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

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+version: '3.7'
+
+services:
+  cbioportal:
+    # 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
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.cbioportal.rule=PathPrefix(`/cbioportal`)"
+      - "traefik.http.routers.cbioportal.service=cbioportal"
+      - "traefik.http.services.cbioportal.loadbalancer.server.port=8080"
+      - "traefik.http.routers.cbioportal.tls=true"
+      - "traefik.http.routers.cbioportal-upload.rule=PathPrefix(`/cbioportal-upload`)"    
+      - "traefik.http.routers.cbioportal-upload.service=cbioportal-upload"
+      - "traefik.http.routers.cbioportal-upload.tls=true"
+      - "traefik.http.services.cbioportal-upload.loadbalancer.server.port=8001" 
+      
+  cbioportal-database:
+    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_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
+ 
+  cbioportal-session:
+    image: cbioportal/session-service:0.6.1
+    container_name: bridgehead-cbioportal-session
+    environment:
+      SERVER_PORT: 5000
+      JAVA_OPTS: -Dspring.data.mongodb.uri=mongodb://cbioportal-session-database:27017/session-service
+    depends_on:
+      - cbioportal-session-database
+
+  cbioportal-session-database:
+    image: mongo:4.2
+    container_name: bridgehead-cbioportal-session-database
+    environment:
+      MONGO_INITDB_DATABASE: session_service
+    volumes:
+      - /var/cache/bridgehead/ccp/cbioportal_session_db_data:/data/db
+      

ccp/modules/cbioportal-setup.sh

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+#!/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"
+  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

ccp/modules/cbioportal.md

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+# CBioPortal Data uploader
+
+
+## Usage
+
+We have integrated an API that allows you to upload data directly to cbioportal without the need to have cbioportal installed in your system.
+
+## Tech stack
+
+We used Flask to add this feature