fix landingpage

Dont test clock skew and priv key for minimal bridgeheads

README.md

@@ -22,6 +22,7 @@ This repository is the starting point for any information and tools you will nee
     - [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)
@@ -33,6 +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:
@@ -51,24 +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.
-
-Note for git and Docker: if you have a local proxy, you will need to adjust your setup appropriately, see [git proxy](https://gist.github.com/evantoli/f8c23a37eb3558ab8765) and [docker proxy](https://docs.docker.com/network/proxy/).
 
 ### Network
 
-A running Bridgehead requires an outgoing HTTPS proxy to communicate with the central components.
+A Bridgehead communicates to all central components via outgoing HTTPS connections.
 
-Additionally, your site might use its own proxy. You should discuss this with your local systems administration. If a proxy is being used, you will need to note down the URL of the proxy. If it is a secure proxy, then you will also need to make a note of its username and password. This information will be used later on during the installation process.
+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/).
 
-Note that git and Docker may also need to be configured to use this proxy. This is a job for your systems administrators.
+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
 
-If there is a site firewall, this needs to be configured so that outgoing calls to the following URLs are allowed: *.dkfz.de, github.com, docker.io, *.docker.io, *.samply.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.
 
-Note for Ubuntu: Please note that the uncomplicated firewall (ufw) is known to conflict with Docker [here](https://github.com/chaifeng/ufw-docker).
+> 📝 Ubuntu's pre-installed uncomplicated firewall (ufw) is known to conflict with Docker, more info [here](https://github.com/chaifeng/ufw-docker).
 
 ## Deployment
 
@@ -101,7 +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.
 
@@ -294,6 +316,32 @@ Once you edited the gitlab config, the bridgehead will autoupdate the config wit
 
 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
@@ -337,8 +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/modules/dnpm-compose.yml

@@ -1,51 +0,0 @@
-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-new.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
-      RUST_LOG: ${RUST_LOG:-info}
-      NO_AUTH: "true"
-    volumes:
-      - /etc/bridgehead/dnpm/local_targets.json:/conf/connect_targets.json:ro
-      - /etc/bridgehead/dnpm/central_targets.json:/conf/central_targets.json:ro
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.dnpm-connect.rule=PathPrefix(`/dnpm-connect`)"
-      - "traefik.http.middlewares.dnpm-connect-strip.stripprefix.prefixes=/dnpm-connect"
-      - "traefik.http.routers.dnpm-connect.middlewares=dnpm-connect-strip"
-      - "traefik.http.services.dnpm-connect.loadbalancer.server.port=8062"
-      - "traefik.http.routers.dnpm-connect.tls=true"
-
-secrets:
-  proxy.pem:
-    file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

bbmri/modules/dnpm-setup.sh

@@ -1,13 +0,0 @@
-#!/bin/bash
-
-if [ -n "${ENABLE_DNPM}" ]; then
-	log INFO "DNPM setup detected (Beam.Connect) -- will start Beam and Beam.Connect for DNPM."
-	OVERRIDE+=" -f ./$PROJECT/modules/dnpm-compose.yml"
-
-	# Set variables required for Beam-Connect
-	DNPM_APPLICATION_SECRET="$(echo \"This is a salt string to generate one consistent password for DNPM. It is not required to be secret.\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
-	DNPM_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
-	DNPM_BROKER_ID="broker.ccp-it.dktk.dkfz.de"
-	DNPM_BROKER_URL="https://${DNPM_BROKER_ID}"
-	DNPM_PROXY_ID="${SITE_ID}.${DNPM_BROKER_ID}"
-fi

bbmri/modules/eric-compose.yml

@@ -2,7 +2,7 @@ version: "3.7"
 
 services:
   focus-eric:
-    image: docker.verbis.dkfz.de/cache/samply/focus:main
+    image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
     container_name: bridgehead-focus-eric
     environment:
       API_KEY: ${ERIC_FOCUS_BEAM_SECRET_SHORT}
@@ -22,7 +22,6 @@ services:
       BROKER_URL: ${ERIC_BROKER_URL}
       PROXY_ID: ${ERIC_PROXY_ID}
       APP_focus_KEY: ${ERIC_FOCUS_BEAM_SECRET_SHORT}
-      APP_monitoring_KEY: ${ERIC_MONITORING_BEAM_SECRET_SHORT}
       PRIVKEY_FILE: /run/secrets/proxy.pem
       ALL_PROXY: http://forward_proxy:3128
       TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
@@ -33,14 +32,5 @@ services:
       - "forward_proxy"
     volumes:
       - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
-      - /srv/docker/bridgehead/bbmri/modules/eric.root.crt.pem:/conf/root.crt.pem:ro
+      - /srv/docker/bridgehead/bbmri/modules/${ERIC_ROOT_CERT}.root.crt.pem:/conf/root.crt.pem:ro
 
-  bridgehead-monitoring:
-    image: docker.verbis.dkfz.de/cache/samply/bridgehead-monitoring:latest
-    container_name: bridgehead-monitoring-eric
-    environment:
-      - BEAM_ID=monitoring.${ERIC_PROXY_ID}
-      - BEAM_API_KEY=${ERIC_MONITORING_BEAM_SECRET_SHORT}
-      - BEAM_PROXY_URL=http://beam-proxy-eric:8081
-    depends_on:
-      - beam-proxy-eric

bbmri/modules/eric-setup.sh

@@ -4,13 +4,25 @@ if [ "${ENABLE_ERIC}" == "true" ]; then
 	log INFO "BBMRI-ERIC setup detected -- will start services for BBMRI-ERIC."
 	OVERRIDE+=" -f ./$PROJECT/modules/eric-compose.yml"
 
-	# Set required variables
+	# The environment needs to be defined in /etc/bridgehead
-	ERIC_BROKER_ID=broker.bbmri.samply.de
+	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
-
-	#Monitoring
-	ERIC_MONITORING_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
 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

@@ -2,7 +2,7 @@ version: "3.7"
 
 services:
   focus-gbn:
-    image: docker.verbis.dkfz.de/cache/samply/focus:main
+    image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
     container_name: bridgehead-focus-gbn
     environment:
       API_KEY: ${GBN_FOCUS_BEAM_SECRET_SHORT}
@@ -22,7 +22,6 @@ services:
       BROKER_URL: ${GBN_BROKER_URL}
       PROXY_ID: ${GBN_PROXY_ID}
       APP_focus_KEY: ${GBN_FOCUS_BEAM_SECRET_SHORT}
-      APP_monitoring_KEY: ${GBN_MONITORING_BEAM_SECRET_SHORT}
       PRIVKEY_FILE: /run/secrets/proxy.pem
       ALL_PROXY: http://forward_proxy:3128
       TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
@@ -33,15 +32,5 @@ services:
       - "forward_proxy"
     volumes:
       - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
-      - /srv/docker/bridgehead/bbmri/modules/gbn.root.crt.pem:/conf/root.crt.pem:ro
+      - /srv/docker/bridgehead/bbmri/modules/${GBN_ROOT_CERT}.root.crt.pem:/conf/root.crt.pem:ro
-
-  bridgehead-monitoring:
-    image: docker.verbis.dkfz.de/cache/samply/bridgehead-monitoring:latest
-    container_name: bridgehead-monitoring-gbn
-    environment:
-      - BEAM_ID=monitoring.${GBN_PROXY_ID}
-      - BEAM_API_KEY=${GBN_MONITORING_BEAM_SECRET_SHORT}
-      - BEAM_PROXY_URL=http://beam-proxy-gbn:8081
-    depends_on:
-      - beam-proxy-gbn
 

bbmri/modules/gbn-setup.sh

@@ -4,13 +4,25 @@ if [ "${ENABLE_GBN}" == "true" ]; then
 	log INFO "GBN setup detected -- will start services for German Biobank Node."
 	OVERRIDE+=" -f ./$PROJECT/modules/gbn-compose.yml"
 
-	# Set required variables
+	# The environment needs to be defined in /etc/bridgehead
-	GBN_BROKER_ID=broker.bbmri.de
+	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
-
-	#Monitoring
-	GBN_MONITORING_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
 fi

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

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

bbmri/vars

@@ -14,7 +14,7 @@ do
 done
 
 SUPPORT_EMAIL=$ERIC_SUPPORT_EMAIL
-BROKER_URL_FOR_PREREQ=$ERIC_BROKER_URL
+BROKER_URL_FOR_PREREQ="${ERIC_BROKER_URL:-$GBN_BROKER_URL}"
 
 if [ -n "$GBN_SUPPORT_EMAIL" ]; then
     SUPPORT_EMAIL=$GBN_SUPPORT_EMAIL
@@ -34,4 +34,4 @@ function do_enroll {
         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

@@ -65,6 +65,23 @@ loadVars() {
 	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 "$ACTION" in
@@ -85,6 +102,11 @@ case "$ACTION" in
 		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

ccp/docker-compose.yml

@@ -19,7 +19,7 @@ services:
       - "traefik.http.routers.blaze_ccp.tls=true"
 
   focus:
-    image: docker.verbis.dkfz.de/cache/samply/focus:main
+    image: docker.verbis.dkfz.de/cache/samply/focus:0.4.0
     container_name: bridgehead-focus
     environment:
       API_KEY: ${FOCUS_BEAM_SECRET_SHORT}
@@ -28,7 +28,7 @@ services:
       BLAZE_URL: "http://bridgehead-ccp-blaze:8080/fhir/"
       BEAM_PROXY_URL: http://beam-proxy:8081
       RETRY_COUNT: ${FOCUS_RETRY_COUNT}
-      OBFUSCATE: "no"
+      EPSILON: 0.28
     depends_on:
       - "beam-proxy"
       - "blaze"
@@ -40,7 +40,6 @@ services:
       BROKER_URL: ${BROKER_URL}
       PROXY_ID: ${PROXY_ID}
       APP_focus_KEY: ${FOCUS_BEAM_SECRET_SHORT}
-      APP_monitoring_KEY: ${CCP_MONITORING_BEAM_SECRET_SHORT}
       PRIVKEY_FILE: /run/secrets/proxy.pem
       ALL_PROXY: http://forward_proxy:3128
       TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
@@ -52,16 +51,6 @@ services:
     volumes:
       - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
       - /srv/docker/bridgehead/ccp/root.crt.pem:/conf/root.crt.pem:ro
-  
-  bridgehead-monitoring:
-    image: docker.verbis.dkfz.de/cache/samply/bridgehead-monitoring:latest
-    container_name: bridgehead-monitoring-ccp
-    environment:
-      - BEAM_ID=monitoring.${PROXY_ID}
-      - BEAM_API_KEY=${CCP_MONITORING_BEAM_SECRET_SHORT}
-      - BEAM_PROXY_URL=http://beam-proxy:8081
-    depends_on:
-      - beam-proxy
 
 
 volumes:

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/ccp-setup.sh

@@ -1,2 +0,0 @@
-#Monitoring
-CCP_MONITORING_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"

ccp/modules/dnpm-compose.yml

@@ -16,10 +16,14 @@ services:
       LOCAL_TARGETS_FILE: "./conf/connect_targets.json"
       HTTP_PROXY: "http://forward_proxy:3128"
       HTTPS_PROXY: "http://forward_proxy:3128"
-      NO_PROXY: beam-proxy,dnpm-backend
+      NO_PROXY: beam-proxy,dnpm-backend,host.docker.internal${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:
@@ -29,3 +33,7 @@ services:
       - "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

@@ -5,6 +5,11 @@ if [ -n "${ENABLE_DNPM}" ]; then
 	OVERRIDE+=" -f ./$PROJECT/modules/dnpm-compose.yml"
 
 	# Set variables required for Beam-Connect
-	DNPM_APPLICATION_SECRET="$(echo \"This is a salt string to generate one consistent password for DNPM. It is not required to be secret.\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
 	DNPM_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
+	# If the DNPM_NO_PROXY variable is set, prefix it with a comma (as it gets added to a comma separated list)
+	if [ -n "${DNPM_NO_PROXY}" ]; then
+		DNPM_ADDITIONAL_NO_PROXY=",${DNPM_NO_PROXY}"
+	else
+		DNPM_ADDITIONAL_NO_PROXY=""
+	fi
 fi

ccp/modules/id-management-compose.yml

@@ -43,7 +43,7 @@ services:
       - patientlist-db
 
   patientlist-db:
-    image: docker.verbis.dkfz.de/cache/postgres:15.1-alpine
+    image: docker.verbis.dkfz.de/cache/postgres:15.6-alpine
     container_name: bridgehead-patientlist-db
     environment:
       POSTGRES_USER: "mainzelliste"

ccp/modules/id-management-setup.sh

@@ -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

@@ -2,7 +2,7 @@ version: "3.7"
 
 services:
   mtba:
-    image: docker.verbis.dkfz.de/cache/samply/mtba:develop
+    image: docker.verbis.dkfz.de/cache/samply/mtba:1.0.0
     container_name: bridgehead-mtba
     environment:
       BLAZE_STORE_URL: http://blaze:8080

ccp/modules/mtba-setup.sh

@@ -1,13 +1,12 @@
 #!/bin/bash
 
 function mtbaSetup() {
-       # TODO: Check if ID-Management Module is activated!
+  if [ -n "$ENABLE_MTBA" ];then
-       if [ -n "$ENABLE_MTBA" ];then
+    log INFO "MTBA setup detected -- will start MTBA Service and CBioPortal."
-               log INFO "MTBA setup detected -- will start MTBA Service and CBioPortal."
+    if [ ! -n "$IDMANAGER_UPLOAD_APIKEY" ]; then
-              if [ ! -n "$IDMANAGER_UPLOAD_APIKEY" ]; then
+      log ERROR "Missing ID-Management Module! Fix this by setting up ID Management:"
-                      log ERROR "Detected MTBA Module configuration but ID-Management Module seems not to be configured!"
+      exit 1;
-                      exit 1;
+    fi
-              fi
+    OVERRIDE+=" -f ./$PROJECT/modules/mtba-compose.yml"
-               OVERRIDE+=" -f ./$PROJECT/modules/mtba-compose.yml"
+  fi
-       fi
 }

ccp/modules/nngm-setup.sh

@@ -1,8 +1,6 @@
 #!/bin/bash
 
-function nngmSetup() {
+if [ -n "$NNGM_CTS_APIKEY" ]; then
-	if [ -n "$NNGM_CTS_APIKEY" ]; then
+  log INFO "nNGM setup detected -- will start nNGM Connector."
-		log INFO "nNGM setup detected -- will start nNGM Connector."
+  OVERRIDE+=" -f ./$PROJECT/modules/nngm-compose.yml"
-		OVERRIDE+=" -f ./$PROJECT/modules/nngm-compose.yml"
+fi
-	fi
-	}

ccp/root-new.crt.pem

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

ccp/vars

@@ -16,5 +16,5 @@ do
 done
 
 idManagementSetup
-nngmSetup
+mtbaSetup
-mtbaSetup
+adt2fhirRestSetup

lib/functions.sh

@@ -9,6 +9,33 @@ detectCompose() {
 	fi
 }
 
+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), $https https proxy"
+	export HTTPS_PROXY_HOST HTTPS_PROXY_PORT HTTPS_PROXY_FULL_URL
+}
+
 exitIfNotRoot() {
   if [ "$EUID" -ne 0 ]; then
     log "ERROR" "Please run as root"
@@ -26,7 +53,7 @@ checkOwner(){
 }
 
 printUsage() {
-	echo "Usage: bridgehead start|stop|is-running|update|install|uninstall|adduser|enroll PROJECTNAME"
+	echo "Usage: bridgehead start|stop|logs|is-running|update|install|uninstall|adduser|enroll PROJECTNAME"
 	echo "PROJECTNAME should be one of ccp|bbmri"
 }
 
@@ -49,7 +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
@@ -188,7 +215,7 @@ function do_enroll_inner {
 		PARAMS+="--admin-email $SUPPORT_EMAIL"
 	fi
 
-	docker run --rm -v /etc/bridgehead/pki:/etc/bridgehead/pki samply/beam-enroll:latest --output-file $PRIVATEKEYFILENAME --proxy-id $MANUAL_PROXY_ID $PARAMS
+	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
 }
 

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 --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/$1"
+        echo -e "$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 --max-time 5 -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/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
   $prerequisite --version 2>&1
   is_available=$?
@@ -67,29 +67,30 @@ log INFO "Checking network access ($BROKER_URL_FOR_PREREQ) ..."
 source /etc/bridgehead/${PROJECT}.conf
 source ${PROJECT}/vars
 
-set +e
+if [ "${PROJECT}" != "minimal" ]; then
-SERVERTIME="$(https_proxy=$HTTPS_PROXY_URL curl -m 5 -s -I $BROKER_URL_FOR_PREREQ 2>&1 | grep -i -e '^Date: ' | sed -e 's/^Date: //i')"
+  set +e
-RET=$?
+  SERVERTIME="$(https_proxy=$HTTPS_PROXY_FULL_URL curl -m 5 -s -I $BROKER_URL_FOR_PREREQ 2>&1 | grep -i -e '^Date: ' | sed -e 's/^Date: //i')"
-set -e
+  RET=$?
-if [ $RET -ne 0 ]; then
+  set -e
-	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."
+  if [ $RET -ne 0 ]; then
-	log WARN "Unable to check clock skew due to previous error."
+	  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."
-else
+  	log WARN "Unable to check clock skew due to previous error."
-	log INFO "Checking clock skew ..."
+  else
+	  log INFO "Checking clock skew ..."
 
-	SERVERTIME_AS_TIMESTAMP=$(date --date="$SERVERTIME" +%s)
+    SERVERTIME_AS_TIMESTAMP=$(date --date="$SERVERTIME" +%s)
-	MYTIME=$(date +%s)
+	  MYTIME=$(date +%s)
-	SKEW=$(($SERVERTIME_AS_TIMESTAMP - $MYTIME))
+	  SKEW=$(($SERVERTIME_AS_TIMESTAMP - $MYTIME))
-	SKEW=$(echo $SKEW | awk -F- '{print $NF}')
+	  SKEW=$(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."
+	  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
+	  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. $SYNCTEXT"
+		  report_error 5 "Your clock is not synchronized (${SKEW}s off). This will cause Samply.Beam's certificate will fail. Please setup time synchronization. $SYNCTEXT"
-		exit 1
+		  exit 1
-	elif [ $SKEW -ge 60 ]; then
+	  elif [ $SKEW -ge 60 ]; then
-		log WARN "Your clock is more than a minute off (${SKEW}s). Consider syncing to a time server. $SYNCTEXT"
+		  log WARN "Your clock is more than a minute off (${SKEW}s). Consider syncing to a time server. $SYNCTEXT"
-	fi
+	  fi
+  fi
 fi
-
 checkPrivKey() {
   if [ -e /etc/bridgehead/pki/${SITE_ID}.priv.pem ]; then
     log INFO "Success - private key found."
@@ -100,7 +101,7 @@ checkPrivKey() {
   return 0
 }
 
-if [[ "$@" =~ "noprivkey" ]]; then
+if [[ "$@" =~ "noprivkey" ||  "${PROJECT}" != "minimal" ]]; then
   log INFO "Skipping check for private key for now."
 else
   checkPrivKey || exit 1

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}"
+    log "INFO" "Git is using proxy ${HTTPS_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 $DIR pull 2>&1)
+    OUT=$(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/} minimal/docker-compose.yml | 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";

minimal/docker-compose.yml

@@ -35,8 +35,8 @@ services:
     image: docker.verbis.dkfz.de/cache/samply/bridgehead-forward-proxy:latest
     environment:
       HTTPS_PROXY: ${HTTPS_PROXY_URL}
-      USERNAME: ${HTTPS_PROXY_USERNAME}
+      HTTPS_PROXY_USERNAME: ${HTTPS_PROXY_USERNAME}
-      PASSWORD: ${HTTPS_PROXY_PASSWORD}
+      HTTPS_PROXY_PASSWORD: ${HTTPS_PROXY_PASSWORD}
     tmpfs:
       - /var/log/squid
       - /var/spool/squid
@@ -45,7 +45,7 @@ services:
 
   landing:
     container_name: bridgehead-landingpage
-    image: docker.verbis.dkfz.de/cache/samply/bridgehead-landingpage:master
+    image: docker.verbis.dkfz.de/cache/samply/bridgehead-landingpage:main
     labels:
       - "traefik.enable=true"
       - "traefik.http.routers.landing.rule=PathPrefix(`/`)"
@@ -55,5 +55,6 @@ services:
       HOST: ${HOST}
       PROJECT: ${PROJECT}
       SITE_NAME: ${SITE_NAME}
+      ENVIRONMENT: "production"
 
 

minimal/modules/dnpm-compose.yml

@@ -18,7 +18,7 @@ services:
       - "forward_proxy"
     volumes:
       - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
-      - /srv/docker/bridgehead/ccp/root-new.crt.pem:/conf/root.crt.pem:ro
+      - /etc/bridgehead/dnpm/aachen.crt.pem:/conf/root.crt.pem:ro
 
   dnpm-beam-connect:
     depends_on: [ dnpm-beam-proxy ]
@@ -32,10 +32,14 @@ services:
       LOCAL_TARGETS_FILE: "./conf/connect_targets.json"
       HTTP_PROXY: http://forward_proxy:3128
       HTTPS_PROXY: http://forward_proxy:3128
-      NO_PROXY: dnpm-beam-proxy,dnpm-backend
+      NO_PROXY: dnpm-beam-proxy,dnpm-backend, host.docker.internal${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:
@@ -46,6 +50,10 @@ services:
       - "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

@@ -5,9 +5,18 @@ if [ -n "${ENABLE_DNPM}" ]; then
 	OVERRIDE+=" -f ./$PROJECT/modules/dnpm-compose.yml"
 
 	# Set variables required for Beam-Connect
-	DNPM_APPLICATION_SECRET="$(echo \"This is a salt string to generate one consistent password for DNPM. It is not required to be secret.\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
 	DNPM_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
-	DNPM_BROKER_ID="broker.ccp-it.dktk.dkfz.de"
+	DNPM_BROKER_ID="dnpm-aachen-broker.samply.de"
 	DNPM_BROKER_URL="https://${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