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Fix environment variables in cbioportal

This commit is contained in:
juarez 2023-11-29 15:46:04 +01:00 committed by djuarezgf
parent 4449beacb5
commit 316398673d
2 changed files with 9 additions and 10 deletions
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11
ccp/modules/cbioportal-compose.yml
View File

@ -2,11 +2,10 @@ version: '3.7'
services: services:
cbioportal: cbioportal:
#image: docker.verbis.dkfz.de/ccp/dktk-cbioportal:latest image: docker.verbis.dkfz.de/ccp/dktk-cbioportal:latest
image: dktk-cbioportal
container_name: bridgehead-cbioportal container_name: bridgehead-cbioportal
environment: environment:
generate_password: ${MYSQL_PASSWORD} DB_PASSWORD: ${CBIOPORTAL_DB_PASSWORD}
depends_on: depends_on:
- cbioportal-database - cbioportal-database
- cbioportal-session - cbioportal-session
@ -25,13 +24,13 @@ services:
environment: environment:
MYSQL_DATABASE: cbioportal MYSQL_DATABASE: cbioportal
MYSQL_USER: cbio_user MYSQL_USER: cbio_user
generate_password: ${MYSQL_PASSWORD} MYSQL_PASSWORD: ${CBIOPORTAL_DB_PASSWORD}
generate_root_password: ${MYSQL_ROOT_PASSWORD} MYSQL_ROOT_PASSWORD: ${CBIOPORTAL_DB_ROOT_PASSWORD}
volumes: volumes:
- /var/cache/bridgehead/ccp/cbioportal_mysql_data:/var/lib/mysql
# TODO: Move sql files to image. Are they really necessary? # TODO: Move sql files to image. Are they really necessary?
- ./cbioportal-cgds.sql:/docker-entrypoint-initdb.d/cgds.sql:ro - ./cbioportal-cgds.sql:/docker-entrypoint-initdb.d/cgds.sql:ro
- ./cbioportal-seed.sql.gz:/docker-entrypoint-initdb.d/seed.sql.gz:ro - ./cbioportal-seed.sql.gz:/docker-entrypoint-initdb.d/seed.sql.gz:ro
- /var/cache/bridgehead/ccp/cbioportal_mysql_data:/var/lib/mysql
cbioportal-session: cbioportal-session:
image: cbioportal/session-service:0.6.1 image: cbioportal/session-service:0.6.1

4
ccp/modules/cbioportal-setup.sh
View File

@ -3,6 +3,6 @@
if [ "$ENABLE_CBIOPORTAL" == true ]; then if [ "$ENABLE_CBIOPORTAL" == true ]; then
log INFO "cBioPortal setup detected -- will start cBioPortal service." log INFO "cBioPortal setup detected -- will start cBioPortal service."
OVERRIDE+=" -f ./$PROJECT/modules/cbioportal-compose.yml" OVERRIDE+=" -f ./$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)" 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)"
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_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 fi