From 0ca5ad76f167e473c61c053f73b7a42b088d429f Mon Sep 17 00:00:00 2001
From: root <root@e260-nb015.inet.dkfz-heidelberg.de>
Date: Tue, 4 Jun 2024 12:11:14 +0200
Subject: [PATCH] Changed: to use the generated passwords from
 cbioportal-setup.sh. Removed: local database files (they have been added in
 the database image named bridgehead-cbioportal-database)

---
 ccp/modules/cbioportal-compose.yml | 22 ++++++++++++++--------
 ccp/modules/cbioportal-setup.sh    |  2 ++
 2 files changed, 16 insertions(+), 8 deletions(-)

diff --git a/ccp/modules/cbioportal-compose.yml b/ccp/modules/cbioportal-compose.yml
index 5ce77e3..a312762 100644
--- a/ccp/modules/cbioportal-compose.yml
+++ b/ccp/modules/cbioportal-compose.yml
@@ -2,12 +2,16 @@ version: '3.7'
 
 services:
   cbioportal:
-    image: docker.verbis.dkfz.de/ccp/dktk-cbioportal:latest
+    # image: docker.verbis.dkfz.de/ccp/dktk-cbioportal:latest
+    image: bridgehead-cbioportal
     container_name: bridgehead-cbioportal
     environment:
       DB_PASSWORD: ${CBIOPORTAL_DB_PASSWORD}
+      # DB_PASSWORD: "password1234"
       HTTP_RELATIVE_PATH: "/cbioportal"
       UPLOAD_HTTP_RELATIVE_PATH: "/cbioportal-upload"
+      UPLOAD_FOLDER: "/app/uploads"
+      EXTRACTED_FOLDER: "/app/study"
     depends_on:
       - cbioportal-database
       - cbioportal-session
@@ -22,19 +26,21 @@ services:
       - "traefik.http.routers.cbioportal-upload.tls=true"
       - "traefik.http.services.cbioportal-upload.loadbalancer.server.port=8001" 
       
-      
-
   cbioportal-database:
-    image: docker.verbis.dkfz.de/ccp/dktk-cbioportal-database:latest
+    restart: unless-stopped
+    # image: docker.verbis.dkfz.de/ccp/dktk-cbioportal-database:latest
+    image: bridgehead-cbioportal-database
     container_name: bridgehead-cbioportal-database
     environment:
-      MYSQL_DATABASE: cbioportal
-      MYSQL_USER: cbio_user
+      MYSQL_DATABASE: "cbioportal"
+      MYSQL_USER: "cbio_user"
       MYSQL_PASSWORD: ${CBIOPORTAL_DB_PASSWORD}
       MYSQL_ROOT_PASSWORD: ${CBIOPORTAL_DB_ROOT_PASSWORD}
+      # MYSQL_PASSWORD: "password1234"
+      # MYSQL_ROOT_PASSWORD: "password12"
     volumes:
-      - /var/cache/bridgehead/ccp/cbioportal_db_data:/var/lib/mysql
-
+     - /var/cache/bridgehead/ccp/cbioportal_db_data:/var/lib/mysql
+ 
   cbioportal-session:
     image: cbioportal/session-service:0.6.1
     container_name: bridgehead-cbioportal-session
diff --git a/ccp/modules/cbioportal-setup.sh b/ccp/modules/cbioportal-setup.sh
index 1458c53..71f0eba 100644
--- a/ccp/modules/cbioportal-setup.sh
+++ b/ccp/modules/cbioportal-setup.sh
@@ -1,5 +1,7 @@
 #!/bin/bash -e
 
+
+ENABLE_CBIOPORTAL=true
  if [ "$ENABLE_CBIOPORTAL" == true ]; then
   log INFO "cBioPortal setup detected -- will start cBioPortal service."
   OVERRIDE+=" -f ./$PROJECT/modules/cbioportal-compose.yml"