refactor: put all modules in a common directory to remove redundancy

.github/scripts/rename_inactive_branches.py

@@ -1,39 +0,0 @@
-import os
-import requests
-from datetime import datetime, timedelta
-
-# Configuration
-GITHUB_TOKEN = os.getenv('GITHUB_TOKEN')
-REPO = 'samply/bridgehead'
-HEADERS = {'Authorization': f'token {GITHUB_TOKEN}', 'Accept': 'application/vnd.github.v3+json'}
-API_URL = f'https://api.github.com/repos/{REPO}/branches'
-INACTIVE_DAYS = 365
-CUTOFF_DATE = datetime.now() - timedelta(days=INACTIVE_DAYS)
-
-# Fetch all branches
-def get_branches():
-    response = requests.get(API_URL, headers=HEADERS)
-    response.raise_for_status()
-    return response.json() if response.status_code == 200 else []
-
-# Rename inactive branches
-def rename_branch(old_name, new_name):
-    rename_url = f'https://api.github.com/repos/{REPO}/branches/{old_name}/rename'
-    response = requests.post(rename_url, json={'new_name': new_name}, headers=HEADERS)
-    response.raise_for_status()
-    print(f"Renamed branch {old_name} to {new_name}" if response.status_code == 201 else f"Failed to rename {old_name}: {response.status_code}")
-
-# Check if the branch is inactive
-def is_inactive(commit_url):
-    last_commit_date = requests.get(commit_url, headers=HEADERS).json()['commit']['committer']['date']
-    return datetime.strptime(last_commit_date, '%Y-%m-%dT%H:%M:%SZ') < CUTOFF_DATE
-
-# Rename inactive branches
-def main():
-    for branch in get_branches():
-        if is_inactive(branch['commit']['url']):
-            #rename_branch(branch['name'], f"archived/{branch['name']}")
-            print(f"[LOG] Branch '{branch['name']}' is inactive and would be renamed to 'archived/{branch['name']}'")
-
-if __name__ == "__main__":
-    main()

.github/workflows/rename-inactive-branches.yml

@@ -1,27 +0,0 @@
-name: Cleanup - Rename Inactive Branches
-
-on:
-  schedule:
-    - cron: '0 0 * * 0'  # Runs every Sunday at midnight
-
-jobs:
-  archive-stale-branches:
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Checkout Repository
-        uses: actions/checkout@v2
-
-      - name: Set up Python
-        uses: actions/setup-python@v2
-        with:
-          python-version: '3.x'
-
-      - name: Install Libraries
-        run: pip install requests
-
-      - name: Run Script to Rename Inactive Branches
-        run: |
-          python .github/scripts/rename_inactive_branches.py
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

README.md

@@ -76,7 +76,7 @@ The following URLs need to be accessible (prefix with `https://`):
   * git.verbis.dkfz.de
 * To fetch docker images
   * docker.verbis.dkfz.de
-  * Official Docker, Inc. URLs (subject to change, see [official list](https://docs.docker.com/desktop/setup/allow-list/))
+  * Official Docker, Inc. URLs (subject to change, see [official list](https://docs.docker.com/desktop/all))
     * hub.docker.com
     * registry-1.docker.io
     * production.cloudflare.docker.com
@@ -154,7 +154,7 @@ Pay special attention to:
 Clone the bridgehead repository:
 ```shell
 sudo mkdir -p /srv/docker/
-sudo git clone -b main https://github.com/samply/bridgehead.git /srv/docker/bridgehead
+sudo git clone https://github.com/samply/bridgehead.git /srv/docker/bridgehead
 ```
 
 Then, run the installation script:
@@ -254,8 +254,6 @@ sh bridgehead uninstall
 
 ## Site-specific configuration
 
-[How to Change Config Access Token](docs/update-access-token.md)
-
 ### HTTPS Access
 
 Even within your internal network, the Bridgehead enforces HTTPS for all services. During the installation, a self-signed, long-lived certificate was created for you. To increase security, you can simply replace the files under `/etc/bridgehead/traefik-tls` with ones from established certification authorities such as [Let's Encrypt](https://letsencrypt.org) or [DFN-AAI](https://www.aai.dfn.de).

bbmri/docker-compose.yml

@@ -4,14 +4,13 @@ version: "3.7"
 
 services:
   blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
+    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
     container_name: bridgehead-bbmri-blaze
     environment:
       BASE_URL: "http://bridgehead-bbmri-blaze:8080"
       JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
       DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
-      DB_BLOCK_CACHE_SIZE: ${BLAZE_MEMORY_CAP}
+      DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP
-      CQL_EXPR_CACHE_SIZE: ${BLAZE_CQL_CACHE_CAP:-32}
       ENFORCE_REFERENTIAL_INTEGRITY: "false"
     volumes:
       - "blaze-data:/app/data"

bbmri/modules/eric-compose.yml

@@ -2,7 +2,7 @@ version: "3.7"
 
 services:
   focus-eric:
-    image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}-bbmri
+    image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
     container_name: bridgehead-focus-eric
     environment:
       API_KEY: ${ERIC_FOCUS_BEAM_SECRET_SHORT}

bbmri/modules/gbn-compose.yml

@@ -2,7 +2,7 @@ version: "3.7"
 
 services:
   focus-gbn:
-    image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}-bbmri
+    image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
     container_name: bridgehead-focus-gbn
     environment:
       API_KEY: ${GBN_FOCUS_BEAM_SECRET_SHORT}

bridgehead

@@ -53,44 +53,17 @@ case "$PROJECT" in
 		;;
 esac
 
-# Loads config variables and runs the projects setup script
 loadVars() {
+	# Load variables from /etc/bridgehead and /srv/docker/bridgehead
 	set -a
-	# Source the project specific config file
 	source /etc/bridgehead/$PROJECT.conf || fail_and_report 1 "/etc/bridgehead/$PROJECT.conf not found"
-	# Source the project specific local config file if present
-	# This file is ignored by git as oposed to the regular config file as it contains private site information like etl auth data
 	if [ -e /etc/bridgehead/$PROJECT.local.conf ]; then
 		log INFO "Applying /etc/bridgehead/$PROJECT.local.conf"
 		source /etc/bridgehead/$PROJECT.local.conf || fail_and_report 1 "Found /etc/bridgehead/$PROJECT.local.conf but failed to import"
 	fi
-	# Set execution environment on main default to prod else test
-	if [[ -z "${ENVIRONMENT+x}" ]]; then
-		if [ "$(git rev-parse --abbrev-ref HEAD)" == "main" ]; then
-			ENVIRONMENT="production"
-		else
-			ENVIRONMENT="test"
-		fi
-	fi
-	# Source the versions of the images components 
-	case "$ENVIRONMENT" in
-		"production")
-			source ./versions/prod
-			;;
-		"test")
-			source ./versions/test
-			;;
-		*)
-			report_error 7 "Environment \"$ENVIRONMENT\" is unknown. Assuming production. FIX THIS!"
-			source ./versions/prod
-			;;
-	esac
 	fetchVarsFromVaultByFile /etc/bridgehead/$PROJECT.conf || fail_and_report 1 "Unable to fetchVarsFromVaultByFile"
 	setHostname
 	optimizeBlazeMemoryUsage
-	# Run project specific setup if it exists
-	# This will ususally modiy the `OVERRIDE` to include all the compose files that the project depends on
-	# This is also where projects specify which modules to load
 	[ -e ./$PROJECT/vars ] && source ./$PROJECT/vars
 	set +a
 
@@ -106,6 +79,26 @@ loadVars() {
 	fi
 	detectCompose
 	setupProxy
+
+	# Set some project-independent default values
+	: ${ENVIRONMENT:=production}
+	export ENVIRONMENT
+
+	case "$ENVIRONMENT" in
+		"production")
+			export FOCUS_TAG=main
+			export BEAM_TAG=main
+			;;
+		"test")
+			export FOCUS_TAG=develop
+			export BEAM_TAG=develop
+			;;
+		*)
+			report_error 7 "Environment \"$ENVIRONMENT\" is unknown. Assuming production. FIX THIS!"
+			export FOCUS_TAG=main
+			export BEAM_TAG=main
+			;;
+	esac
 }
 
 case "$ACTION" in

cce/docker-compose.yml

@@ -2,7 +2,7 @@ version: "3.7"
 
 services:
   blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
+    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
     container_name: bridgehead-cce-blaze
     environment:
       BASE_URL: "http://bridgehead-cce-blaze:8080"

cce/modules/lens-compose.yml

@@ -1,33 +0,0 @@
-version: "3.7"
-services:
-  landing:
-    container_name: lens_federated-search
-    image: docker.verbis.dkfz.de/ccp/lens:${SITE_ID}
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.landing.rule=PathPrefix(`/`)"
-      - "traefik.http.services.landing.loadbalancer.server.port=80"
-      - "traefik.http.routers.landing.tls=true"
-
-  spot:
-    image: docker.verbis.dkfz.de/ccp-private/central-spot
-    environment:
-      BEAM_SECRET: "${FOCUS_BEAM_SECRET_SHORT}"
-      BEAM_URL: http://beam-proxy:8081
-      BEAM_PROXY_ID: ${SITE_ID}
-      BEAM_BROKER_ID: ${BROKER_ID}
-      BEAM_APP_ID: "focus"
-      PROJECT_METADATA: "cce_supervisors"
-    depends_on:
-      - "beam-proxy"
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.services.spot.loadbalancer.server.port=8080"
-      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowmethods=GET,OPTIONS,POST"
-      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolalloworiginlist=https://${HOST}"
-      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowcredentials=true"
-      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolmaxage=-1"
-      - "traefik.http.routers.spot.rule=Host(`${HOST}`) && PathPrefix(`/backend`)"
-      - "traefik.http.middlewares.stripprefix_spot.stripprefix.prefixes=/backend"
-      - "traefik.http.routers.spot.tls=true"
-      - "traefik.http.routers.spot.middlewares=corsheaders2,stripprefix_spot"

cce/modules/lens-setup.sh

@@ -1,5 +0,0 @@
-#!/bin/bash
-
-if [ -n "$ENABLE_LENS" ];then
-  OVERRIDE+=" -f ./$PROJECT/modules/lens-compose.yml"
-fi

cce/vars

@@ -7,7 +7,7 @@ SUPPORT_EMAIL=manoj.waikar@dkfz-heidelberg.de
 PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
 BROKER_URL_FOR_PREREQ=$BROKER_URL
 
-for module in $PROJECT/modules/*.sh
+for module in common/*.sh
 do
     log DEBUG "sourcing $module"
     source $module

ccp/docker-compose.yml

@@ -2,14 +2,13 @@ version: "3.7"
 
 services:
   blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
+    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
     container_name: bridgehead-ccp-blaze
     environment:
       BASE_URL: "http://bridgehead-ccp-blaze:8080"
       JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
       DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
-      DB_BLOCK_CACHE_SIZE: ${BLAZE_MEMORY_CAP}
+      DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP
-      CQL_EXPR_CACHE_SIZE: ${BLAZE_CQL_CACHE_CAP:-32}
       ENFORCE_REFERENTIAL_INTEGRITY: "false"
     volumes:
       - "blaze-data:/app/data"
@@ -22,7 +21,7 @@ services:
       - "traefik.http.routers.blaze_ccp.tls=true"
 
   focus:
-    image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}-dktk
+    image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
     container_name: bridgehead-focus
     environment:
       API_KEY: ${FOCUS_BEAM_SECRET_SHORT}
@@ -33,7 +32,6 @@ services:
       RETRY_COUNT: ${FOCUS_RETRY_COUNT}
       EPSILON: 0.28
       QUERIES_TO_CACHE: '/queries_to_cache.conf'
-      ENDPOINT_TYPE: ${FOCUS_ENDPOINT_TYPE:-blaze}
     volumes:
       - /srv/docker/bridgehead/ccp/queries_to_cache.conf:/queries_to_cache.conf
     depends_on:
@@ -59,6 +57,7 @@ services:
       - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
       - /srv/docker/bridgehead/ccp/root.crt.pem:/conf/root.crt.pem:ro
 
+
 volumes:
   blaze-data:
 

ccp/modules/dnpm-node-compose.yml

@@ -1,99 +0,0 @@
-version: "3.7"
-
-services:
-  dnpm-mysql:
-    image: mysql:9
-    healthcheck:
-      test: [ "CMD", "mysqladmin" ,"ping", "-h", "localhost" ]
-      interval: 3s
-      timeout: 5s
-      retries: 5
-    environment:
-      MYSQL_ROOT_HOST: "%"
-      MYSQL_ROOT_PASSWORD: ${DNPM_MYSQL_ROOT_PASSWORD}
-    volumes:
-      - /var/cache/bridgehead/dnpm/mysql:/var/lib/mysql
-
-  dnpm-authup:
-    image: authup/authup:latest
-    container_name: bridgehead-dnpm-authup
-    volumes:
-      - /var/cache/bridgehead/dnpm/authup:/usr/src/app/writable
-    depends_on:
-      dnpm-mysql:
-        condition: service_healthy
-    command: server/core start
-    environment:
-      - PUBLIC_URL=https://${HOST}/auth/
-      - AUTHORIZE_REDIRECT_URL=https://${HOST}
-      - ROBOT_ADMIN_ENABLED=true
-      - ROBOT_ADMIN_SECRET=${DNPM_AUTHUP_SECRET}
-      - ROBOT_ADMIN_SECRET_RESET=true
-      - DB_TYPE=mysql
-      - DB_HOST=dnpm-mysql
-      - DB_USERNAME=root
-      - DB_PASSWORD=${DNPM_MYSQL_ROOT_PASSWORD}
-      - DB_DATABASE=auth
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.middlewares.authup-strip.stripprefix.prefixes=/auth"
-      - "traefik.http.routers.dnpm-auth.middlewares=authup-strip"
-      - "traefik.http.routers.dnpm-auth.rule=PathPrefix(`/auth`)"
-      - "traefik.http.services.dnpm-auth.loadbalancer.server.port=3000"
-      - "traefik.http.routers.dnpm-auth.tls=true"
-
-  dnpm-portal:
-    image: ghcr.io/dnpm-dip/portal:latest
-    container_name: bridgehead-dnpm-portal
-    environment:
-      - NUXT_API_URL=http://dnpm-backend:9000/
-      - NUXT_PUBLIC_API_URL=https://${HOST}/api/
-      - NUXT_AUTHUP_URL=http://dnpm-authup:3000/
-      - NUXT_PUBLIC_AUTHUP_URL=https://${HOST}/auth/
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.dnpm-frontend.rule=PathPrefix(`/`)"
-      - "traefik.http.services.dnpm-frontend.loadbalancer.server.port=3000"
-      - "traefik.http.routers.dnpm-frontend.tls=true"
-
-  dnpm-backend:
-    container_name: bridgehead-dnpm-backend
-    image: ghcr.io/dnpm-dip/backend:latest
-    environment:
-      - LOCAL_SITE=${ZPM_SITE}:${SITE_NAME}   # Format: {Site-ID}:{Site-name}, e.g. UKT:Tübingen
-      - RD_RANDOM_DATA=${DNPM_SYNTH_NUM:--1}
-      - MTB_RANDOM_DATA=${DNPM_SYNTH_NUM:--1}
-      - HATEOAS_HOST=https://${HOST}
-      - CONNECTOR_TYPE=broker
-      - AUTHUP_URL=robot://system:${DNPM_AUTHUP_SECRET}@http://dnpm-authup:3000
-    volumes:
-      - /etc/bridgehead/dnpm/config:/dnpm_config
-      - /var/cache/bridgehead/dnpm/backend-data:/dnpm_data
-    depends_on:
-      dnpm-authup:
-        condition: service_healthy
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.services.dnpm-backend.loadbalancer.server.port=9000"
-      # expose everything
-      - "traefik.http.routers.dnpm-backend.rule=PathPrefix(`/api`)"
-      - "traefik.http.routers.dnpm-backend.tls=true"
-      - "traefik.http.routers.dnpm-backend.service=dnpm-backend"
-      # except ETL
-      - "traefik.http.routers.dnpm-backend-etl.rule=PathRegexp(`^/api(/.*)?etl(/.*)?$`)"
-      - "traefik.http.routers.dnpm-backend-etl.tls=true"
-      - "traefik.http.routers.dnpm-backend-etl.service=dnpm-backend"
-      # this needs an ETL processor with support for basic auth
-      - "traefik.http.routers.dnpm-backend-etl.middlewares=auth"
-      # except peer-to-peer
-      - "traefik.http.routers.dnpm-backend-peer.rule=PathRegexp(`^/api(/.*)?/peer2peer(/.*)?$`)"
-      - "traefik.http.routers.dnpm-backend-peer.tls=true"
-      - "traefik.http.routers.dnpm-backend-peer.service=dnpm-backend"
-      - "traefik.http.routers.dnpm-backend-peer.middlewares=dnpm-backend-peer"
-      # this effectively denies all requests
-      # this is okay, because requests from peers don't go through Traefik
-      - "traefik.http.middlewares.dnpm-backend-peer.ipWhiteList.sourceRange=0.0.0.0/32"
-
-  landing:
-    labels:
-      - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"

ccp/modules/dnpm-node-setup.sh

@@ -1,16 +0,0 @@
-#!/bin/bash
-
-if [ -n "${ENABLE_DNPM_NODE}" ]; then
-	log INFO "DNPM setup detected -- will start DNPM:DIP node."
-	OVERRIDE+=" -f ./$PROJECT/modules/dnpm-node-compose.yml"
-
-	# Set variables required for BwHC Node. ZPM_SITE is assumed to be set in /etc/bridgehead/<project>.conf
-	if [ -z "${ZPM_SITE+x}" ]; then
-		log ERROR "Mandatory variable ZPM_SITE not defined!"
-		exit 1
-	fi
-    mkdir -p /var/cache/bridgehead/dnpm/ || fail_and_report 1 "Failed to create '/var/cache/bridgehead/dnpm/'. Please run sudo './bridgehead install $PROJECT' again to fix the permissions."
-    DNPM_SYNTH_NUM=${DNPM_SYNTH_NUM:--1}
-    DNPM_MYSQL_ROOT_PASSWORD="$(generate_simple_password 'dnpm mysql')"
-    DNPM_AUTHUP_SECRET="$(generate_simple_password 'dnpm authup')"
-fi

ccp/modules/exporter-compose.yml

@@ -1,72 +0,0 @@
-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: "${EXPORTER_OPAL_PASSWORD}"
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.exporter_ccp.rule=PathPrefix(`/ccp-exporter`)"
-      - "traefik.http.services.exporter_ccp.loadbalancer.server.port=8092"
-      - "traefik.http.routers.exporter_ccp.tls=true"
-      - "traefik.http.middlewares.exporter_ccp_strip.stripprefix.prefixes=/ccp-exporter"
-      - "traefik.http.routers.exporter_ccp.middlewares=exporter_ccp_strip"
-    volumes:
-      - "/var/cache/bridgehead/ccp/exporter-files:/app/exporter-files/output"
-
-  exporter-db:
-    image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
-    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"
-
-  focus:
-    environment:
-      EXPORTER_URL: "http://exporter:8092"
-      EXPORTER_API_KEY: "${EXPORTER_API_KEY}"

ccp/modules/exporter-setup.sh

@@ -1,8 +0,0 @@
-#!/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="$(echo \"This is a salt string to generate one consistent password for the exporter. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
-  EXPORTER_API_KEY="$(echo \"This is a salt string to generate one consistent API KEY for the exporter. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 64)"
-fi

ccp/modules/ovis-compose.yml

@@ -1,112 +0,0 @@
-version: '3.7'
-
-services:
-
-  ovis-traefik-forward-auth:
-      image: quay.io/oauth2-proxy/oauth2-proxy:latest
-      environment:
-        - http_proxy=${http_proxy:-http://forward_proxy:3128}
-        - https_proxy=${https_proxy:-http://forward_proxy:3128}
-        - OAUTH2_PROXY_PROVIDER=oidc
-        - OAUTH2_PROXY_SKIP_PROVIDER_BUTTON=true
-        - OAUTH2_PROXY_OIDC_ISSUER_URL=${OAUTH_ISSUER_URL}
-        - OAUTH2_PROXY_CLIENT_ID=${OAUTH_CLIENT_ID}
-        - OAUTH2_PROXY_CLIENT_SECRET=${OAUTH_CLIENT_SECRET}
-        - OAUTH2_PROXY_COOKIE_SECRET=${AUTHENTICATION_SECRET}
-        - OAUTH2_PROXY_COOKIE_DOMAINS=.${HOST:-localhost}
-        - OAUTH2_PROXY_COOKIE_REFRESH=4m
-        - OAUTH2_PROXY_COOKIE_EXPIRE=24h
-        - OAUTH2_PROXY_HTTP_ADDRESS=:4180
-        - OAUTH2_PROXY_REVERSE_PROXY=true
-        - OAUTH2_PROXY_WHITELIST_DOMAINS=.${HOST:-localhost}
-        - OAUTH2_PROXY_UPSTREAMS=static://202
-        - OAUTH2_PROXY_EMAIL_DOMAINS=*
-        #- OAUTH2_PROXY_ALLOWED_GROUPS=app-ovis
-        #- OAUTH2_PROXY_ERRORS_TO_INFO_LOG=true
-        - OAUTH2_PROXY_CODE_CHALLENGE_METHOD=S256
-        # For some reason, login.verbis.dkfz.de does not have a "groups" scope but this comes automatically through a
-        # scope called microprofile-jwt. Remove the following line once we have a "groups" scope.
-        - OAUTH2_PROXY_SCOPE=openid profile email
-        # Pass Authorization Header and some user information to spot
-        - OAUTH2_PROXY_SET_AUTHORIZATION_HEADER=true
-        - OAUTH2_PROXY_SET_XAUTHREQUEST=true
-      labels:
-        - "traefik.enable=true"
-        - "traefik.http.middlewares.ovis-traefik-forward-auth.forwardauth.address=http://ovis-traefik-forward-auth:4180"
-        - "traefik.http.middlewares.ovis-traefik-forward-auth.forwardauth.authResponseHeaders=Authorization, X-Forwarded-User, X-Auth-Request-User, X-Auth-Request-Email"
-        - "traefik.http.services.ovis-traefik-forward-auth.loadbalancer.server.port=4180"
-        - "traefik.http.routers.oauth2.rule=Host(`${HOST:-localhost}`) && PathPrefix(`/oauth2-ovis/`)"
-        - "traefik.http.routers.oauth2.tls=true"
-
-  fhir-transformer:
-    image: docker.verbis.dkfz.de/ovis/adt-mon-gql-fhir-transformer:latest
-    restart: on-failure
-    environment:
-      - FHIR_SERVER_URL=${FHIR_SERVER_URL:-http://bridgehead-ccp-blaze:8080/fhir}
-      - FHIR_USERNAME=${FHIR_USERNAME}
-      - FHIR_PASSWORD=${FHIR_PASSWORD}
-    volumes:
-      - /var/cache/bridgehead/ccp/ovis/shared_data:/app/output
-
-  mongo:
-    image: mongo:${MONGO_VER:-latest}
-    restart: always
-    command: mongod
-      - /var/cache/bridgehead/ccp/ovis/mongo/init/init.js:/docker-entrypoint-initdb.d/init.js
-
-  backend:
-    image: docker.verbis.dkfz.de/ovis/adt-mon-gql-backend:latest
-    restart: always
-    user: root
-    working_dir: /app
-    environment:
-      - APOLLO_PORT=${APOLLO_PORT:-4001}
-      - CREDOS_PORT=${CREDOS_PORT:-4000}
-      - MONGO_VER=latest
-      - CORS_ORIGIN=*
-      - DB=${DB:-onc_test}
-      - ADRESS=${ADRESS:-mongodb://mongo:27017}
-    depends_on:
-      - mongo
-      - fhir-transformer
-    healthcheck:
-      test: ["CMD", "curl", "-f", "http://localhost:${APOLLO_PORT:-4001}/health"]
-      interval: 5s
-      timeout: 3s
-      retries: 5
-      start_period: 10s
-    entrypoint: >
-      sh -c "
-        # First run the initialization process
-        while [ ! -f /shared/omock.json ]; do
-          echo 'Waiting for omock.json...'
-          sleep 5
-        done;
-        mkdir -p ./prep &&
-        cp /shared/omock.json ./prep/omock.json &&
-        node ./mgDB/prep/preprocessor.mjs &&
-        echo 'Processing complete' &&
-        exec node --watch index.js"
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.ovis-backend.rule=Host(`${HOST:-localhost}`) && PathPrefix(`/graphql`)"
-      - "traefik.http.routers.ovis-backend.tls=true"
-      - "traefik.http.services.ovis-backend.loadbalancer.server.port=${APOLLO_PORT:-4001}"
-    volumes:
-      - /var/cache/bridgehead/ccp/ovis/shared_data:/shared
-
-  frontend:
-    image: docker.verbis.dkfz.de/ovis/adt-mon-gql-frontend:latest
-    restart: always
-    environment:
-      - PUBLIC_GRAPHQL_URL=https://${HOST:-localhost}/graphql
-    depends_on:
-      backend:
-        condition: service_healthy
-    working_dir: /app
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.ovis-frontend.tls=true"
-      - "traefik.http.routers.ovis-frontend.rule=Host(`${HOST:-localhost}`)"
-      - "traefik.http.routers.ovis-frontend.middlewares=traefik-forward-auth"
-      - "traefik.http.services.ovis-frontend.loadbalancer.server.port=5173"

ccp/modules/ovis-setup.sh

@@ -1,108 +0,0 @@
-#!/bin/bash -e
-
-if [ -n "$ENABLE_OVIS" ];then
-    # Setup MongoDB initialization directory if it doesn't exist
-    mkdir -p "/var/cache/bridgehead/ccp/ovis/mongo/init"
-    
-    # Generate MongoDB initialization script directly
-    cat > "/var/cache/bridgehead/ccp/ovis/mongo/init/init.js" << 'EOF'
-db = db.getSiblingDB("test_credos");
-db.createCollection("user");
-db.user.insertMany([{
-    "_id": "OVIS-Root",
-    "createdAt": new Date(),
-    "createdBy": "system",
-    "role": "super-admin",
-    "status": "active",
-    "pseudonymization": false,
-    "darkMode": false,
-    "colorTheme": "CCCMunich",
-    "language":  "de",
-}]);
-
-db = db.getSiblingDB("onc_test");
-db.createCollection("user");
-db.user.insertMany([{
-    "_id": "OVIS-Root",
-    "createdAt": new Date(),
-    "createdBy": "system",
-    "role": "super-admin",
-    "status": "active",
-    "pseudonymization": false,
-    "darkMode": false,
-    "colorTheme": "CCCMunich",
-    "language":  "de",
-}]);
-
-db.ops.insertMany([
-    {"OPSC_4":"1-40","OPS_Gruppen_Text":"Biopsie ohne Inzision an Nervensystem und endokrinen Organen "},
-    {"OPSC_4":"1-44","OPS_Gruppen_Text":"Biopsie ohne Inzision an den Verdauungsorganen"},
-    {"OPSC_4":"1-40","OPS_Gruppen_Text":"Biopsie ohne Inzision an anderen Organen und Geweben"},
-    {"OPSC_4":"1-50","OPS_Gruppen_Text":"Biopsie an Haut, Mamma, Knochen und Muskeln durch Inzision"},
-    {"OPSC_4":"1-51","OPS_Gruppen_Text":"Biopsie an Nervengewebe, Hypophyse, Corpus pineale durch Inzision und Trepanation von Schädelknochen "},
-    {"OPSC_4":"1-55","OPS_Gruppen_Text":"Biopsie an anderen Verdauungsorganen, Zwerchfell und (Retro-)Peritoneum durch Inzision "},
-    {"OPSC_4":"1-56","OPS_Gruppen_Text":"Biopsie an Harnwegen und männlichen Geschlechtsorgannen durch Inzision"},
-    {"OPSC_4":"1-58","OPS_Gruppen_Text":"Biopsie an anderen Organen durch Inzision "},
-    {"OPSC_4":"1-63","OPS_Gruppen_Text":"Diagnostische Endoskopie des oberen Verdauungstraktes"},
-    {"OPSC_4":"1-65","OPS_Gruppen_Text":"Diagnostische Endoskopie des unteren Verdauungstraktes"},
-    {"OPSC_4":"1-69","OPS_Gruppen_Text":"Diagnostische Endoskopie durch Inzision und intraoperativ "},
-    {"OPSC_4":"5-01","OPS_Gruppen_Text":"Inzision (Trepanation) und Exzision an Schädel, Gehirn und Hirnhäuten"},
-    {"OPSC_4":"5-02","OPS_Gruppen_Text":"Andere Operationen  an Schädel, Gehirn und Hirnhäuten"},
-    {"OPSC_4":"5-03","OPS_Gruppen_Text":"Operationen an Rückenmark, Rückenmarkhäuten und Spinalkanal"},
-    {"OPSC_4":"5-05","OPS_Gruppen_Text":"Andere Operationen an Nerven und Nervenganglien "},
-    {"OPSC_4":"5-06","OPS_Gruppen_Text":"Operationen an Schilddrüse und Nebenschilddrüse "},
-    {"OPSC_4":"5-07","OPS_Gruppen_Text":"Operationen an anderen endokrinen Drüsen "},
-    {"OPSC_4":"5-20","OPS_Gruppen_Text":"Andere Operationen an Mittel- und Innenohr "},
-    {"OPSC_4":"5-25","OPS_Gruppen_Text":"Operationen an der Zunge "},
-    {"OPSC_4":"5-31","OPS_Gruppen_Text":"Andere Larynxoperationen und Operationen an der Trachea "},
-    {"OPSC_4":"5-32","OPS_Gruppen_Text":"Exzision und Resektion an Lunge und Bronchus "},
-    {"OPSC_4":"5-33","OPS_Gruppen_Text":"Andere Operationen an Lunge und Bronchus"},
-    {"OPSC_4":"5-34","OPS_Gruppen_Text":"Operationen an Brustwand, Pleura, Mediastinum und Zwerchfell "},
-    {"OPSC_4":"5-37","OPS_Gruppen_Text":"Rhythmuschirurgie und andere Operationen an Herz und Perikard"},
-    {"OPSC_4":"5-38","OPS_Gruppen_Text":"Inzision, Exzision und Verschluß von Blutgefäßen "},
-    {"OPSC_4":"5-39","OPS_Gruppen_Text":"Andere Operationen an Blutgefäßen "},
-    {"OPSC_4":"5-40","OPS_Gruppen_Text":"Operationen am Lymphgewebe "},
-    {"OPSC_4":"5-41","OPS_Gruppen_Text":"Operationen an Milz und Knochenmark "},
-    {"OPSC_4":"5-42","OPS_Gruppen_Text":"Operationen am Ösophagus "},
-    {"OPSC_4":"5-43","OPS_Gruppen_Text":"Inzision, Exzision und Resektion am Magen "},
-    {"OPSC_4":"5-44","OPS_Gruppen_Text":"Erweiterte Magenresektion und andere Operationen am Magen "},
-    {"OPSC_4":"5-45","OPS_Gruppen_Text":"Inzision, Exzision, Resektion und Anastomose an Dünn- und Dickdarm "},
-    {"OPSC_4":"5-46","OPS_Gruppen_Text":"Andere Operationen an Dünn- und Dickdarm "},
-    {"OPSC_4":"5-47","OPS_Gruppen_Text":"Operationen an der Appendix "},
-    {"OPSC_4":"5-48","OPS_Gruppen_Text":"Operationen am Rektum "},
-    {"OPSC_4":"5-49","OPS_Gruppen_Text":"Operationen am Anus "},
-    {"OPSC_4":"5-50","OPS_Gruppen_Text":"Operationen an der Leber "},
-    {"OPSC_4":"5-51","OPS_Gruppen_Text":"Operationen an Gallenblase und Gallenwegen "},
-    {"OPSC_4":"5-52","OPS_Gruppen_Text":"Operationen am Pankreas "},
-    {"OPSC_4":"5-53","OPS_Gruppen_Text":"Verschluß abdominaler Hernien "},
-    {"OPSC_4":"5-54","OPS_Gruppen_Text":"Andere Operationen in der Bauchregion "},
-    {"OPSC_4":"5-55","OPS_Gruppen_Text":"Operationen an der Niere "},
-    {"OPSC_4":"5-56","OPS_Gruppen_Text":"Operationen am Ureter "},
-    {"OPSC_4":"5-57","OPS_Gruppen_Text":"Operationen an der Harnblase "},
-    {"OPSC_4":"5-59","OPS_Gruppen_Text":"Andere Operationen an den Harnorganen "},
-    {"OPSC_4":"5-60","OPS_Gruppen_Text":"Operationen an Prostata und Vesiculae seminales "},
-    {"OPSC_4":"5-61","OPS_Gruppen_Text":"Operationen an Skrotum und Tunica vaginalis testis"},
-    {"OPSC_4":"5-62","OPS_Gruppen_Text":"Operationen am Hoden "},
-    {"OPSC_4":"5-65","OPS_Gruppen_Text":"Operationen am Ovar "},
-    {"OPSC_4":"5-68","OPS_Gruppen_Text":"Inzision, Exzision und Exstirpation des Uterus "},
-    {"OPSC_4":"5-70","OPS_Gruppen_Text":"Operationen an Vagina und Douglasraum "},
-    {"OPSC_4":"5-71","OPS_Gruppen_Text":"Operationen an der Vulva "},
-    {"OPSC_4":"5-85","OPS_Gruppen_Text":"Operationen an Muskeln, Sehnen, Faszien und Schleimbeuteln"},
-    {"OPSC_4":"5-87","OPS_Gruppen_Text":"Exzision und Resektion der Mamma "},
-    {"OPSC_4":"5-89","OPS_Gruppen_Text":"Operationen an Haut und Unterhaut "},
-    {"OPSC_4":"5-90","OPS_Gruppen_Text":"Operative Wiederherstellung und Rekonstruktion von Haut und Unterhaut"},
-    {"OPSC_4":"5-91","OPS_Gruppen_Text":"Andere Operationen an Haut und Unterhaut "},
-    {"OPSC_4":"5-93","OPS_Gruppen_Text":"Angaben zum Transplantat und zu verwendeten Materialien"},
-    {"OPSC_4":"5-98","OPS_Gruppen_Text":"Spezielle Operationstechniken und Operationen bei speziellen Versorgungssituationen "},
-    {"OPSC_4":"8-13","OPS_Gruppen_Text":"Manipulation am Harntrakt"},
-    {"OPSC_4":"8-14","OPS_Gruppen_Text":"Therapeutische Kathedirisierung, Aspiration, Punktion und Spülung "},
-    {"OPSC_4":"8-15","OPS_Gruppen_Text":"Therapeutische Aspiration und Entleerung durch Punktion "},
-    {"OPSC_4":"8-17","OPS_Gruppen_Text":"Spülung (Lavage) "},
-    {"OPSC_4":"8-19","OPS_Gruppen_Text":"Verbände "},
-    {"OPSC_4":"8-77","OPS_Gruppen_Text":"Maßnahmen im Rahmen der Reanimation "},
-    {"OPSC_4":"8-92","OPS_Gruppen_Text":"Neurologisches Monitoring "},
-])
-EOF
-    
-    OVERRIDE+=" -f ./$PROJECT/modules/ovis-compose.yml"
-fi

ccp/modules/teiler-setup.sh

@@ -1,9 +0,0 @@
-#!/bin/bash -e
-
-if [ "$ENABLE_TEILER" == true ];then
-  log INFO "Teiler setup detected -- will start Teiler services."
-  OVERRIDE+=" -f ./$PROJECT/modules/teiler-compose.yml"
-  TEILER_DEFAULT_LANGUAGE=DE
-  TEILER_DEFAULT_LANGUAGE_LOWER_CASE=${TEILER_DEFAULT_LANGUAGE,,}
-  add_public_oidc_redirect_url "/ccp-teiler/*"
-fi

ccp/vars

@@ -20,7 +20,7 @@ OIDC_GROUP_CLAIM="groups"
 
 POSTGRES_TAG=15.6-alpine
 
-for module in $PROJECT/modules/*.sh
+for module in common/*.sh
 do
     log DEBUG "sourcing $module"
     source $module

common/blaze-secondary-compose.yml

@@ -2,7 +2,7 @@ version: "3.7"
 
 services:
   blaze-secondary:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
+    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
     container_name: bridgehead-ccp-blaze-secondary
     environment:
       BASE_URL: "http://bridgehead-ccp-blaze-secondary:8080"

common/blaze-secondary-setup.sh

@@ -3,7 +3,7 @@
 function blazeSecondarySetup() {
   if [ -n "$ENABLE_SECONDARY_BLAZE" ]; then
     log INFO "Secondary Blaze setup detected -- will start second blaze."
-    OVERRIDE+=" -f ./$PROJECT/modules/blaze-secondary-compose.yml"
+    OVERRIDE+=" -f ./common/blaze-secondary-compose.yml"
     #make oBDS2FHIR ignore ID-Management and replace target Blaze
     PATIENTLIST_URL=" "
     STORE_PATH="http://blaze-secondary:8080/fhir"

common/datashield-compose.yml

@@ -151,7 +151,7 @@ services:
       --pass-access-token=false
     labels:
       - "traefik.enable=true"
-      - "traefik.http.routers.oauth2_proxy.rule=PathPrefix(`/oauth2`)"
+      - "traefik.http.routers.oauth2_proxy.rule=Host(`${HOST}`) && PathPrefix(`/oauth2`)"
       - "traefik.http.services.oauth2_proxy.loadbalancer.server.port=4180"
       - "traefik.http.routers.oauth2_proxy.tls=true"
     environment:

common/datashield-setup.sh

@@ -10,7 +10,7 @@ if [ "$ENABLE_DATASHIELD" == true ]; then
   add_private_oidc_redirect_url "${OAUTH2_CALLBACK}"
 
   log INFO "DataSHIELD setup detected -- will start DataSHIELD services."
-  OVERRIDE+=" -f ./$PROJECT/modules/datashield-compose.yml"
+  OVERRIDE+=" -f ./common/datashield-compose.yml"
   EXPORTER_OPAL_PASSWORD="$(generate_password \"exporter in Opal\")"
   TOKEN_MANAGER_OPAL_PASSWORD="$(generate_password \"Token Manager in Opal\")"
   OPAL_DB_PASSWORD="$(echo \"Opal DB\" | generate_simple_password)"
@@ -23,7 +23,7 @@ if [ "$ENABLE_DATASHIELD" == true ]; then
     openssl req -x509 -newkey rsa:4096 -nodes -keyout /tmp/bridgehead/opal-key.pem -out /tmp/bridgehead/opal-cert.pem -days 3650 -subj "/CN=opal/C=DE"
   fi
   mkdir -p /tmp/bridgehead/opal-map
-  sites="$(cat ./$PROJECT/modules/datashield-sites.json)"
+  sites="$(cat ./common/datashield-sites.json)"
   echo "$sites" | docker_jq -n --args '{"sites": input | map({
     "name": .,
     "id": .,

common/datashield-sites.json

@@ -0,0 +1,15 @@
+[
+    "berlin",
+    "muenchen-lmu",
+    "dresden",
+    "freiburg",
+    "muenchen-tum",
+    "tuebingen",
+    "mainz",
+    "frankfurt",
+    "essen",
+    "dktk-datashield-test",
+    "dktk-test",
+    "mannheim",
+    "central-ds-orchestrator"
+]

common/dnpm-compose.yml

@@ -13,7 +13,7 @@ services:
       PROXY_APIKEY: ${DNPM_BEAM_SECRET_SHORT}
       APP_ID: dnpm-connect.${PROXY_ID}
       DISCOVERY_URL: "./conf/central_targets.json"
-      LOCAL_TARGETS_FILE: "/conf/connect_targets.json"
+      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,host.docker.internal${DNPM_ADDITIONAL_NO_PROXY}
@@ -25,7 +25,7 @@ services:
     volumes:
       - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
       - /etc/bridgehead/dnpm/local_targets.json:/conf/connect_targets.json:ro
-      - /srv/docker/bridgehead/minimal/modules/dnpm-central-targets.json:/conf/central_targets.json:ro
+      - /etc/bridgehead/dnpm/central_targets.json:/conf/central_targets.json:ro
     labels:
       - "traefik.enable=true"
       - "traefik.http.routers.dnpm-connect.rule=PathPrefix(`/dnpm-connect`)"

common/dnpm-node-compose.yml

@@ -0,0 +1,34 @@
+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=${ZPM_SITE}
+      - N_RANDOM_FILES=${DNPM_SYNTH_NUM}
+    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"

common/dnpm-node-setup.sh

@@ -0,0 +1,28 @@
+#!/bin/bash
+
+if [ -n "${ENABLE_DNPM_NODE}" ]; then
+	log INFO "DNPM setup detected (BwHC Node) -- will start BwHC node."
+	OVERRIDE+=" -f ./common/dnpm-node-compose.yml"
+
+	# Set variables required for BwHC Node. ZPM_SITE is assumed to be set in /etc/bridgehead/<project>.conf
+	DNPM_APPLICATION_SECRET="$(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 "${DNPM_DATA_DIR+x}" ]; then
+		log ERROR "Mandatory variable DNPM_DATA_DIR not defined!"
+		exit 1
+	fi
+	DNPM_SYNTH_NUM=${DNPM_SYNTH_NUM:-0}
+	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

common/dnpm-setup.sh

@@ -2,7 +2,7 @@
 
 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"
+	OVERRIDE+=" -f ./common/dnpm-compose.yml"
 
 	# Set variables required for Beam-Connect
 	DNPM_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"

common/exporter-setup.sh

@@ -2,7 +2,7 @@
 
 if [ "$ENABLE_EXPORTER" == true ]; then
   log INFO "Exporter setup detected -- will start Exporter service."
-  OVERRIDE+=" -f ./$PROJECT/modules/exporter-compose.yml"
+  OVERRIDE+=" -f ./common/exporter-compose.yml"
   EXPORTER_DB_PASSWORD="$(echo \"This is a salt string to generate one consistent password for the exporter. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
   EXPORTER_API_KEY="$(echo \"This is a salt string to generate one consistent API KEY for the exporter. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 64)"
 fi

common/fhir2sql-compose.yml

@@ -23,7 +23,3 @@ services:
       POSTGRES_DB: "dashboard"
     volumes:
       - "/var/cache/bridgehead/ccp/dashboard-db:/var/lib/postgresql/data"
-
-  focus:
-    environment:
-      POSTGRES_CONNECTION_STRING: "postgresql://dashboard:${DASHBOARD_DB_PASSWORD}@dashboard-db/dashboard"

common/fhir2sql-setup.sh

@@ -2,7 +2,6 @@
 
 if [ "$ENABLE_FHIR2SQL" == true ]; then
   log INFO "Dashboard setup detected -- will start Dashboard backend and FHIR2SQL service."
-  OVERRIDE+=" -f ./$PROJECT/modules/fhir2sql-compose.yml"
+  OVERRIDE+=" -f ./common/fhir2sql-compose.yml"
   DASHBOARD_DB_PASSWORD="$(generate_simple_password 'fhir2sql')"
-  FOCUS_ENDPOINT_TYPE="blaze-and-sql"
 fi

common/id-management-compose.yml

@@ -19,18 +19,10 @@ services:
       - traefik-forward-auth
     labels:
       - "traefik.enable=true"
-      # Router with Authentication
       - "traefik.http.routers.id-manager.rule=PathPrefix(`/id-manager`)"
+      - "traefik.http.services.id-manager.loadbalancer.server.port=8080"
       - "traefik.http.routers.id-manager.tls=true"
       - "traefik.http.routers.id-manager.middlewares=traefik-forward-auth-idm"
-      - "traefik.http.routers.id-manager.service=id-manager-service"
-      # Router without Authentication
-      - "traefik.http.routers.id-manager-compatibility.rule=PathPrefix(`/id-manager/paths/translator/getIds`)"
-      - "traefik.http.routers.id-manager-compatibility.tls=true"
-      - "traefik.http.routers.id-manager-compatibility.service=id-manager-service"
-      # Definition of Service
-      - "traefik.http.services.id-manager-service.loadbalancer.server.port=8080"
-      - "traefik.http.services.id-manager-service.loadbalancer.server.scheme=http"
 
   patientlist:
     image: docker.verbis.dkfz.de/bridgehead/mainzelliste
@@ -65,7 +57,7 @@ services:
       - "/tmp/bridgehead/patientlist/:/docker-entrypoint-initdb.d/"
 
   traefik-forward-auth:
-    image: docker.verbis.dkfz.de/cache/oauth2-proxy/oauth2-proxy:latest
+    image: docker.verbis.dkfz.de/cache/oauth2-proxy/oauth2-proxy:v7.6.0
     environment:
       - http_proxy=http://forward_proxy:3128
       - https_proxy=http://forward_proxy:3128
@@ -75,7 +67,6 @@ services:
       - OAUTH2_PROXY_CLIENT_ID=bridgehead-${SITE_ID}
       - OAUTH2_PROXY_CLIENT_SECRET=${IDMANAGER_AUTH_CLIENT_SECRET}
       - OAUTH2_PROXY_COOKIE_SECRET=${IDMANAGER_AUTH_COOKIE_SECRET}
-      - OAUTH2_PROXY_COOKIE_NAME=_BRIDGEHEAD_oauth2_idm
       - OAUTH2_PROXY_COOKIE_DOMAINS=.${HOST}
       - OAUTH2_PROXY_HTTP_ADDRESS=:4180
       - OAUTH2_PROXY_REVERSE_PROXY=true
@@ -101,12 +92,5 @@ services:
       forward_proxy:
         condition: service_healthy
 
-  ccp-patient-project-identificator:
-    image: docker.verbis.dkfz.de/cache/samply/ccp-patient-project-identificator
-    container_name: bridgehead-ccp-patient-project-identificator
-    environment:
-      MAINZELLISTE_APIKEY: ${IDMANAGER_LOCAL_PATIENTLIST_APIKEY}
-      SITE_NAME: ${IDMANAGEMENT_FRIENDLY_ID}
-
 volumes:
   patientlist-db-data:

common/id-management-setup.sh

@@ -3,7 +3,7 @@
 function idManagementSetup() {
 	if [ -n "$IDMANAGER_UPLOAD_APIKEY" ]; then
 		log INFO "id-management setup detected -- will start id-management (mainzelliste & magicpl)."
-		OVERRIDE+=" -f ./ccp/modules/id-management-compose.yml"
+		OVERRIDE+=" -f ./common/id-management-compose.yml"
 
 		# Auto Generate local Passwords
 		PATIENTLIST_POSTGRES_PASSWORD="$(echo \"id-management-module-db-password-salt\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"

common/lens-setup.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+
+if [ -n "$ENABLE_LENS" ];then
+  OVERRIDE+=" -f ./common/lens-compose.yml"
+fi

common/mtba-setup.sh

@@ -6,7 +6,7 @@ function mtbaSetup() {
     if [ ! -n "$IDMANAGER_UPLOAD_APIKEY" ]; then
       log ERROR "Missing ID-Management Module! Fix this by setting up ID Management:"
     fi
-    OVERRIDE+=" -f ./$PROJECT/modules/mtba-compose.yml"
+    OVERRIDE+=" -f ./common/mtba-compose.yml"
     add_private_oidc_redirect_url "/mtba/*"
   fi
 }

common/nngm-compose.yml

@@ -12,6 +12,7 @@ services:
       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`)"

common/nngm-setup.sh

@@ -2,5 +2,5 @@
 
 if [ -n "$NNGM_CTS_APIKEY" ]; then
   log INFO "nNGM setup detected -- will start nNGM Connector."
-  OVERRIDE+=" -f ./$PROJECT/modules/nngm-compose.yml"
+  OVERRIDE+=" -f ./common/nngm-compose.yml"
 fi

common/obds2fhir-rest-compose.yml

@@ -10,6 +10,7 @@ services:
       SALT: ${LOCAL_SALT}
       KEEP_INTERNAL_ID: ${KEEP_INTERNAL_ID:-false}
       MAINZELLISTE_URL: ${PATIENTLIST_URL:-http://patientlist:8080/patientlist}
+    restart: always
     labels:
       - "traefik.enable=true"
       - "traefik.http.routers.obds2fhir-rest.rule=PathPrefix(`/obds2fhir-rest`) || PathPrefix(`/adt2fhir-rest`)"

common/obds2fhir-rest-setup.sh

@@ -7,7 +7,7 @@ function obds2fhirRestSetup() {
       log ERROR "Missing ID-Management Module! Fix this by setting up ID Management:"
       PATIENTLIST_URL=" "
     fi
-    OVERRIDE+=" -f ./ccp/modules/obds2fhir-rest-compose.yml"
+    OVERRIDE+=" -f ./common/obds2fhir-rest-compose.yml"
     LOCAL_SALT="$(echo \"local-random-salt\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
   fi
 }

common/teiler-setup.sh

@@ -2,7 +2,7 @@
 
 if [ "$ENABLE_TEILER" == true ];then
   log INFO "Teiler setup detected -- will start Teiler services."
-  OVERRIDE+=" -f ./$PROJECT/modules/teiler-compose.yml"
+  OVERRIDE+=" -f ./common/teiler-compose.yml"
   TEILER_DEFAULT_LANGUAGE=DE
   TEILER_DEFAULT_LANGUAGE_LOWER_CASE=${TEILER_DEFAULT_LANGUAGE,,}
   add_public_oidc_redirect_url "/ccp-teiler/*"

dhki/docker-compose.yml

@@ -2,7 +2,7 @@ version: "3.7"
 
 services:
   blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
+    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
     container_name: bridgehead-dhki-blaze
     environment:
       BASE_URL: "http://bridgehead-dhki-blaze:8080"

dhki/vars

@@ -10,19 +10,11 @@ BROKER_URL_FOR_PREREQ=$BROKER_URL
 
 POSTGRES_TAG=15.6-alpine
 
-for module in ccp/modules/*.sh
+for module in common/*.sh
 do
     log DEBUG "sourcing $module"
     source $module
 done
 
 idManagementSetup
-obds2fhirRestSetup
+obds2fhirRestSetup
-
-for module in modules/*.sh
-do
-    log DEBUG "sourcing $module"
-    source $module
-done
-
-transfairSetup

docs/update-access-token.md

@@ -1,42 +0,0 @@
-## How to Change Config Access Token
-
-### 1. Generate a New Access Token
-
-1. Go to your Git configuration repository provider, it might be either [git.verbis.dkfz.de](https://git.verbis.dkfz.de) or [gitlab.bbmri-eric.eu](https://gitlab.bbmri-eric.eu).  
-2. Navigate to the configuration repository for your site.  
-3. Go to **Settings → Access Tokens** to check if your Access Token is valid or expired.  
-   - **If expired**, create a new Access Token.  
-4. Configure the new Access Token with the following settings:  
-   - **Expiration date**: One year from today, minus one day.  
-   - **Role**: Developer.  
-   - **Scope**: Only `read_repository`.  
-5. Save the newly generated Access Token in a secure location.  
-
----
-
-### 2. Replace the Old Access Token
-
-1. Navigate to `/etc/bridgehead` in your system.  
-2. Run the following command to retrieve the current Git remote URL:  
-   ```bash
-   git remote get-url origin
-   ```
-   Example output:  
-   ```
-   https://name40dkfz-heidelberg.de:<old_access_token>@git.verbis.dkfz.de/bbmri-bridgehead-configs/test.git
-   ```
-3. Replace `<old_access_token>` with your new Access Token in the URL.  
-4. Set the updated URL using the following command:  
-   ```bash
-   git remote set-url origin https://name40dkfz-heidelberg.de:<new_access_token>@git.verbis.dkfz.de/bbmri-bridgehead-configs/test.git
-   
-   ```
-
-5. Start the Bridgehead update service by running:  
-   ```bash
-   systemctl start bridgehead-update@<project>
-   ```
-6. View the output to ensure the update process is successful:  
-   ```bash
-   journalctl -u bridgehead-update@<project> -f
-   ```

itcc/docker-compose.yml

@@ -2,7 +2,7 @@ version: "3.7"
 
 services:
   blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
+    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
     container_name: bridgehead-itcc-blaze
     environment:
       BASE_URL: "http://bridgehead-itcc-blaze:8080"

itcc/modules/lens-setup.sh

@@ -1,5 +0,0 @@
-#!/bin/bash
-
-if [ -n "$ENABLE_LENS" ];then
-  OVERRIDE+=" -f ./$PROJECT/modules/lens-compose.yml"
-fi

itcc/vars

@@ -7,7 +7,7 @@ SUPPORT_EMAIL=arturo.macias@dkfz-heidelberg.de
 PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
 BROKER_URL_FOR_PREREQ=$BROKER_URL
 
-for module in $PROJECT/modules/*.sh
+for module in common/*.sh
 do
     log DEBUG "sourcing $module"
     source $module

kr/docker-compose.yml

@@ -1,12 +1,8 @@
 version: "3.7"
 
 services:
-  landing:
-    deploy:
-      replicas: 0 #deactivate landing page
-
   blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
+    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
     container_name: bridgehead-kr-blaze
     environment:
       BASE_URL: "http://bridgehead-kr-blaze:8080"

kr/modules/exporter.md

@@ -1,15 +0,0 @@
-# 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.

kr/modules/lens-compose.yml

@@ -1,35 +0,0 @@
-version: "3.7"
-services:
-  landing:
-    deploy:
-      replicas: 1 #reactivate if lens is in use
-    container_name: lens_federated-search
-    image: docker.verbis.dkfz.de/ccp/lens:${SITE_ID}
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.landing.rule=PathPrefix(`/`)"
-      - "traefik.http.services.landing.loadbalancer.server.port=80"
-      - "traefik.http.routers.landing.tls=true"
-
-  spot:
-    image: docker.verbis.dkfz.de/ccp-private/central-spot
-    environment:
-      BEAM_SECRET: "${FOCUS_BEAM_SECRET_SHORT}"
-      BEAM_URL: http://beam-proxy:8081
-      BEAM_PROXY_ID: ${SITE_ID}
-      BEAM_BROKER_ID: ${BROKER_ID}
-      BEAM_APP_ID: "focus"
-      PROJECT_METADATA: "kr_supervisors"
-    depends_on:
-      - "beam-proxy"
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.services.spot.loadbalancer.server.port=8080"
-      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowmethods=GET,OPTIONS,POST"
-      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolalloworiginlist=https://${HOST}"
-      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowcredentials=true"
-      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolmaxage=-1"
-      - "traefik.http.routers.spot.rule=Host(`${HOST}`) && PathPrefix(`/backend`)"
-      - "traefik.http.middlewares.stripprefix_spot.stripprefix.prefixes=/backend"
-      - "traefik.http.routers.spot.tls=true"
-      - "traefik.http.routers.spot.middlewares=corsheaders2,stripprefix_spot"

kr/modules/lens-setup.sh

@@ -1,5 +0,0 @@
-#!/bin/bash
-
-if [ -n "$ENABLE_LENS" ];then
-  OVERRIDE+=" -f ./$PROJECT/modules/lens-compose.yml"
-fi

kr/modules/obds2fhir-rest-compose.yml

@@ -1,19 +0,0 @@
-version: "3.7"
-
-services:
-  obds2fhir-rest:
-    container_name: bridgehead-obds2fhir-rest
-    image: docker.verbis.dkfz.de/ccp/obds2fhir-rest:main
-    environment:
-      IDTYPE: BK_${IDMANAGEMENT_FRIENDLY_ID}_L-ID
-      MAINZELLISTE_APIKEY: ${IDMANAGER_LOCAL_PATIENTLIST_APIKEY}
-      SALT: ${LOCAL_SALT}
-      KEEP_INTERNAL_ID: ${KEEP_INTERNAL_ID:-false}
-      MAINZELLISTE_URL: ${PATIENTLIST_URL:-http://patientlist:8080/patientlist}
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.obds2fhir-rest.rule=PathPrefix(`/obds2fhir-rest`) || PathPrefix(`/adt2fhir-rest`)"
-      - "traefik.http.middlewares.obds2fhir-rest_strip.stripprefix.prefixes=/obds2fhir-rest,/adt2fhir-rest"
-      - "traefik.http.services.obds2fhir-rest.loadbalancer.server.port=8080"
-      - "traefik.http.routers.obds2fhir-rest.tls=true"
-      - "traefik.http.routers.obds2fhir-rest.middlewares=obds2fhir-rest_strip,auth"

kr/modules/obds2fhir-rest-setup.sh

@@ -1,13 +0,0 @@
-#!/bin/bash
-
-function obds2fhirRestSetup() {
-  if [ -n "$ENABLE_OBDS2FHIR_REST" ]; then
-    log INFO "oBDS2FHIR-REST setup detected -- will start obds2fhir-rest module."
-    if [ ! -n "$IDMANAGER_UPLOAD_APIKEY" ]; then
-      log ERROR "Missing ID-Management Module! Fix this by setting up ID Management:"
-      PATIENTLIST_URL=" "
-    fi
-    OVERRIDE+=" -f ./$PROJECT/modules/obds2fhir-rest-compose.yml"
-    LOCAL_SALT="$(echo \"local-random-salt\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
-  fi
-}

kr/modules/teiler-compose.yml

@@ -1,81 +0,0 @@
-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: "${TEILER_DEFAULT_LANGUAGE_LOWER_CASE}"
-      HTTP_RELATIVE_PATH: "/ccp-teiler"
-
-  teiler-dashboard:
-    image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:develop
-    container_name: bridgehead-teiler-dashboard
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.teiler_dashboard_ccp.rule=PathPrefix(`/ccp-teiler-dashboard`)"
-      - "traefik.http.services.teiler_dashboard_ccp.loadbalancer.server.port=80"
-      - "traefik.http.routers.teiler_dashboard_ccp.tls=true"
-      - "traefik.http.middlewares.teiler_dashboard_ccp_strip.stripprefix.prefixes=/ccp-teiler-dashboard"
-      - "traefik.http.routers.teiler_dashboard_ccp.middlewares=teiler_dashboard_ccp_strip"
-    environment:
-      DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
-      TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend"
-      OIDC_URL: "${OIDC_URL}"
-      OIDC_REALM: "${OIDC_REALM}"
-      OIDC_CLIENT_ID: "${OIDC_PUBLIC_CLIENT_ID}"
-      OIDC_TOKEN_GROUP: "${OIDC_GROUP_CLAIM}"
-      TEILER_ADMIN_NAME: "${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: "${OIDC_USER_GROUP}"
-      TEILER_ADMIN: "${OIDC_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
-    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: "${HOST}"
-      DEFAULT_LANGUAGE: "${TEILER_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

kr/modules/teiler.md

@@ -1,19 +0,0 @@
-# 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.

kr/vars

@@ -7,7 +7,7 @@ SUPPORT_EMAIL=arturo.macias@dkfz-heidelberg.de
 PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
 BROKER_URL_FOR_PREREQ=$BROKER_URL
 
-for module in $PROJECT/modules/*.sh
+for module in common/*.sh
 do
     log DEBUG "sourcing $module"
     source $module

lib/functions.sh

@@ -116,7 +116,7 @@ assertVarsNotEmpty() {
 	MISSING_VARS=""
 
 	for VAR in $@; do
-		if [ -z "${!VAR}" ]; then
+	if [ -z "${!VAR}" ]; then
 			MISSING_VARS+="$VAR "
 		fi
 	done
@@ -171,10 +171,8 @@ optimizeBlazeMemoryUsage() {
 		if [ $available_system_memory_chunks -eq 0 ]; then
 			log WARN "Only ${BLAZE_MEMORY_CAP} system memory available for Blaze. If your Blaze stores more than 128000 fhir ressources it will run significally slower."
 			export BLAZE_RESOURCE_CACHE_CAP=128000;
-			export BLAZE_CQL_CACHE_CAP=32;
 		else
 			export BLAZE_RESOURCE_CACHE_CAP=$((available_system_memory_chunks * 312500))
-			export BLAZE_CQL_CACHE_CAP=$((($system_memory_in_mb/4)/16));
 		fi
 	fi
 }
@@ -318,7 +316,7 @@ function sync_secrets() {
         docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest
 
     set -a # Export variables as environment variables
-    source /var/cache/bridgehead/secrets/oidc
+    source /var/cache/bridgehead/secrets/*
     set +a # Export variables in the regular way
 }
 

lib/gitlab-token-helper.sh

@@ -1,11 +0,0 @@
-#!/bin/bash
-
-[ "$1" = "get" ] || exit
-
-source /var/cache/bridgehead/secrets/gitlab_token
-
-# Any non-empty username works, only the token matters
-cat << EOF
-username=bk
-password=$BRIDGEHEAD_CONFIG_REPO_TOKEN
-EOF

lib/gitpassword.sh

@@ -0,0 +1,41 @@
+#!/bin/bash
+
+if [ "$1" != "get" ]; then
+	echo "Usage: $0 get"
+	exit 1
+fi
+
+baseDir() {
+	# see https://stackoverflow.com/questions/59895
+	SOURCE=${BASH_SOURCE[0]}
+	while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
+		DIR=$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )
+		SOURCE=$(readlink "$SOURCE")
+		[[ $SOURCE != /* ]] && SOURCE=$DIR/$SOURCE # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
+        done
+        DIR=$( cd -P "$( dirname "$SOURCE" )/.." >/dev/null 2>&1 && pwd )
+        echo $DIR
+}
+
+BASE=$(baseDir)
+cd $BASE
+
+source lib/functions.sh
+
+assertVarsNotEmpty SITE_ID || fail_and_report 1 "gitpassword.sh failed: SITE_ID is empty."
+
+PARAMS="$(cat)"
+GITHOST=$(echo "$PARAMS" | grep "^host=" | sed 's/host=\(.*\)/\1/g')
+
+fetchVarsFromVault GIT_PASSWORD
+
+if [ -z "${GIT_PASSWORD}" ]; then
+	fail_and_report 1 "gitpassword.sh failed: Git password not found."
+fi
+
+cat <<EOF
+protocol=https
+host=$GITHOST
+username=bk-${SITE_ID}
+password=${GIT_PASSWORD}
+EOF

lib/prerequisites.sh

@@ -3,16 +3,14 @@
 source lib/functions.sh
 
 detectCompose
-CONFIG_DIR="/etc/bridgehead/"
-COMPONENT_DIR="/srv/docker/bridgehead/"
 
 if ! id "bridgehead" &>/dev/null; then
   log ERROR "User bridgehead does not exist. Please run bridgehead install $PROJECT"
   exit 1
 fi
 
-checkOwner "${CONFIG_DIR}" bridgehead || exit 1
+checkOwner /srv/docker/bridgehead bridgehead || exit 1
-checkOwner "${COMPONENT_DIR}" bridgehead || exit 1
+checkOwner /etc/bridgehead bridgehead || exit 1
 
 ## Check if user is a su
 log INFO "Checking if all prerequisites are met ..."
@@ -34,31 +32,31 @@ fi
 log INFO "Checking configuration ..."
 
 ## Download submodule
-if [ ! -d "${CONFIG_DIR}" ]; then
+if [ ! -d "/etc/bridgehead/" ]; then
-  fail_and_report 1 "Please set up the config folder at ${CONFIG_DIR}. Instruction are in the readme."
+  fail_and_report 1 "Please set up the config folder at /etc/bridgehead. Instruction are in the readme."
 fi
 
 # TODO: Check all required variables here in a generic loop
 
 #check if project env is present
-if [ -d "${CONFIG_DIR}${PROJECT}.conf" ]; then
+if [ -d "/etc/bridgehead/${PROJECT}.conf" ]; then
-   fail_and_report 1 "Project config not found. Please copy the template from ${PROJECT} and put it under ${CONFIG_DIR}${PROJECT}.conf."
+   fail_and_report 1 "Project config not found. Please copy the template from ${PROJECT} and put it under /etc/bridgehead-config/${PROJECT}.conf."
 fi
 
 # TODO: Make sure you're in the right directory, or, even better, be independent from the working directory.
 
 log INFO "Checking ssl cert for accessing bridgehead via https"
 
-if [ ! -d "${CONFIG_DIR}traefik-tls" ]; then
+if [ ! -d "/etc/bridgehead/traefik-tls" ]; then
   log WARN "TLS certs for accessing bridgehead via https missing, we'll now create a self-signed one. Please consider getting an officially signed one (e.g. via Let's Encrypt ...) and put into /etc/bridgehead/traefik-tls"
   mkdir -p /etc/bridgehead/traefik-tls
 fi
 
-if [ ! -e "${CONFIG_DIR}traefik-tls/fullchain.pem" ]; then
+if [ ! -e "/etc/bridgehead/traefik-tls/fullchain.pem" ]; then
   openssl req -x509 -newkey rsa:4096 -nodes -keyout /etc/bridgehead/traefik-tls/privkey.pem -out /etc/bridgehead/traefik-tls/fullchain.pem -days 3650 -subj "/CN=$HOST"
 fi
 
-if [ -e "${CONFIG_DIR}"vault.conf ]; then
+if [ -e /etc/bridgehead/vault.conf ]; then
   if [ "$(stat -c "%a %U" /etc/bridgehead/vault.conf)" != "600 bridgehead" ]; then
     fail_and_report 1 "/etc/bridgehead/vault.conf has wrong owner/permissions. To correct this issue, run chmod 600 /etc/bridgehead/vault.conf && chown bridgehead /etc/bridgehead/vault.conf."
   fi
@@ -66,7 +64,7 @@ fi
 
 log INFO "Checking network access ($BROKER_URL_FOR_PREREQ) ..."
 
-source "${CONFIG_DIR}${PROJECT}".conf
+source /etc/bridgehead/${PROJECT}.conf
 source ${PROJECT}/vars
 
 if [ "${PROJECT}" != "minimal" ]; then
@@ -94,10 +92,10 @@ if [ "${PROJECT}" != "minimal" ]; then
   fi
 fi
 checkPrivKey() {
-  if [ -e "${CONFIG_DIR}pki/${SITE_ID}.priv.pem" ]; then
+  if [ -e /etc/bridgehead/pki/${SITE_ID}.priv.pem ]; then
     log INFO "Success - private key found."
   else
-    log ERROR "Unable to find private key at ${CONFIG_DIR}pki/${SITE_ID}.priv.pem. To fix, please run\n  bridgehead enroll ${PROJECT}\nand follow the instructions."
+    log ERROR "Unable to find private key at /etc/bridgehead/pki/${SITE_ID}.priv.pem. To fix, please run\n  bridgehead enroll ${PROJECT}\nand follow the instructions."
     return 1
   fi
   return 0
@@ -109,11 +107,6 @@ else
   checkPrivKey || exit 1
 fi
 
-for dir in  "${CONFIG_DIR}" "${COMPONENT_DIR}"; do
-  log INFO "Checking branch: $(cd $dir && echo "$dir $(git branch --show-current)")"
-  hc_send log "Checking branch: $(cd $dir && echo "$dir $(git branch --show-current)")"
-done
-
 log INFO "Success - all prerequisites are met!"
 hc_send log "Success - all prerequisites are met!"
 

lib/update-bridgehead.sh

@@ -19,7 +19,7 @@ fi
 
 hc_send log "Checking for bridgehead updates ..."
 
-CONFFILE=/etc/bridgehead/$PROJECT.conf
+CONFFILE=/etc/bridgehead/$1.conf
 
 if [ ! -e $CONFFILE ]; then
   fail_and_report 1 "Configuration file $CONFFILE not found."
@@ -33,43 +33,7 @@ export SITE_ID
 checkOwner /srv/docker/bridgehead bridgehead || fail_and_report 1 "Update failed: Wrong permissions in /srv/docker/bridgehead"
 checkOwner /etc/bridgehead bridgehead || fail_and_report 1 "Update failed: Wrong permissions in /etc/bridgehead"
 
-# Use Secret Sync to validate the GitLab token in /var/cache/bridgehead/secrets/gitlab_token.
+CREDHELPER="/srv/docker/bridgehead/lib/gitpassword.sh"
-# If it is missing or expired, Secret Sync will create a new token and write it to the file.
-# The git credential helper reads the token from the file during git pull.
-mkdir -p /var/cache/bridgehead/secrets
-touch /var/cache/bridgehead/secrets/gitlab_token # the file has to exist to be mounted correctly in the Docker container
-log "INFO" "Running Secret Sync for the GitLab token"
-docker pull docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest # make sure we have the latest image
-docker run --rm \
-  -v /var/cache/bridgehead/secrets/gitlab_token:/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 NO_PROXY=localhost,127.0.0.1 \
-  -e ALL_PROXY=$HTTPS_PROXY_FULL_URL \
-  -e PROXY_ID=$PROXY_ID \
-  -e BROKER_URL=$BROKER_URL \
-  -e GITLAB_PROJECT_ACCESS_TOKEN_PROVIDER=secret-sync-central.oidc-client-enrollment.$BROKER_ID \
-  -e SECRET_DEFINITIONS=GitLabProjectAccessToken:BRIDGEHEAD_CONFIG_REPO_TOKEN: \
-  docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest
-if [ $? -eq 0 ]; then
-  log "INFO" "Secret Sync was successful"
-  # In the past we used to hardcode tokens into the repository URL. We have to remove those now for the git credential helper to become effective.
-  CLEAN_REPO="$(git -C /etc/bridgehead remote get-url origin | sed -E 's|https://[^@]+@|https://|')"
-  git -C /etc/bridgehead remote set-url origin "$CLEAN_REPO"
-  # Set the git credential helper
-  git -C /etc/bridgehead config credential.helper /srv/docker/bridgehead/lib/gitlab-token-helper.sh
-else
-  log "WARN" "Secret Sync failed"
-  # Remove the git credential helper
-  git -C /etc/bridgehead config --unset credential.helper
-fi
-
-# In the past the git credential helper was also set for /srv/docker/bridgehead but never used.
-# Let's remove it to avoid confusion. This line can be removed at some point the future when we
-# believe that it was removed on all/most production servers.
-git -C /srv/docker/bridgehead config --unset credential.helper
 
 CHANGES=""
 
@@ -81,6 +45,10 @@ for DIR in /etc/bridgehead $(pwd); do
   if [ -n "$OUT" ]; then
     report_error log "The working directory $DIR is modified. Changed files: $OUT"
   fi
+  if [ "$(git -C $DIR config --get credential.helper)" != "$CREDHELPER" ]; then
+    log "INFO" "Configuring repo to use bridgehead git credential helper."
+    git -C $DIR config credential.helper "$CREDHELPER"
+  fi
   old_git_hash="$(git -C $DIR rev-parse --verify HEAD)"
   if [ -z "$HTTPS_PROXY_FULL_URL" ]; then
     log "INFO" "Git is using no proxy!"
@@ -90,8 +58,7 @@ for DIR in /etc/bridgehead $(pwd); do
     OUT=$(retry 5 git -c http.proxy=$HTTPS_PROXY_FULL_URL -c https.proxy=$HTTPS_PROXY_FULL_URL -C $DIR fetch 2>&1 && retry 5 git -c http.proxy=$HTTPS_PROXY_FULL_URL -c https.proxy=$HTTPS_PROXY_FULL_URL -C $DIR pull 2>&1)
   fi
   if [ $? -ne 0 ]; then
-    OUT_SAN=$(echo $OUT | sed -E 's|://[^:]+:[^@]+@|://credentials@|g')
+    report_error log "Unable to update git $DIR: $OUT"
-    report_error log "Unable to update git $DIR: $OUT_SAN"
   fi
 
   new_git_hash="$(git -C $DIR rev-parse --verify HEAD)"

minimal/docker-compose.yml

@@ -10,13 +10,13 @@ services:
       - --providers.docker=true
       - --providers.docker.exposedbydefault=false
       - --providers.file.directory=/configuration/
-      - --api.dashboard=false
+      - --api.dashboard=true
       - --accesslog=true
       - --entrypoints.web.http.redirections.entrypoint.to=websecure
       - --entrypoints.web.http.redirections.entrypoint.scheme=https
     labels:
       - "traefik.enable=true"
-      - "traefik.http.routers.dashboard.rule=PathPrefix(`/dashboard/`)"
+      - "traefik.http.routers.dashboard.rule=PathPrefix(`/api`) || PathPrefix(`/dashboard`)"
       - "traefik.http.routers.dashboard.entrypoints=websecure"
       - "traefik.http.routers.dashboard.service=api@internal"
       - "traefik.http.routers.dashboard.tls=true"

minimal/modules/dnpm-central-targets.json

@@ -1,142 +0,0 @@
-{
-    "sites": [
-        {
-            "id": "UKFR",
-            "name": "Freiburg",
-            "virtualhost": "ukfr.dnpm.de",
-            "beamconnect": "dnpm-connect.dnpm-bridge.broker.ccp-it.dktk.dkfz.de"
-        },
-        {
-            "id": "UKHD",
-            "name": "Heidelberg",
-            "virtualhost": "ukhd.dnpm.de",
-            "beamconnect": "dnpm-connect.dnpm-bridge.broker.ccp-it.dktk.dkfz.de"
-        },
-        {
-            "id": "UKT",
-            "name": "Tübingen",
-            "virtualhost": "ukt.dnpm.de",
-            "beamconnect": "dnpm-connect.dnpm-bridge.broker.ccp-it.dktk.dkfz.de"
-        },
-        {
-            "id": "UKU",
-            "name": "Ulm",
-            "virtualhost": "uku.dnpm.de",
-            "beamconnect": "dnpm-connect.dnpm-bridge.broker.ccp-it.dktk.dkfz.de"
-        },
-        {
-            "id": "UM",
-            "name": "Mainz",
-            "virtualhost": "um.dnpm.de",
-            "beamconnect": "dnpm-connect.dnpm-bridge.broker.ccp-it.dktk.dkfz.de"
-        },
-        {
-            "id": "UKMR",
-            "name": "Marburg",
-            "virtualhost": "ukmr.dnpm.de",
-            "beamconnect": "dnpm-connect.dnpm-bridge.broker.ccp-it.dktk.dkfz.de"
-        },
-        {
-            "id": "UKE",
-            "name": "Hamburg",
-            "virtualhost": "uke.dnpm.de",
-            "beamconnect": "dnpm-connect.dnpm-bridge.broker.ccp-it.dktk.dkfz.de"
-        },
-        {
-            "id": "UKA",
-            "name": "Aachen",
-            "virtualhost": "uka.dnpm.de",
-            "beamconnect": "dnpm-connect.dnpm-bridge.broker.ccp-it.dktk.dkfz.de"
-        },
-        {
-            "id": "Charite",
-            "name": "Berlin",
-            "virtualhost": "charite.dnpm.de",
-            "beamconnect": "dnpm-connect.berlin-test.broker.ccp-it.dktk.dkfz.de"
-        },
-        {
-            "id": "MRI",
-            "name": "Muenchen-tum",
-            "virtualhost": "mri.dnpm.de",
-            "beamconnect": "dnpm-connect.muenchen-tum.broker.ccp-it.dktk.dkfz.de"
-        },
-        {
-            "id": "KUM",
-            "name": "Muenchen-lmu",
-            "virtualhost": "kum.dnpm.de",
-            "beamconnect": "dnpm-connect.muenchen-lmu.broker.ccp-it.dktk.dkfz.de"
-        },
-        {
-            "id": "MHH",
-            "name": "Hannover",
-            "virtualhost": "mhh.dnpm.de",
-            "beamconnect": "dnpm-connect.hannover.broker.ccp-it.dktk.dkfz.de"
-        },
-        {
-            "id": "UKDD",
-            "name": "dresden-dnpm",
-            "virtualhost": "ukdd.dnpm.de",
-            "beamconnect": "dnpm-connect.dresden-dnpm.broker.ccp-it.dktk.dkfz.de"
-        },
-        {
-            "id": "UKB",
-            "name": "Bonn",
-            "virtualhost": "ukb.dnpm.de",
-            "beamconnect": "dnpm-connect.bonn-dnpm.broker.ccp-it.dktk.dkfz.de"
-        },
-        {
-            "id": "UKD",
-            "name": "Duesseldorf",
-            "virtualhost": "ukd.dnpm.de",
-            "beamconnect": "dnpm-connect.duesseldorf-dnpm.broker.ccp-it.dktk.dkfz.de"
-        },
-        {
-            "id": "UKK",
-            "name": "Koeln",
-            "virtualhost": "ukk.dnpm.de",
-            "beamconnect": "dnpm-connect.dnpm-bridge.broker.ccp-it.dktk.dkfz.de"
-        },
-        {
-            "id": "UME",
-            "name": "Essen",
-            "virtualhost": "ume.dnpm.de",
-            "beamconnect": "dnpm-connect.essen.broker.ccp-it.dktk.dkfz.de"
-        },
-        {
-            "id": "UKM",
-            "name": "Muenster",
-            "virtualhost": "ukm.dnpm.de",
-            "beamconnect": "dnpm-connect.muenster-dnpm.broker.ccp-it.dktk.dkfz.de"
-        },
-        {
-            "id": "UKF",
-            "name": "Frankfurt",
-            "virtualhost": "ukf.dnpm.de",
-            "beamconnect": "dnpm-connect.frankfurt.broker.ccp-it.dktk.dkfz.de"
-        },
-        {
-            "id": "UMG",
-            "name": "Goettingen",
-            "virtualhost": "umg.dnpm.de",
-            "beamconnect": "dnpm-connect.goettingen.broker.ccp-it.dktk.dkfz.de"
-        },
-        {
-            "id": "UKW",
-            "name": "Würzburg",
-            "virtualhost": "ukw.dnpm.de",
-            "beamconnect": "dnpm-connect.wuerzburg-dnpm.broker.ccp-it.dktk.dkfz.de"
-        },
-        {
-            "id": "UKSH",
-            "name": "Schleswig-Holstein",
-            "virtualhost": "uksh.dnpm.de",
-            "beamconnect": "dnpm-connect.uksh-dnpm.broker.ccp-it.dktk.dkfz.de"
-        },
-        {
-            "id": "TKT",
-            "name": "Test",
-            "virtualhost": "tkt.dnpm.de",
-            "beamconnect": "dnpm-connect.tobias-develop.broker.ccp-it.dktk.dkfz.de"
-        }
-    ]
-}

minimal/modules/dnpm-compose.yml

@@ -29,7 +29,7 @@ services:
       PROXY_APIKEY: ${DNPM_BEAM_SECRET_SHORT}
       APP_ID: dnpm-connect.${DNPM_PROXY_ID}
       DISCOVERY_URL: "./conf/central_targets.json"
-      LOCAL_TARGETS_FILE: "/conf/connect_targets.json"
+      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, host.docker.internal${DNPM_ADDITIONAL_NO_PROXY}
@@ -41,7 +41,7 @@ services:
     volumes:
       - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
       - /etc/bridgehead/dnpm/local_targets.json:/conf/connect_targets.json:ro
-      - /srv/docker/bridgehead/minimal/modules/dnpm-central-targets.json:/conf/central_targets.json:ro
+      - /etc/bridgehead/dnpm/central_targets.json:/conf/central_targets.json:ro
     labels:
       - "traefik.enable=true"
       - "traefik.http.routers.dnpm-connect.rule=PathPrefix(`/dnpm-connect`)"

minimal/modules/dnpm-node-compose.yml

@@ -1,99 +1,34 @@
 version: "3.7"
 
 services:
-  dnpm-mysql:
-    image: mysql:9
-    healthcheck:
-      test: [ "CMD", "mysqladmin" ,"ping", "-h", "localhost" ]
-      interval: 3s
-      timeout: 5s
-      retries: 5
-    environment:
-      MYSQL_ROOT_HOST: "%"
-      MYSQL_ROOT_PASSWORD: ${DNPM_MYSQL_ROOT_PASSWORD}
-    volumes:
-      - /var/cache/bridgehead/dnpm/mysql:/var/lib/mysql
-
-  dnpm-authup:
-    image: authup/authup:latest
-    container_name: bridgehead-dnpm-authup
-    volumes:
-      - /var/cache/bridgehead/dnpm/authup:/usr/src/app/writable
-    depends_on:
-      dnpm-mysql:
-        condition: service_healthy
-    command: server/core start
-    environment:
-      - PUBLIC_URL=https://${HOST}/auth/
-      - AUTHORIZE_REDIRECT_URL=https://${HOST}
-      - ROBOT_ADMIN_ENABLED=true
-      - ROBOT_ADMIN_SECRET=${DNPM_AUTHUP_SECRET}
-      - ROBOT_ADMIN_SECRET_RESET=true
-      - DB_TYPE=mysql
-      - DB_HOST=dnpm-mysql
-      - DB_USERNAME=root
-      - DB_PASSWORD=${DNPM_MYSQL_ROOT_PASSWORD}
-      - DB_DATABASE=auth
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.middlewares.authup-strip.stripprefix.prefixes=/auth/"
-      - "traefik.http.routers.dnpm-auth.middlewares=authup-strip"
-      - "traefik.http.routers.dnpm-auth.rule=PathPrefix(`/auth`)"
-      - "traefik.http.services.dnpm-auth.loadbalancer.server.port=3000"
-      - "traefik.http.routers.dnpm-auth.tls=true"
-
-  dnpm-portal:
-    image: ghcr.io/dnpm-dip/portal:latest
-    container_name: bridgehead-dnpm-portal
-    environment:
-      - NUXT_API_URL=http://dnpm-backend:9000/
-      - NUXT_PUBLIC_API_URL=https://${HOST}/api/
-      - NUXT_AUTHUP_URL=http://dnpm-authup:3000/
-      - NUXT_PUBLIC_AUTHUP_URL=https://${HOST}/auth/
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.dnpm-frontend.rule=PathPrefix(`/`)"
-      - "traefik.http.services.dnpm-frontend.loadbalancer.server.port=3000"
-      - "traefik.http.routers.dnpm-frontend.tls=true"
-
   dnpm-backend:
+    image: ghcr.io/kohlbacherlab/bwhc-backend:1.0-snapshot-broker-connector
     container_name: bridgehead-dnpm-backend
-    image: ghcr.io/dnpm-dip/backend:latest
     environment:
-      - LOCAL_SITE=${ZPM_SITE}:${SITE_NAME}   # Format: {Site-ID}:{Site-name}, e.g. UKT:Tübingen
+      - ZPM_SITE=${ZPM_SITE}
-      - RD_RANDOM_DATA=${DNPM_SYNTH_NUM:--1}
+      - N_RANDOM_FILES=${DNPM_SYNTH_NUM}
-      - MTB_RANDOM_DATA=${DNPM_SYNTH_NUM:--1}
-      - HATEOAS_HOST=https://${HOST}
-      - CONNECTOR_TYPE=broker
-      - AUTHUP_URL=robot://system:${DNPM_AUTHUP_SECRET}@http://dnpm-authup:3000
     volumes:
-      - /etc/bridgehead/dnpm/config:/dnpm_config
+      - /etc/bridgehead/dnpm:/bwhc_config:ro
-      - /var/cache/bridgehead/dnpm/backend-data:/dnpm_data
+      - ${DNPM_DATA_DIR}:/bwhc_data
-    depends_on:
-      dnpm-authup:
-        condition: service_healthy
     labels:
       - "traefik.enable=true"
-      - "traefik.http.services.dnpm-backend.loadbalancer.server.port=9000"
+      - "traefik.http.routers.bwhc-backend.rule=PathPrefix(`/bwhc`)"
-      # expose everything
+      - "traefik.http.services.bwhc-backend.loadbalancer.server.port=9000"
-      - "traefik.http.routers.dnpm-backend.rule=PathPrefix(`/api`)"
+      - "traefik.http.routers.bwhc-backend.tls=true"
-      - "traefik.http.routers.dnpm-backend.tls=true"
-      - "traefik.http.routers.dnpm-backend.service=dnpm-backend"
-      # except ETL
-      - "traefik.http.routers.dnpm-backend-etl.rule=PathRegexp(`^/api(/.*)?etl(/.*)?$`)"
-      - "traefik.http.routers.dnpm-backend-etl.tls=true"
-      - "traefik.http.routers.dnpm-backend-etl.service=dnpm-backend"
-      # this needs an ETL processor with support for basic auth
-      - "traefik.http.routers.dnpm-backend-etl.middlewares=auth"
-      # except peer-to-peer
-      - "traefik.http.routers.dnpm-backend-peer.rule=PathRegexp(`^/api(/.*)?/peer2peer(/.*)?$`)"
-      - "traefik.http.routers.dnpm-backend-peer.tls=true"
-      - "traefik.http.routers.dnpm-backend-peer.service=dnpm-backend"
-      - "traefik.http.routers.dnpm-backend-peer.middlewares=dnpm-backend-peer"
-      # this effectively denies all requests
-      # this is okay, because requests from peers don't go through Traefik
-      - "traefik.http.middlewares.dnpm-backend-peer.ipWhiteList.sourceRange=0.0.0.0/32"
 
-  landing:
+  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.http.routers.landing.rule=PathPrefix(`/landing`)"
+      - "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

@@ -1,16 +1,28 @@
 #!/bin/bash
 
 if [ -n "${ENABLE_DNPM_NODE}" ]; then
-	log INFO "DNPM setup detected -- will start DNPM:DIP node."
+	log INFO "DNPM setup detected (BwHC Node) -- will start BwHC node."
 	OVERRIDE+=" -f ./$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
-    mkdir -p /var/cache/bridgehead/dnpm/ || fail_and_report 1 "Failed to create '/var/cache/bridgehead/dnpm/'. Please run sudo './bridgehead install $PROJECT' again to fix the permissions."
+	if [ -z "${DNPM_DATA_DIR+x}" ]; then
-    DNPM_SYNTH_NUM=${DNPM_SYNTH_NUM:--1}
+		log ERROR "Mandatory variable DNPM_DATA_DIR not defined!"
-    DNPM_MYSQL_ROOT_PASSWORD="$(generate_simple_password 'dnpm mysql')"
+		exit 1
-    DNPM_AUTHUP_SECRET="$(generate_simple_password 'dnpm authup')"
+	fi
+	DNPM_SYNTH_NUM=${DNPM_SYNTH_NUM:-0}
+	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/nngm-compose.yml

@@ -11,6 +11,7 @@ services:
       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`)"

modules/transfair-compose.yml

@@ -1,51 +0,0 @@
-
-services:
-  transfair:
-    image: docker.verbis.dkfz.de/cache/samply/transfair:latest
-    container_name: bridgehead-transfair
-    environment:
-      # NOTE: Those 3 variables need only to be passed if their set, otherwise transfair will complain about empty url values
-      - INSTITUTE_TTP_URL
-      - INSTITUTE_TTP_API_KEY
-      - PROJECT_ID_SYSTEM
-      - FHIR_REQUEST_URL=${FHIR_REQUEST_URL}
-      - FHIR_INPUT_URL=${FHIR_INPUT_URL}
-      - FHIR_OUTPUT_URL=${FHIR_OUTPUT_URL:-http://blaze:8080}
-      - FHIR_REQUEST_CREDENTIALS=${FHIR_REQUEST_CREDENTIALS}
-      - FHIR_INPUT_CREDENTIALS=${FHIR_INPUT_CREDENTIALS}
-      - FHIR_OUTPUT_CREDENTIALS=${FHIR_OUTPUT_CREDENTIALS}
-      - EXCHANGE_ID_SYSTEM=${EXCHANGE_ID_SYSTEM:-SESSION_ID}
-      - DATABASE_URL=sqlite://transfair/data_requests.sql?mode=rwc
-      - RUST_LOG=${RUST_LOG:-info}
-    volumes:
-      - /var/cache/bridgehead/${PROJECT}/transfair:/transfair
-
-  transfair-input-blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
-    container_name: bridgehead-transfair-input-blaze
-    environment:
-      BASE_URL: "http://bridgehead-transfair-input-blaze:8080"
-      JAVA_TOOL_OPTIONS: "-Xmx1024m"
-      DB_BLOCK_CACHE_SIZE: 1024
-      CQL_EXPR_CACHE_SIZE: 8
-      ENFORCE_REFERENTIAL_INTEGRITY: "false"
-    volumes:
-      - "transfair-input-blaze-data:/app/data"
-    profiles: ["transfair-input-blaze"]
-
-  transfair-request-blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
-    container_name: bridgehead-transfair-requests-blaze
-    environment:
-      BASE_URL: "http://bridgehead-transfair-requests-blaze:8080"
-      JAVA_TOOL_OPTIONS: "-Xmx1024m"
-      DB_BLOCK_CACHE_SIZE: 1024
-      CQL_EXPR_CACHE_SIZE: 8
-      ENFORCE_REFERENTIAL_INTEGRITY: "false"
-    volumes:
-      - "transfair-request-blaze-data:/app/data"
-    profiles: ["transfair-request-blaze"]
-
-volumes:
-  transfair-input-blaze-data:
-  transfair-request-blaze-data:

modules/transfair-setup.sh

@@ -1,22 +0,0 @@
-#!/bin/bash -e
-
-function transfairSetup() {
-    if [[ -n "$INSTITUTE_TTP_URL" || -n "$EXCHANGE_ID_SYSTEM" ]]; then
-        echo "Starting transfair."
-	    OVERRIDE+=" -f ./modules/transfair-compose.yml"
-	    if [ -n "$FHIR_INPUT_URL" ]; then
-		    log INFO "TransFAIR input fhir store set to external $FHIR_INPUT_URL"
-	    else
-		    log INFO "TransFAIR input fhir store not set writing to internal blaze"
-		    FHIR_INPUT_URL="http://transfair-input-blaze:8080"
-		    OVERRIDE+=" --profile transfair-input-blaze"
-	    fi
-	    if [ -n "$FHIR_REQUEST_URL" ]; then
-		    log INFO "TransFAIR request fhir store set to external $FHIR_REQUEST_URL"
-	    else
-		    log INFO "TransFAIR request fhir store not set writing to internal blaze"
-		    FHIR_REQUEST_URL="http://transfair-requests-blaze:8080"
-		    OVERRIDE+=" --profile transfair-request-blaze"
-	    fi
-    fi
-}

versions/prod

@@ -1,2 +0,0 @@
-FOCUS_TAG=main
-BEAM_TAG=main

versions/test

@@ -1,2 +0,0 @@
-FOCUS_TAG=develop
-BEAM_TAG=develop