Changed: image used for cbioportal and teiler backend

- used image for cbioportal in cbioportal-compose to the Harbor image

- Ran tests to make sure cbioportal and cbioportal API work in Teiler backend.

.gitignore

@@ -1,7 +1,7 @@
 ##Ignore site configuration
 .gitmodules
 site-config/*
-
+.idea
 ## Ignore site configuration
 */docker-compose.override.yml
 

README.md

@@ -34,6 +34,10 @@ This repository is the starting point for any information and tools you will nee
 
 ## Requirements
 
+The data protection group at your site will probably want to know exactly what our software does with patient data, and you may need to get their approval before you are allowed to install a Bridgehead. To help you with this, we have provided some data protection concepts:
+
+- [Germany](https://www.bbmri.de/biobanking/it/infrastruktur/datenschutzkonzept/)
+
 ### Hardware
 
 Hardware requirements strongly depend on the specific use-cases of your network as well as on the data it is going to serve. Most use-cases are well-served with the following configuration:

bbmri/modules/directory-sync-compose.yml

@@ -1,3 +1,5 @@
+version: "3.7"
+
 services:
   directory_sync_service:
     image: "docker.verbis.dkfz.de/cache/samply/directory_sync_service"

bbmri/modules/dnpm-compose.yml

@@ -18,7 +18,7 @@ services:
       - "forward_proxy"
     volumes:
       - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
-      - /srv/docker/bridgehead/ccp/root-new.crt.pem:/conf/root.crt.pem:ro
+      - /srv/docker/bridgehead/ccp/root.crt.pem:/conf/root.crt.pem:ro
 
   dnpm-beam-connect:
     depends_on: [ dnpm-beam-proxy ]
@@ -32,9 +32,11 @@ services:
       LOCAL_TARGETS_FILE: "./conf/connect_targets.json"
       HTTP_PROXY: http://forward_proxy:3128
       HTTPS_PROXY: http://forward_proxy:3128
-      NO_PROXY: dnpm-beam-proxy,dnpm-backend
+      NO_PROXY: dnpm-beam-proxy,dnpm-backend, host.docker.internal
       RUST_LOG: ${RUST_LOG:-info}
       NO_AUTH: "true"
+    extra_host:
+      - "host.docker.internal:host-gateway"
     volumes:
       - /etc/bridgehead/dnpm/local_targets.json:/conf/connect_targets.json:ro
       - /etc/bridgehead/dnpm/central_targets.json:/conf/central_targets.json:ro

bbmri/modules/dnpm-node-compose.yml

@@ -0,0 +1,33 @@
+version: "3.7"
+
+services:
+  dnpm-backend:
+    image: ghcr.io/kohlbacherlab/bwhc-backend:1.0-snapshot-broker-connector
+    container_name: bridgehead-dnpm-backend
+    environment:
+      - ZPM_SITE=${ZPM_SITE}
+    volumes:
+      - /etc/bridgehead/dnpm:/bwhc_config:ro
+      - ${DNPM_DATA_DIR}:/bwhc_data
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.bwhc-backend.rule=PathPrefix(`/bwhc`)"
+      - "traefik.http.services.bwhc-backend.loadbalancer.server.port=9000"
+      - "traefik.http.routers.bwhc-backend.tls=true"
+
+  dnpm-frontend:
+    image: ghcr.io/kohlbacherlab/bwhc-frontend:2209
+    container_name: bridgehead-dnpm-frontend
+    links:
+      - dnpm-backend
+    environment:
+      - NUXT_HOST=0.0.0.0
+      - NUXT_PORT=8080
+      - BACKEND_PROTOCOL=https
+      - BACKEND_HOSTNAME=$HOST
+      - BACKEND_PORT=443
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.bwhc-frontend.rule=PathPrefix(`/`)"
+      - "traefik.http.services.bwhc-frontend.loadbalancer.server.port=8080"
+      - "traefik.http.routers.bwhc-frontend.tls=true"

bbmri/modules/dnpm-node-setup.sh

@@ -0,0 +1,27 @@
+#!/bin/bash
+
+if [ -n "${ENABLE_DNPM_NODE}" ]; then
+	log INFO "DNPM setup detected (BwHC Node) -- will start BwHC node."
+	OVERRIDE+=" -f ./$PROJECT/modules/dnpm-node-compose.yml"
+
+	# Set variables required for BwHC Node. ZPM_SITE is assumed to be set in /etc/bridgehead/<project>.conf
+	DNPM_APPLICATION_SECRET="$(echo \"This is a salt string to generate one consistent password for DNPM. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
+	if [ -z "${ZPM_SITE+x}" ]; then
+		log ERROR "Mandatory variable ZPM_SITE not defined!"
+		exit 1
+	fi
+	if [ -z "${DNPM_DATA_DIR+x}" ]; then
+		log ERROR "Mandatory variable DNPM_DATA_DIR not defined!"
+		exit 1
+	fi
+			if grep -q 'traefik.http.routers.landing.rule=PathPrefix(`/landing`)' /srv/docker/bridgehead/minimal/docker-compose.override.yml 2>/dev/null; then
+				echo "Override of landing page url already in place"
+			else
+				echo "Adding override of landing page url"
+				if [ -f /srv/docker/bridgehead/minimal/docker-compose.override.yml ]; then
+					echo -e '  landing:\n    labels:\n      - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"' >> /srv/docker/bridgehead/minimal/docker-compose.override.yml
+				else
+					echo -e 'version: "3.7"\nservices:\n  landing:\n    labels:\n      - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"' >> /srv/docker/bridgehead/minimal/docker-compose.override.yml
+				fi
+			fi
+fi

bbmri/modules/dnpm-setup.sh

@@ -5,7 +5,6 @@ if [ -n "${ENABLE_DNPM}" ]; then
 	OVERRIDE+=" -f ./$PROJECT/modules/dnpm-compose.yml"
 
 	# Set variables required for Beam-Connect
-	DNPM_APPLICATION_SECRET="$(echo \"This is a salt string to generate one consistent password for DNPM. It is not required to be secret.\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
 	DNPM_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
 	DNPM_BROKER_ID="broker.ccp-it.dktk.dkfz.de"
 	DNPM_BROKER_URL="https://${DNPM_BROKER_ID}"

bbmri/modules/eric-compose.yml

@@ -2,7 +2,7 @@ version: "3.7"
 
 services:
   focus-eric:
-    image: docker.verbis.dkfz.de/cache/samply/focus:main
+    image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
     container_name: bridgehead-focus-eric
     environment:
       API_KEY: ${ERIC_FOCUS_BEAM_SECRET_SHORT}
@@ -32,5 +32,5 @@ services:
       - "forward_proxy"
     volumes:
       - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
-      - /srv/docker/bridgehead/bbmri/modules/eric.root.crt.pem:/conf/root.crt.pem:ro
+      - /srv/docker/bridgehead/bbmri/modules/${ERIC_ROOT_CERT}.root.crt.pem:/conf/root.crt.pem:ro
 

bbmri/modules/eric-setup.sh

@@ -4,8 +4,23 @@ if [ "${ENABLE_ERIC}" == "true" ]; then
 	log INFO "BBMRI-ERIC setup detected -- will start services for BBMRI-ERIC."
 	OVERRIDE+=" -f ./$PROJECT/modules/eric-compose.yml"
 
-	# Set required variables
-	ERIC_BROKER_ID=broker.bbmri.samply.de
+	# The environment needs to be defined in /etc/bridgehead
+	case "$ENVIRONMENT" in
+		"production")
+			export ERIC_BROKER_ID=broker.bbmri.samply.de
+			export ERIC_ROOT_CERT=eric
+			;;
+		"test")
+			export ERIC_BROKER_ID=broker-test.bbmri-test.samply.de
+			export ERIC_ROOT_CERT=eric.test
+			;;
+		*)
+			report_error 6 "Environment \"$ENVIRONMENT\" is unknown. Assuming production. FIX THIS!"
+			export ERIC_BROKER_ID=broker.bbmri.samply.de
+			export ERIC_ROOT_CERT=eric
+			;;
+	esac
+
 	ERIC_BROKER_URL=https://${ERIC_BROKER_ID}
 	ERIC_PROXY_ID=${SITE_ID}.${ERIC_BROKER_ID}
 	ERIC_FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"

bbmri/modules/eric.test.root.crt.pem

@@ -0,0 +1,20 @@
+-----BEGIN CERTIFICATE-----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+-----END CERTIFICATE-----

bbmri/modules/gbn-compose.yml

@@ -2,7 +2,7 @@ version: "3.7"
 
 services:
   focus-gbn:
-    image: docker.verbis.dkfz.de/cache/samply/focus:main
+    image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
     container_name: bridgehead-focus-gbn
     environment:
       API_KEY: ${GBN_FOCUS_BEAM_SECRET_SHORT}
@@ -32,5 +32,5 @@ services:
       - "forward_proxy"
     volumes:
       - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
-      - /srv/docker/bridgehead/bbmri/modules/gbn.root.crt.pem:/conf/root.crt.pem:ro
+      - /srv/docker/bridgehead/bbmri/modules/${GBN_ROOT_CERT}.root.crt.pem:/conf/root.crt.pem:ro
 

bbmri/modules/gbn-setup.sh

@@ -4,8 +4,23 @@ if [ "${ENABLE_GBN}" == "true" ]; then
 	log INFO "GBN setup detected -- will start services for German Biobank Node."
 	OVERRIDE+=" -f ./$PROJECT/modules/gbn-compose.yml"
 
-	# Set required variables
-	GBN_BROKER_ID=broker.bbmri.de
+	# The environment needs to be defined in /etc/bridgehead
+	case "$ENVIRONMENT" in
+		"production")
+			export GBN_BROKER_ID=broker.bbmri.de
+			export GBN_ROOT_CERT=gbn
+			;;
+		"test")
+			export GBN_BROKER_ID=broker.test.bbmri.de
+			export GBN_ROOT_CERT=gbn.test
+			;;
+		*)
+			report_error 6 "Environment \"$ENVIRONMENT\" is unknown. Assuming production. FIX THIS!"
+			export GBN_BROKER_ID=broker.bbmri.de
+			export GBN_ROOT_CERT=gbn
+			;;
+	esac
+	
 	GBN_BROKER_URL=https://${GBN_BROKER_ID}
 	GBN_PROXY_ID=${SITE_ID}.${GBN_BROKER_ID}
 	GBN_FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"

bbmri/modules/gbn.test.root.crt.pem

@@ -0,0 +1,20 @@
+-----BEGIN CERTIFICATE-----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+-----END CERTIFICATE-----

bridgehead

@@ -41,6 +41,7 @@ case "$PROJECT" in
 		;;
 esac
 
+# TODO: Please add proper documentation for variable priorities (1. secrets, 2. vars, 3. PROJECT.local.conf, 4. PROJECT.conf, 5. ???
 loadVars() {
 	# Load variables from /etc/bridgehead and /srv/docker/bridgehead
 	set -a
@@ -50,6 +51,7 @@ loadVars() {
 		source /etc/bridgehead/$PROJECT.local.conf || fail_and_report 1 "Found /etc/bridgehead/$PROJECT.local.conf but failed to import"
 	fi
 	fetchVarsFromVaultByFile /etc/bridgehead/$PROJECT.conf || fail_and_report 1 "Unable to fetchVarsFromVaultByFile"
+	setHostname
 	[ -e ./$PROJECT/vars ] && source ./$PROJECT/vars
 	set +a
 
@@ -64,8 +66,23 @@ loadVars() {
 		OVERRIDE+=" -f ./$PROJECT/docker-compose.override.yml"
 	fi
 	detectCompose
-	setHostname
 	setupProxy
+
+	# Set some project-independent default values
+	: ${ENVIRONMENT:=production}
+
+	case "$ENVIRONMENT" in
+		"production")
+			export FOCUS_TAG=main
+			;;
+		"test")
+			export FOCUS_TAG=develop
+			;;
+		*)
+			report_error 7 "Environment \"$ENVIRONMENT\" is unknown. Assuming production. FIX THIS!"
+			export FOCUS_TAG=main
+			;;
+	esac
 }
 
 case "$ACTION" in
@@ -73,6 +90,7 @@ case "$ACTION" in
 		loadVars
 		hc_send log "Bridgehead $PROJECT startup: Checking requirements ..."
 		checkRequirements
+        sync_secrets
 		hc_send log "Bridgehead $PROJECT startup: Requirements checked out. Now starting bridgehead ..."
 		exec $COMPOSE -p $PROJECT -f ./minimal/docker-compose.yml -f ./$PROJECT/docker-compose.yml $OVERRIDE up --abort-on-container-exit
 		;;

ccp/docker-compose.yml

@@ -52,6 +52,12 @@ services:
       - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
       - /srv/docker/bridgehead/ccp/root.crt.pem:/conf/root.crt.pem:ro
 
+  traefik:
+    labels:
+      - "traefik.http.middlewares.oidcAuth.forwardAuth.address=http://oauth2_proxy:4180/"
+      - "traefik.http.middlewares.oidcAuth.forwardAuth.trustForwardHeader=true"
+      - "traefik.http.middlewares.oidcAuth.forwardAuth.authResponseHeaders=X-Auth-Request-Access-Token,Authorization"
+
 
 volumes:
   blaze-data:

ccp/modules/cbioportal-compose.yml

@@ -0,0 +1,53 @@
+version: '3.7'
+
+services:
+  cbioportal:
+    # image: docker.verbis.dkfz.de/ccp/dktk-cbioportal:latest
+    image: dktk-cbioportal
+    container_name: bridgehead-cbioportal
+    environment:
+      DB_PASSWORD: ${CBIOPORTAL_DB_PASSWORD}
+      HTTP_RELATIVE_PATH: "/cbioportal"
+      UPLOAD_HTTP_RELATIVE_PATH: "/cbioportal-upload"
+    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:
+    image: docker.verbis.dkfz.de/ccp/dktk-cbioportal-database:latest
+    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}
+    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

@@ -0,0 +1,8 @@
+#!/bin/bash -e
+
+ 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

@@ -0,0 +1,10 @@
+# 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

ccp/modules/datashield-compose.yml

@@ -0,0 +1,161 @@
+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: "${RSTUDIO_ADMIN_PASSWORD}" # It is required, even if the authentication is disabled
+      DISABLE_AUTH: "true" # https://rocker-project.org/images/versioned/rstudio.html#how-to-use
+      HTTP_RELATIVE_PATH: "/rstudio"
+      ALL_PROXY: "http://forward_proxy:3128" # https://rocker-project.org/use/networking.html
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.rstudio_ccp.rule=PathPrefix(`/rstudio`)"
+      - "traefik.http.services.rstudio_ccp.loadbalancer.server.port=8787"
+      - "traefik.http.middlewares.rstudio_ccp_strip.stripprefix.prefixes=/rstudio"
+      - "traefik.http.routers.rstudio_ccp.tls=true"
+      - "traefik.http.routers.rstudio_ccp.middlewares=oidcAuth,rstudio_ccp_strip"
+    networks:
+      - rstudio
+
+  opal:
+    container_name: bridgehead-opal
+    image: docker.verbis.dkfz.de/ccp/dktk-opal:latest
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.opal_ccp.rule=PathPrefix(`/opal`)"
+      - "traefik.http.services.opal_ccp.loadbalancer.server.port=8080"
+      - "traefik.http.routers.opal_ccp.tls=true"
+    links:
+      - opal-rserver
+      - opal-db
+    environment:
+      JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC -Dhttps.proxyHost=forward_proxy -Dhttps.proxyPort=3128"
+      # OPAL_ADMINISTRATOR_USER: "administrator" # This line is kept for informational purposes
+      OPAL_ADMINISTRATOR_PASSWORD: "${OPAL_ADMIN_PASSWORD}"
+      POSTGRESDATA_HOST: "opal-db"
+      POSTGRESDATA_DATABASE: "opal"
+      POSTGRESDATA_USER: "opal"
+      POSTGRESDATA_PASSWORD: "${OPAL_DB_PASSWORD}"
+      ROCK_HOSTS: "opal-rserver:8085"
+      APP_URL: "https://${HOST}/opal"
+      APP_CONTEXT_PATH: "/opal"
+      OPAL_PRIVATE_KEY: "/run/secrets/opal-key.pem"
+      OPAL_CERTIFICATE: "/run/secrets/opal-cert.pem"
+      KEYCLOAK_URL: "${KEYCLOAK_URL}"
+      KEYCLOAK_REALM: "${KEYCLOAK_REALM}"
+      KEYCLOAK_CLIENT_ID: "${KEYCLOAK_PRIVATE_CLIENT_ID}"
+      KEYCLOAK_CLIENT_SECRET: "${OIDC_CLIENT_SECRET}"
+      KEYCLOAK_ADMIN_GROUP: "${KEYCLOAK_ADMIN_GROUP}"
+      TOKEN_MANAGER_PASSWORD: "${TOKEN_MANAGER_OPAL_PASSWORD}"
+      EXPORTER_PASSWORD: "${EXPORTER_OPAL_PASSWORD}"
+      BEAM_APP_ID: token-manager.${PROXY_ID}
+      BEAM_SECRET: ${TOKEN_MANAGER_SECRET}
+      BEAM_DATASHIELD_PROXY: request-manager
+    volumes:
+      - "/var/cache/bridgehead/ccp/opal-metadata-db:/srv" # Opal metadata
+    secrets:
+      - opal-cert.pem
+      - opal-key.pem
+
+  opal-db:
+    container_name: bridgehead-opal-db
+    image: docker.verbis.dkfz.de/cache/postgres:15.4-alpine
+    environment:
+      POSTGRES_PASSWORD: "${OPAL_DB_PASSWORD}" # Set in datashield-setup.sh
+      POSTGRES_USER: "opal"
+      POSTGRES_DB: "opal"
+    volumes:
+      - "/var/cache/bridgehead/ccp/opal-db:/var/lib/postgresql/data" # Opal project data (imported from exporter)
+
+  opal-rserver:
+    container_name: bridgehead-opal-rserver
+    image: docker.verbis.dkfz.de/ccp/dktk-rserver # datashield/rock-base + dsCCPhos
+    tmpfs:
+      - /srv
+
+  beam-connect:
+    image: docker.verbis.dkfz.de/cache/samply/beam-connect:develop
+    container_name: bridgehead-datashield-connect
+    environment:
+      PROXY_URL: "http://beam-proxy:8081"
+      TLS_CA_CERTIFICATES_DIR: /run/secrets
+      APP_ID: datashield-connect.${SITE_ID}.${BROKER_ID}
+      PROXY_APIKEY: ${DATASHIELD_CONNECT_SECRET}
+      DISCOVERY_URL: "./map/central.json"
+      LOCAL_TARGETS_FILE: "./map/local.json"
+      NO_AUTH: "true"
+    secrets:
+      - opal-cert.pem
+    depends_on:
+      - beam-proxy
+    volumes:
+      - /tmp/bridgehead/opal-map/:/map/:ro
+    networks:
+      - default
+      - rstudio
+  
+  traefik:
+    networks:
+      - default
+      - rstudio
+  forward_proxy:
+    networks:
+      - default
+      - rstudio
+
+  beam-proxy:
+    environment:
+      APP_datashield-connect_KEY: ${DATASHIELD_CONNECT_SECRET}
+      APP_token-manager_KEY: ${TOKEN_MANAGER_SECRET}
+
+  # TODO: Allow users of group /DataSHIELD and KEYCLOAK_USER_GROUP at the same time:
+  # Maybe a solution would be (https://oauth2-proxy.github.io/oauth2-proxy/docs/configuration/overview/):
+  # --allowed-groups=/DataSHIELD,KEYCLOAK_USER_GROUP
+  oauth2_proxy:
+    image: quay.io/oauth2-proxy/oauth2-proxy
+    container_name: bridgehead_oauth2_proxy
+    command: >-
+      --allowed-group=/DataSHIELD
+      --oidc-groups-claim=${KEYCLOAK_GROUP_CLAIM}
+      --auth-logging=true
+      --whitelist-domain=${HOST}
+      --http-address="0.0.0.0:4180"
+      --reverse-proxy=true
+      --upstream="static://202"
+      --email-domain="*"
+      --cookie-name="_BRIDGEHEAD_oauth2"
+      --cookie-secret="${OAUTH2_PROXY_SECRET}"
+      --cookie-expire="12h"
+      --cookie-secure="true"
+      --cookie-httponly="true"
+      #OIDC settings
+      --provider="keycloak-oidc"
+      --provider-display-name="VerbIS Login"
+      --client-id="${KEYCLOAK_PRIVATE_CLIENT_ID}"
+      --client-secret="${OIDC_CLIENT_SECRET}"
+      --redirect-url="https://${HOST}${OAUTH2_CALLBACK}"
+      --oidc-issuer-url="${KEYCLOAK_ISSUER_URL}"
+      --scope="openid email profile"
+      --code-challenge-method="S256"
+      --skip-provider-button=true
+      #X-Forwarded-Header settings - true/false depending on your needs
+      --pass-basic-auth=true
+      --pass-user-headers=false
+      --pass-access-token=false
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.oauth2_proxy.rule=Host(`${HOST}`) && PathPrefix(`/oauth2`, `/oauth2/callback`)"
+      - "traefik.http.services.oauth2_proxy.loadbalancer.server.port=4180"
+      - "traefik.http.routers.oauth2_proxy.tls=true"
+
+secrets:
+  opal-cert.pem:
+    file: /tmp/bridgehead/opal-cert.pem
+  opal-key.pem:
+    file: /tmp/bridgehead/opal-key.pem
+
+networks:
+  rstudio:

ccp/modules/datashield-import-template.xml

@@ -0,0 +1,157 @@
+<template id="opal-ccp" source-id="blaze-store" opal-project="ccp-demo" target-id="opal" >
+
+  <container csv-filename="Patient-${TIMESTAMP}.csv" opal-table="patient" opal-entity-type="Patient">
+    <attribute csv-column="patient-id" opal-value-type="text" primary-key="true" val-fhir-path="Patient.id.value" anonym="Pat" op="EXTRACT_RELATIVE_ID"/>
+    <attribute csv-column="dktk-id-global" opal-value-type="text" val-fhir-path="Patient.identifier.where(type.coding.code = 'Global').value.value"/>
+    <attribute csv-column="dktk-id-lokal" opal-value-type="text" val-fhir-path="Patient.identifier.where(type.coding.code = 'Lokal').value.value" />
+    <attribute csv-column="geburtsdatum" opal-value-type="date" val-fhir-path="Patient.birthDate.value"/>
+    <attribute csv-column="geschlecht" opal-value-type="text" val-fhir-path="Patient.gender.value" />
+    <attribute csv-column="datum_des_letztbekannten_vitalstatus" opal-value-type="date" val-fhir-path="Observation.where(code.coding.code = '75186-7').effective.value" join-fhir-path="/Observation.where(code.coding.code = '75186-7').subject.reference.value"/>
+    <attribute csv-column="vitalstatus" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '75186-7').value.coding.code.value" join-fhir-path="/Observation.where(code.coding.code = '75186-7').subject.reference.value"/>
+    <!--fehlt in ADT2FHIR--><attribute csv-column="tod_tumorbedingt" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '68343-3').value.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.value" join-fhir-path="/Observation.where(code.coding.code = '68343-3').subject.reference.value"/>
+    <!--fehlt in ADT2FHIR--><attribute csv-column="todesursachen" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '68343-3').value.coding.where(system = 'http://dktk.dkfz.de/fhir/onco/core/CodeSystem/JNUCS').code.value" join-fhir-path="/Observation.where(code.coding.code = '68343-3').subject.reference.value"/>
+  </container>
+
+  <container csv-filename="Diagnosis-${TIMESTAMP}.csv" opal-table="diagnosis" opal-entity-type="Diagnosis">
+    <attribute csv-column="diagnosis-id" primary-key="true" opal-value-type="text" val-fhir-path="Condition.id.value" anonym="Dia" op="EXTRACT_RELATIVE_ID"/>
+    <attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="Condition.subject.reference.value" anonym="Pat"/>
+    <attribute csv-column="primaerdiagnose" opal-value-type="text" val-fhir-path="Condition.code.coding.code.value"/>
+    <attribute csv-column="tumor_diagnosedatum" opal-value-type="date" val-fhir-path="Condition.onset.value"/>
+    <attribute csv-column="primaertumor_diagnosetext" opal-value-type="text" val-fhir-path="Condition.code.text.value"/>
+    <attribute csv-column="version_des_icd-10_katalogs" opal-value-type="integer" val-fhir-path="Condition.code.coding.version.value"/>
+    <attribute csv-column="lokalisation" opal-value-type="text" val-fhir-path="Condition.bodySite.coding.where(system = 'urn:oid:2.16.840.1.113883.6.43.1').code.value"/>
+    <attribute csv-column="icd-o_katalog_topographie_version" opal-value-type="text" val-fhir-path="Condition.bodySite.coding.where(system = 'urn:oid:2.16.840.1.113883.6.43.1').version.value"/>
+    <attribute csv-column="seitenlokalisation_nach_adt-gekid" opal-value-type="text" val-fhir-path="Condition.bodySite.coding.where(system = 'http://dktk.dkfz.de/fhir/onco/core/CodeSystem/SeitenlokalisationCS').code.value"/>
+  </container>
+
+  <container csv-filename="Progress-${TIMESTAMP}.csv" opal-table="progress" opal-entity-type="Progress">
+<!--it would be better to generate a an ID, instead of extracting the ClinicalImpression id-->
+    <attribute csv-column="progress-id" primary-key="true" opal-value-type="text" val-fhir-path="ClinicalImpression.id.value" anonym="Pro" op="EXTRACT_RELATIVE_ID"/>
+    <attribute csv-column="diagnosis-id" opal-value-type="text" val-fhir-path="ClinicalImpression.problem.reference.value" anonym="Dia"/>
+    <attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="ClinicalImpression.subject.reference.value" anonym="Pat" />
+    <attribute csv-column="untersuchungs-_befunddatum_im_verlauf" opal-value-type="date" val-fhir-path="ClinicalImpression.effective.value" />
+    <!-- just for evaluation: redundant to Untersuchungs-, Befunddatum im Verlauf-->
+    <attribute csv-column="datum_lokales_oder_regionaeres_rezidiv" opal-value-type="date" val-fhir-path="Observation.where(code.coding.code = 'LA4583-6').effective.value" join-fhir-path="ClinicalImpression.finding.itemReference.reference.value" />
+    <attribute csv-column="gesamtbeurteilung_tumorstatus" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21976-6').value.coding.code.value" join-fhir-path="ClinicalImpression.finding.itemReference.reference.value"/>
+    <attribute csv-column="lokales_oder_regionaeres_rezidiv" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = 'LA4583-6').value.coding.code.value" join-fhir-path="ClinicalImpression.finding.itemReference.reference.value"/>
+    <attribute csv-column="lymphknoten-rezidiv" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = 'LA4370-8').value.coding.code.value" join-fhir-path="ClinicalImpression.finding.itemReference.reference.value" />
+    <attribute csv-column="fernmetastasen" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = 'LA4226-2').value.coding.code.value" join-fhir-path="ClinicalImpression.finding.itemReference.reference.value" />
+  </container>
+
+  <container csv-filename="Histology-${TIMESTAMP}.csv" opal-table="histology" opal-entity-type="Histology" >
+    <attribute csv-column="histology-id" primary-key="true" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '59847-4').id" anonym="His" op="EXTRACT_RELATIVE_ID"/>
+    <attribute csv-column="diagnosis-id" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '59847-4').focus.reference.value" anonym="Dia"/>
+    <attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '59847-4').subject.reference.value" anonym="Pat" />
+    <attribute csv-column="histologie_datum" opal-value-type="date" val-fhir-path="Observation.where(code.coding.code = '59847-4').effective.value"/>
+    <attribute csv-column="icd-o_katalog_morphologie_version" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '59847-4').value.coding.version.value" />
+    <attribute csv-column="morphologie" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '59847-4').value.coding.code.value"/>
+    <attribute csv-column="morphologie-freitext" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '59847-4').value.text.value"/>
+    <attribute csv-column="grading" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '59542-1').value.coding.code.value" join-fhir-path="Observation.where(code.coding.code = '59847-4').hasMember.reference.value"/>
+  </container>
+
+
+  <container csv-filename="Metastasis-${TIMESTAMP}.csv" opal-table="metastasis" opal-entity-type="Metastasis" >
+    <attribute csv-column="metastasis-id" primary-key="true" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21907-1').id" anonym="Met" op="EXTRACT_RELATIVE_ID"/>
+    <attribute csv-column="diagnosis-id" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21907-1').focus.reference.value" anonym="Dia"/>
+    <attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21907-1').subject.reference.value" anonym="Pat" />
+    <attribute csv-column="datum_fernmetastasen" opal-value-type="date" val-fhir-path="Observation.where(code.coding.code = '21907-1').effective.value"/>
+    <attribute csv-column="fernmetastasen_vorhanden" opal-value-type="boolean" val-fhir-path="Observation.where(code.coding.code = '21907-1').value.coding.code.value"/>
+    <attribute csv-column="lokalisation_fernmetastasen" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21907-1').bodySite.coding.code.value"/>
+  </container>
+
+  <container csv-filename="TNM-${TIMESTAMP}.csv" opal-table="tnm" opal-entity-type="TNM">
+    <attribute csv-column="tnm-id" primary-key="true" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').id" anonym="TNM" op="EXTRACT_RELATIVE_ID"/>
+    <attribute csv-column="diagnosis-id" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').focus.reference.value" anonym="Dia"/>
+    <attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').subject.reference.value" anonym="Pat" />
+    <attribute csv-column="datum_der_tnm_dokumentation_datum_befund" opal-value-type="date" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').effective.value"/>
+    <attribute csv-column="uicc_stadium" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').value.coding.code.value"/>
+    <attribute csv-column="tnm-t" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').component.where(code.coding.code = '21905-5' or code.coding.code = '21899-0').value.coding.code.value"/>
+    <attribute csv-column="tnm-n" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').component.where(code.coding.code = '21906-3' or code.coding.code = '21900-6').value.coding.code.value"/>
+    <attribute csv-column="tnm-m" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').component.where(code.coding.code = '21907-1' or code.coding.code = '21901-4').value.coding.code.value"/>
+    <attribute csv-column="c_p_u_preefix_t" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').component.where(code.coding.code = '21905-5' or code.coding.code = '21899-0').extension('http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Extension-TNMcpuPraefix').value.coding.code.value"/>
+    <attribute csv-column="c_p_u_preefix_n" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').component.where(code.coding.code = '21906-3' or code.coding.code = '21900-6').extension('http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Extension-TNMcpuPraefix').value.coding.code.value"/>
+    <attribute csv-column="c_p_u_preefix_m" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').component.where(code.coding.code = '21907-1' or code.coding.code = '21901-4').extension('http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Extension-TNMcpuPraefix').value.coding.code.value"/>
+    <attribute csv-column="tnm-y-symbol" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').component.where(code.coding.code = '59479-6' or code.coding.code = '59479-6').value.coding.code.value"/>
+    <attribute csv-column="tnm-r-symbol" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').component.where(code.coding.code = '21983-2' or code.coding.code = '21983-2').value.coding.code.value"/>
+    <attribute csv-column="tnm-m-symbol" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').component.where(code.coding.code = '42030-7' or code.coding.code = '42030-7').value.coding.code.value"/>
+    <!--nur bei UICC, nicht in ADT2FHIR--><attribute csv-column="tnm-version" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').value.coding.version.value"/>
+  </container>
+
+
+  <container csv-filename="System-Therapy-${TIMESTAMP}.csv" opal-table="system-therapy" opal-entity-type="SystemTherapy">
+    <attribute csv-column="system-therapy-id" primary-key="true" opal-value-type="text" val-fhir-path="MedicationStatement.id" anonym="Sys" op="EXTRACT_RELATIVE_ID"/>
+    <attribute csv-column="diagnosis-id" opal-value-type="text" val-fhir-path="MedicationStatement.reasonReference.reference.value" anonym="Dia"/>
+    <attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="MedicationStatement.subject.reference.value" anonym="Pat" />
+    <attribute csv-column="systemische_therapie_stellung_zu_operativer_therapie" opal-value-type="text" val-fhir-path="MedicationStatement.extension('http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Extension-StellungZurOp').value.coding.code.value"/>
+    <attribute csv-column="intention_chemotherapie" opal-value-type="text" val-fhir-path="MedicationStatement.extension('http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Extension-SYSTIntention').value.coding.code.value"/>
+    <attribute csv-column="therapieart" opal-value-type="text" val-fhir-path="MedicationStatement.category.coding.code.value"/>
+    <attribute csv-column="systemische_therapie_beginn" opal-value-type="date" val-fhir-path="MedicationStatement.effective.start.value"/>
+    <attribute csv-column="systemische_therapie_ende" opal-value-type="date" val-fhir-path="MedicationStatement.effective.end.value"/>
+    <attribute csv-column="systemische_therapie_protokoll" opal-value-type="text" val-fhir-path="MedicationStatement.extension('http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Extension-SystemischeTherapieProtokoll').value.text.value"/>
+    <attribute csv-column="systemische_therapie_substanzen" opal-value-type="text" val-fhir-path="MedicationStatement.medication.text.value"/>
+    <attribute csv-column="chemotherapie" opal-value-type="boolean" val-fhir-path="MedicationStatement.where(category.coding.code = 'CH').exists().value" />
+    <attribute csv-column="hormontherapie" opal-value-type="boolean" val-fhir-path="MedicationStatement.where(category.coding.code = 'HO').exists().value" />
+    <attribute csv-column="immuntherapie" opal-value-type="boolean" val-fhir-path="MedicationStatement.where(category.coding.code = 'IM').exists().value" />
+    <attribute csv-column="knochenmarktransplantation" opal-value-type="boolean" val-fhir-path="MedicationStatement.where(category.coding.code = 'KM').exists().value" />
+    <attribute csv-column="abwartende_strategie" opal-value-type="boolean" val-fhir-path="MedicationStatement.where(category.coding.code = 'WS').exists().value" />
+  </container>
+
+
+  <container csv-filename="Surgery-${TIMESTAMP}.csv" opal-table="surgery" opal-entity-type="Surgery">
+    <attribute csv-column="surgery-id" primary-key="true" opal-value-type="text" val-fhir-path="Procedure.where(category.coding.code = 'OP').id" anonym="Sur" op="EXTRACT_RELATIVE_ID"/>
+    <attribute csv-column="diagnosis-id" opal-value-type="text" val-fhir-path="Procedure.where(category.coding.code = 'OP').reasonReference.reference.value" anonym="Dia"/>
+    <attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="Procedure.where(category.coding.code = 'OP').subject.reference.value" anonym="Pat" />
+    <attribute csv-column="ops-code" opal-value-type="text" val-fhir-path="Procedure.where(category.coding.code = 'OP').code.coding.code.value"/>
+    <attribute csv-column="datum_der_op" opal-value-type="date" val-fhir-path="Procedure.where(category.coding.code = 'OP').performed.value"/>
+    <attribute csv-column="intention_op" opal-value-type="text" val-fhir-path="Procedure.extension('http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Extension-OPIntention').value.coding.code.value"/>
+    <attribute csv-column="lokale_beurteilung_resttumor" opal-value-type="text" val-fhir-path="Procedure.where(category.coding.code = 'OP').outcome.coding.where(system = 'http://dktk.dkfz.de/fhir/onco/core/CodeSystem/LokaleBeurteilungResidualstatusCS').code.value" />
+    <attribute csv-column="gesamtbeurteilung_resttumor" opal-value-type="text" val-fhir-path="Procedure.where(category.coding.code = 'OP').outcome.coding.where(system = 'http://dktk.dkfz.de/fhir/onco/core/CodeSystem/GesamtbeurteilungResidualstatusCS').code.value"  />
+  </container>
+
+
+  <container csv-filename="Radiation-Therapy-${TIMESTAMP}.csv" opal-table="radiation-therapy" opal-entity-type="RadiationTherapy">
+    <attribute csv-column="radiation-therapy-id" primary-key="true" opal-value-type="text" val-fhir-path="Procedure.where(category.coding.code = 'ST').id" anonym="Rad" op="EXTRACT_RELATIVE_ID"/>
+    <attribute csv-column="diagnosis-id" opal-value-type="text" val-fhir-path="Procedure.where(category.coding.code = 'ST').reasonReference.reference.value" anonym="Dia"/>
+    <attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="Procedure.where(category.coding.code = 'ST').subject.reference.value" anonym="Pat" />
+    <attribute csv-column="strahlentherapie_stellung_zu_operativer_therapie" opal-value-type="text" val-fhir-path="Procedure.extension('http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Extension-StellungZurOp').value.coding.code.value"/>
+    <attribute csv-column="intention_strahlentherapie" opal-value-type="text" val-fhir-path="Procedure.extension('http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Extension-SYSTIntention').value.coding.code.value" />
+    <attribute csv-column="strahlentherapie_beginn" opal-value-type="date" val-fhir-path="Procedure.where(category.coding.code = 'ST').performed.start.value"/>
+    <attribute csv-column="strahlentherapie_ende" opal-value-type="date" val-fhir-path="Procedure.where(category.coding.code = 'ST').performed.end.value"/>
+  </container>
+
+
+  <container csv-filename="Molecular-Marker-${TIMESTAMP}.csv" opal-table="molecular-marker" opal-entity-type="MolecularMarker">
+    <attribute csv-column="mol-marker-id" primary-key="true" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '69548-6').id" anonym="Mol" op="EXTRACT_RELATIVE_ID"/>
+    <attribute csv-column="diagnosis-id" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '69548-6').focus.reference.value" anonym="Dia" />
+    <attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '69548-6').subject.reference.value" anonym="Pat" />
+    <attribute csv-column="datum_der_datenerhebung" opal-value-type="date" val-fhir-path="Observation.where(code.coding.code = '69548-6').effective.value"/>
+    <attribute csv-column="marker" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '69548-6').component.value.coding.code.value"/>
+    <attribute csv-column="status_des_molekularen_markers" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '69548-6').value.coding.code.value" />
+    <attribute csv-column="zusaetzliche_alternative_dokumentation" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '69548-6').value.text.value"/>
+  </container>
+
+
+  <container csv-filename="Sample-${TIMESTAMP}.csv" opal-table="sample" opal-entity-type="Sample">
+    <attribute csv-column="sample-id" primary-key="true" opal-value-type="text" val-fhir-path="Specimen.id" anonym="Sam" op="EXTRACT_RELATIVE_ID"/>
+    <attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="Specimen.subject.reference.value" anonym="Pat" />
+    <attribute csv-column="entnahmedatum" opal-value-type="date" val-fhir-path="Specimen.collection.collectedDateTime.value"/>
+    <attribute csv-column="probenart" opal-value-type="text" val-fhir-path="Specimen.type.coding.code.value"/>
+    <attribute csv-column="status" opal-value-type="text" val-fhir-path="Specimen.status.code.value"/>
+    <attribute csv-column="projekt" opal-value-type="text" val-fhir-path="Specimen.identifier.system.value"/>
+   <!-- @TODO: it is still necessary to clarify whether it would not be better to take the quantity of collection.quantity -->
+    <attribute csv-column="menge" opal-value-type="integer" val-fhir-path="Specimen.container.specimenQuantity.value.value"/>
+    <attribute csv-column="einheit" opal-value-type="text" val-fhir-path="Specimen.container.specimenQuantity.unit.value"/>
+    <attribute csv-column="aliquot" opal-value-type="text" val-fhir-path="Specimen.parent.reference.exists().value" />
+  </container>
+
+
+
+
+  <fhir-rev-include>Observation:patient</fhir-rev-include>
+  <fhir-rev-include>Condition:patient</fhir-rev-include>
+  <fhir-rev-include>ClinicalImpression:patient</fhir-rev-include>
+  <fhir-rev-include>MedicationStatement:patient</fhir-rev-include>
+  <fhir-rev-include>Procedure:patient</fhir-rev-include>
+  <fhir-rev-include>Specimen:patient</fhir-rev-include>
+
+</template>

ccp/modules/datashield-mappings.json

@@ -0,0 +1,13 @@
+[
+    "berlin",
+    "muenchen-lmu",
+    "dresden",
+    "freiburg",
+    "muenchen-tum",
+    "tuebingen",
+    "mainz",
+    "frankfurt",
+    "essen",
+    "dktk-datashield-test",
+    "dktk-test"
+]

ccp/modules/datashield-setup.sh

@@ -0,0 +1,33 @@
+#!/bin/bash -e
+
+if [ "$ENABLE_DATASHIELD" == true ]; then
+  log INFO "DataSHIELD setup detected -- will start DataSHIELD services."
+  OVERRIDE+=" -f ./$PROJECT/modules/datashield-compose.yml"
+  EXPORTER_OPAL_PASSWORD="$(generate_password \"exporter in Opal\")"
+  TOKEN_MANAGER_OPAL_PASSWORD="$(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
+    mkdir -p /tmp/bridgehead/
+    chown -R bridgehead:docker /tmp/bridgehead/
+    openssl req -x509 -newkey rsa:4096 -nodes -keyout /tmp/bridgehead/opal-key.pem -out /tmp/bridgehead/opal-cert.pem -days 3650 -subj "/CN=opal/C=DE"
+    chmod g+r /tmp/bridgehead/opal-key.pem
+  fi
+  mkdir -p /tmp/bridgehead/opal-map
+  jq -n '{"sites": input | map({
+    "name": .,
+    "id": .,
+    "virtualhost": "\(.):443",
+    "beamconnect": "datashield-connect.\(.).'"$BROKER_ID"'"
+  })}' ./$PROJECT/modules/datashield-mappings.json > /tmp/bridgehead/opal-map/central.json
+  jq -n '[{
+    "external": "'"$SITE_ID"':443",
+    "internal": "opal:8443",
+    "allowed": input | map("datashield-connect.\(.).'"$BROKER_ID"'")
+  }]' ./$PROJECT/modules/datashield-mappings.json > /tmp/bridgehead/opal-map/local.json
+  chown -R bridgehead:docker /tmp/bridgehead/
+  add_private_oidc_redirect_url "/opal/*"
+fi

ccp/modules/datashield.md

@@ -0,0 +1,28 @@
+# DataSHIELD
+This module constitutes the infrastructure to run DataSHIELD within the bridghead. 
+For more information about DataSHIELD, please visit https://www.datashield.org/
+
+## R-Studio
+To connect to the different bridgeheads of the CCP through DataSHIELD, you can use your own R-Studio environment.
+However, this R-Studio has already installed the DataSHIELD libraries and is integrated within the bridgehead.
+This can save you some time for extra configuration of your R-Studio environment.
+
+## Opal
+This is the core of DataSHIELD. It is made up of Opal, a Postgres database and an R-server.
+For more information about Opal, please visit https://opaldoc.obiba.org
+
+### Opal
+Opal is OBiBa’s core database application for biobanks. 
+
+### Opal-DB
+Opal requires a database to import the data for DataSHIELD. We use a Postgres instance as database. 
+The data is imported within the bridgehead through the exporter.
+
+### Opal-R-Server
+R-Server to execute R scripts in DataSHIELD.
+
+## Beam
+### Beam-Connect
+Beam-Connect is used to route http(s) traffic through beam to enable R-Studio to access data from other bridgeheads that have datashield enabled.
+### Beam-Proxy
+The usual beam proxy used for communication.

ccp/modules/dnpm-compose.yml

@@ -16,9 +16,11 @@ services:
       LOCAL_TARGETS_FILE: "./conf/connect_targets.json"
       HTTP_PROXY: "http://forward_proxy:3128"
       HTTPS_PROXY: "http://forward_proxy:3128"
-      NO_PROXY: beam-proxy,dnpm-backend
+      NO_PROXY: beam-proxy,dnpm-backend,host.docker.internal
       RUST_LOG: ${RUST_LOG:-info}
       NO_AUTH: "true"
+    extra_hosts:
+      - "host.docker.internal:host-gateway"
     volumes:
       - /etc/bridgehead/dnpm/local_targets.json:/conf/connect_targets.json:ro
       - /etc/bridgehead/dnpm/central_targets.json:/conf/central_targets.json:ro

ccp/modules/dnpm-node-compose.yml

@@ -0,0 +1,33 @@
+version: "3.7"
+
+services:
+  dnpm-backend:
+    image: ghcr.io/kohlbacherlab/bwhc-backend:1.0-snapshot-broker-connector
+    container_name: bridgehead-dnpm-backend
+    environment:
+      - ZPM_SITE=${ZPM_SITE}
+    volumes:
+      - /etc/bridgehead/dnpm:/bwhc_config:ro
+      - ${DNPM_DATA_DIR}:/bwhc_data
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.bwhc-backend.rule=PathPrefix(`/bwhc`)"
+      - "traefik.http.services.bwhc-backend.loadbalancer.server.port=9000"
+      - "traefik.http.routers.bwhc-backend.tls=true"
+
+  dnpm-frontend:
+    image: ghcr.io/kohlbacherlab/bwhc-frontend:2209
+    container_name: bridgehead-dnpm-frontend
+    links:
+      - dnpm-backend
+    environment:
+      - NUXT_HOST=0.0.0.0
+      - NUXT_PORT=8080
+      - BACKEND_PROTOCOL=https
+      - BACKEND_HOSTNAME=$HOST
+      - BACKEND_PORT=443
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.bwhc-frontend.rule=PathPrefix(`/`)"
+      - "traefik.http.services.bwhc-frontend.loadbalancer.server.port=8080"
+      - "traefik.http.routers.bwhc-frontend.tls=true"

ccp/modules/dnpm-node-setup.sh

@@ -0,0 +1,27 @@
+#!/bin/bash
+
+if [ -n "${ENABLE_DNPM_NODE}" ]; then
+	log INFO "DNPM setup detected (BwHC Node) -- will start BwHC node."
+	OVERRIDE+=" -f ./$PROJECT/modules/dnpm-node-compose.yml"
+
+	# Set variables required for BwHC Node. ZPM_SITE is assumed to be set in /etc/bridgehead/<project>.conf
+	DNPM_APPLICATION_SECRET="$(echo \"This is a salt string to generate one consistent password for DNPM. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
+	if [ -z "${ZPM_SITE+x}" ]; then
+		log ERROR "Mandatory variable ZPM_SITE not defined!"
+		exit 1
+	fi
+	if [ -z "${DNPM_DATA_DIR+x}" ]; then
+		log ERROR "Mandatory variable DNPM_DATA_DIR not defined!"
+		exit 1
+	fi
+			if grep -q 'traefik.http.routers.landing.rule=PathPrefix(`/landing`)' /srv/docker/bridgehead/minimal/docker-compose.override.yml 2>/dev/null; then
+				echo "Override of landing page url already in place"
+			else
+				echo "Adding override of landing page url"
+				if [ -f /srv/docker/bridgehead/minimal/docker-compose.override.yml ]; then
+					echo -e '  landing:\n    labels:\n      - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"' >> /srv/docker/bridgehead/minimal/docker-compose.override.yml
+				else
+					echo -e 'version: "3.7"\nservices:\n  landing:\n    labels:\n      - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"' >> /srv/docker/bridgehead/minimal/docker-compose.override.yml
+				fi
+			fi
+fi

ccp/modules/dnpm-setup.sh

@@ -1,10 +1,9 @@
-#!/bin/bash
+#!/bin/bash -e
 
 if [ -n "${ENABLE_DNPM}" ]; then
 	log INFO "DNPM setup detected (Beam.Connect) -- will start Beam.Connect for DNPM."
 	OVERRIDE+=" -f ./$PROJECT/modules/dnpm-compose.yml"
 
 	# Set variables required for Beam-Connect
-	DNPM_APPLICATION_SECRET="$(echo \"This is a salt string to generate one consistent password for DNPM. It is not required to be secret.\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
 	DNPM_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
 fi

ccp/modules/export-and-qb.curl-templates

@@ -0,0 +1,6 @@
+# Full Excel Export
+curl --location --request POST 'https://${HOST}/ccp-exporter/request?query=Patient&query-format=FHIR_PATH&template-id=ccp&output-format=EXCEL' \
+--header 'x-api-key: ${EXPORT_API_KEY}'
+
+# QB
+curl --location --request POST 'https://${HOST}/ccp-reporter/generate?template-id=ccp'

ccp/modules/exporter-compose.yml

@@ -0,0 +1,67 @@
+version: "3.7"
+
+services:
+  exporter:
+    image: docker.verbis.dkfz.de/ccp/dktk-exporter:latest
+    container_name: bridgehead-ccp-exporter
+    environment:
+      JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
+      LOG_LEVEL: "INFO"
+      EXPORTER_API_KEY: "${EXPORTER_API_KEY}" # Set in exporter-setup.sh
+      CROSS_ORIGINS: "https://${HOST}"
+      EXPORTER_DB_USER: "exporter"
+      EXPORTER_DB_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
+      EXPORTER_DB_URL: "jdbc:postgresql://exporter-db:5432/exporter"
+      HTTP_RELATIVE_PATH: "/ccp-exporter"
+      SITE: "${SITE_ID}"
+      HTTP_SERVLET_REQUEST_SCHEME: "https"
+      OPAL_PASSWORD: "${EXPORTER_OPAL_PASSWORD}"
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.exporter_ccp.rule=PathPrefix(`/ccp-exporter`)"
+      - "traefik.http.services.exporter_ccp.loadbalancer.server.port=8092"
+      - "traefik.http.routers.exporter_ccp.tls=true"
+      - "traefik.http.middlewares.exporter_ccp_strip.stripprefix.prefixes=/ccp-exporter"
+      - "traefik.http.routers.exporter_ccp.middlewares=exporter_ccp_strip"
+    volumes:
+      - "/var/cache/bridgehead/ccp/exporter-files:/app/exporter-files/output"
+
+  exporter-db:
+    image: docker.verbis.dkfz.de/cache/postgres:15.4-alpine
+    container_name: bridgehead-ccp-exporter-db
+    environment:
+      POSTGRES_USER: "exporter"
+      POSTGRES_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
+      POSTGRES_DB: "exporter"
+    volumes:
+      # Consider removing this volume once we find a solution to save Lens-queries to be executed in the explorer.
+      - "/var/cache/bridgehead/ccp/exporter-db:/var/lib/postgresql/data"
+
+  reporter:
+    image: docker.verbis.dkfz.de/ccp/dktk-reporter:latest
+    container_name: bridgehead-ccp-reporter
+    environment:
+      JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
+      LOG_LEVEL: "INFO"
+      CROSS_ORIGINS: "https://${HOST}"
+      HTTP_RELATIVE_PATH: "/ccp-reporter"
+      SITE: "${SITE_ID}"
+      EXPORTER_API_KEY: "${EXPORTER_API_KEY}" # Set in exporter-setup.sh
+      EXPORTER_URL: "http://exporter:8092"
+      LOG_FHIR_VALIDATION: "false"
+      HTTP_SERVLET_REQUEST_SCHEME: "https"
+
+    # In this initial development state of the bridgehead, we are trying to have so many volumes as possible.
+    # However, in the first executions in the CCP sites, this volume seems to be very important. A report is
+    # a process that can take several hours, because it depends on the exporter.
+    # There is a risk that the bridgehead restarts, losing the already created export.
+
+    volumes:
+      - "/var/cache/bridgehead/ccp/reporter-files:/app/reports"
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.reporter_ccp.rule=PathPrefix(`/ccp-reporter`)"
+      - "traefik.http.services.reporter_ccp.loadbalancer.server.port=8095"
+      - "traefik.http.routers.reporter_ccp.tls=true"
+      - "traefik.http.middlewares.reporter_ccp_strip.stripprefix.prefixes=/ccp-reporter"
+      - "traefik.http.routers.reporter_ccp.middlewares=reporter_ccp_strip"

ccp/modules/exporter-setup.sh

@@ -0,0 +1,8 @@
+#!/bin/bash -e
+
+if [ "$ENABLE_EXPORTER" == true ]; then
+  log INFO "Exporter setup detected -- will start Exporter service."
+  OVERRIDE+=" -f ./$PROJECT/modules/exporter-compose.yml"
+  EXPORTER_DB_PASSWORD="$(echo \"This is a salt string to generate one consistent password for the exporter. It is not required to be secret.\" | openssl rsautl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
+  EXPORTER_API_KEY="$(echo \"This is a salt string to generate one consistent API KEY for the exporter. It is not required to be secret.\" | openssl rsautl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 64)"
+fi

ccp/modules/exporter.md

@@ -0,0 +1,15 @@
+# Exporter and Reporter
+
+
+## Exporter
+The exporter is a REST API that exports the data of the different databases of the bridgehead in a set of tables.
+It can accept different output formats as CSV, Excel, JSON or XML. It can also export data into Opal.
+
+## Exporter-DB
+It is a database to save queries for its execution in the exporter. 
+The exporter manages also the different executions of the same query in through the database.
+
+## Reporter
+This component is a plugin of the exporter that allows to create more complex Excel reports described in templates.
+It is compatible with different template engines as Groovy, Thymeleaf,...
+It is perfect to generate a document as our traditional CCP quality report.

ccp/modules/id-management-compose.yml

@@ -1,4 +1,5 @@
 version: "3.7"
+
 services:
   id-manager:
     image: docker.verbis.dkfz.de/bridgehead/magicpl
@@ -43,7 +44,7 @@ services:
       - patientlist-db
 
   patientlist-db:
-    image: docker.verbis.dkfz.de/cache/postgres:15.4-alpine
+    image: docker.verbis.dkfz.de/cache/postgres:15.6-alpine
     container_name: bridgehead-patientlist-db
     environment:
       POSTGRES_USER: "mainzelliste"

ccp/modules/id-management-setup.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/bin/bash -e
 
 function idManagementSetup() {
 	if [ -n "$IDMANAGER_UPLOAD_APIKEY" ]; then

ccp/modules/login-compose.yml

@@ -0,0 +1,47 @@
+version: "3.7"
+
+services:
+
+  login-db:
+    image: docker.verbis.dkfz.de/cache/postgres:15.4-alpine
+    container_name: bridgehead-login-db
+    environment:
+      POSTGRES_USER: "keycloak"
+      POSTGRES_PASSWORD: "${KEYCLOAK_DB_PASSWORD}" # Set in login-setup.sh
+      POSTGRES_DB: "keycloak"
+    tmpfs:
+      - /var/lib/postgresql/data
+# Consider removing this comment once we have collected experience in production.
+#    volumes:
+#      - "bridgehead-login-db:/var/lib/postgresql/data"
+
+  login:
+    image: docker.verbis.dkfz.de/ccp/dktk-keycloak:latest
+    container_name: bridgehead-login
+    environment:
+      KEYCLOAK_ADMIN: "admin"
+      KEYCLOAK_ADMIN_PASSWORD: "${LDM_AUTH}"
+      TEILER_ADMIN: "${PROJECT}"
+      TEILER_ADMIN_PASSWORD: "${LDM_AUTH}"
+      TEILER_ADMIN_FIRST_NAME: "${OPERATOR_FIRST_NAME}"
+      TEILER_ADMIN_LAST_NAME: "${OPERATOR_LAST_NAME}"
+      TEILER_ADMIN_EMAIL: "${OPERATOR_EMAIL}"
+      KC_DB_PASSWORD: "${KEYCLOAK_DB_PASSWORD}" # Set in login-setup.sh
+      KC_HOSTNAME_URL: "https://${HOST}/login"
+      KC_HOSTNAME_STRICT: "false"
+      KC_PROXY_ADDRESS_FORWARDING: "true"
+      TEILER_ORCHESTRATOR_EXTERN_URL: "https://${HOST}/ccp-teiler"
+    command:
+      - start-dev --import-realm --proxy edge --http-relative-path=/login
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.login.rule=PathPrefix(`/login`)"
+      - "traefik.http.services.login.loadbalancer.server.port=8080"
+      - "traefik.http.routers.login.tls=true"
+    depends_on:
+      - login-db
+
+# Consider removing this comment once we have collected experience in production.
+#volumes:
+#  bridgehead-login-db:
+#    name: "bridgehead-login-db"

ccp/modules/login-setup.sh

@@ -0,0 +1,7 @@
+#!/bin/bash -e
+
+if [ "$ENABLE_LOGIN" == true ]; then
+  log INFO "Login setup detected -- will start Login services."
+  OVERRIDE+=" -f ./$PROJECT/modules/login-compose.yml"
+  KEYCLOAK_DB_PASSWORD="$(generate_password \"local Keycloak\")"
+fi

ccp/modules/login.md

@@ -0,0 +1,13 @@
+# Login
+The login component is a local Keycloak instance. In the future will be replaced by the central keycloak instance
+or maybe can be used to add local identity providers to the bridgehead or just to simplify the configuration of
+the central keycloak instance for the integration of every new bridgehead.
+The basic configuration of our Keycloak instance is contained in a small json file.
+
+### Teiler User
+Currently, the local keycloak is used by the teiler. There is a basic admin user in the basic configuration of keycloak.
+The user can be configured with the environment variables TEILER_ADMIN_XXX.
+
+## Login-DB
+Keycloak requires a local database for its configuration. However, as we use an initial json configuration file, if no
+local identity provider is configured nor any local user, theoretically we don't need a volume for the login.

ccp/modules/mtba-compose.yml

@@ -2,7 +2,8 @@ version: "3.7"
 
 services:
   mtba:
-    image: docker.verbis.dkfz.de/cache/samply/mtba:latest
+    #image: docker.verbis.dkfz.de/cache/samply/mtba:latest
+    image: docker.verbis.dkfz.de/cache/samply/mtba:develop
     container_name: bridgehead-mtba
     environment:
       BLAZE_STORE_URL: http://blaze:8080
@@ -11,22 +12,30 @@ services:
       ID_MANAGER_API_KEY: ${IDMANAGER_UPLOAD_APIKEY}
       ID_MANAGER_PSEUDONYM_ID_TYPE: BK_${IDMANAGEMENT_FRIENDLY_ID}_L-ID
       ID_MANAGER_URL: http://id-manager:8080/id-manager
-      PATIENT_CSV_FIRST_NAME_HEADER: ${MTBA_PATIENT_CSV_FIRST_NAME_HEADER}
-      PATIENT_CSV_LAST_NAME_HEADER: ${MTBA_PATIENT_CSV_LAST_NAME_HEADER}
-      PATIENT_CSV_GENDER_HEADER: ${MTBA_PATIENT_CSV_GENDER_HEADER}
-      PATIENT_CSV_BIRTHDAY_HEADER: ${MTBA_PATIENT_CSV_BIRTHDAY_HEADER}
+      PATIENT_CSV_FIRST_NAME_HEADER: ${MTBA_PATIENT_CSV_FIRST_NAME_HEADER:-FIRST_NAME}
+      PATIENT_CSV_LAST_NAME_HEADER: ${MTBA_PATIENT_CSV_LAST_NAME_HEADER:-LAST_NAME}
+      PATIENT_CSV_GENDER_HEADER: ${MTBA_PATIENT_CSV_GENDER_HEADER:-GENDER}
+      PATIENT_CSV_BIRTHDAY_HEADER: ${MTBA_PATIENT_CSV_BIRTHDAY_HEADER:-BIRTHDAY}
       CBIOPORTAL_URL:  http://cbioportal:8080
-      FILE_CHARSET: ${MTBA_FILE_CHARSET}
-      FILE_END_OF_LINE: ${MTBA_FILE_END_OF_LINE}
-      CSV_DELIMITER: ${MTBA_CSV_DELIMITER}
+      FILE_CHARSET: ${MTBA_FILE_CHARSET:-UTF-8}
+      FILE_END_OF_LINE: ${MTBA_FILE_END_OF_LINE:-LF}
+      CSV_DELIMITER: ${MTBA_CSV_DELIMITER:-TAB}
+      HTTP_RELATIVE_PATH: "/mtba"
+      KEYCLOAK_ADMIN_GROUP: "${KEYCLOAK_ADMIN_GROUP}"
+      KEYCLOAK_CLIENT_ID: "${KEYCLOAK_PRIVATE_CLIENT_ID}"
+      KEYCLOAK_CLIENT_SECRET: "${OIDC_CLIENT_SECRET}"
+      KEYCLOAK_REALM: "${KEYCLOAK_REALM}"
+      KEYCLOAK_URL: "${KEYCLOAK_URL}"
+
     labels:
       - "traefik.enable=true"
-      - "traefik.http.routers.mtba.rule=PathPrefix(`/`)"
-      - "traefik.http.services.mtba.loadbalancer.server.port=80"
-      - "traefik.http.routers.mtba.tls=true"
+      - "traefik.http.routers.mtba_ccp.rule=PathPrefix(`/mtba`)"
+      - "traefik.http.services.mtba_ccp.loadbalancer.server.port=8480"
+      - "traefik.http.routers.mtba_ccp.tls=true"
+
     volumes:
-      - /tmp/bridgehead/mtba/input:/app/input
-      - /tmp/bridgehead/mtba/persist:/app/persist
+      - /var/cache/bridgehead/ccp/mtba/input:/app/input
+      - /var/cache/bridgehead/ccp/mtba/persist:/app/persist
 
   # TODO: Include CBioPortal in Deployment ...
   # NOTE: CBioPortal can't load data while the system is running. So after import of data bridgehead needs to be restarted!

ccp/modules/mtba-setup.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/bin/bash -e
 
 function mtbaSetup() {
   if [ -n "$ENABLE_MTBA" ];then
@@ -8,5 +8,6 @@ function mtbaSetup() {
       exit 1;
     fi
     OVERRIDE+=" -f ./$PROJECT/modules/mtba-compose.yml"
+    add_private_oidc_redirect_url "/mtba/*"
   fi
-}
+}

ccp/modules/mtba.md

@@ -0,0 +1,6 @@
+# Molecular Tumor Board Alliance (MTBA)
+
+In this module, the genetic data to import is stored in a directory (/tmp/bridgehead/mtba/input). A process checks
+regularly if there are files in the directory. The files are pseudonomized when the IDAT is provided. The files are
+combined with clinical data of the blaze and imported in cBioPortal. On the other hand, this files are also imported in
+Blaze.

ccp/modules/nngm-compose.yml

@@ -1,4 +1,5 @@
 version: "3.7"
+
 volumes:
   nngm-rest:
 
@@ -21,9 +22,6 @@ services:
       - "traefik.http.routers.connector.middlewares=connector_strip,auth-nngm"
     volumes:
       - nngm-rest:/var/log
-
   traefik:
     labels:
       - "traefik.http.middlewares.auth-nngm.basicauth.users=${NNGM_AUTH}"
-
-

ccp/modules/nngm-setup.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/bin/bash -e
 
 if [ -n "$NNGM_CTS_APIKEY" ]; then
   log INFO "nNGM setup detected -- will start nNGM Connector."

ccp/modules/teiler-compose.yml

@@ -0,0 +1,82 @@
+version: "3.7"
+
+services:
+
+  teiler-orchestrator:
+    image: docker.verbis.dkfz.de/cache/samply/teiler-orchestrator:latest
+    container_name: bridgehead-teiler-orchestrator
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.teiler_orchestrator_ccp.rule=PathPrefix(`/ccp-teiler`)"
+      - "traefik.http.services.teiler_orchestrator_ccp.loadbalancer.server.port=9000"
+      - "traefik.http.routers.teiler_orchestrator_ccp.tls=true"
+      - "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://${HOST}/ccp-teiler-backend"
+      TEILER_DASHBOARD_URL: "https://${HOST}/ccp-teiler-dashboard"
+      DEFAULT_LANGUAGE: "${DEFAULT_LANGUAGE_LOWER_CASE}"
+      HTTP_RELATIVE_PATH: "/ccp-teiler"
+
+  teiler-dashboard:
+    image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:latest
+    container_name: bridgehead-teiler-dashboard
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.teiler_dashboard_ccp.rule=PathPrefix(`/ccp-teiler-dashboard`)"
+      - "traefik.http.services.teiler_dashboard_ccp.loadbalancer.server.port=80"
+      - "traefik.http.routers.teiler_dashboard_ccp.tls=true"
+      - "traefik.http.middlewares.teiler_dashboard_ccp_strip.stripprefix.prefixes=/ccp-teiler-dashboard"
+      - "traefik.http.routers.teiler_dashboard_ccp.middlewares=teiler_dashboard_ccp_strip"
+    environment:
+      DEFAULT_LANGUAGE: "${DEFAULT_LANGUAGE}"
+      TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend"
+      KEYCLOAK_URL: "${KEYCLOAK_URL}"
+      KEYCLOAK_REALM: "${KEYCLOAK_REALM}"
+      KEYCLOAK_CLIENT_ID: "${KEYCLOAK_PUBLIC_CLIENT_ID}"
+      KEYCLOAK_TOKEN_GROUP: "${KEYCLOAK_GROUP_CLAIM}"
+      TEILER_ADMIN_NAME: "${OPERATOR_FIRST_NAME} ${OPERATOR_LAST_NAME}"
+      TEILER_ADMIN_EMAIL: "${OPERATOR_EMAIL}"
+      TEILER_ADMIN_PHONE: "${OPERATOR_PHONE}"
+      TEILER_PROJECT: "${PROJECT}"
+      EXPORTER_API_KEY: "${EXPORTER_API_KEY}"
+      TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler"
+      TEILER_DASHBOARD_HTTP_RELATIVE_PATH: "/ccp-teiler-dashboard"
+      TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler"
+      TEILER_USER: "${KEYCLOAK_USER_GROUP}"
+      TEILER_ADMIN: "${KEYCLOAK_ADMIN_GROUP}"
+      REPORTER_DEFAULT_TEMPLATE_ID: "ccp-qb"
+      EXPORTER_DEFAULT_TEMPLATE_ID: "ccp"
+
+
+  teiler-backend:
+    # image: docker.verbis.dkfz.de/ccp/dktk-teiler-backend:latest
+    image: dktk-teiler-backend
+    container_name: bridgehead-teiler-backend
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.teiler_backend_ccp.rule=PathPrefix(`/ccp-teiler-backend`)"
+      - "traefik.http.services.teiler_backend_ccp.loadbalancer.server.port=8085"
+      - "traefik.http.routers.teiler_backend_ccp.tls=true"
+      - "traefik.http.middlewares.teiler_backend_ccp_strip.stripprefix.prefixes=/ccp-teiler-backend"
+      - "traefik.http.routers.teiler_backend_ccp.middlewares=teiler_backend_ccp_strip"
+    environment:
+      LOG_LEVEL: "INFO"
+      APPLICATION_PORT: "8085"
+      APPLICATION_ADDRESS: "${HOST}"
+      DEFAULT_LANGUAGE: "${DEFAULT_LANGUAGE}"
+      CONFIG_ENV_VAR_PATH: "/run/secrets/ccp.conf"
+      TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler"
+      TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler"
+      TEILER_DASHBOARD_DE_URL: "https://${HOST}/ccp-teiler-dashboard/de"
+      TEILER_DASHBOARD_EN_URL: "https://${HOST}/ccp-teiler-dashboard/en"
+      CENTRAX_URL: "${CENTRAXX_URL}"
+      HTTP_PROXY: "http://forward_proxy:3128"
+      ENABLE_MTBA: "${ENABLE_MTBA}"
+      ENABLE_DATASHIELD: "${ENABLE_DATASHIELD}"
+    secrets:
+      - ccp.conf
+
+secrets:
+  ccp.conf:
+    file: /etc/bridgehead/ccp.conf

ccp/modules/teiler-setup.sh

@@ -0,0 +1,7 @@
+#!/bin/bash -e
+
+if [ "$ENABLE_TEILER" == true ];then
+  log INFO "Teiler setup detected -- will start Teiler services."
+  OVERRIDE+=" -f ./$PROJECT/modules/teiler-compose.yml"
+  add_public_oidc_redirect_url "/ccp-teiler/*"
+fi

ccp/modules/teiler.md

@@ -0,0 +1,19 @@
+# Teiler
+This module orchestrates the different microfrontends of the bridgehead as a single page application.  
+
+## Teiler Orchestrator
+Single SPA component that consists on the root HTML site of the single page application and a javascript code that
+gets the information about the microfrontend calling the teiler backend and is responsible for registering them. With the
+resulting mapping, it can initialize, mount and unmount the required microfrontends on the fly. 
+
+The microfrontends run independently in different containers and can be based on different frameworks (Angular, Vue, React,...)
+This microfrontends can run as single alone but need an extension with Single-SPA (https://single-spa.js.org/docs/ecosystem).
+There are also available three templates (Angular, Vue, React) to be directly extended to be used directly in the teiler.
+
+## Teiler Dashboard
+It consists on the main dashboard and a set of embedded services.
+### Login
+user and password in ccp.local.conf
+
+## Teiler Backend
+In this component, the microfrontends are configured.

ccp/root-new.crt.pem

@@ -1,20 +0,0 @@
------BEGIN CERTIFICATE-----
-MIIDNTCCAh2gAwIBAgIUN7yzueIZzwpe8PaPEIMY8zoH+eMwDQYJKoZIhvcNAQEL
-BQAwFjEUMBIGA1UEAxMLQnJva2VyLVJvb3QwHhcNMjMwNTIzMTAxNzIzWhcNMzMw
-NTIwMTAxNzUzWjAWMRQwEgYDVQQDEwtCcm9rZXItUm9vdDCCASIwDQYJKoZIhvcN
-AQEBBQADggEPADCCAQoCggEBAN5JAj+HydSGaxvA0AOcrXVTZ9FfsH0cMVBlQb72
-bGZgrRvkqtB011TNXZfsHl7rPxCY61DcsDJfFq3+8VHT+S9HE0qV1bEwP+oA3xc4
-Opq77av77cNNOqDC7h+jyPhHcUaE33iddmrH9Zn2ofWTSkKHHu3PAe5udCrc2QnD
-4PLRF6gqiEY1mcGknJrXj1ff/X0nRY/m6cnHNXz0Cvh8oPOtbdfGgfZjID2/fJNP
-fNoNKqN+5oJAZ+ZZ9id9rBvKj1ivW3F2EoGjZF268SgZzc5QrM/D1OpSBQf5SF/V
-qUPcQTgt9ry3YR+SZYazLkfKMEOWEa0WsqJVgXdQ6FyergcCAwEAAaN7MHkwDgYD
-VR0PAQH/BAQDAgEGMA8GA1UdEwEB/wQFMAMBAf8wHQYDVR0OBBYEFEa70kcseqU5
-bHx2zSt4bG21HokhMB8GA1UdIwQYMBaAFEa70kcseqU5bHx2zSt4bG21HokhMBYG
-A1UdEQQPMA2CC0Jyb2tlci1Sb290MA0GCSqGSIb3DQEBCwUAA4IBAQCGmE7NXW4T
-6J4mV3b132cGEMD7grx5JeiXK5EHMlswUS+Odz0NcBNzhUHdG4WVMbrilHbI5Ua+
-6jdKx5WwnqzjQvElP0MCw6sH/35gbokWgk1provOP99WOFRsQs+9Sm8M2XtMf9HZ
-m3wABwU/O+dhZZ1OT1PjSZD0OKWKqH/KvlsoF5R6P888KpeYFiIWiUNS5z21Jm8A
-ZcllJjiRJ60EmDwSUOQVJJSMOvtr6xTZDZLtAKSN8zN08lsNGzyrFwqjDwU0WTqp
-scMXEGBsWQjlvxqDnXyljepR0oqRIjOvgrWaIgbxcnu98tK/OdBGwlAPKNUW7Crr
-vO+eHxl9iqd4
------END CERTIFICATE-----

ccp/vars

@@ -7,7 +7,25 @@ SUPPORT_EMAIL=support-ccp@dkfz-heidelberg.de
 PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
 
 BROKER_URL_FOR_PREREQ=$BROKER_URL
+DEFAULT_LANGUAGE=DE
+DEFAULT_LANGUAGE_LOWER_CASE=${DEFAULT_LANGUAGE,,}
+ENABLE_EXPORTER=true
+ENABLE_TEILER=true
+#ENABLE_DATASHIELD=true
 
+KEYCLOAK_USER_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})"
+KEYCLOAK_ADMIN_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})_Verwalter"
+KEYCLOAK_PRIVATE_CLIENT_ID=${SITE_ID}-private
+KEYCLOAK_PUBLIC_CLIENT_ID=${SITE_ID}-public
+# TODO: Change Keycloak Realm to productive. "test-realm-01" is only for testing
+KEYCLOAK_REALM="${KEYCLOAK_REALM:-test-realm-01}"
+KEYCLOAK_URL="https://login.verbis.dkfz.de"
+KEYCLOAK_ISSUER_URL="${KEYCLOAK_URL}/realms/${KEYCLOAK_REALM}"
+KEYCLOAK_GROUP_CLAIM="groups"
+OAUTH2_CALLBACK=/oauth2/callback
+OAUTH2_PROXY_SECRET="$(echo \"This is a salt string to generate one consistent encryption key for the oauth2_proxy. It is not required to be secret.\" | openssl rsautl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 32)"
+
+add_private_oidc_redirect_url "${OAUTH2_CALLBACK}"
 
 for module in $PROJECT/modules/*.sh
 do
@@ -17,4 +35,4 @@ done
 
 idManagementSetup
 mtbaSetup
-adt2fhirRestSetup
+adt2fhirRestSetup

lib/functions.sh

@@ -239,3 +239,109 @@ add_basic_auth_user() {
  	log DEBUG "Saving clear text credentials in $FILE. If wanted, delete them manually."
    sed -i "/^$NAME/ s|$|\n# User: $USER\n# Password: $PASSWORD|" $FILE
 }
+
+OIDC_PUBLIC_REDIRECT_URLS=${OIDC_PUBLIC_REDIRECT_URLS:-""}
+OIDC_PRIVATE_REDIRECT_URLS=${OIDC_PRIVATE_REDIRECT_URLS:-""}
+
+# Add a redirect url to the public oidc client of the bridgehead
+function add_public_oidc_redirect_url() {
+    if [[ $OIDC_PUBLIC_REDIRECT_URLS == "" ]]; then
+        OIDC_PUBLIC_REDIRECT_URLS+="$(generate_redirect_urls $1)"
+    else 
+        OIDC_PUBLIC_REDIRECT_URLS+=",$(generate_redirect_urls $1)"
+    fi
+}
+
+# Add a redirect url to the private oidc client of the bridgehead
+function add_private_oidc_redirect_url() {
+    if [[ $OIDC_PRIVATE_REDIRECT_URLS == "" ]]; then
+        OIDC_PRIVATE_REDIRECT_URLS+="$(generate_redirect_urls $1)"
+    else 
+        OIDC_PRIVATE_REDIRECT_URLS+=",$(generate_redirect_urls $1)"
+    fi
+}
+
+function sync_secrets() {
+    local delimiter=$'\x1E'
+    local secret_sync_args=""
+    if [[ $OIDC_PRIVATE_REDIRECT_URLS != "" ]]; then
+        secret_sync_args="OIDC:OIDC_CLIENT_SECRET:private;$OIDC_PRIVATE_REDIRECT_URLS"
+    fi
+    if [[ $OIDC_PRIVATE_REDIRECT_URLS != "" ]]; then
+        if [[ $secret_sync_args == "" ]]; then
+            secret_sync_args="OIDC:OIDC_PUBLIC:public;$OIDC_PUBLIC_REDIRECT_URLS"
+        else 
+            secret_sync_args+="${delimiter}OIDC:OIDC_PUBLIC:public;$OIDC_PUBLIC_REDIRECT_URLS"
+        fi
+    fi
+    if [[ $secret_sync_args == "" ]]; then
+        return
+    fi
+    mkdir -p /var/cache/bridgehead/secrets/
+    touch /var/cache/bridgehead/secrets/oidc
+    chown -R bridgehead:docker /var/cache/bridgehead/secrets
+    # The oidc provider will need to be switched based on the project at some point I guess
+    docker run --rm \
+        -v /var/cache/bridgehead/secrets/oidc:/usr/local/cache \
+        -v $PRIVATEKEYFILENAME:/run/secrets/privkey.pem:ro \
+        -v /srv/docker/bridgehead/$PROJECT/root.crt.pem:/run/secrets/root.crt.pem:ro \
+        -v /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro \
+        -e TLS_CA_CERTIFICATES_DIR=/conf/trusted-ca-certs \
+        -e HTTPS_PROXY=$HTTPS_PROXY_FULL_URL \
+        -e PROXY_ID=$PROXY_ID \
+        -e BROKER_URL=$BROKER_URL \
+        -e OIDC_PROVIDER=secret-sync-central.oidc-client-enrollment.$BROKER_ID \
+        -e SECRET_DEFINITIONS=$secret_sync_args \
+        docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest
+    set -a # Export variables as environment variables
+    source /var/cache/bridgehead/secrets/*
+    set +a # Export variables in the regular way
+}
+
+capitalize_first_letter() {
+    input="$1"
+    capitalized="$(tr '[:lower:]' '[:upper:]' <<< ${input:0:1})${input:1}"
+    echo "$capitalized"
+}
+
+# Generate a string of ',' separated string of redirect urls relative to $HOST.
+# $1 will be appended to the url
+# If the host looks like dev-jan.inet.dkfz-heidelberg.de it will generate urls with dev-jan and the original $HOST as url Authorities
+function generate_redirect_urls(){
+    local redirect_urls="https://${HOST}$1"
+    local host_without_proxy="$(echo "$HOST" | cut -d '.' -f1)"
+    # Only append second url if its different and the host is not an ip address
+    if [[ "$HOST" != "$host_without_proxy" && ! "$HOST" =~ ^[0-9]+\.[0-9]+\.[0-9]+\.[0-9]+$ ]]; then
+        redirect_urls+=",https://$host_without_proxy$1"
+    fi
+    echo "$redirect_urls"
+}
+
+# This password contains at least one special char, a random number and a random upper and lower case letter
+generate_password(){
+  local seed_text="$1"
+  local seed_num=$(awk 'BEGIN{FS=""} NR==1{print $10}' /etc/bridgehead/pki/${SITE_ID}.priv.pem | od -An -tuC)
+  local nums="1234567890"
+  local n=$(echo "$seed_num" | awk '{print $1 % 10}')
+  local random_digit=${nums:$n:1}
+  local n=$(echo "$seed_num" | awk '{print $1 % 26}')
+  local upper="ABCDEFGHIJKLMNOPQRSTUVWXYZ"
+  local lower="abcdefghijklmnopqrstuvwxyz"
+  local random_upper=${upper:$n:1}
+  local random_lower=${lower:$n:1}
+  local n=$(echo "$seed_num" | awk '{print $1 % 8}')
+  local special='@#$%^&+='
+  local random_special=${special:$n:1}
+
+  local combined_text="This is a salt string to generate one consistent password for ${seed_text}. It is not required to be secret."
+  local main_password=$(echo "${combined_text}" | openssl rsautl -sign -inkey "/etc/bridgehead/pki/${SITE_ID}.priv.pem" 2> /dev/null | base64 | head -c 26 | sed 's/\//A/g')
+
+  echo "${main_password}${random_digit}${random_upper}${random_lower}${random_special}"
+}
+
+# This password only contains alphanumeric characters
+generate_simple_password(){
+  local seed_text="$1"
+  local combined_text="This is a salt string to generate one consistent password for ${seed_text}. It is not required to be secret."
+  echo "${combined_text}" | openssl rsautl -sign -inkey "/etc/bridgehead/pki/${SITE_ID}.priv.pem" 2> /dev/null | base64 | head -c 26 | sed 's/[+\/]/A/g'
+}

minimal/modules/dnpm-compose.yml

@@ -18,7 +18,7 @@ services:
       - "forward_proxy"
     volumes:
       - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
-      - /srv/docker/bridgehead/ccp/root-new.crt.pem:/conf/root.crt.pem:ro
+      - /srv/docker/bridgehead/ccp/root.crt.pem:/conf/root.crt.pem:ro
 
   dnpm-beam-connect:
     depends_on: [ dnpm-beam-proxy ]
@@ -32,9 +32,11 @@ services:
       LOCAL_TARGETS_FILE: "./conf/connect_targets.json"
       HTTP_PROXY: http://forward_proxy:3128
       HTTPS_PROXY: http://forward_proxy:3128
-      NO_PROXY: dnpm-beam-proxy,dnpm-backend
+      NO_PROXY: dnpm-beam-proxy,dnpm-backend, host.docker.internal
       RUST_LOG: ${RUST_LOG:-info}
       NO_AUTH: "true"
+    extra_hosts:
+      - "host.docker.internal:host-gateway"
     volumes:
       - /etc/bridgehead/dnpm/local_targets.json:/conf/connect_targets.json:ro
       - /etc/bridgehead/dnpm/central_targets.json:/conf/central_targets.json:ro

minimal/modules/dnpm-node-compose.yml

@@ -0,0 +1,33 @@
+version: "3.7"
+
+services:
+  dnpm-backend:
+    image: ghcr.io/kohlbacherlab/bwhc-backend:1.0-snapshot-broker-connector
+    container_name: bridgehead-dnpm-backend
+    environment:
+      - ZPM_SITE=${ZPM_SITE}
+    volumes:
+      - /etc/bridgehead/dnpm:/bwhc_config:ro
+      - ${DNPM_DATA_DIR}:/bwhc_data
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.bwhc-backend.rule=PathPrefix(`/bwhc`)"
+      - "traefik.http.services.bwhc-backend.loadbalancer.server.port=9000"
+      - "traefik.http.routers.bwhc-backend.tls=true"
+
+  dnpm-frontend:
+    image: ghcr.io/kohlbacherlab/bwhc-frontend:2209
+    container_name: bridgehead-dnpm-frontend
+    links:
+      - dnpm-backend
+    environment:
+      - NUXT_HOST=0.0.0.0
+      - NUXT_PORT=8080
+      - BACKEND_PROTOCOL=https
+      - BACKEND_HOSTNAME=$HOST
+      - BACKEND_PORT=443
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.bwhc-frontend.rule=PathPrefix(`/`)"
+      - "traefik.http.services.bwhc-frontend.loadbalancer.server.port=8080"
+      - "traefik.http.routers.bwhc-frontend.tls=true"

minimal/modules/dnpm-node-setup.sh

@@ -0,0 +1,27 @@
+#!/bin/bash
+
+if [ -n "${ENABLE_DNPM_NODE}" ]; then
+	log INFO "DNPM setup detected (BwHC Node) -- will start BwHC node."
+	OVERRIDE+=" -f ./$PROJECT/modules/dnpm-node-compose.yml"
+
+	# Set variables required for BwHC Node. ZPM_SITE is assumed to be set in /etc/bridgehead/<project>.conf
+	DNPM_APPLICATION_SECRET="$(echo \"This is a salt string to generate one consistent password for DNPM. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
+	if [ -z "${ZPM_SITE+x}" ]; then
+		log ERROR "Mandatory variable ZPM_SITE not defined!"
+		exit 1
+	fi
+	if [ -z "${DNPM_DATA_DIR+x}" ]; then
+		log ERROR "Mandatory variable DNPM_DATA_DIR not defined!"
+		exit 1
+	fi
+			if grep -q 'traefik.http.routers.landing.rule=PathPrefix(`/landing`)' /srv/docker/bridgehead/minimal/docker-compose.override.yml 2>/dev/null; then
+				echo "Override of landing page url already in place"
+			else
+				echo "Adding override of landing page url"
+				if [ -f /srv/docker/bridgehead/minimal/docker-compose.override.yml ]; then
+					echo -e '  landing:\n    labels:\n      - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"' >> /srv/docker/bridgehead/minimal/docker-compose.override.yml
+				else
+					echo -e 'version: "3.7"\nservices:\n  landing:\n    labels:\n      - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"' >> /srv/docker/bridgehead/minimal/docker-compose.override.yml
+				fi
+			fi
+fi

minimal/modules/dnpm-setup.sh

@@ -5,9 +5,12 @@ if [ -n "${ENABLE_DNPM}" ]; then
 	OVERRIDE+=" -f ./$PROJECT/modules/dnpm-compose.yml"
 
 	# Set variables required for Beam-Connect
-	DNPM_APPLICATION_SECRET="$(echo \"This is a salt string to generate one consistent password for DNPM. It is not required to be secret.\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
 	DNPM_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
 	DNPM_BROKER_ID="broker.ccp-it.dktk.dkfz.de"
 	DNPM_BROKER_URL="https://${DNPM_BROKER_ID}"
+	if [ -z ${BROKER_URL_FOR_PREREQ+x} ]; then
+		BROKER_URL_FOR_PREREQ=$DNPM_BROKER_URL
+		log DEBUG "No Broker for clock check set; using $DNPM_BROKER_URL"
+	fi
 	DNPM_PROXY_ID="${SITE_ID}.${DNPM_BROKER_ID}"
 fi

minimal/modules/nngm-compose.yml

@@ -0,0 +1,29 @@
+version: "3.7"
+volumes:
+  nngm-rest:
+
+services:
+  connector:
+    container_name: bridgehead-connector
+    image: docker.verbis.dkfz.de/ccp/nngm-rest:main
+    environment:
+      CTS_MAGICPL_API_KEY: ${NNGM_MAGICPL_APIKEY}
+      CTS_API_KEY: ${NNGM_CTS_APIKEY}
+      CRYPT_KEY: ${NNGM_CRYPTKEY}
+      #CTS_MAGICPL_SITE: ${SITE_ID}TODO
+    restart: always
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.connector.rule=PathPrefix(`/nngm-connector`)"
+      - "traefik.http.middlewares.connector_strip.stripprefix.prefixes=/nngm-connector"
+      - "traefik.http.services.connector.loadbalancer.server.port=8080"
+      - "traefik.http.routers.connector.tls=true"
+      - "traefik.http.routers.connector.middlewares=connector_strip,auth-nngm"
+    volumes:
+      - nngm-rest:/var/log
+
+  traefik:
+    labels:
+      - "traefik.http.middlewares.auth-nngm.basicauth.users=${NNGM_AUTH}"
+
+

minimal/modules/nngm-setup.sh

@@ -0,0 +1,6 @@
+#!/bin/bash
+
+if [ -n "$NNGM_CTS_APIKEY" ]; then
+  log INFO "nNGM setup detected -- will start nNGM Connector."
+  OVERRIDE+=" -f ./$PROJECT/modules/nngm-compose.yml"
+fi