Remove R-Studio

README.md

@@ -399,6 +399,7 @@ The Exporter is a dedicated service for extracting and exporting Bridgehead data
 
 ```bash
 ENABLE_EXPORTER=true
+```
 
 #### Data Quality Report
 To assess the quality and plausibility of your imported data, the Reporter component is pre-configured to generate Excel reports with data quality metrics and statistical analyses. Reporter is part of the Exporter and can be enabled by setting the same environment variable in your `<PROJECT>.conf` file:

bbmri/modules/teiler-compose.yml

@@ -13,8 +13,8 @@ services:
       - "traefik.http.middlewares.teiler_orchestrator_bbmri_strip.stripprefix.prefixes=/bbmri-teiler"
       - "traefik.http.routers.teiler_orchestrator_bbmri.middlewares=teiler_orchestrator_bbmri_strip"
     environment:
-      TEILER_BACKEND_URL: "https://${HOST}/bbmri-teiler-backend"
+      TEILER_BACKEND_URL: "/bbmri-teiler-backend"
-      TEILER_DASHBOARD_URL: "https://${HOST}/bbmri-teiler-dashboard"
+      TEILER_DASHBOARD_URL: "/bbmri-teiler-dashboard"
       DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE_LOWER_CASE}"
       HTTP_RELATIVE_PATH: "/bbmri-teiler"
 
@@ -30,8 +30,8 @@ services:
       - "traefik.http.routers.teiler_dashboard_bbmri.middlewares=teiler_dashboard_bbmri_strip"
     environment:
       DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
-      TEILER_BACKEND_URL: "https://${HOST}/bbmri-teiler-backend"
+      TEILER_BACKEND_URL: "/bbmri-teiler-backend"
-      TEILER_DASHBOARD_URL: "https://${HOST}/bbmri-teiler-dashboard"
+      TEILER_DASHBOARD_URL: "/bbmri-teiler-dashboard"
       OIDC_URL: "${OIDC_URL}"
       OIDC_CLIENT_ID: "${OIDC_PUBLIC_CLIENT_ID}"
       OIDC_TOKEN_GROUP: "${OIDC_GROUP_CLAIM}"
@@ -40,7 +40,7 @@ services:
       TEILER_ADMIN_PHONE: "${OPERATOR_PHONE}"
       TEILER_PROJECT: "${PROJECT}"
       EXPORTER_API_KEY: "${EXPORTER_API_KEY}"
-      TEILER_ORCHESTRATOR_URL: "https://${HOST}/bbmri-teiler"
+      TEILER_ORCHESTRATOR_URL: "/bbmri-teiler"
       TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/bbmri-teiler"
       TEILER_USER: "${OIDC_USER_GROUP}"
       TEILER_ADMIN: "${OIDC_ADMIN_GROUP}"
@@ -61,10 +61,9 @@ services:
     environment:
       LOG_LEVEL: "INFO"
       APPLICATION_PORT: "8085"
-      APPLICATION_ADDRESS: "${HOST}"
       DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
       TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/bbmri-teiler"
-      TEILER_ORCHESTRATOR_URL: "https://${HOST}/bbmri-teiler"
+      TEILER_ORCHESTRATOR_URL: "/bbmri-teiler"
-      TEILER_DASHBOARD_DE_URL: "https://${HOST}/bbmri-teiler-dashboard/de"
+      TEILER_DASHBOARD_DE_URL: "/bbmri-teiler-dashboard/de"
-      TEILER_DASHBOARD_EN_URL: "https://${HOST}/bbmri-teiler-dashboard/en"
+      TEILER_DASHBOARD_EN_URL: "/bbmri-teiler-dashboard/en"
       HTTP_PROXY: "http://forward_proxy:3128"

ccp/modules/datashield-compose.yml

@@ -1,25 +1,6 @@
 version: "3.7"
 
 services:
-  rstudio:
-    container_name: bridgehead-rstudio
-    image: docker.verbis.dkfz.de/ccp/dktk-rstudio:latest
-    environment:
-      #DEFAULT_USER: "rstudio" # This line is kept for informational purposes
-      PASSWORD: "${RSTUDIO_ADMIN_PASSWORD}" # It is required, even if the authentication is disabled
-      DISABLE_AUTH: "true" # https://rocker-project.org/images/versioned/rstudio.html#how-to-use
-      HTTP_RELATIVE_PATH: "/rstudio"
-      ALL_PROXY: "http://forward_proxy:3128" # https://rocker-project.org/use/networking.html
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.rstudio_ccp.rule=PathPrefix(`/rstudio`)"
-      - "traefik.http.services.rstudio_ccp.loadbalancer.server.port=8787"
-      - "traefik.http.middlewares.rstudio_ccp_strip.stripprefix.prefixes=/rstudio"
-      - "traefik.http.routers.rstudio_ccp.tls=true"
-      - "traefik.http.routers.rstudio_ccp.middlewares=oidcAuth,rstudio_ccp_strip"
-    networks:
-      - rstudio
-
   opal:
     container_name: bridgehead-opal
     image: docker.verbis.dkfz.de/ccp/dktk-opal:latest
@@ -94,7 +75,6 @@ services:
       - /tmp/bridgehead/opal-map/:/map/:ro
     networks:
       - default
-      - rstudio
 
   traefik:
     labels:
@@ -103,11 +83,9 @@ services:
       - "traefik.http.middlewares.oidcAuth.forwardAuth.authResponseHeaders=X-Auth-Request-Access-Token,Authorization"
     networks:
       - default
-      - rstudio
   forward_proxy:
     networks:
       - default
-      - rstudio
 
   beam-proxy:
     environment:
@@ -165,6 +143,3 @@ secrets:
     file: /tmp/bridgehead/opal-cert.pem
   opal-key.pem:
     file: /tmp/bridgehead/opal-key.pem
-
-networks:
-  rstudio:

ccp/modules/datashield-setup.sh

@@ -15,7 +15,6 @@ if [ "$ENABLE_DATASHIELD" == true ]; then
   TOKEN_MANAGER_OPAL_PASSWORD="$(generate_password \"Token Manager in Opal\")"
   OPAL_DB_PASSWORD="$(echo \"Opal DB\" | generate_simple_password)"
   OPAL_ADMIN_PASSWORD="$(generate_password \"admin password for Opal\")"
-  RSTUDIO_ADMIN_PASSWORD="$(generate_password \"admin password for R-Studio\")"
   DATASHIELD_CONNECT_SECRET="$(echo \"DataShield Connect\" | generate_simple_password)"
   TOKEN_MANAGER_SECRET="$(echo \"Token Manager\" | generate_simple_password)"
   if [ ! -e /tmp/bridgehead/opal-cert.pem ]; then

ccp/modules/teiler-compose.yml

@@ -13,8 +13,8 @@ services:
       - "traefik.http.middlewares.teiler_orchestrator_ccp_strip.stripprefix.prefixes=/ccp-teiler"
       - "traefik.http.routers.teiler_orchestrator_ccp.middlewares=teiler_orchestrator_ccp_strip"
     environment:
-      TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend"
+      TEILER_BACKEND_URL: "/ccp-teiler-backend"
-      TEILER_DASHBOARD_URL: "https://${HOST}/ccp-teiler-dashboard"
+      TEILER_DASHBOARD_URL: "/ccp-teiler-dashboard"
       DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE_LOWER_CASE}"
       HTTP_RELATIVE_PATH: "/ccp-teiler"
 
@@ -30,8 +30,8 @@ services:
       - "traefik.http.routers.teiler_dashboard_ccp.middlewares=teiler_dashboard_ccp_strip"
     environment:
       DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
-      TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend"
+      TEILER_BACKEND_URL: "/ccp-teiler-backend"
-      TEILER_DASHBOARD_URL: "https://${HOST}/ccp-teiler-dashboard"
+      TEILER_DASHBOARD_URL: "/ccp-teiler-dashboard"
       OIDC_URL: "${OIDC_URL}"
       OIDC_CLIENT_ID: "${OIDC_PUBLIC_CLIENT_ID}"
       OIDC_TOKEN_GROUP: "${OIDC_GROUP_CLAIM}"
@@ -40,7 +40,7 @@ services:
       TEILER_ADMIN_PHONE: "${OPERATOR_PHONE}"
       TEILER_PROJECT: "${PROJECT}"
       EXPORTER_API_KEY: "${EXPORTER_API_KEY}"
-      TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler"
+      TEILER_ORCHESTRATOR_URL: "/ccp-teiler"
       TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler"
       TEILER_USER: "${OIDC_USER_GROUP}"
       TEILER_ADMIN: "${OIDC_ADMIN_GROUP}"
@@ -61,12 +61,11 @@ services:
     environment:
       LOG_LEVEL: "INFO"
       APPLICATION_PORT: "8085"
-      APPLICATION_ADDRESS: "${HOST}"
       DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
       TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler"
-      TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler"
+      TEILER_ORCHESTRATOR_URL: "/ccp-teiler"
-      TEILER_DASHBOARD_DE_URL: "https://${HOST}/ccp-teiler-dashboard/de"
+      TEILER_DASHBOARD_DE_URL: "/ccp-teiler-dashboard/de"
-      TEILER_DASHBOARD_EN_URL: "https://${HOST}/ccp-teiler-dashboard/en"
+      TEILER_DASHBOARD_EN_URL: "/ccp-teiler-dashboard/en"
       HTTP_PROXY: "http://forward_proxy:3128"
       ENABLE_MTBA: "${ENABLE_MTBA}"
       ENABLE_DATASHIELD: "${ENABLE_DATASHIELD}"

modules/transfair-compose.yml

@@ -10,6 +10,7 @@ services:
       - TTP_GW_SOURCE
       - TTP_GW_EPIX_DOMAIN
       - TTP_GW_GPAS_DOMAIN
+      - TTP_TYPE
       - TTP_AUTH
       - PROJECT_ID_SYSTEM
       - FHIR_REQUEST_URL=${FHIR_REQUEST_URL}
@@ -25,7 +26,6 @@ services:
       - TLS_DISABLE=${TRANSFAIR_TLS_DISABLE:-false}
       - NO_PROXY=${TRANSFAIR_NO_PROXIES}
       - ALL_PROXY=http://forward_proxy:3128
-    command: dic ${TTP_TYPE}
     volumes:
       - /var/cache/bridgehead/${PROJECT}/transfair:/transfair
       - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro