From 316398673d896de9e0aaf6a911da9999b438e5a5 Mon Sep 17 00:00:00 2001 From: juarez Date: Wed, 29 Nov 2023 15:46:04 +0100 Subject: [PATCH] Fix environment variables in cbioportal --- ccp/modules/cbioportal-compose.yml | 15 +++++++-------- ccp/modules/cbioportal-setup.sh | 4 ++-- 2 files changed, 9 insertions(+), 10 deletions(-) diff --git a/ccp/modules/cbioportal-compose.yml b/ccp/modules/cbioportal-compose.yml index 6e58e38..eea98ff 100644 --- a/ccp/modules/cbioportal-compose.yml +++ b/ccp/modules/cbioportal-compose.yml @@ -2,11 +2,10 @@ version: '3.7' services: cbioportal: - #image: docker.verbis.dkfz.de/ccp/dktk-cbioportal:latest - image: dktk-cbioportal + image: docker.verbis.dkfz.de/ccp/dktk-cbioportal:latest container_name: bridgehead-cbioportal environment: - generate_password: ${MYSQL_PASSWORD} + DB_PASSWORD: ${CBIOPORTAL_DB_PASSWORD} depends_on: - cbioportal-database - cbioportal-session @@ -25,13 +24,13 @@ services: environment: MYSQL_DATABASE: cbioportal MYSQL_USER: cbio_user - generate_password: ${MYSQL_PASSWORD} - generate_root_password: ${MYSQL_ROOT_PASSWORD} + MYSQL_PASSWORD: ${CBIOPORTAL_DB_PASSWORD} + MYSQL_ROOT_PASSWORD: ${CBIOPORTAL_DB_ROOT_PASSWORD} volumes: + - /var/cache/bridgehead/ccp/cbioportal_mysql_data:/var/lib/mysql # TODO: Move sql files to image. Are they really necessary? - - ./cbioportal-cgds.sql:/docker-entrypoint-initdb.d/cgds.sql:ro - - ./cbioportal-seed.sql.gz:/docker-entrypoint-initdb.d/seed.sql.gz:ro - - /var/cache/bridgehead/ccp/cbioportal_mysql_data:/var/lib/mysql + - ./cbioportal-cgds.sql:/docker-entrypoint-initdb.d/cgds.sql:ro + - ./cbioportal-seed.sql.gz:/docker-entrypoint-initdb.d/seed.sql.gz:ro cbioportal-session: image: cbioportal/session-service:0.6.1 diff --git a/ccp/modules/cbioportal-setup.sh b/ccp/modules/cbioportal-setup.sh index 9aaf781..10b3d6a 100644 --- a/ccp/modules/cbioportal-setup.sh +++ b/ccp/modules/cbioportal-setup.sh @@ -3,6 +3,6 @@ if [ "$ENABLE_CBIOPORTAL" == true ]; then log INFO "cBioPortal setup detected -- will start cBioPortal service." OVERRIDE+=" -f ./$PROJECT/modules/cbioportal-compose.yml" - generate_password="$(echo \"This is a salt string to generate one consistent password for the cbioportal database. It is not required to be secret.\" | openssl rsautl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)" - generate_root_password="$(echo \"This is a salt string to generate one consistent root password for the cbioportal database. It is not required to be secret.\" | openssl rsautl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 64)" + CBIOPORTAL_DB_PASSWORD="$(echo \"This is a salt string to generate one consistent password for the cbioportal database. It is not required to be secret.\" | openssl rsautl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)" + CBIOPORTAL_DB_ROOT_PASSWORD="$(echo \"This is a salt string to generate one consistent root password for the cbioportal database. It is not required to be secret.\" | openssl rsautl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 64)" fi