Add Opal

ccp/modules/opal-compose.yml

@@ -0,0 +1,79 @@
+version: "3.7"
+
+services:
+
+  ############################################ DataSHIELD Client (Rocker R-Studio)
+  rstudio:
+    image: docker.verbis.dkfz.de/dktk/bridgehead-rstudio:latest
+    container_name: bridgehead-rstudio
+    #TODO: Connect with Keycloak: https://rocker-project.org/images/versioned/rstudio.html
+    environment:
+      USER: "ruser"
+      PASSWORD: "${RSTUDIO_PASSWORD}"
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.login.rule=PathPrefix(`/rstudio`)"
+      - "traefik.http.services.login.loadbalancer.server.port=8787"
+      - "traefik.http.routers.login.tls=true"
+    volumes:
+      - "rstudio-config:/home/rstudio/.config/rstudio"
+      - "rstudio-workspace:/home/rstudio/workspace"
+      - "rstudio-user-files:/home/user-files"
+
+  ############################################ DataSHIELD Server (Opal)
+  opal:
+    image: obiba/opal:4.5
+    container_name: bridgehead-opal
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.login.rule=PathPrefix(`/opal`)"
+      - "traefik.http.services.login.loadbalancer.server.port=8080" #TODO: HTTPS -> 8443
+      - "traefik.http.routers.login.tls=true"
+    links:
+      - opal-rserver
+      - opal-mongo
+      - opal-db
+    environment:
+      JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
+      # OPAL_ADMINISTRATOR_USER: "administrator"
+      OPAL_ADMINISTRATOR_PASSWORD: "${OPAL_ADMINISTRATOR_PASSWORD}"
+      MONGO_HOST: "opal-mongo"
+      MONGO_PORT: "27017"
+      POSTGRESDATA_HOST: "opal-db"
+      POSTGRESDATA_DATABASE: "opal"
+      POSTGRESDATA_USER: "opal"
+      POSTGRESDATA_PASSWORD: "${OPAL_DB_PASSWORD}"
+
+      ROCK_HOSTS: "opal-rserver:8085"
+    volumes:
+      - "opal:/srv"
+
+  opal-mongo: # IDs
+    image: mongo:4.2 # TODO: Update mongo:6.0.4
+    container_name: bridgehead-opal-mongo
+
+  opal-db: # Data
+    image: postgres:15.1
+    container_name: bridgehead-opal-db
+    environment:
+      POSTGRES_PASSWORD: "${OPAL_DB_PASSWORD}"
+      POSTGRES_USER: "opal"
+      POSTGRES_DB: "opal"
+    volumes:
+      - "opal-db:/var/lib/postgresql/data"
+
+  opal-rserver:
+    image: datashield/rock-base:6.2-R4.2  # https://datashield.discourse.group/t/ds-aggregate-method-error/416/4
+    container_name: bridgehead-opal-rserver
+
+volumes:
+  rstudio-config:
+    name: "rstudio-config"
+  rstudio-workspace:
+    name: "rstudio-workspace"
+  rstudio-user-files:
+    name: "rstudio-user-files"
+  opal-db:
+    name: "opal-db"
+  opal:
+    name: "opal"

ccp/modules/opal-setup.sh

@@ -0,0 +1,7 @@
+#!/bin/bash
+
+if [ "$ENABLE_OPAL" == true ];then
+  log INFO "Opal setup detected -- will start Opal services."
+  OVERRIDE+=" -f ./$PROJECT/modules/opal-compose.yml"
+fi
+OPAL_DB_PASSWORD="$(echo \"This is a salt string to generate one consistent password. It is not required to be secret.\" | openssl rsautl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"

ccp/modules/teiler-ui-compose.yml

@@ -241,26 +241,26 @@ services:
       TEILER_APP24_INMENU: "false"
       TEILER_APP25_NAME: "dialog-tests"
       TEILER_APP25_INMENU: "false"
-  #    TEILER_APP26_NAME: "opal"
+      TEILER_APP26_NAME: "opal"
-  #    TEILER_APP26_TITLE: "Opal"
+      TEILER_APP26_TITLE: "Opal"
-  #    TEILER_APP26_DESCRIPTION: "Opal is OBiBa’s core database application for biobanks."
+      TEILER_APP26_DESCRIPTION: "Opal is OBiBa’s core database application for biobanks."
-  #    TEILER_APP26_SOURCEURL: "http://localhost:8880"
+      TEILER_APP26_SOURCEURL: "https://${HOST}/opal"
-  #    TEILER_APP26_ROLES: "TEILER_USER"
+      TEILER_APP26_ROLES: "TEILER_USER"
-  #    TEILER_APP26_ISACTIVATED: "true"
+      TEILER_APP26_ISACTIVATED: "true"
-  #    TEILER_APP26_ICONSOURCEURL: "https://www.obiba.org/assets/themes/bootstrap/img/obiba-logo-small.png"
+      TEILER_APP26_ICONSOURCEURL: "https://www.obiba.org/assets/themes/bootstrap/img/obiba-logo-small.png"
-  #    TEILER_APP26_ORDER: "19"
+      TEILER_APP26_ORDER: "19"
-  #    TEILER_APP26_ISEXTERNALLINK: "true"
+      TEILER_APP26_ISEXTERNALLINK: "true"
-  #    TEILER_APP26_ISLOCAL: "true"
+      TEILER_APP26_ISLOCAL: "true"
-  #    TEILER_APP27_NAME: "rstudio"
+      TEILER_APP27_NAME: "rstudio"
-  #    TEILER_APP27_TITLE: "R Studio"
+      TEILER_APP27_TITLE: "R Studio"
-  #    TEILER_APP27_DESCRIPTION: "RStudio is an integrated development environment (IDE) for R and Python."
+      TEILER_APP27_DESCRIPTION: "RStudio is an integrated development environment (IDE) for R and Python."
-  #    TEILER_APP27_SOURCEURL: "http://localhost:8787"
+      TEILER_APP27_SOURCEURL: "https://${HOST}/rstudio"
-  #    TEILER_APP27_ROLES: "TEILER_USER"
+      TEILER_APP27_ROLES: "TEILER_USER"
-  #    TEILER_APP27_ISACTIVATED: "true"
+      TEILER_APP27_ISACTIVATED: "true"
-  #    TEILER_APP27_ICONSOURCEURL: "https://rstudio.com/wp-content/uploads/2018/10/RStudio-Logo-Flat.png"
+      TEILER_APP27_ICONSOURCEURL: "https://rstudio.com/wp-content/uploads/2018/10/RStudio-Logo-Flat.png"
-  #    TEILER_APP27_ORDER: "20"
+      TEILER_APP27_ORDER: "20"
-  #    TEILER_APP27_ISEXTERNALLINK: "true"
+      TEILER_APP27_ISEXTERNALLINK: "true"
-  #    TEILER_APP27_ISLOCAL: "true"
+      TEILER_APP27_ISLOCAL: "true"
 
 volumes:
   login-db: