssl=.*||' | \ + sed 's|db.connection_string=.*|db.connection_string=jdbc:mysql://cbioportal-database:3306/cbioportal?useSSL=false&allowPublicKeyRetrieval=true|' \ > portal.properties - name: 'Start cbioportal-docker-compose' working-directory: ./cbioportal-docker-compose diff --git a/docker/web-and-data/docker-entrypoint.sh b/docker/web-and-data/docker-entrypoint.sh index 9e1b9abf098..b474a216d5b 100755 --- a/docker/web-and-data/docker-entrypoint.sh +++ b/docker/web-and-data/docker-entrypoint.sh @@ -114,7 +114,7 @@ _main() { # available, otherwise use portal.properties if [ -n "$SHOW_DEBUG_INFO" ] && [ "$SHOW_DEBUG_INFO" != "false" ]; then echo "Using database config:" - #parse_db_params_from_config_and_command_line $@ + parse_db_params_from_config_and_command_line $@ fi check_db_connection $@ diff --git a/test/integration/docker-compose-localbuild.yml b/test/integration/docker-compose-localbuild.yml index 958c75492a8..cd3d8adc17e 100644 --- a/test/integration/docker-compose-localbuild.yml +++ b/test/integration/docker-compose-localbuild.yml @@ -13,3 +13,5 @@ services: # and running - $PORTAL_SOURCE_DIR:/cbioportal/ - $PORTAL_SOURCE_DIR/portal/target/cbioportal.war:/app.war + # TODO: remove line below after upgrade of cbioportal-docker-compose to > v5.3.20 + - $PORTAL_SOURCE_DIR/docker/web-and-data/docker-entrypoint.sh:/usr/local/bin/docker-entrypoint.sh