remove readme

Co-authored-by: Tobias Kussel <TKussel@users.noreply.github.com>

.github/scripts/rename_inactive_branches.py

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

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

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

README.md

@@ -254,8 +254,6 @@ sh bridgehead uninstall
 
 ## Site-specific configuration
 
-[How to Change Config Access Token](docs/update-access-token.md)
-
 ### HTTPS Access
 
 Even within your internal network, the Bridgehead enforces HTTPS for all services. During the installation, a self-signed, long-lived certificate was created for you. To increase security, you can simply replace the files under `/etc/bridgehead/traefik-tls` with ones from established certification authorities such as [Let's Encrypt](https://letsencrypt.org) or [DFN-AAI](https://www.aai.dfn.de).

bbmri/docker-compose.yml

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

bbmri/modules/eric-compose.yml

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

bbmri/modules/gbn-compose.yml

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

cce/docker-compose.yml

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

ccp/docker-compose.yml

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

ccp/modules/blaze-secondary-compose.yml

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

ccp/modules/datashield-compose.yml

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

ccp/modules/dnpm-compose.yml

@@ -13,7 +13,7 @@ services:
       PROXY_APIKEY: ${DNPM_BEAM_SECRET_SHORT}
       APP_ID: dnpm-connect.${PROXY_ID}
       DISCOVERY_URL: "./conf/central_targets.json"
-      LOCAL_TARGETS_FILE: "/conf/connect_targets.json"
+      LOCAL_TARGETS_FILE: "./conf/connect_targets.json"
       HTTP_PROXY: "http://forward_proxy:3128"
       HTTPS_PROXY: "http://forward_proxy:3128"
       NO_PROXY: beam-proxy,dnpm-backend,host.docker.internal${DNPM_ADDITIONAL_NO_PROXY}
@@ -25,7 +25,7 @@ services:
     volumes:
       - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
       - /etc/bridgehead/dnpm/local_targets.json:/conf/connect_targets.json:ro
-      - /srv/docker/bridgehead/minimal/modules/dnpm-central-targets.json:/conf/central_targets.json:ro
+      - /etc/bridgehead/dnpm/central_targets.json:/conf/central_targets.json:ro
     labels:
       - "traefik.enable=true"
       - "traefik.http.routers.dnpm-connect.rule=PathPrefix(`/dnpm-connect`)"

ccp/modules/dnpm-node-compose.yml

@@ -1,103 +1,34 @@
 version: "3.7"
 
 services:
-  dnpm-mysql:
-    image: mysql:9
-    healthcheck:
-      test: [ "CMD", "mysqladmin" ,"ping", "-h", "localhost" ]
-      interval: 3s
-      timeout: 5s
-      retries: 5
-    environment:
-      MYSQL_ROOT_HOST: "%"
-      MYSQL_ROOT_PASSWORD: ${DNPM_MYSQL_ROOT_PASSWORD}
-    volumes:
-      - /var/cache/bridgehead/dnpm/mysql:/var/lib/mysql
-
-  dnpm-authup:
-    image: authup/authup:latest
-    container_name: bridgehead-dnpm-authup
-    volumes:
-      - /var/cache/bridgehead/dnpm/authup:/usr/src/app/writable
-    depends_on:
-      dnpm-mysql:
-        condition: service_healthy
-    command: server/core start
-    environment:
-      - PUBLIC_URL=https://${HOST}/auth/
-      - AUTHORIZE_REDIRECT_URL=https://${HOST}
-      - ROBOT_ADMIN_ENABLED=true
-      - ROBOT_ADMIN_SECRET=${DNPM_AUTHUP_SECRET}
-      - ROBOT_ADMIN_SECRET_RESET=true
-      - DB_TYPE=mysql
-      - DB_HOST=dnpm-mysql
-      - DB_USERNAME=root
-      - DB_PASSWORD=${DNPM_MYSQL_ROOT_PASSWORD}
-      - DB_DATABASE=auth
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.middlewares.authup-strip.stripprefix.prefixes=/auth"
-      - "traefik.http.routers.dnpm-auth.middlewares=authup-strip"
-      - "traefik.http.routers.dnpm-auth.rule=PathPrefix(`/auth`)"
-      - "traefik.http.services.dnpm-auth.loadbalancer.server.port=3000"
-      - "traefik.http.routers.dnpm-auth.tls=true"
-
-  dnpm-portal:
-    image: ghcr.io/dnpm-dip/portal:latest
-    container_name: bridgehead-dnpm-portal
-    environment:
-      - NUXT_API_URL=http://dnpm-backend:9000/
-      - NUXT_PUBLIC_API_URL=https://${HOST}/api/
-      - NUXT_AUTHUP_URL=http://dnpm-authup:3000/
-      - NUXT_PUBLIC_AUTHUP_URL=https://${HOST}/auth/
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.dnpm-frontend.rule=PathPrefix(`/`)"
-      - "traefik.http.services.dnpm-frontend.loadbalancer.server.port=3000"
-      - "traefik.http.routers.dnpm-frontend.tls=true"
-
   dnpm-backend:
+    image: ghcr.io/kohlbacherlab/bwhc-backend:1.0-snapshot-broker-connector
     container_name: bridgehead-dnpm-backend
-    image: ghcr.io/dnpm-dip/backend:latest
     environment:
-      - LOCAL_SITE=${ZPM_SITE}:${SITE_NAME}   # Format: {Site-ID}:{Site-name}, e.g. UKT:Tübingen
+      - ZPM_SITE=${ZPM_SITE}
-      - RD_RANDOM_DATA=${DNPM_SYNTH_NUM:--1}
+      - N_RANDOM_FILES=${DNPM_SYNTH_NUM}
-      - MTB_RANDOM_DATA=${DNPM_SYNTH_NUM:--1}
-      - HATEOAS_HOST=https://${HOST}
-      - CONNECTOR_TYPE=broker
-      - AUTHUP_URL=robot://system:${DNPM_AUTHUP_SECRET}@http://dnpm-authup:3000
     volumes:
-      - /etc/bridgehead/dnpm/config:/dnpm_config
+      - /etc/bridgehead/dnpm:/bwhc_config:ro
-      - /var/cache/bridgehead/dnpm/backend-data:/dnpm_data
+      - ${DNPM_DATA_DIR}:/bwhc_data
-    depends_on:
-      dnpm-authup:
-        condition: service_healthy
     labels:
       - "traefik.enable=true"
-      - "traefik.http.services.dnpm-backend.loadbalancer.server.port=9000"
+      - "traefik.http.routers.bwhc-backend.rule=PathPrefix(`/bwhc`)"
-      # expose everything
+      - "traefik.http.services.bwhc-backend.loadbalancer.server.port=9000"
-      - "traefik.http.routers.dnpm-backend.rule=PathPrefix(`/api`)"
+      - "traefik.http.routers.bwhc-backend.tls=true"
-      - "traefik.http.routers.dnpm-backend.tls=true"
-      - "traefik.http.routers.dnpm-backend.service=dnpm-backend"
-      # except ETL
-      - "traefik.http.routers.dnpm-backend-etl.rule=PathRegexp(`^/api(/.*)?etl(/.*)?$`)"
-      - "traefik.http.routers.dnpm-backend-etl.tls=true"
-      - "traefik.http.routers.dnpm-backend-etl.service=dnpm-backend"
-      # TODO: add to minimal and document
-      - "traefik.http.middlewares.rewrite-mtbfile.replacepathregex.regex=^(.*)/MTBFile$"
-      - "traefik.http.middlewares.rewrite-mtbfile.replacepathregex.replacement=$1"
-      - "traefik.http.routers.dnpm-backend-etl.middlewares=rewrite-mtbfile"
-      # this needs an ETL processor with support for basic auth
-      - "traefik.http.routers.dnpm-backend-etl.middlewares=auth"
-      # except peer-to-peer
-      - "traefik.http.routers.dnpm-backend-peer.rule=PathRegexp(`^/api(/.*)?/peer2peer(/.*)?$`)"
-      - "traefik.http.routers.dnpm-backend-peer.tls=true"
-      - "traefik.http.routers.dnpm-backend-peer.service=dnpm-backend"
-      - "traefik.http.routers.dnpm-backend-peer.middlewares=dnpm-backend-peer"
-      # this effectively denies all requests
-      # this is okay, because requests from peers don't go through Traefik
-      - "traefik.http.middlewares.dnpm-backend-peer.ipWhiteList.sourceRange=0.0.0.0/32"
 
-  landing:
+  dnpm-frontend:
+    image: ghcr.io/kohlbacherlab/bwhc-frontend:2209
+    container_name: bridgehead-dnpm-frontend
+    links:
+      - dnpm-backend
+    environment:
+      - NUXT_HOST=0.0.0.0
+      - NUXT_PORT=8080
+      - BACKEND_PROTOCOL=https
+      - BACKEND_HOSTNAME=$HOST
+      - BACKEND_PORT=443
     labels:
-      - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"
+      - "traefik.enable=true"
+      - "traefik.http.routers.bwhc-frontend.rule=PathPrefix(`/`)"
+      - "traefik.http.services.bwhc-frontend.loadbalancer.server.port=8080"
+      - "traefik.http.routers.bwhc-frontend.tls=true"

ccp/modules/dnpm-node-setup.sh

@@ -1,16 +1,28 @@
 #!/bin/bash
 
 if [ -n "${ENABLE_DNPM_NODE}" ]; then
-	log INFO "DNPM setup detected -- will start DNPM:DIP node."
+	log INFO "DNPM setup detected (BwHC Node) -- will start BwHC node."
 	OVERRIDE+=" -f ./$PROJECT/modules/dnpm-node-compose.yml"
 
 	# Set variables required for BwHC Node. ZPM_SITE is assumed to be set in /etc/bridgehead/<project>.conf
+	DNPM_APPLICATION_SECRET="$(echo \"This is a salt string to generate one consistent password for DNPM. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
 	if [ -z "${ZPM_SITE+x}" ]; then
 		log ERROR "Mandatory variable ZPM_SITE not defined!"
 		exit 1
 	fi
-    mkdir -p /var/cache/bridgehead/dnpm/ || fail_and_report 1 "Failed to create '/var/cache/bridgehead/dnpm/'. Please run sudo './bridgehead install $PROJECT' again to fix the permissions."
+	if [ -z "${DNPM_DATA_DIR+x}" ]; then
-	DNPM_SYNTH_NUM=${DNPM_SYNTH_NUM:--1}
+		log ERROR "Mandatory variable DNPM_DATA_DIR not defined!"
-    DNPM_MYSQL_ROOT_PASSWORD="$(generate_simple_password 'dnpm mysql')"
+		exit 1
-    DNPM_AUTHUP_SECRET="$(generate_simple_password 'dnpm authup')"
+	fi
+	DNPM_SYNTH_NUM=${DNPM_SYNTH_NUM:-0}
+	if grep -q 'traefik.http.routers.landing.rule=PathPrefix(`/landing`)' /srv/docker/bridgehead/minimal/docker-compose.override.yml 2>/dev/null; then
+		echo "Override of landing page url already in place"
+	else
+		echo "Adding override of landing page url"
+		if [ -f /srv/docker/bridgehead/minimal/docker-compose.override.yml ]; then
+			echo -e '  landing:\n    labels:\n      - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"' >> /srv/docker/bridgehead/minimal/docker-compose.override.yml
+		else
+			echo -e 'version: "3.7"\nservices:\n  landing:\n    labels:\n      - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"' >> /srv/docker/bridgehead/minimal/docker-compose.override.yml
+		fi
+	fi
 fi

ccp/modules/exporter-compose.yml

@@ -65,8 +65,3 @@ services:
       - "traefik.http.routers.reporter_ccp.tls=true"
       - "traefik.http.middlewares.reporter_ccp_strip.stripprefix.prefixes=/ccp-reporter"
       - "traefik.http.routers.reporter_ccp.middlewares=reporter_ccp_strip"
-
-  focus:
-    environment:
-      EXPORTER_URL: "http://exporter:8092"
-      EXPORTER_API_KEY: "${EXPORTER_API_KEY}"

ccp/modules/fhir2sql-compose.yml

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

ccp/modules/fhir2sql-setup.sh

@@ -4,5 +4,4 @@ if [ "$ENABLE_FHIR2SQL" == true ]; then
   log INFO "Dashboard setup detected -- will start Dashboard backend and FHIR2SQL service."
   OVERRIDE+=" -f ./$PROJECT/modules/fhir2sql-compose.yml"
   DASHBOARD_DB_PASSWORD="$(generate_simple_password 'fhir2sql')"
-  FOCUS_ENDPOINT_TYPE="blaze-and-sql"
 fi

ccp/modules/id-management-compose.yml

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

ccp/modules/nngm-compose.yml

@@ -12,6 +12,7 @@ services:
       CTS_API_KEY: ${NNGM_CTS_APIKEY}
       CRYPT_KEY: ${NNGM_CRYPTKEY}
       #CTS_MAGICPL_SITE: ${SITE_ID}TODO
+    restart: always
     labels:
       - "traefik.enable=true"
       - "traefik.http.routers.connector.rule=PathPrefix(`/nngm-connector`)"

ccp/modules/obds2fhir-rest-compose.yml

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

dhki/docker-compose.yml

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

docs/update-access-token.md

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

itcc/docker-compose.yml

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

kr/docker-compose.yml

@@ -6,7 +6,7 @@ services:
       replicas: 0 #deactivate landing page
 
   blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
+    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
     container_name: bridgehead-kr-blaze
     environment:
       BASE_URL: "http://bridgehead-kr-blaze:8080"

kr/modules/obds2fhir-rest-compose.yml

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

lib/functions.sh

@@ -171,10 +171,8 @@ optimizeBlazeMemoryUsage() {
 		if [ $available_system_memory_chunks -eq 0 ]; then
 			log WARN "Only ${BLAZE_MEMORY_CAP} system memory available for Blaze. If your Blaze stores more than 128000 fhir ressources it will run significally slower."
 			export BLAZE_RESOURCE_CACHE_CAP=128000;
-			export BLAZE_CQL_CACHE_CAP=32;
 		else
 			export BLAZE_RESOURCE_CACHE_CAP=$((available_system_memory_chunks * 312500))
-			export BLAZE_CQL_CACHE_CAP=$((($system_memory_in_mb/4)/16));
 		fi
 	fi
 }

lib/update-bridgehead.sh

@@ -58,8 +58,7 @@ for DIR in /etc/bridgehead $(pwd); do
     OUT=$(retry 5 git -c http.proxy=$HTTPS_PROXY_FULL_URL -c https.proxy=$HTTPS_PROXY_FULL_URL -C $DIR fetch 2>&1 && retry 5 git -c http.proxy=$HTTPS_PROXY_FULL_URL -c https.proxy=$HTTPS_PROXY_FULL_URL -C $DIR pull 2>&1)
   fi
   if [ $? -ne 0 ]; then
-    OUT_SAN=$(echo $OUT | sed -E 's|://[^:]+:[^@]+@|://credentials@|g')
+    report_error log "Unable to update git $DIR: $OUT"
-    report_error log "Unable to update git $DIR: $OUT_SAN"
   fi
 
   new_git_hash="$(git -C $DIR rev-parse --verify HEAD)"

minimal/docker-compose.yml

@@ -16,7 +16,7 @@ services:
       - --entrypoints.web.http.redirections.entrypoint.scheme=https
     labels:
       - "traefik.enable=true"
-      - "traefik.http.routers.dashboard.rule=PathPrefix(`/dashboard/`)"
+      - "traefik.http.routers.dashboard.rule=PathPrefix(`/api`) || PathPrefix(`/dashboard/`)"
       - "traefik.http.routers.dashboard.entrypoints=websecure"
       - "traefik.http.routers.dashboard.service=api@internal"
       - "traefik.http.routers.dashboard.tls=true"

minimal/modules/dnpm-central-targets.json

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

minimal/modules/dnpm-compose.yml

@@ -29,7 +29,7 @@ services:
       PROXY_APIKEY: ${DNPM_BEAM_SECRET_SHORT}
       APP_ID: dnpm-connect.${DNPM_PROXY_ID}
       DISCOVERY_URL: "./conf/central_targets.json"
-      LOCAL_TARGETS_FILE: "/conf/connect_targets.json"
+      LOCAL_TARGETS_FILE: "./conf/connect_targets.json"
       HTTP_PROXY: http://forward_proxy:3128
       HTTPS_PROXY: http://forward_proxy:3128
       NO_PROXY: dnpm-beam-proxy,dnpm-backend, host.docker.internal${DNPM_ADDITIONAL_NO_PROXY}
@@ -41,7 +41,7 @@ services:
     volumes:
       - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
       - /etc/bridgehead/dnpm/local_targets.json:/conf/connect_targets.json:ro
-      - /srv/docker/bridgehead/minimal/modules/dnpm-central-targets.json:/conf/central_targets.json:ro
+      - /etc/bridgehead/dnpm/central_targets.json:/conf/central_targets.json:ro
     labels:
       - "traefik.enable=true"
       - "traefik.http.routers.dnpm-connect.rule=PathPrefix(`/dnpm-connect`)"

minimal/modules/dnpm-node-compose.yml

@@ -1,99 +1,34 @@
 version: "3.7"
 
 services:
-  dnpm-mysql:
-    image: mysql:9
-    healthcheck:
-      test: [ "CMD", "mysqladmin" ,"ping", "-h", "localhost" ]
-      interval: 3s
-      timeout: 5s
-      retries: 5
-    environment:
-      MYSQL_ROOT_HOST: "%"
-      MYSQL_ROOT_PASSWORD: ${DNPM_MYSQL_ROOT_PASSWORD}
-    volumes:
-      - /var/cache/bridgehead/dnpm/mysql:/var/lib/mysql
-
-  dnpm-authup:
-    image: authup/authup:latest
-    container_name: bridgehead-dnpm-authup
-    volumes:
-      - /var/cache/bridgehead/dnpm/authup:/usr/src/app/writable
-    depends_on:
-      dnpm-mysql:
-        condition: service_healthy
-    command: server/core start
-    environment:
-      - PUBLIC_URL=https://${HOST}/auth/
-      - AUTHORIZE_REDIRECT_URL=https://${HOST}
-      - ROBOT_ADMIN_ENABLED=true
-      - ROBOT_ADMIN_SECRET=${DNPM_AUTHUP_SECRET}
-      - ROBOT_ADMIN_SECRET_RESET=true
-      - DB_TYPE=mysql
-      - DB_HOST=dnpm-mysql
-      - DB_USERNAME=root
-      - DB_PASSWORD=${DNPM_MYSQL_ROOT_PASSWORD}
-      - DB_DATABASE=auth
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.middlewares.authup-strip.stripprefix.prefixes=/auth/"
-      - "traefik.http.routers.dnpm-auth.middlewares=authup-strip"
-      - "traefik.http.routers.dnpm-auth.rule=PathPrefix(`/auth`)"
-      - "traefik.http.services.dnpm-auth.loadbalancer.server.port=3000"
-      - "traefik.http.routers.dnpm-auth.tls=true"
-
-  dnpm-portal:
-    image: ghcr.io/dnpm-dip/portal:latest
-    container_name: bridgehead-dnpm-portal
-    environment:
-      - NUXT_API_URL=http://dnpm-backend:9000/
-      - NUXT_PUBLIC_API_URL=https://${HOST}/api/
-      - NUXT_AUTHUP_URL=http://dnpm-authup:3000/
-      - NUXT_PUBLIC_AUTHUP_URL=https://${HOST}/auth/
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.dnpm-frontend.rule=PathPrefix(`/`)"
-      - "traefik.http.services.dnpm-frontend.loadbalancer.server.port=3000"
-      - "traefik.http.routers.dnpm-frontend.tls=true"
-
   dnpm-backend:
+    image: ghcr.io/kohlbacherlab/bwhc-backend:1.0-snapshot-broker-connector
     container_name: bridgehead-dnpm-backend
-    image: ghcr.io/dnpm-dip/backend:latest
     environment:
-      - LOCAL_SITE=${ZPM_SITE}:${SITE_NAME}   # Format: {Site-ID}:{Site-name}, e.g. UKT:Tübingen
+      - ZPM_SITE=${ZPM_SITE}
-      - RD_RANDOM_DATA=${DNPM_SYNTH_NUM:--1}
+      - N_RANDOM_FILES=${DNPM_SYNTH_NUM}
-      - MTB_RANDOM_DATA=${DNPM_SYNTH_NUM:--1}
-      - HATEOAS_HOST=https://${HOST}
-      - CONNECTOR_TYPE=broker
-      - AUTHUP_URL=robot://system:${DNPM_AUTHUP_SECRET}@http://dnpm-authup:3000
     volumes:
-      - /etc/bridgehead/dnpm/config:/dnpm_config
+      - /etc/bridgehead/dnpm:/bwhc_config:ro
-      - /var/cache/bridgehead/dnpm/backend-data:/dnpm_data
+      - ${DNPM_DATA_DIR}:/bwhc_data
-    depends_on:
-      dnpm-authup:
-        condition: service_healthy
     labels:
       - "traefik.enable=true"
-      - "traefik.http.services.dnpm-backend.loadbalancer.server.port=9000"
+      - "traefik.http.routers.bwhc-backend.rule=PathPrefix(`/bwhc`)"
-      # expose everything
+      - "traefik.http.services.bwhc-backend.loadbalancer.server.port=9000"
-      - "traefik.http.routers.dnpm-backend.rule=PathPrefix(`/api`)"
+      - "traefik.http.routers.bwhc-backend.tls=true"
-      - "traefik.http.routers.dnpm-backend.tls=true"
-      - "traefik.http.routers.dnpm-backend.service=dnpm-backend"
-      # except ETL
-      - "traefik.http.routers.dnpm-backend-etl.rule=PathRegexp(`^/api(/.*)?etl(/.*)?$`)"
-      - "traefik.http.routers.dnpm-backend-etl.tls=true"
-      - "traefik.http.routers.dnpm-backend-etl.service=dnpm-backend"
-      # this needs an ETL processor with support for basic auth
-      - "traefik.http.routers.dnpm-backend-etl.middlewares=auth"
-      # except peer-to-peer
-      - "traefik.http.routers.dnpm-backend-peer.rule=PathRegexp(`^/api(/.*)?/peer2peer(/.*)?$`)"
-      - "traefik.http.routers.dnpm-backend-peer.tls=true"
-      - "traefik.http.routers.dnpm-backend-peer.service=dnpm-backend"
-      - "traefik.http.routers.dnpm-backend-peer.middlewares=dnpm-backend-peer"
-      # this effectively denies all requests
-      # this is okay, because requests from peers don't go through Traefik
-      - "traefik.http.middlewares.dnpm-backend-peer.ipWhiteList.sourceRange=0.0.0.0/32"
 
-  landing:
+  dnpm-frontend:
+    image: ghcr.io/kohlbacherlab/bwhc-frontend:2209
+    container_name: bridgehead-dnpm-frontend
+    links:
+      - dnpm-backend
+    environment:
+      - NUXT_HOST=0.0.0.0
+      - NUXT_PORT=8080
+      - BACKEND_PROTOCOL=https
+      - BACKEND_HOSTNAME=$HOST
+      - BACKEND_PORT=443
     labels:
-      - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"
+      - "traefik.enable=true"
+      - "traefik.http.routers.bwhc-frontend.rule=PathPrefix(`/`)"
+      - "traefik.http.services.bwhc-frontend.loadbalancer.server.port=8080"
+      - "traefik.http.routers.bwhc-frontend.tls=true"

minimal/modules/dnpm-node-setup.sh

@@ -1,16 +1,28 @@
 #!/bin/bash
 
 if [ -n "${ENABLE_DNPM_NODE}" ]; then
-	log INFO "DNPM setup detected -- will start DNPM:DIP node."
+	log INFO "DNPM setup detected (BwHC Node) -- will start BwHC node."
 	OVERRIDE+=" -f ./$PROJECT/modules/dnpm-node-compose.yml"
 
 	# Set variables required for BwHC Node. ZPM_SITE is assumed to be set in /etc/bridgehead/<project>.conf
+	DNPM_APPLICATION_SECRET="$(echo \"This is a salt string to generate one consistent password for DNPM. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
 	if [ -z "${ZPM_SITE+x}" ]; then
 		log ERROR "Mandatory variable ZPM_SITE not defined!"
 		exit 1
 	fi
-    mkdir -p /var/cache/bridgehead/dnpm/ || fail_and_report 1 "Failed to create '/var/cache/bridgehead/dnpm/'. Please run sudo './bridgehead install $PROJECT' again to fix the permissions."
+	if [ -z "${DNPM_DATA_DIR+x}" ]; then
-	DNPM_SYNTH_NUM=${DNPM_SYNTH_NUM:--1}
+		log ERROR "Mandatory variable DNPM_DATA_DIR not defined!"
-    DNPM_MYSQL_ROOT_PASSWORD="$(generate_simple_password 'dnpm mysql')"
+		exit 1
-    DNPM_AUTHUP_SECRET="$(generate_simple_password 'dnpm authup')"
+	fi
+	DNPM_SYNTH_NUM=${DNPM_SYNTH_NUM:-0}
+	if grep -q 'traefik.http.routers.landing.rule=PathPrefix(`/landing`)' /srv/docker/bridgehead/minimal/docker-compose.override.yml 2>/dev/null; then
+		echo "Override of landing page url already in place"
+	else
+		echo "Adding override of landing page url"
+		if [ -f /srv/docker/bridgehead/minimal/docker-compose.override.yml ]; then
+			echo -e '  landing:\n    labels:\n      - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"' >> /srv/docker/bridgehead/minimal/docker-compose.override.yml
+		else
+			echo -e 'version: "3.7"\nservices:\n  landing:\n    labels:\n      - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"' >> /srv/docker/bridgehead/minimal/docker-compose.override.yml
+		fi
+	fi
 fi

minimal/modules/nngm-compose.yml

@@ -11,6 +11,7 @@ services:
       CTS_API_KEY: ${NNGM_CTS_APIKEY}
       CRYPT_KEY: ${NNGM_CRYPTKEY}
       #CTS_MAGICPL_SITE: ${SITE_ID}TODO
+    restart: always
     labels:
       - "traefik.enable=true"
       - "traefik.http.routers.connector.rule=PathPrefix(`/nngm-connector`)"