samply/bridgehead
1
0
Fork 0
mirror of https://github.com/samply/bridgehead.git synced 2025-11-04 08:20:17 +01:00
Code Issues Packages Projects Releases Wiki Activity

Fix environment variables in cbioportal

Browse Source
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
Download Patch File Download Diff File Expand all files Collapse all files

15
ccp/modules/cbioportal-compose.yml
View File

@@ -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

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

@@ -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