chore: update datashield beam-connect mappings

fix: Generate public oidc client when there is no private client

.gitignore

@@ -1,6 +1,9 @@
 ##Ignore site configuration
 .gitmodules
 site-config/*
-
+.idea
 ## Ignore site configuration
 */docker-compose.override.yml
+
+## MAC OS
+.DS_Store

README.md

@@ -21,6 +21,8 @@ This repository is the starting point for any information and tools you will nee
     - [HTTPS Access](#https-access)
     - [TLS terminating proxies](#tls-terminating-proxies)
     - [File structure](#file-structure)
+    - [BBMRI-ERIC Directory entry needed](#bbmri-eric-directory-entry-needed)
+    - [Loading data](#loading-data)
 4. [Things you should know](#things-you-should-know)
     - [Auto-Updates](#auto-updates)
     - [Auto-Backups](#auto-backups)
@@ -32,6 +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:
@@ -50,16 +56,41 @@ Ensure the following software (or newer) is installed:
 - docker >= 20.10.1
 - docker-compose >= 2.xx (`docker-compose` and `docker compose` are both supported).
 - systemd
+- curl
 
 We recommend to install Docker(-compose) from its official sources as described on the [Docker website](https://docs.docker.com).
 
-Note for Ubuntu: Please note that snap versions of Docker are not supported.
+> 📝 Note for Ubuntu: Snap versions of Docker are not supported.
 
 ### Network
 
-Since it needs to carry sensitive patient data, Bridgeheads are intended to be deployed within your institution's secure network and behave well even in networks in strict security settings, e.g. firewall rules. The only connectivity required is an outgoing HTTPS proxy. TLS termination is supported, too (see [below](#tls-terminating-proxies))
+A Bridgehead communicates to all central components via outgoing HTTPS connections.
 
-Note for Ubuntu: Please note that the uncomplicated firewall (ufw) is known to conflict with Docker [here](https://github.com/chaifeng/ufw-docker).
+Your site might require an outgoing proxy (i.e. HTTPS forward proxy) to connect to external servers; you should discuss this with your local systems administration. In that case, you will need to note down the URL of the proxy. If the proxy requires authentication, you will also need to make a note of its username and password. This information will be used later on during the installation process. TLS terminating proxies are also supported, see [here](#tls-terminating-proxies). Apart from the Bridgehead itself, you may also need to configure the proxy server in [git](https://gist.github.com/evantoli/f8c23a37eb3558ab8765) and [docker](https://docs.docker.com/network/proxy/).
+
+The following URLs need to be accessible (prefix with `https://`):
+* To fetch code and configuration from git repositories
+  * github.com
+  * 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/all))
+    * hub.docker.com
+    * registry-1.docker.io
+    * production.cloudflare.docker.com
+* To report bridgeheads operational status
+  * healthchecks.verbis.dkfz.de
+* only for DKTK/CCP
+  * broker.ccp-it.dktk.dkfz.de
+* only for BBMRI-ERIC
+  * broker.bbmri.samply.de
+  * gitlab.bbmri-eric.eu
+* only for German Biobank Node
+  * broker.bbmri.de
+
+> 📝 This URL list is subject to change. Instead of the individual names, we highly recommend whitelisting wildcard domains: *.dkfz.de, github.com, *.docker.com, *.docker.io, *.samply.de, *.bbmri.de.
+
+> 📝 Ubuntu's pre-installed uncomplicated firewall (ufw) is known to conflict with Docker, more info [here](https://github.com/chaifeng/ufw-docker).
 
 ## Deployment
 
@@ -92,7 +123,7 @@ Mention:
 We will set the repository up for you. We will then send you:
 
 - A Repository Short Name (RSN). Beware: this is distinct from your site name.
-- Repository URL containing the acces token eg. https://BH_Dummy:dummy_token@git.verbis.dkfz.de/bbmri-bridgehead-configs/dummy.git
+- Repository URL containing the acces token eg. https://BH_Dummy:dummy_token@git.verbis.dkfz.de/<project>-bridgehead-configs/dummy.git
 
 During the installation, your Bridgehead will download your site's configuration from GitLab and you can review the details provided to us by email.
 
@@ -140,7 +171,7 @@ cd /srv/docker/bridgehead
 sudo ./bridgehead enroll <PROJECT>
 ```
 
-... and follow the instructions on the screen. You should then be prompted to do the next step:
+... and follow the instructions on the screen. Please send your default Collection ID and the display name of your site together with the certificate request when you enroll. You should then be prompted to do the next step:
 
 ### Starting and stopping your Bridgehead
 
@@ -228,6 +259,21 @@ Even within your internal network, the Bridgehead enforces HTTPS for all service
 
 All of the Bridgehead's outgoing connections are secured by transport encryption (TLS) and a Bridgehead will refuse to connect if certificate verification fails. If your local forward proxy server performs TLS termination, please place its CA certificate in `/etc/bridgehead/trusted-ca-certs` as a `.pem` file, e.g. `/etc/bridgehead/trusted-ca-certs/mylocalca.pem`. Then, all Bridgehead components will pick up this certificate and trust it for outgoing connections.
 
+To find the certificate file, first run the following:
+
+```
+curl -v https://broker.bbmri.samply.de/v1/health
+```
+
+In the output, look out for the line:
+
+
+```
+successfully set certificate verify locations:
+```
+
+Here a file will be mentioned, perhaps in the directory /etc/ssl/certs. The exact location  will depend on your operating system. This is the file that you need to copy.
+
 ### File structure
 
 - `/srv/docker/bridgehead` contains this git repository with the shell scripts and *project-specific configuration*. In here, all files are identical for all sites. You should not make any changes here.
@@ -240,36 +286,69 @@ All of the Bridgehead's outgoing connections are secured by transport encryption
 
 Your Bridgehead's actual data is not stored in the above directories, but in named docker volumes, see `docker volume ls` and `docker volume inspect <volume_name>`.
 
-### Directory sync
+### BBMRI-ERIC Directory entry needed
 
-This is an optional feature for bbmri projects. It keeps the [BBMRI Directory](https://directory.bbmri-eric.eu/) up to date with your local data eg. number of samples. It also updates the local FHIR store with the latest contact details etc. from the Directory.  You must explicitly set your country specific directory url, username and password to enable this feature.
+If you run a biobank, you should be listed together with your collections with in the [Directory](https://directory.bbmri-eric.eu), a BBMRI-ERIC project that catalogs biobanks.
+
+To do this, contact the BBMRI-ERIC national node for the country where your biobank is based, see [the list of nodes](http://www.bbmri-eric.eu/national-nodes/).
+
+Once you have added your biobank to the Directory you got persistent identifier (PID) for your biobank and unique identifiers (IDs) for your collections. The collection IDs are necessary for the biospecimens assigning to the collections and later in the data flows between BBMRI-ERIC tools. In case you cannot distribute all your biospecimens within collections via assigning the collection IDs, **you should choose one of your sample collections as a default collection for your biobank**. This collection will be automatically used to label any samples that have not been assigned a collection ID in your ETL process. Make a note of this default collection ID, you will need it later on in the installation process.
+
+### Directory sync tool
+
+The Bridgehead's **Directory Sync** is an optional feature that keeps the Directory up to date with your local data, e.g. number of samples. Conversely, it also updates the local FHIR store with the latest contact details etc. from the Directory. You must explicitly set your country specific directory URL, username and password to enable this feature.
 
 Full details can be found in [directory_sync_service](https://github.com/samply/directory_sync_service).
 
 To enable it, you will need to set these variables to the ```bbmri.conf``` file of your GitLab repository. Here is an example config:
 
 ```
-### Directory sync service
 DS_DIRECTORY_URL=https://directory.bbmri-eric.eu
 DS_DIRECTORY_USER_NAME=your_directory_username
 DS_DIRECTORY_USER_PASS=qwdnqwswdvqHBVGFR9887
 DS_TIMER_CRON="0 22 * * *"
 ```
-You must contact the Directory for your national node to find the URL, and to register as a user.
+You must contact the Directory team for your national node to find the URL, and to register as a user.
 
 Additionally, you should choose when you want Directory sync to run. In the example above, this is set to happen at 10 pm every evening. You can modify this to suit your requirements. The timer specification should follow the [cron](https://crontab.guru) convention.
 
-Once you edited the gitlab config. The bridgehead will autoupdate the config with the values and will sync the data.
+Once you edited the gitlab config, the bridgehead will autoupdate the config with the values and will sync the data.
 
 There will be a delay before the effects of Directory sync become visible. First, you will need to wait until the time you have specified in ```TIMER_CRON```. Second, the information will then be synchronized from your national node with the central European Directory. This can take up to 24 hours.
 
+### Loading data
+
+The data accessed by the federated search is held in the Bridgehead in a FHIR store (we use Blaze).
+
+You can load data into this store by using its FHIR API:
+
+```
+https://<Name of your server>/bbmri-localdatamanagement/fhir
+```
+The name of your server will generally be the full name of the VM that the Bridgehead runs on. You can alternatively supply an IP address.
+
+The FHIR API uses basic auth. You can find the credentials in `/etc/bridgehead/<project>.local.conf`.
+
+Note that if you don't have a DNS certificate for the Bridgehead, you will need to allow an insecure connection. E.g. with curl, use the `-k` flag.
+
+The storage space on your hard drive will depend on the number of FHIR resources that you intend to generate. This will be the sum of the number of patients/subjects, the number of samples, the number of conditions/diseases and the number of observations. As a general rule of thumb, you can assume that each resource will consume about 2 kilobytes of disk space.
+
+For more information on Blaze performance, please refer to [import performance](https://github.com/samply/blaze/blob/master/docs/performance/import.md).
+
+#### ETL for BBMRI and GBA
+
+Normally, you will need to build your own ETL to feed the Bridgehead. However, there is one case where a short cut might be available:
+- If you are using CentraXX as a BIMS and you have a FHIR-Export License, then you can employ standard mapping scripts that access the CentraXX-internal data structures and map the data onto the BBMRI FHIR profile. It may be necessary to adjust a few parameters, but this is nonetheless significantly easier than writing your own ETL.
+
+You can find the profiles for generating FHIR in [Simplifier](https://simplifier.net/bbmri.de/~resources?category=Profile).
+
 ## Things you should know
 
 ### Auto-Updates
 
 Your Bridgehead will automatically and regularly check for updates. Whenever something has been updates (e.g., one of the git repositories or one of the docker images), your Bridgehead is automatically restarted. This should happen automatically and does not need any configuration.
 
-If you would like to understand what happens exactly and when, please check the systemd units deployed during the [installation](#base-installation) via `systemctl cat bridgehead-update@<PROJECT>.service` and `systemctl cat bridgehead-update@<PROJECT.timer`.
+If you would like to understand what happens exactly and when, please check the systemd units deployed during the [installation](#base-installation) via `systemctl cat bridgehead-update@<PROJECT>.service` and `systemctl cat bridgehead-update@<PROJECT>.timer`.
 
 ### Auto-Backups
 
@@ -306,8 +385,28 @@ Installation under WSL ought to work, but we have not tested this.
 
 ### Docker Daemon Proxy Configuration
 
-Docker has a background daemon, responsible for downloading images and starting them. Sometimes, proxy configuration from your system won't carry over and it will fail to download images. In that case, configure the proxy for this daemon as described in the [official documentation](https://docs.docker.com).
+Docker has a background daemon, responsible for downloading images and starting them. Sometimes, proxy configuration from your system won't carry over and it will fail to download images. In that case, you'll need to configure the proxy inside the system unit of docker by creating the file `/etc/systemd/system/docker.service.d/proxy.conf` with the following content:
 
+``` ini
+[Service]
+Environment="HTTP_PROXY=http://proxy.example.com:3128"
+Environment="HTTPS_PROXY=https://proxy.example.com:3128"
+Environment="NO_PROXY=localhost,127.0.0.1,some-local-docker-registry.example.com,.corp"
+```
+
+After saving the configuration file, you'll need to reload the system daemon for the changes to take effect:
+
+``` shell
+sudo systemctl daemon-reload
+```
+
+and restart the docker daemon:
+
+``` shell
+sudo systemctl restart docker
+```
+
+For more information, please consult the [official documentation](https://docs.docker.com/config/daemon/systemd/#httphttps-proxy).
 
 ### Monitoring
 

bbmri/directory-sync.sh

@@ -1,8 +0,0 @@
-#!/bin/bash
-
-function dirSetup() {
-	if [ -n "$DS_DIRECTORY_USER_NAME" ]; then
-		log INFO "Directory sync setup detected -- will start directory sync service."
-		OVERRIDE+=" -f ./$PROJECT/directory-sync-compose.yml"
-	fi
-}

bbmri/docker-compose.yml

@@ -1,65 +1,16 @@
 version: "3.7"
 
+# This includes only the shared persistence for BBMRI-ERIC and GBN. Federation components are included as modules, see vars.
+
 services:
-  traefik:
-    container_name: bridgehead-traefik
-    image: docker.verbis.dkfz.de/cache/traefik:latest
-    command:
-      - --entrypoints.web.address=:80
-      - --entrypoints.websecure.address=:443
-      - --providers.docker=true
-      - --providers.docker.exposedbydefault=false
-      - --providers.file.directory=/configuration/
-      - --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(`/api`) || PathPrefix(`/dashboard`)"
-      - "traefik.http.routers.dashboard.entrypoints=websecure"
-      - "traefik.http.routers.dashboard.service=api@internal"
-      - "traefik.http.routers.dashboard.tls=true"
-      - "traefik.http.routers.dashboard.middlewares=auth"
-      - "traefik.http.middlewares.auth.basicauth.users=${LDM_LOGIN}"
-    ports:
-      - 80:80
-      - 443:443
-    volumes:
-      - /etc/bridgehead/traefik-tls:/certs:ro
-      - ../lib/traefik-configuration/:/configuration:ro
-      - /var/run/docker.sock:/var/run/docker.sock:ro
-
-  forward_proxy:
-    container_name: bridgehead-forward-proxy
-    image: docker.verbis.dkfz.de/cache/samply/bridgehead-forward-proxy:latest
-    environment:
-      HTTPS_PROXY: ${HTTPS_PROXY_URL}
-      USERNAME: ${HTTPS_PROXY_USERNAME}
-      PASSWORD: ${HTTPS_PROXY_PASSWORD}
-    volumes:
-      - /etc/bridgehead/trusted-ca-certs:/docker/custom-certs/:ro
-
-  landing:
-    container_name: bridgehead-landingpage
-    image: docker.verbis.dkfz.de/cache/samply/bridgehead-landingpage:master
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.landing.rule=PathPrefix(`/`)"
-      - "traefik.http.services.landing.loadbalancer.server.port=80"
-      - "traefik.http.routers.landing.tls=true"
-    environment:
-      HOST: ${HOST}
-      PROJECT: ${PROJECT}
-      SITE_NAME: ${SITE_NAME}
-
   blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.19
+    image: docker.verbis.dkfz.de/cache/samply/blaze:latest
     container_name: bridgehead-bbmri-blaze
     environment:
       BASE_URL: "http://bridgehead-bbmri-blaze:8080"
-      JAVA_TOOL_OPTIONS: "-Xmx4g"
-      LOG_LEVEL: "debug"
+      JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
+      DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
+      DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP
       ENFORCE_REFERENTIAL_INTEGRITY: "false"
     volumes:
       - "blaze-data:/app/data"
@@ -71,43 +22,10 @@ services:
       - "traefik.http.routers.blaze_ccp.middlewares=ccp_b_strip,auth"
       - "traefik.http.routers.blaze_ccp.tls=true"
 
-  focus:
-    image: docker.verbis.dkfz.de/cache/samply/focus:develop
-    container_name: bridgehead-focus
-    environment:
-      API_KEY: ${FOCUS_BEAM_SECRET_SHORT}
-      BEAM_APP_ID_LONG: focus.${PROXY_ID}
-      PROXY_ID: ${PROXY_ID}
-      BLAZE_URL: "http://bridgehead-bbmri-blaze:8080/fhir/"
-      BEAM_PROXY_URL: http://beam-proxy:8081
-      RETRY_COUNT: ${FOCUS_RETRY_COUNT}
-    depends_on:
-      - "beam-proxy"
-      - "blaze"
-
-  beam-proxy:
-    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
-    container_name: bridgehead-beam-proxy
-    environment:
-      BROKER_URL: ${BROKER_URL}
-      PROXY_ID: ${PROXY_ID}
-      APP_0_ID: focus
-      APP_0_KEY: ${FOCUS_BEAM_SECRET_SHORT}
-      PRIVKEY_FILE: /run/secrets/proxy.pem
-      ALL_PROXY: http://forward_proxy:3128
-      TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
-      ROOTCERT_FILE: /conf/root.crt.pem
-    secrets:
-      - proxy.pem
-    depends_on:
-      - "forward_proxy"
-    volumes:
-      - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
-      - ./root.crt.pem:/conf/root.crt.pem:ro
-
 volumes:
   blaze-data:
 
+# used in modules *-locator.yml
 secrets:
   proxy.pem:
     file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

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/directory-sync.sh

@@ -0,0 +1,6 @@
+#!/bin/bash
+
+if [ -n "${DS_DIRECTORY_USER_NAME}" ]; then
+	log INFO "Directory sync setup detected -- will start directory sync service."
+	OVERRIDE+=" -f ./$PROJECT/modules/directory-sync-compose.yml"
+fi

bbmri/modules/eric-compose.yml

@@ -0,0 +1,36 @@
+version: "3.7"
+
+services:
+  focus-eric:
+    image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
+    container_name: bridgehead-focus-eric
+    environment:
+      API_KEY: ${ERIC_FOCUS_BEAM_SECRET_SHORT}
+      BEAM_APP_ID_LONG: focus.${ERIC_PROXY_ID}
+      PROXY_ID: ${ERIC_PROXY_ID}
+      BLAZE_URL: "http://blaze:8080/fhir/"
+      BEAM_PROXY_URL: http://beam-proxy-eric:8081
+      RETRY_COUNT: ${FOCUS_RETRY_COUNT}
+    depends_on:
+      - "beam-proxy-eric"
+      - "blaze"
+
+  beam-proxy-eric:
+    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
+    container_name: bridgehead-beam-proxy-eric
+    environment:
+      BROKER_URL: ${ERIC_BROKER_URL}
+      PROXY_ID: ${ERIC_PROXY_ID}
+      APP_focus_KEY: ${ERIC_FOCUS_BEAM_SECRET_SHORT}
+      PRIVKEY_FILE: /run/secrets/proxy.pem
+      ALL_PROXY: http://forward_proxy:3128
+      TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
+      ROOTCERT_FILE: /conf/root.crt.pem
+    secrets:
+      - proxy.pem
+    depends_on:
+      - "forward_proxy"
+    volumes:
+      - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
+      - /srv/docker/bridgehead/bbmri/modules/${ERIC_ROOT_CERT}.root.crt.pem:/conf/root.crt.pem:ro
+

bbmri/modules/eric-setup.sh

@@ -0,0 +1,28 @@
+#!/bin/bash
+
+if [ "${ENABLE_ERIC}" == "true" ]; then
+	log INFO "BBMRI-ERIC setup detected -- will start services for BBMRI-ERIC."
+	OVERRIDE+=" -f ./$PROJECT/modules/eric-compose.yml"
+
+	# 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)"
+	ERIC_SUPPORT_EMAIL=bridgehead@helpdesk.bbmri-eric.eu
+fi

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

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

bbmri/modules/gbn-compose.yml

@@ -0,0 +1,36 @@
+version: "3.7"
+
+services:
+  focus-gbn:
+    image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
+    container_name: bridgehead-focus-gbn
+    environment:
+      API_KEY: ${GBN_FOCUS_BEAM_SECRET_SHORT}
+      BEAM_APP_ID_LONG: focus.${GBN_PROXY_ID}
+      PROXY_ID: ${GBN_PROXY_ID}
+      BLAZE_URL: "http://blaze:8080/fhir/"
+      BEAM_PROXY_URL: http://beam-proxy-gbn:8081
+      RETRY_COUNT: ${FOCUS_RETRY_COUNT}
+    depends_on:
+      - "beam-proxy-gbn"
+      - "blaze"
+
+  beam-proxy-gbn:
+    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
+    container_name: bridgehead-beam-proxy-gbn
+    environment:
+      BROKER_URL: ${GBN_BROKER_URL}
+      PROXY_ID: ${GBN_PROXY_ID}
+      APP_focus_KEY: ${GBN_FOCUS_BEAM_SECRET_SHORT}
+      PRIVKEY_FILE: /run/secrets/proxy.pem
+      ALL_PROXY: http://forward_proxy:3128
+      TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
+      ROOTCERT_FILE: /conf/root.crt.pem
+    secrets:
+      - proxy.pem
+    depends_on:
+      - "forward_proxy"
+    volumes:
+      - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
+      - /srv/docker/bridgehead/bbmri/modules/${GBN_ROOT_CERT}.root.crt.pem:/conf/root.crt.pem:ro
+

bbmri/modules/gbn-setup.sh

@@ -0,0 +1,28 @@
+#!/bin/bash
+
+if [ "${ENABLE_GBN}" == "true" ]; then
+	log INFO "GBN setup detected -- will start services for German Biobank Node."
+	OVERRIDE+=" -f ./$PROJECT/modules/gbn-compose.yml"
+
+	# 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)"
+	GBN_SUPPORT_EMAIL=feedback@germanbiobanknode.de
+fi

bbmri/modules/gbn.root.crt.pem

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

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

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

bbmri/vars

@@ -1,11 +1,37 @@
-BROKER_ID=broker.bbmri.samply.de
-BROKER_URL=https://${BROKER_ID}
-PROXY_ID=${SITE_ID}.${BROKER_ID}
-FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
+# Makes sense for all European Biobanks
+: ${ENABLE_ERIC:=true}
+
+# Makes only sense for German Biobanks
+: ${ENABLE_GBN:=false}
+
 FOCUS_RETRY_COUNT=32
-SUPPORT_EMAIL=bridgehead@helpdesk.bbmri-eric.eu
 PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
 
-# This will load directory-sync setup.
-source $PROJECT/directory-sync.sh
-dirSetup
+for module in $PROJECT/modules/*.sh
+do
+    log DEBUG "sourcing $module"
+    source $module
+done
+
+SUPPORT_EMAIL=$ERIC_SUPPORT_EMAIL
+BROKER_URL_FOR_PREREQ="${ERIC_BROKER_URL:-$GBN_BROKER_URL}"
+
+if [ -n "$GBN_SUPPORT_EMAIL" ]; then
+    SUPPORT_EMAIL=$GBN_SUPPORT_EMAIL
+fi
+
+function do_enroll {
+    COUNT=0
+    if [ "$ENABLE_ERIC" == "true" ]; then
+        do_enroll_inner $ERIC_PROXY_ID $ERIC_SUPPORT_EMAIL
+        COUNT=$((COUNT+1))
+    fi
+    if [ "$ENABLE_GBN" == "true" ]; then
+        do_enroll_inner $GBN_PROXY_ID $GBN_SUPPORT_EMAIL
+        COUNT=$((COUNT+1))
+    fi
+    if [ $COUNT -ge 2 ]; then
+        echo
+        echo "You just received $COUNT certificate signing requests (CSR). Please send $COUNT e-mails, with 1 CSR each, to the respective e-mail address."
+    fi
+}

bridgehead

@@ -32,6 +32,9 @@ case "$PROJECT" in
 	bbmri)
 		#nothing extra to do
 		;;
+	minimal)
+		#nothing extra to do
+		;;
 	*)
 		printUsage
 		exit 1
@@ -47,16 +50,39 @@ loadVars() {
 		source /etc/bridgehead/$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
+	optimizeBlazeMemoryUsage
 	[ -e ./$PROJECT/vars ] && source ./$PROJECT/vars
 	set +a
 
 	OVERRIDE=${OVERRIDE:=""}
+	# minimal contains shared components, so potential overrides must be applied in every project
+	if [ -f "minimal/docker-compose.override.yml" ]; then
+		log INFO "Applying Bridgehead common components override (minimal/docker-compose.override.yml)"
+		OVERRIDE+=" -f ./minimal/docker-compose.override.yml"
+	fi
 	if [ -f "$PROJECT/docker-compose.override.yml" ]; then
 		log INFO "Applying $PROJECT/docker-compose.override.yml"
 		OVERRIDE+=" -f ./$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 "$ACTION" in
@@ -64,20 +90,27 @@ case "$ACTION" in
 		loadVars
 		hc_send log "Bridgehead $PROJECT startup: Checking requirements ..."
 		checkRequirements
+		sync_secrets
 		hc_send log "Bridgehead $PROJECT startup: Requirements checked out. Now starting bridgehead ..."
-		export LDM_LOGIN=$(getLdmPassword)
-		exec $COMPOSE -f ./$PROJECT/docker-compose.yml $OVERRIDE up --abort-on-container-exit
+		exec $COMPOSE -p $PROJECT -f ./minimal/docker-compose.yml -f ./$PROJECT/docker-compose.yml $OVERRIDE up --abort-on-container-exit
 		;;
 	stop)
 		loadVars
-		# HACK: This is tempoarily to properly shut down false bridgehead instances (bridgehead-ccp instead ccp)
-		$COMPOSE -p bridgehead-$PROJECT -f ./$PROJECT/docker-compose.yml $OVERRIDE down
-		exec $COMPOSE -f ./$PROJECT/docker-compose.yml $OVERRIDE down
+		# Kill stale secret-sync instances if present
+		docker kill $(docker ps -q --filter ancestor=docker.verbis.dkfz.de/cache/samply/secret-sync-local) 2>/dev/null || true
+		# HACK: This is temporarily to properly shut down false bridgehead instances (bridgehead-ccp instead ccp)
+		$COMPOSE -p bridgehead-$PROJECT -f ./minimal/docker-compose.yml -f ./$PROJECT/docker-compose.yml $OVERRIDE down
+		exec $COMPOSE -p $PROJECT -f ./minimal/docker-compose.yml -f ./$PROJECT/docker-compose.yml $OVERRIDE down
 		;;
 	is-running)
 		bk_is_running
 		exit $?
 		;;
+	logs)
+		loadVars
+		shift 2
+		exec $COMPOSE -p $PROJECT -f ./minimal/docker-compose.yml -f ./$PROJECT/docker-compose.yml $OVERRIDE logs -f $@
+		;;
 	update)
 		loadVars
 		exec ./lib/update-bridgehead.sh $PROJECT
@@ -95,14 +128,17 @@ case "$ACTION" in
 	uninstall)
 		exec ./lib/uninstall-bridgehead.sh $PROJECT
 		;;
+	adduser)
+		loadVars
+		log "INFO" "Adding encrypted credentials in /etc/bridgehead/$PROJECT.local.conf"
+    		read -p "Please choose the component (LDM_AUTH|NNGM_AUTH) you want to add a user to : " COMPONENT
+    		read -p "Please enter a username: " USER
+    		read -s -p "Please enter a password (will not be echoed): "$'\n' PASSWORD
+    		add_basic_auth_user $USER $PASSWORD $COMPONENT $PROJECT
+		;;
 	enroll)
 		loadVars
-		if [ -e $PRIVATEKEYFILENAME ]; then
-			log ERROR "Private key already exists at $PRIVATEKEYFILENAME. Please delete first to proceed."
-			exit 1
-		fi
-		docker run --rm -ti -v /etc/bridgehead/pki:/etc/bridgehead/pki samply/beam-enroll:latest --output-file $PRIVATEKEYFILENAME --proxy-id $PROXY_ID --admin-email $SUPPORT_EMAIL
-		chmod 600 $PRIVATEKEYFILENAME
+		do_enroll $PROXY_ID
 		;;
 	preRun | preUpdate)
 		fixPermissions

ccp/docker-compose.yml

@@ -1,65 +1,14 @@
 version: "3.7"
 
 services:
-  traefik:
-    container_name: bridgehead-traefik
-    image: docker.verbis.dkfz.de/cache/traefik:latest
-    command:
-      - --entrypoints.web.address=:80
-      - --entrypoints.websecure.address=:443
-      - --providers.docker=true
-      - --providers.docker.exposedbydefault=false
-      - --providers.file.directory=/configuration/
-      - --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(`/api`) || PathPrefix(`/dashboard`)"
-      - "traefik.http.routers.dashboard.entrypoints=websecure"
-      - "traefik.http.routers.dashboard.service=api@internal"
-      - "traefik.http.routers.dashboard.tls=true"
-      - "traefik.http.routers.dashboard.middlewares=auth"
-      - "traefik.http.middlewares.auth.basicauth.users=${LDM_LOGIN}"
-    ports:
-      - 80:80
-      - 443:443
-    volumes:
-      - /etc/bridgehead/traefik-tls:/certs:ro
-      - ../lib/traefik-configuration/:/configuration:ro
-      - /var/run/docker.sock:/var/run/docker.sock:ro
-
-  forward_proxy:
-    container_name: bridgehead-forward-proxy
-    image: docker.verbis.dkfz.de/cache/samply/bridgehead-forward-proxy:latest
-    environment:
-      HTTPS_PROXY: ${HTTPS_PROXY_URL}
-      USERNAME: ${HTTPS_PROXY_USERNAME}
-      PASSWORD: ${HTTPS_PROXY_PASSWORD}
-    volumes:
-      - /etc/bridgehead/trusted-ca-certs:/docker/custom-certs/:ro
-
-  landing:
-    container_name: bridgehead-landingpage
-    image: docker.verbis.dkfz.de/cache/samply/bridgehead-landingpage:master
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.landing.rule=PathPrefix(`/`)"
-      - "traefik.http.services.landing.loadbalancer.server.port=80"
-      - "traefik.http.routers.landing.tls=true"
-    environment:
-      HOST: ${HOST}
-      PROJECT: ${PROJECT}
-      SITE_NAME: ${SITE_NAME}
-
   blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.19
+    image: docker.verbis.dkfz.de/cache/samply/blaze:latest
     container_name: bridgehead-ccp-blaze
     environment:
       BASE_URL: "http://bridgehead-ccp-blaze:8080"
-      JAVA_TOOL_OPTIONS: "-Xmx4g"
-      LOG_LEVEL: "debug"
+      JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
+      DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
+      DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP
       ENFORCE_REFERENTIAL_INTEGRITY: "false"
     volumes:
       - "blaze-data:/app/data"
@@ -71,15 +20,17 @@ services:
       - "traefik.http.routers.blaze_ccp.middlewares=ccp_b_strip,auth"
       - "traefik.http.routers.blaze_ccp.tls=true"
 
-  spot:
-    image: docker.verbis.dkfz.de/cache/samply/spot:latest
-    container_name: bridgehead-spot
+  focus:
+    image: docker.verbis.dkfz.de/cache/samply/focus:0.4.4
+    container_name: bridgehead-focus
     environment:
-      SECRET: ${SPOT_BEAM_SECRET_LONG}
-      APPID: spot
+      API_KEY: ${FOCUS_BEAM_SECRET_SHORT}
+      BEAM_APP_ID_LONG: focus.${PROXY_ID}
       PROXY_ID: ${PROXY_ID}
-      LDM_URL: http://bridgehead-ccp-blaze:8080/fhir
-      BEAM_PROXY: http://beam-proxy:8081
+      BLAZE_URL: "http://bridgehead-ccp-blaze:8080/fhir/"
+      BEAM_PROXY_URL: http://beam-proxy:8081
+      RETRY_COUNT: ${FOCUS_RETRY_COUNT}
+      EPSILON: 0.28
     depends_on:
       - "beam-proxy"
       - "blaze"
@@ -90,10 +41,7 @@ services:
     environment:
       BROKER_URL: ${BROKER_URL}
       PROXY_ID: ${PROXY_ID}
-      APP_0_ID: spot
-      APP_0_KEY: ${SPOT_BEAM_SECRET_SHORT}
-      APP_1_ID: report-hub
-      APP_1_KEY: ${REPORTHUB_BEAM_SECRET_SHORT}
+      APP_focus_KEY: ${FOCUS_BEAM_SECRET_SHORT}
       PRIVKEY_FILE: /run/secrets/proxy.pem
       ALL_PROXY: http://forward_proxy:3128
       TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
@@ -104,7 +52,7 @@ services:
       - "forward_proxy"
     volumes:
       - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
-      - ./root.crt.pem:/conf/root.crt.pem:ro
+      - /srv/docker/bridgehead/ccp/root.crt.pem:/conf/root.crt.pem:ro
 
 
 volumes:

ccp/exliquid-compose.yml

@@ -1,34 +0,0 @@
-version: "3.7"
-
-services:
-  exliquid-task-store:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.19
-    container_name: bridgehead-exliquid-task-store
-    environment:
-      BASE_URL: "http://bridgehead-exliquid-task-store:8080"
-      JAVA_TOOL_OPTIONS: "-Xmx1g"
-    volumes:
-    - "exliquid-task-store-data:/app/data"
-    labels:
-      - "traefik.enable=false"
-
-  exliquid-report-hub:
-    image: docker.verbis.dkfz.de/cache/samply/report-hub:latest
-    container_name: bridgehead-exliquid-report-hub
-    environment:
-      SPRING_WEBFLUX_BASE_PATH: "/exliquid"
-      JAVA_TOOL_OPTIONS: "-Xmx1g"
-      APP_BEAM_APPID: "report-hub.${PROXY_ID}"
-      APP_BEAM_SECRET: ${REPORTHUB_BEAM_SECRET_SHORT}
-      APP_BEAM_PROXY_BASEURL: http://beam-proxy:8081
-      APP_TASKSTORE_BASEURL: "http://bridgehead-exliquid-task-store:8080/fhir"
-      APP_DATASTORE_BASEURL:  http://bridgehead-ccp-blaze:8080/fhir
-    restart: always
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.report-ccp.rule=PathPrefix(`/exliquid`)"
-      - "traefik.http.services.report-ccp.loadbalancer.server.port=8080"
-      - "traefik.http.routers.report-ccp.tls=true"
-
-volumes:
-  exliquid-task-store-data:

ccp/exliquid-setup.sh

@@ -1,19 +0,0 @@
-#!/bin/bash
-
-function exliquidSetup() {
-	case ${SITE_ID} in
-		berlin|dresden|essen|frankfurt|freiburg|luebeck|mainz|muenchen-lmu|muenchen-tum|mannheim|tuebingen)
-			EXLIQUID=1
-			;;
-		dktk-test)
-			EXLIQUID=1
-			;;
-		*)
-			EXLIQUID=0
-			;;
-	esac
-	if [[ $EXLIQUID -eq 1 ]]; then
-		log INFO "EXLIQUID setup detected -- will start Report-Hub."
-		OVERRIDE+=" -f ./$PROJECT/exliquid-compose.yml"
-	fi
-}

ccp/modules/adt2fhir-rest-compose.yml

@@ -0,0 +1,18 @@
+version: "3.7"
+
+services:
+  adt2fhir-rest:
+    container_name: bridgehead-adt2fhir-rest
+    image: docker.verbis.dkfz.de/ccp/adt2fhir-rest:main
+    environment:
+      IDTYPE: BK_${IDMANAGEMENT_FRIENDLY_ID}_L-ID
+      MAINZELLISTE_APIKEY: ${IDMANAGER_LOCAL_PATIENTLIST_APIKEY}
+      SALT: ${LOCAL_SALT}
+    restart: always
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.adt2fhir-rest.rule=PathPrefix(`/adt2fhir-rest`)"
+      - "traefik.http.middlewares.adt2fhir-rest_strip.stripprefix.prefixes=/adt2fhir-rest"
+      - "traefik.http.services.adt2fhir-rest.loadbalancer.server.port=8080"
+      - "traefik.http.routers.adt2fhir-rest.tls=true"
+      - "traefik.http.routers.adt2fhir-rest.middlewares=adt2fhir-rest_strip,auth"

ccp/modules/adt2fhir-rest-setup.sh

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+function adt2fhirRestSetup() {
+  if [ -n "$ENABLE_ADT2FHIR_REST" ]; then
+    log INFO "ADT2FHIR-REST setup detected -- will start adt2fhir-rest API."
+    if [ ! -n "$IDMANAGER_LOCAL_PATIENTLIST_APIKEY" ]; then
+      log ERROR "Missing ID-Management Module! Fix this by setting up ID Management:"
+      exit 1;
+    fi
+    OVERRIDE+=" -f ./$PROJECT/modules/adt2fhir-rest-compose.yml"
+    LOCAL_SALT="$(echo \"local-random-salt\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
+  fi
+}

ccp/modules/datashield-compose.yml

@@ -0,0 +1,87 @@
+version: "3.7"
+
+services:
+  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://${HOST}/opal"
+      APP_CONTEXT_PATH: "/opal"
+      OPAL_PRIVATE_KEY: "/run/secrets/opal-key.pem"
+      OPAL_CERTIFICATE: "/run/secrets/opal-cert.pem"
+      OIDC_URL: "${OIDC_URL}"
+      OIDC_REALM: "${OIDC_REALM}"
+      OIDC_CLIENT_ID: "${OIDC_PRIVATE_CLIENT_ID}"
+      OIDC_CLIENT_SECRET: "${OIDC_CLIENT_SECRET}"
+      OIDC_ADMIN_GROUP: "${OIDC_ADMIN_GROUP}"
+      TOKEN_MANAGER_PASSWORD: "${TOKEN_MANAGER_OPAL_PASSWORD}"
+      EXPORTER_PASSWORD: "${EXPORTER_OPAL_PASSWORD}"
+      BEAM_APP_ID: token-manager.${PROXY_ID}
+      BEAM_SECRET: ${TOKEN_MANAGER_SECRET}
+      BEAM_DATASHIELD_PROXY: request-manager
+    volumes:
+      - "/var/cache/bridgehead/ccp/opal-metadata-db:/srv" # Opal metadata
+    secrets:
+      - opal-cert.pem
+      - opal-key.pem
+
+  opal-db:
+    container_name: bridgehead-opal-db
+    image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
+    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
+
+  beam-proxy:
+    environment:
+      APP_datashield-connect_KEY: ${DATASHIELD_CONNECT_SECRET}
+      APP_token-manager_KEY: ${TOKEN_MANAGER_SECRET}
+
+secrets:
+  opal-cert.pem:
+    file: /tmp/bridgehead/opal-cert.pem
+  opal-key.pem:
+    file: /tmp/bridgehead/opal-key.pem

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-setup.sh

@@ -0,0 +1,33 @@
+#!/bin/bash -e
+
+if [ "$ENABLE_DATASHIELD" == true ]; then
+  # HACK: This only works because exporter-setup.sh and teiler-setup.sh are sourced after datashield-setup.sh
+  if [ -z "${ENABLE_EXPORTER}" ] || [ "${ENABLE_EXPORTER}" != "true" ]; then
+    log WARN "The ENABLE_EXPORTER variable is either not set or not set to 'true'."
+  fi
+  log INFO "DataSHIELD setup detected -- will start DataSHIELD services."
+  OVERRIDE+=" -f ./$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\")"
+  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/
+    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
+  echo '{"sites": []}' >/tmp/bridgehead/opal-map/central.json
+  echo '[{
+    "external": "'$SITE_ID':443",
+    "internal": "opal:8443",
+    "allowed": ["central-ds-orchestrator.'$BROKER_ID'"]
+  }]' > /tmp/bridgehead/opal-map/local.json
+  if [ "$USER" == "root" ]; then
+    chown -R bridgehead:docker /tmp/bridgehead
+    chmod g+wr /tmp/bridgehead/opal-map/*
+    chmod g+r /tmp/bridgehead/opal-key.pem
+  fi
+  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

@@ -0,0 +1,39 @@
+version: "3.7"
+
+services:
+  beam-proxy:
+    environment:
+      APP_dnpm-connect_KEY: ${DNPM_BEAM_SECRET_SHORT}
+  dnpm-beam-connect:
+    depends_on: [ beam-proxy ]
+    image: docker.verbis.dkfz.de/cache/samply/beam-connect:develop
+    container_name: bridgehead-dnpm-beam-connect
+    environment:
+      PROXY_URL: http://beam-proxy:8081
+      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"
+      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}
+      RUST_LOG: ${RUST_LOG:-info}
+      NO_AUTH: "true"
+      TLS_CA_CERTIFICATES_DIR: ./conf/trusted-ca-certs
+    extra_hosts:
+      - "host.docker.internal:host-gateway"
+    volumes:
+      - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
+      - /etc/bridgehead/dnpm/local_targets.json:/conf/connect_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`)"
+      - "traefik.http.middlewares.dnpm-connect-strip.stripprefix.prefixes=/dnpm-connect"
+      - "traefik.http.routers.dnpm-connect.middlewares=dnpm-connect-strip"
+      - "traefik.http.services.dnpm-connect.loadbalancer.server.port=8062"
+      - "traefik.http.routers.dnpm-connect.tls=true"
+
+  dnpm-echo:
+    image: docker.verbis.dkfz.de/cache/samply/bridgehead-echo:latest
+    container_name: bridgehead-dnpm-echo

ccp/modules/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"

ccp/modules/dnpm-node-setup.sh

@@ -0,0 +1,28 @@
+#!/bin/bash
+
+if [ -n "${ENABLE_DNPM_NODE}" ]; then
+	log INFO "DNPM setup detected (BwHC Node) -- will start BwHC node."
+	OVERRIDE+=" -f ./$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
+	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

ccp/modules/dnpm-setup.sh

@@ -0,0 +1,15 @@
+#!/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_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
+	# If the DNPM_NO_PROXY variable is set, prefix it with a comma (as it gets added to a comma separated list)
+	if [ -n "${DNPM_NO_PROXY}" ]; then
+		DNPM_ADDITIONAL_NO_PROXY=",${DNPM_NO_PROXY}"
+	else
+		DNPM_ADDITIONAL_NO_PROXY=""
+	fi
+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 +1,80 @@
+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"
+
+  file-dispatcher:
+    image: docker.verbis.dkfz.de/cache/samply/file-dispatcher:latest
+    environment:
+      - BEAM_ID=file-dispatcher.${PROXY_ID}
+      - PROJECT_MANAGER_ID=project-manager.request-manager.${BROKER_ID}
+      - BEAM_SECRET=${FILE_DISPATCHER_BEAM_SECRET} # Generated in exporter-setup.sh
+      - BEAM_URL=http://beam-proxy:8081
+      - EXPORTER_URL=http://exporter:8092
+  
+  beam-proxy:
+    environment:
+      - APP_file-dispatcher_KEY=${FILE_DISPATCHER_BEAM_SECRET}

ccp/modules/exporter-setup.sh

@@ -0,0 +1,9 @@
+#!/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)"
+  FILE_DISPATCHER_BEAM_SECRET="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
+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

@@ -1,10 +1,12 @@
 version: "3.7"
+
 services:
   id-manager:
     image: docker.verbis.dkfz.de/bridgehead/magicpl
     container_name: bridgehead-id-manager
     environment:
       TOMCAT_REVERSEPROXY_FQDN: ${HOST}
+      TOMCAT_REVERSEPROXY_SSL: "true"
       MAGICPL_SITE: ${IDMANAGEMENT_FRIENDLY_ID}
       MAGICPL_ALLOWED_ORIGINS: https://${HOST}
       MAGICPL_LOCAL_PATIENTLIST_APIKEY: ${IDMANAGER_LOCAL_PATIENTLIST_APIKEY}
@@ -42,7 +44,7 @@ services:
       - patientlist-db
 
   patientlist-db:
-    image: docker.verbis.dkfz.de/cache/postgres:15.1-alpine
+    image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
     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 "$IDMANAGER_UPLOAD_APIKEY" ]; then
@@ -6,7 +6,7 @@ function idManagementSetup() {
 		OVERRIDE+=" -f ./$PROJECT/modules/id-management-compose.yml"
 
 		# Auto Generate local Passwords
-		PATIENTLIST_POSTGRES_PASSWORD="$(echo \"id-management-module-db-password-salt\" | openssl rsautl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
+		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)"
 		IDMANAGER_LOCAL_PATIENTLIST_APIKEY="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
 
 		# Transform Seeds Configuration to pass it to the Mainzelliste Container
@@ -39,6 +39,7 @@ function applySpecialCases() {
 	result="$1";
 	result="${result/Lmu/LMU}";
 	result="${result/Tum/TUM}";
+	result="${result/Dktk Test/Teststandort}";
 	echo "$result";
 }
 

ccp/modules/mtba-compose.yml

@@ -11,22 +11,30 @@ 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: ${MTBA_CSV_DELIMITER:-TAB}
+      HTTP_RELATIVE_PATH: "/mtba"
+      OIDC_ADMIN_GROUP: "${OIDC_ADMIN_GROUP}"
+      OIDC_CLIENT_ID: "${OIDC_PRIVATE_CLIENT_ID}"
+      OIDC_CLIENT_SECRET: "${OIDC_CLIENT_SECRET}"
+      OIDC_REALM: "${OIDC_REALM}"
+      OIDC_URL: "${OIDC_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

@@ -0,0 +1,13 @@
+#!/bin/bash -e
+
+function mtbaSetup() {
+  if [ -n "$ENABLE_MTBA" ];then
+    log INFO "MTBA setup detected -- will start MTBA Service and CBioPortal."
+    if [ ! -n "$IDMANAGER_UPLOAD_APIKEY" ]; then
+      log ERROR "Missing ID-Management Module! Fix this by setting up ID Management:"
+      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:
 
@@ -18,7 +19,9 @@ services:
       - "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"
+      - "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

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

ccp/modules/teiler-compose.yml

@@ -0,0 +1,81 @@
+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

ccp/modules/teiler-setup.sh

@@ -0,0 +1,9 @@
+#!/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/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/nngm-setup.sh

@@ -1,24 +0,0 @@
-#!/bin/bash
-##nNGM vars:
-#NNGM_MAGICPL_APIKEY
-#NNGM_CTS_APIKEY
-#NNGM_CRYPTKEY
-
-function nngmSetup() {
-	if [ -n "$NNGM_CTS_APIKEY" ]; then
-		log INFO "nNGM setup detected -- will start nNGM Connector."
-		OVERRIDE+=" -f ./$PROJECT/nngm-compose.yml"
-	fi
-	}
-
-function mtbaSetup() {
-	# TODO: Check if ID-Management Module is activated!
-	if [ -n "$ENABLE_MTBA" ];then
-		log INFO "MTBA setup detected -- will start MTBA Service and CBioPortal."
-		if [ ! -n "$IDMANAGER_UPLOAD_APIKEY" ]; then
-			log ERROR "Detected MTBA Module configuration but ID-Management Module seems not to be configured!"
-			exit 1;
-		fi
-		OVERRIDE+=" -f ./$PROJECT/mtba-compose.yml"
-	fi
-}

ccp/root.crt.pem

@@ -1,20 +1,20 @@
 -----BEGIN CERTIFICATE-----
-MIIDNTCCAh2gAwIBAgIUMeGRSrNPhRdQ1tU7uK5+lUa4f38wDQYJKoZIhvcNAQEL
-BQAwFjEUMBIGA1UEAxMLQnJva2VyLVJvb3QwHhcNMjIwOTI5MTQxMjU1WhcNMzIw
-OTI2MTQxMzI1WjAWMRQwEgYDVQQDEwtCcm9rZXItUm9vdDCCASIwDQYJKoZIhvcN
-AQEBBQADggEPADCCAQoCggEBAMYyroOUeb27mYzClOrjCmgIceLalsFA0aVCh5mZ
-KtP8+1U3oq/7exP30gXiJojxW7xoerfyQY9s0Sz5YYbxYbuskFOYEtyAILB/pxgd
-+k+J3tlZKolpfmo7WT5tZiHxH/zjrtAYGnuB2xPHRMCWh/tHYrELgXQuilNol24y
-GBa1plTlARy0aKEDUHp87WLhD2qH7B8sFlLgo0+gunE1UtR2HMSPF45w3VXszyG6
-fJNrAj0yPnKy3Dm1BMO3jDO2e0A9lCQ71a4j4TeKePfCk1xCArSu6PpiwiacKplF
-c6CRR6KrWVm2g+8Y2hFcOBG/Py2xusm3PWbpylGq6vtFRkkCAwEAAaN7MHkwDgYD
-VR0PAQH/BAQDAgEGMA8GA1UdEwEB/wQFMAMBAf8wHQYDVR0OBBYEFEFxD6BQwQO5
-xsJ+3cvZypsnh6dDMB8GA1UdIwQYMBaAFEFxD6BQwQO5xsJ+3cvZypsnh6dDMBYG
-A1UdEQQPMA2CC0Jyb2tlci1Sb290MA0GCSqGSIb3DQEBCwUAA4IBAQB5zTeIhV/3
-3Am6O144EFtnIeaZ2w0D6aEHqHAZp50vJv3+uQfOliCOzgw7VDxI4Zz2JALjlR/i
-uOYHsu3YIRMIOmPOjqrdDJa6auB0ufL4oUPfCRln7Fh0f3JVlz3BUoHsSDt949p4
-g0nnsciL2JHuzlqjn7Jyt3L7dAHrlFKulCcuidG5D3cqXrRCbF83f+k3TC/HRiNd
-25oMi7I4MP/SOCdfQGUGIsHIf/0hSm3pNjDOrC/XuI/8gh2f5io+Y8V+hMwMBcm4
-JbH8bdyBB+EIhsNbTwf2MWntD5bmg47sf7hh23aNvKXI67Li1pTI2t1CqiGnFR0U
-fCEpeaEAHs0k
------END CERTIFICATE-----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+-----END CERTIFICATE-----

ccp/vars

@@ -1,19 +1,31 @@
-BROKER_ID=broker.dev.ccp-it.dktk.dkfz.de
+BROKER_ID=broker.ccp-it.dktk.dkfz.de
 BROKER_URL=https://${BROKER_ID}
 PROXY_ID=${SITE_ID}.${BROKER_ID}
-SPOT_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
-SPOT_BEAM_SECRET_LONG="ApiKey spot.${PROXY_ID} ${SPOT_BEAM_SECRET_SHORT}"
-REPORTHUB_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
-REPORTHUB_BEAM_SECRET_LONG="ApiKey report-hub.${PROXY_ID} ${REPORTHUB_BEAM_SECRET_SHORT}"
+FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
+FOCUS_RETRY_COUNT=32
 SUPPORT_EMAIL=support-ccp@dkfz-heidelberg.de
 PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
 
-# This will load id-management setup. Effective only if id-management configuration is defined.
-source $PROJECT/modules/id-management-setup.sh
+BROKER_URL_FOR_PREREQ=$BROKER_URL
+
+OIDC_USER_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})"
+OIDC_ADMIN_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})_Verwalter"
+OIDC_PRIVATE_CLIENT_ID=${SITE_ID}-private
+OIDC_PUBLIC_CLIENT_ID=${SITE_ID}-public
+# Use "test-realm-01" for testing
+OIDC_REALM="${OIDC_REALM:-master}"
+OIDC_URL="https://login.verbis.dkfz.de"
+OIDC_ISSUER_URL="${OIDC_URL}/realms/${OIDC_REALM}"
+OIDC_GROUP_CLAIM="groups"
+
+POSTGRES_TAG=15.6-alpine
+
+for module in $PROJECT/modules/*.sh
+do
+    log DEBUG "sourcing $module"
+    source $module
+done
+
 idManagementSetup
-# This will load nngm setup. Effective only if nngm configuration is defined.
-source $PROJECT/nngm-setup.sh
-nngmSetup
-source $PROJECT/exliquid-setup.sh
-exliquidSetup
-mtbaSetup
+mtbaSetup
+adt2fhirRestSetup

lib/functions.sh

@@ -9,12 +9,31 @@ detectCompose() {
 	fi
 }
 
-getLdmPassword() {
-	if [ -n "$LDM_PASSWORD" ]; then
-		docker run --rm docker.verbis.dkfz.de/cache/httpd:alpine htpasswd -nb $PROJECT $LDM_PASSWORD | tr -d '\n' | tr -d '\r'
-	else
-		echo -n ""
+setupProxy() {
+	### Note: As the current data protection concepts do not allow communication via HTTP,
+	### we are not setting a proxy for HTTP requests.
+
+	local http="no"
+	local https="no"
+	if [ $HTTPS_PROXY_URL ]; then
+		local proto="$(echo $HTTPS_PROXY_URL | grep :// | sed -e 's,^\(.*://\).*,\1,g')"
+		local fqdn="$(echo ${HTTPS_PROXY_URL/$proto/})"
+		local hostport=$(echo $HTTPS_PROXY_URL | sed -e "s,$proto,,g" | cut -d/ -f1)
+		HTTPS_PROXY_HOST="$(echo $hostport | sed -e 's,:.*,,g')"
+		HTTPS_PROXY_PORT="$(echo $hostport | sed -e 's,^.*:,:,g' -e 's,.*:\([0-9]*\).*,\1,g' -e 's,[^0-9],,g')"
+		if [[ ! -z "$HTTPS_PROXY_USERNAME" && ! -z "$HTTPS_PROXY_PASSWORD" ]]; then
+			local proto="$(echo $HTTPS_PROXY_URL | grep :// | sed -e 's,^\(.*://\).*,\1,g')"
+			local fqdn="$(echo ${HTTPS_PROXY_URL/$proto/})"
+			HTTPS_PROXY_FULL_URL="$(echo $proto$HTTPS_PROXY_USERNAME:$HTTPS_PROXY_PASSWORD@$fqdn)"
+			https="authenticated"
+		else
+			HTTPS_PROXY_FULL_URL=$HTTPS_PROXY_URL
+			https="unauthenticated"
+		fi
 	fi
+
+	log INFO "Configuring proxy servers: $http http proxy (we're not supporting unencrypted comms), $https https proxy"
+	export HTTPS_PROXY_HOST HTTPS_PROXY_PORT HTTPS_PROXY_FULL_URL
 }
 
 exitIfNotRoot() {
@@ -34,7 +53,7 @@ checkOwner(){
 }
 
 printUsage() {
-	echo "Usage: bridgehead start|stop|is-running|update|install|uninstall|enroll PROJECTNAME"
+	echo "Usage: bridgehead start|stop|logs|is-running|update|install|uninstall|adduser|enroll PROJECTNAME"
 	echo "PROJECTNAME should be one of ccp|bbmri"
 }
 
@@ -57,7 +76,7 @@ fetchVarsFromVault() {
 
 	set +e
 
-	PASS=$(BW_MASTERPASS="$BW_MASTERPASS" BW_CLIENTID="$BW_CLIENTID" BW_CLIENTSECRET="$BW_CLIENTSECRET" docker run --rm -e BW_MASTERPASS -e BW_CLIENTID -e BW_CLIENTSECRET -e http_proxy samply/bridgehead-vaultfetcher $@)
+	PASS=$(BW_MASTERPASS="$BW_MASTERPASS" BW_CLIENTID="$BW_CLIENTID" BW_CLIENTSECRET="$BW_CLIENTSECRET" docker run --rm -e BW_MASTERPASS -e BW_CLIENTID -e BW_CLIENTSECRET -e http_proxy docker.verbis.dkfz.de/cache/samply/bridgehead-vaultfetcher:latest $@)
 	RET=$?
 
 	if [ $RET -ne 0 ]; then
@@ -136,6 +155,28 @@ setHostname() {
 	fi
 }
 
+# This function optimizes the usage of memory through blaze, according to the official performance tuning guide:
+#   https://github.com/samply/blaze/blob/master/docs/tuning-guide.md
+# Short summary of the adjustments made:
+# - set blaze memory cap to a quarter of the system memory
+# - set db block cache size to a quarter of the system memory
+# - limit resource count allowed in blaze to 1,25M per 4GB available system memory
+optimizeBlazeMemoryUsage() {
+	if [ -z "$BLAZE_MEMORY_CAP" ]; then
+	   system_memory_in_mb=$(LC_ALL=C free -m | grep 'Mem:' | awk '{print $2}');
+	   export BLAZE_MEMORY_CAP=$(($system_memory_in_mb/4));
+	fi
+	if [ -z "$BLAZE_RESOURCE_CACHE_CAP" ]; then
+		available_system_memory_chunks=$((BLAZE_MEMORY_CAP / 1000))
+		if [ $available_system_memory_chunks -eq 0 ]; then
+			log WARN "Only ${BLAZE_MEMORY_CAP} system memory available for Blaze. If your Blaze stores more than 128000 fhir ressources it will run significally slower."
+			export BLAZE_RESOURCE_CACHE_CAP=128000;
+		else
+			export BLAZE_RESOURCE_CACHE_CAP=$((available_system_memory_chunks * 312500))
+		fi
+	fi
+}
+
 # Takes 1) The Backup Directory Path 2) The name of the Service to be backuped
 # Creates 3 Backups: 1) For the past seven days 2) For the current month and 3) for each calendar week
 createEncryptedPostgresBackup(){
@@ -171,7 +212,7 @@ function retry {
 
 function bk_is_running {
 	detectCompose
-	RUNNING="$($COMPOSE -p $PROJECT -f ./$PROJECT/docker-compose.yml $OVERRIDE ps -q)"
+	RUNNING="$($COMPOSE -p $PROJECT -f minimal/docker-compose.yml -f ./$PROJECT/docker-compose.yml $OVERRIDE ps -q)"
 	NUMBEROFRUNNING=$(echo "$RUNNING" | wc -l)
 	if [ $NUMBEROFRUNNING -ge 2 ]; then
 		return 0
@@ -180,6 +221,149 @@ function bk_is_running {
 	fi
 }
 
-##Setting Network properties
-# currently not needed
-#export HOSTIP=$(MSYS_NO_PATHCONV=1 docker run --rm --add-host=host.docker.internal:host-gateway ubuntu cat /etc/hosts | grep 'host.docker.internal' | awk '{print $1}');
+function do_enroll_inner {
+	PARAMS=""
+	
+	MANUAL_PROXY_ID="${1:-$PROXY_ID}"
+	if [ -z "$MANUAL_PROXY_ID" ]; then
+		log ERROR "No Proxy ID set"
+		exit 1
+	else
+		log INFO "Enrolling Beam Proxy Id $MANUAL_PROXY_ID"
+	fi
+
+	SUPPORT_EMAIL="${2:-$SUPPORT_EMAIL}"
+	if [ -n "$SUPPORT_EMAIL" ]; then
+		PARAMS+="--admin-email $SUPPORT_EMAIL"
+	fi
+
+	docker run --rm -v /etc/bridgehead/pki:/etc/bridgehead/pki docker.verbis.dkfz.de/cache/samply/beam-enroll:latest --output-file $PRIVATEKEYFILENAME --proxy-id $MANUAL_PROXY_ID $PARAMS
+	chmod 600 $PRIVATEKEYFILENAME
+}
+
+function do_enroll {
+	do_enroll_inner $@
+}
+
+add_basic_auth_user() {
+   USER="${1}"
+   PASSWORD="${2}"
+   NAME="${3}"
+   PROJECT="${4}"
+   FILE="/etc/bridgehead/${PROJECT}.local.conf"
+   ENCRY_CREDENTIALS="$(docker run --rm docker.verbis.dkfz.de/cache/httpd:alpine htpasswd -nb $USER $PASSWORD  | tr -d '\n' | tr -d '\r')"
+   if [ -f $FILE ] && grep -R -q "$NAME=" $FILE # if a specific basic auth user already exists:
+   then
+     sed -i "/$NAME/ s|='|='$ENCRY_CREDENTIALS,|" $FILE
+   else
+     echo -e "\n## Basic Authentication Credentials for:\n$NAME='$ENCRY_CREDENTIALS'" >> $FILE;
+   fi
+ 	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_PUBLIC_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/ || fail_and_report 1 "Failed to create '/var/cache/bridgehead/secrets/'. Please run sudo './bridgehead install $PROJECT' again."
+    touch /var/cache/bridgehead/secrets/oidc
+    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 NO_PROXY=localhost,127.0.0.1 \
+        -e ALL_PROXY=$HTTPS_PROXY_FULL_URL \
+        -e PROXY_ID=$PROXY_ID \
+        -e BROKER_URL=$BROKER_URL \
+        -e OIDC_PROVIDER=secret-sync-central.oidc-client-enrollment.$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 "${combined_text}" | sha1sum | openssl pkeyutl -sign -inkey "/etc/bridgehead/pki/${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}" | sha1sum | openssl pkeyutl -sign -inkey "/etc/bridgehead/pki/${SITE_ID}.priv.pem" 2> /dev/null | base64 | head -c 26 | sed 's/[+\/]/A/g'
+}

lib/install-bridgehead.sh

@@ -29,12 +29,16 @@ bridgehead ALL= NOPASSWD: BRIDGEHEAD${PROJECT^^}
 EOF
 
 # TODO: Determine whether this should be located in setup-bridgehead (triggered through bridgehead install) or in update bridgehead (triggered every hour)
-if [ -z "$LDM_PASSWORD" ]; then
-  log "INFO" "Now generating a password for the local data management. Please save the password for your ETL process!"
+if [ -z "$LDM_AUTH" ]; then
+  log "INFO" "Now generating basic auth for the local data management (see adduser in bridgehead for more information). "
   generated_passwd="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 32)"
+  add_basic_auth_user $PROJECT $generated_passwd "LDM_AUTH" $PROJECT
+fi
 
-  log "INFO" "Your generated credentials are:\n            user: $PROJECT\n            password: $generated_passwd"
-  echo -e "## Local Data Management Basic Authentication\n# User: $PROJECT\nLDM_PASSWORD=$generated_passwd" >> /etc/bridgehead/${PROJECT}.local.conf;
+if [ ! -z "$NNGM_CTS_APIKEY" ] && [ -z "$NNGM_AUTH" ]; then
+  log "INFO" "Now generating basic auth for nNGM upload API (see adduser in bridgehead for more information). "
+  generated_passwd="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 32)"
+  add_basic_auth_user "nngm" $generated_passwd "NNGM_AUTH" $PROJECT
 fi
 
 log "INFO" "Registering system units for bridgehead and bridgehead-update"

lib/monitoring.sh

@@ -47,8 +47,8 @@ function hc_send(){
 
     if [ -n "$2" ]; then
         MSG="$2\n\nDocker stats:\n$UPTIME"
-        echo -e "$MSG" | https_proxy=$HTTPS_PROXY_URL curl -A "$USER_AGENT" -s -o /dev/null -X POST --data-binary @- "$HCURL"/"$1" || log WARN "Monitoring failed: Unable to send data to $HCURL/$1"
+        echo -e "$MSG" | https_proxy=$HTTPS_PROXY_FULL_URL curl --max-time 5 -A "$USER_AGENT" -s -o /dev/null -X POST --data-binary @- "$HCURL"/"$1" || log WARN "Monitoring failed: Unable to send data to $HCURL/$1"
     else
-        https_proxy=$HTTPS_PROXY_URL curl -A "$USER_AGENT" -s -o /dev/null "$HCURL"/"$1" || log WARN "Monitoring failed: Unable to send data to $HCURL/$1"
+        https_proxy=$HTTPS_PROXY_FULL_URL curl --max-time 5 -A "$USER_AGENT" -s -o /dev/null "$HCURL"/"$1" || log WARN "Monitoring failed: Unable to send data to $HCURL/$1"
     fi
 }

lib/prepare-system.sh

@@ -52,6 +52,9 @@ case "$PROJECT" in
 	bbmri)
 		site_configuration_repository_middle="git.verbis.dkfz.de/bbmri-bridgehead-configs/"
 		;;
+	minimal)
+		site_configuration_repository_middle="git.verbis.dkfz.de/minimal-bridgehead-configs/"
+		;;
 	*)
 		log ERROR "Internal error, this should not happen."
         exit 1
@@ -68,8 +71,12 @@ if [ -d /etc/bridgehead ]; then
     fi
 elif [[ "$DEV_MODE" == "NODEV" ]]; then
     log "INFO" "Now cloning your site configuration repository for you."
-    read -p "Please enter your site: " site
-    read -s -p "Please enter the bridgehead's access token for your site configuration repository (will not be echoed): " access_token
+    if [ -z "$site" ]; then
+        read -p "Please enter your site: " site
+    fi
+    if [ -z "$access_token" ]; then
+        read -s -p "Please enter the bridgehead's access token for your site configuration repository (will not be echoed): " access_token
+    fi
     site_configuration_repository_url="https://bytoken:${access_token}@${site_configuration_repository_middle}$(echo $site | tr '[:upper:]' '[:lower:]').git"
     git clone $site_configuration_repository_url /etc/bridgehead
     if [ $? -gt 0 ]; then
@@ -82,6 +89,9 @@ elif [[ "$DEV_MODE" == "DEV" ]]; then
 fi
 
 chown -R bridgehead /etc/bridgehead /srv/docker/bridgehead
+mkdir -p /tmp/bridgehead /var/cache/bridgehead
+chown -R bridgehead:docker /tmp/bridgehead /var/cache/bridgehead
+chmod -R g+wr /var/cache/bridgehead /tmp/bridgehead
 
 log INFO "System preparation is completed and configuration is present."
 

lib/prerequisites.sh

@@ -14,7 +14,7 @@ checkOwner /etc/bridgehead bridgehead || exit 1
 
 ## Check if user is a su
 log INFO "Checking if all prerequisites are met ..."
-prerequisites="git docker"
+prerequisites="git docker curl"
 for prerequisite in $prerequisites; do
   $prerequisite --version 2>&1
   is_available=$?
@@ -62,6 +62,35 @@ if [ -e /etc/bridgehead/vault.conf ]; then
   fi
 fi
 
+log INFO "Checking network access ($BROKER_URL_FOR_PREREQ) ..."
+
+source /etc/bridgehead/${PROJECT}.conf
+source ${PROJECT}/vars
+
+if [ "${PROJECT}" != "minimal" ]; then
+  set +e
+  SERVERTIME="$(https_proxy=$HTTPS_PROXY_FULL_URL curl -m 5 -s -I $BROKER_URL_FOR_PREREQ 2>&1 | grep -i -e '^Date: ' | sed -e 's/^Date: //i')"
+  RET=$?
+  set -e
+  if [ $RET -ne 0 ]; then
+	  log WARN "Unable to connect to Samply.Beam broker at $BROKER_URL_FOR_PREREQ. Please check your proxy settings.\nThe currently configured proxy was \"$HTTPS_PROXY_URL\". This error is normal when using proxy authentication."
+  	log WARN "Unable to check clock skew due to previous error."
+  else
+	  log INFO "Checking clock skew ..."
+
+    SERVERTIME_AS_TIMESTAMP=$(date --date="$SERVERTIME" +%s)
+	  MYTIME=$(date +%s)
+	  SKEW=$(($SERVERTIME_AS_TIMESTAMP - $MYTIME))
+	  SKEW=$(echo $SKEW | awk -F- '{print $NF}')
+	  SYNCTEXT="For example, consider entering a correct NTP server (e.g. your institution's Active Directory Domain Controller in /etc/systemd/timesyncd.conf (option NTP=) and restart systemd-timesyncd."
+	  if [ $SKEW -ge 300 ]; then
+		  report_error 5 "Your clock is not synchronized (${SKEW}s off). This will cause Samply.Beam's certificate will fail. Please setup time synchronization. $SYNCTEXT"
+		  exit 1
+	  elif [ $SKEW -ge 60 ]; then
+		  log WARN "Your clock is more than a minute off (${SKEW}s). Consider syncing to a time server. $SYNCTEXT"
+	  fi
+  fi
+fi
 checkPrivKey() {
   if [ -e /etc/bridgehead/pki/${SITE_ID}.priv.pem ]; then
     log INFO "Success - private key found."
@@ -69,15 +98,16 @@ checkPrivKey() {
     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
-  log INFO "Success - all prerequisites are met!"
-  hc_send log "Success - all prerequisites are met!"
   return 0
 }
 
-if [[ "$@" =~ "noprivkey" ]]; then
+if [[ "$@" =~ "noprivkey" ||  "${PROJECT}" != "minimal" ]]; then
   log INFO "Skipping check for private key for now."
 else
   checkPrivKey || exit 1
 fi
 
+log INFO "Success - all prerequisites are met!"
+hc_send log "Success - all prerequisites are met!"
+
 exit 0

lib/update-bridgehead.sh

@@ -30,7 +30,7 @@ source $CONFFILE
 assertVarsNotEmpty SITE_ID || fail_and_report 1 "Update failed: SITE_ID empty"
 export SITE_ID
 
-checkOwner . bridgehead || fail_and_report 1 "Update failed: Wrong permissions in $(pwd)"
+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"
 
 CREDHELPER="/srv/docker/bridgehead/lib/gitpassword.sh"
@@ -50,12 +50,12 @@ for DIR in /etc/bridgehead $(pwd); do
     git -C $DIR config credential.helper "$CREDHELPER"
   fi
   old_git_hash="$(git -C $DIR rev-parse --verify HEAD)"
-  if [ -z "$HTTP_PROXY_URL" ]; then
+  if [ -z "$HTTPS_PROXY_FULL_URL" ]; then
     log "INFO" "Git is using no proxy!"
     OUT=$(retry 5 git -C $DIR fetch 2>&1 && retry 5 git -C $DIR pull 2>&1)
   else
-    log "INFO" "Git is using proxy ${HTTP_PROXY_URL} from ${CONFFILE}"
-    OUT=$(retry 5 git -c http.proxy=$HTTP_PROXY_URL -c https.proxy=$HTTPS_PROXY_URL -C $DIR fetch 2>&1 && retry 5 git -c http.proxy=$HTTP_PROXY_URL -c https.proxy=$HTTPS_PROXY_URL -C $DIR pull 2>&1)
+    log "INFO" "Git is using proxy ${HTTPS_PROXY_URL} from ${CONFFILE}"
+    OUT=$(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
     report_error log "Unable to update git $DIR: $OUT"
@@ -86,7 +86,7 @@ done
 # Check docker updates
 log "INFO" "Checking for updates to running docker images ..."
 docker_updated="false"
-for IMAGE in $(cat $PROJECT/docker-compose.yml ${OVERRIDE//-f/} | grep -v "^#" | grep "image:" | sed -e 's_^.*image: \(.*\).*$_\1_g; s_\"__g'); do
+for IMAGE in $($COMPOSE -p $PROJECT -f ./minimal/docker-compose.yml -f ./$PROJECT/docker-compose.yml $OVERRIDE config | grep "image:" | sed -e 's_^.*image: \(.*\).*$_\1_g; s_\"__g'); do
   log "INFO" "Checking for Updates of Image: $IMAGE"
   if docker pull $IMAGE | grep "Downloaded newer image"; then
     CHANGE="Image $IMAGE updated."
@@ -116,7 +116,7 @@ if [ -n "${BACKUP_DIRECTORY}" ]; then
     mkdir -p "$BACKUP_DIRECTORY"
     chown -R "$BACKUP_DIRECTORY" bridgehead;
   fi
-  checkOwner "$BACKUP_DIRECTORY" bridgehead || fail_and_report 1 "Automatic maintenance failed: Wrong permissions for backup directory $(pwd)"
+  checkOwner "$BACKUP_DIRECTORY" bridgehead || fail_and_report 1 "Automatic maintenance failed: Wrong permissions for backup directory $BACKUP_DIRECTORY"
   # Collect all container names that contain '-db'
   BACKUP_SERVICES="$(docker ps --filter name=-db --format "{{.Names}}" | tr "\n" "\ ")"
   log INFO "Performing automatic maintenance: Creating Backups for $BACKUP_SERVICES";
@@ -139,6 +139,15 @@ else
   log WARN "Automated backups are disabled (variable AUTO_BACKUPS != \"true\")"
 fi
 
+#TODO: the following block can be deleted after successful update at all sites
+if [ ! -z "$LDM_PASSWORD" ]; then
+  FILE="/etc/bridgehead/$PROJECT.local.conf"
+  log "INFO" "Migrating LDM_PASSWORD to encrypted credentials in $FILE"
+  add_basic_auth_user $PROJECT $LDM_PASSWORD "LDM_AUTH" $PROJECT
+  add_basic_auth_user $PROJECT $LDM_PASSWORD "NNGM_AUTH" $PROJECT
+  sed -i "/LDM_PASSWORD/{d;}" $FILE
+fi
+
 exit 0
 
 # TODO: Print last commit explicit

minimal/docker-compose.yml

@@ -0,0 +1,57 @@
+version: "3.7"
+
+services:
+  traefik:
+    container_name: bridgehead-traefik
+    image: docker.verbis.dkfz.de/cache/traefik:latest
+    command:
+      - --entrypoints.web.address=:80
+      - --entrypoints.websecure.address=:443
+      - --providers.docker=true
+      - --providers.docker.exposedbydefault=false
+      - --providers.file.directory=/configuration/
+      - --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(`/api`) || PathPrefix(`/dashboard`)"
+      - "traefik.http.routers.dashboard.entrypoints=websecure"
+      - "traefik.http.routers.dashboard.service=api@internal"
+      - "traefik.http.routers.dashboard.tls=true"
+      - "traefik.http.routers.dashboard.middlewares=auth"
+      - "traefik.http.middlewares.auth.basicauth.users=${LDM_AUTH}"
+    ports:
+      - 80:80
+      - 443:443
+    volumes:
+      - /etc/bridgehead/traefik-tls:/certs:ro
+      - ../lib/traefik-configuration/:/configuration:ro
+      - /var/run/docker.sock:/var/run/docker.sock:ro
+
+  forward_proxy:
+    container_name: bridgehead-forward-proxy
+    image: docker.verbis.dkfz.de/cache/samply/bridgehead-forward-proxy:latest
+    environment:
+      HTTPS_PROXY: ${HTTPS_PROXY_URL}
+      HTTPS_PROXY_USERNAME: ${HTTPS_PROXY_USERNAME}
+      HTTPS_PROXY_PASSWORD: ${HTTPS_PROXY_PASSWORD}
+    tmpfs:
+      - /var/log/squid
+      - /var/spool/squid
+    volumes:
+      - /etc/bridgehead/trusted-ca-certs:/docker/custom-certs/:ro
+
+  landing:
+    container_name: bridgehead-landingpage
+    image: docker.verbis.dkfz.de/cache/samply/bridgehead-landingpage:main
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.landing.rule=PathPrefix(`/`)"
+      - "traefik.http.services.landing.loadbalancer.server.port=80"
+      - "traefik.http.routers.landing.tls=true"
+    environment:
+      HOST: ${HOST}
+      PROJECT: ${PROJECT}
+      SITE_NAME: ${SITE_NAME}

minimal/modules/dnpm-compose.yml

@@ -0,0 +1,59 @@
+version: "3.7"
+
+services:
+  dnpm-beam-proxy:
+    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
+    container_name: bridgehead-dnpm-beam-proxy
+    environment:
+      BROKER_URL: ${DNPM_BROKER_URL}
+      PROXY_ID: ${DNPM_PROXY_ID}
+      APP_dnpm-connect_KEY: ${DNPM_BEAM_SECRET_SHORT}
+      PRIVKEY_FILE: /run/secrets/proxy.pem
+      ALL_PROXY: http://forward_proxy:3128
+      TLS_CA_CERTIFICATES_DIR: ./conf/trusted-ca-certs
+      ROOTCERT_FILE: ./conf/root.crt.pem
+    secrets:
+      - proxy.pem
+    depends_on:
+      - "forward_proxy"
+    volumes:
+      - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
+      - /srv/docker/bridgehead/ccp/root.crt.pem:/conf/root.crt.pem:ro
+
+  dnpm-beam-connect:
+    depends_on: [ dnpm-beam-proxy ]
+    image: docker.verbis.dkfz.de/cache/samply/beam-connect:develop
+    container_name: bridgehead-dnpm-beam-connect
+    environment:
+      PROXY_URL: http://dnpm-beam-proxy:8081
+      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"
+      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}
+      RUST_LOG: ${RUST_LOG:-info}
+      NO_AUTH: "true"
+      TLS_CA_CERTIFICATES_DIR: ./conf/trusted-ca-certs
+    extra_hosts:
+      - "host.docker.internal:host-gateway"
+    volumes:
+      - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
+      - /etc/bridgehead/dnpm/local_targets.json:/conf/connect_targets.json:ro
+      - /etc/bridgehead/dnpm/central_targets.json:/conf/central_targets.json:ro
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.dnpm-connect.rule=PathPrefix(`/dnpm-connect`)"
+      - "traefik.http.middlewares.dnpm-connect-strip.stripprefix.prefixes=/dnpm-connect"
+      - "traefik.http.routers.dnpm-connect.middlewares=dnpm-connect-strip"
+      - "traefik.http.services.dnpm-connect.loadbalancer.server.port=8062"
+      - "traefik.http.routers.dnpm-connect.tls=true"
+
+  dnpm-echo:
+    image: docker.verbis.dkfz.de/cache/samply/bridgehead-echo:latest
+    container_name: bridgehead-dnpm-echo
+
+secrets:
+  proxy.pem:
+    file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

minimal/modules/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"

minimal/modules/dnpm-node-setup.sh

@@ -0,0 +1,28 @@
+#!/bin/bash
+
+if [ -n "${ENABLE_DNPM_NODE}" ]; then
+	log INFO "DNPM setup detected (BwHC Node) -- will start BwHC node."
+	OVERRIDE+=" -f ./$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
+	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/dnpm-setup.sh

@@ -0,0 +1,22 @@
+#!/bin/bash
+
+if [ -n "${ENABLE_DNPM}" ]; then
+	log DEBUG "DNPM setup detected (Beam.Connect) -- will start Beam and Beam.Connect for DNPM."
+	OVERRIDE+=" -f ./$PROJECT/modules/dnpm-compose.yml"
+
+	# Set variables required for Beam-Connect
+	DNPM_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
+	DNPM_BROKER_ID="broker.ccp-it.dktk.dkfz.de"
+	DNPM_BROKER_URL="https://${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}.${DNPM_BROKER_ID}"
+	# If the DNPM_NO_PROXY variable is set, prefix it with a comma (as it gets added to a comma separated list)
+	if [ -n "${DNPM_NO_PROXY}" ]; then
+		DNPM_ADDITIONAL_NO_PROXY=",${DNPM_NO_PROXY}"
+	else
+		DNPM_ADDITIONAL_NO_PROXY=""
+	fi
+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

minimal/vars

@@ -0,0 +1,6 @@
+for module in $PROJECT/modules/*.sh
+do
+    log DEBUG "sourcing $module"
+    source $module
+done
+PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem