Whitespace formatting

When a OIDC provider is configured, you'll get redirected to authup by Keycloak which redirects you to the DNPM:DIP. 

Currently the url looks like this: https://myserver/authup//someurl
and produces an error. Manually removing the additional / fixes the issue.

README.md

@@ -254,6 +254,8 @@ 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

@@ -4,7 +4,7 @@ version: "3.7"
 
 services:
   blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
+    image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
     container_name: bridgehead-bbmri-blaze
     environment:
       BASE_URL: "http://bridgehead-bbmri-blaze:8080"

cce/docker-compose.yml

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

ccp/docker-compose.yml

@@ -2,7 +2,7 @@ version: "3.7"
 
 services:
   blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
+    image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
     container_name: bridgehead-ccp-blaze
     environment:
       BASE_URL: "http://bridgehead-ccp-blaze:8080"
@@ -11,7 +11,6 @@ services:
       DB_BLOCK_CACHE_SIZE: ${BLAZE_MEMORY_CAP}
       CQL_EXPR_CACHE_SIZE: ${BLAZE_CQL_CACHE_CAP:-32}
       ENFORCE_REFERENTIAL_INTEGRITY: "false"
-      LOG_LEVEL: ${LOG_LEVEL_BLAZE:-WARN}
     volumes:
       - "blaze-data:/app/data"
     labels:
@@ -35,7 +34,6 @@ services:
       EPSILON: 0.28
       QUERIES_TO_CACHE: '/queries_to_cache.conf'
       ENDPOINT_TYPE: ${FOCUS_ENDPOINT_TYPE:-blaze}
-      RUST_LOG: ${LOG_LEVEL_FOCUS:-WARN}
     volumes:
       - /srv/docker/bridgehead/ccp/queries_to_cache.conf:/queries_to_cache.conf
     depends_on:
@@ -53,7 +51,6 @@ services:
       ALL_PROXY: http://forward_proxy:3128
       TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
       ROOTCERT_FILE: /conf/root.crt.pem
-      RUST_LOG: ${LOG_LEVEL_FOCUS:-WARN}
     secrets:
       - proxy.pem
     depends_on:

ccp/modules/blaze-secondary-compose.yml

@@ -2,7 +2,7 @@ version: "3.7"
 
 services:
   blaze-secondary:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
+    image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
     container_name: bridgehead-ccp-blaze-secondary
     environment:
       BASE_URL: "http://bridgehead-ccp-blaze-secondary:8080"
@@ -10,7 +10,6 @@ services:
       DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
       DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP
       ENFORCE_REFERENTIAL_INTEGRITY: "false"
-      LOG_LEVEL: ${LOG_LEVEL_BLAZE:-WARN}
     volumes:
       - "blaze-secondary-data:/app/data"
     labels:

ccp/modules/datashield-compose.yml

@@ -10,7 +10,6 @@ services:
       DISABLE_AUTH: "true" # https://rocker-project.org/images/versioned/rstudio.html#how-to-use
       HTTP_RELATIVE_PATH: "/rstudio"
       ALL_PROXY: "http://forward_proxy:3128" # https://rocker-project.org/use/networking.html
-      LOG_LEVEL: ${LOG_LEVEL_RSTUDIO:-WARN}
     labels:
       - "traefik.enable=true"
       - "traefik.http.routers.rstudio_ccp.rule=PathPrefix(`/rstudio`)"
@@ -55,7 +54,6 @@ services:
       BEAM_APP_ID: token-manager.${PROXY_ID}
       BEAM_SECRET: ${TOKEN_MANAGER_SECRET}
       BEAM_DATASHIELD_PROXY: request-manager
-      LOG_LEVEL: ${LOG_LEVEL_OPAL:-WARN}
     volumes:
       - "/var/cache/bridgehead/ccp/opal-metadata-db:/srv" # Opal metadata
     secrets:
@@ -77,8 +75,6 @@ services:
     image: docker.verbis.dkfz.de/ccp/dktk-rserver # datashield/rock-base + dsCCPhos
     tmpfs:
       - /srv
-    environment:
-      LOG_LEVEL: ${LOG_LEVEL_OPAL:-WARN}
 
   beam-connect:
     image: docker.verbis.dkfz.de/cache/samply/beam-connect:develop
@@ -91,7 +87,6 @@ services:
       DISCOVERY_URL: "./map/central.json"
       LOCAL_TARGETS_FILE: "./map/local.json"
       NO_AUTH: "true"
-      RUST_LOG: ${LOG_LEVEL_BEAMCONNECT:-WARN}
     secrets:
       - opal-cert.pem
     depends_on:

ccp/modules/dnpm-compose.yml

@@ -13,11 +13,11 @@ 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}
-      RUST_LOG: ${LOG_LEVEL_BEAMCONNECTDNPM:-WARN}
+      RUST_LOG: ${RUST_LOG:-info}
       NO_AUTH: "true"
       TLS_CA_CERTIFICATES_DIR: ./conf/trusted-ca-certs
     extra_hosts:
@@ -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
-      - /etc/bridgehead/dnpm/central_targets.json:/conf/central_targets.json:ro
+      - /srv/docker/bridgehead/minimal/modules/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

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

ccp/modules/dnpm-node-setup.sh

@@ -1,28 +1,16 @@
 #!/bin/bash
 
 if [ -n "${ENABLE_DNPM_NODE}" ]; then
-	log INFO "DNPM setup detected (BwHC Node) -- will start BwHC node."
+	log INFO "DNPM setup detected -- will start DNPM:DIP node."
 	OVERRIDE+=" -f ./$PROJECT/modules/dnpm-node-compose.yml"
 
 	# Set variables required for BwHC Node. ZPM_SITE is assumed to be set in /etc/bridgehead/<project>.conf
-	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
+    mkdir -p /var/cache/bridgehead/dnpm/ || fail_and_report 1 "Failed to create '/var/cache/bridgehead/dnpm/'. Please run sudo './bridgehead install $PROJECT' again to fix the permissions."
-		log ERROR "Mandatory variable DNPM_DATA_DIR not defined!"
+    DNPM_SYNTH_NUM=${DNPM_SYNTH_NUM:--1}
-		exit 1
+    DNPM_MYSQL_ROOT_PASSWORD="$(generate_simple_password 'dnpm mysql')"
-	fi
+    DNPM_AUTHUP_SECRET="$(generate_simple_password 'dnpm authup')"
-	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

@@ -6,6 +6,7 @@ services:
     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"
@@ -15,7 +16,6 @@ services:
       SITE: "${SITE_ID}"
       HTTP_SERVLET_REQUEST_SCHEME: "https"
       OPAL_PASSWORD: "${EXPORTER_OPAL_PASSWORD}"
-      LOG_LEVEL: ${LOG_LEVEL_EXPORTER:-WARN}
     labels:
       - "traefik.enable=true"
       - "traefik.http.routers.exporter_ccp.rule=PathPrefix(`/ccp-exporter`)"
@@ -42,6 +42,7 @@ services:
     container_name: bridgehead-ccp-reporter
     environment:
       JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
+      LOG_LEVEL: "INFO"
       CROSS_ORIGINS: "https://${HOST}"
       HTTP_RELATIVE_PATH: "/ccp-reporter"
       SITE: "${SITE_ID}"
@@ -49,7 +50,6 @@ services:
       EXPORTER_URL: "http://exporter:8092"
       LOG_FHIR_VALIDATION: "false"
       HTTP_SERVLET_REQUEST_SCHEME: "https"
-      LOG_LEVEL: ${LOG_LEVEL_REPORTER:-WARN}
 
     # 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
@@ -69,4 +69,4 @@ services:
   focus:
     environment:
       EXPORTER_URL: "http://exporter:8092"
-      AUTH_HEADER: "${EXPORTER_API_KEY}"
+      EXPORTER_API_KEY: "${EXPORTER_API_KEY}"

ccp/modules/id-management-compose.yml

@@ -14,7 +14,6 @@ services:
       MAGICPL_CONNECTOR_APIKEY: ${IDMANAGER_READ_APIKEY}
       MAGICPL_CENTRAL_PATIENTLIST_APIKEY: ${IDMANAGER_CENTRAL_PATIENTLIST_APIKEY}
       MAGICPL_CONTROLNUMBERGENERATOR_APIKEY: ${IDMANAGER_CONTROLNUMBERGENERATOR_APIKEY}
-      ML_LOG_LEVEL: ${LOG_LEVEL_IDMANAGER:-WARN}
     depends_on:
       - patientlist
       - traefik-forward-auth
@@ -45,8 +44,6 @@ services:
       - ML_UPLOAD_API_KEY=${IDMANAGER_UPLOAD_APIKEY}
       # Add Variables from /etc/patientlist-id-generators.env
       - PATIENTLIST_SEEDS_TRANSFORMED
-      - ML_LOG_LEVEL=${LOG_LEVEL_PATIENTLIST:-WARN}
-      #TODO confirm LOG_LEVEL
     labels:
       - "traefik.enable=true"
       - "traefik.http.routers.patientlist.rule=PathPrefix(`/patientlist`)"
@@ -105,11 +102,11 @@ services:
         condition: service_healthy
 
   ccp-patient-project-identificator:
-    image: samply/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: ${SITE_NAME}
+      SITE_NAME: ${IDMANAGEMENT_FRIENDLY_ID}
 
 volumes:
   patientlist-db-data:

ccp/modules/mtba-compose.yml

@@ -25,7 +25,6 @@ services:
       OIDC_CLIENT_SECRET: "${OIDC_CLIENT_SECRET}"
       OIDC_REALM: "${OIDC_REALM}"
       OIDC_URL: "${OIDC_URL}"
-      LOG_LEVEL: ${LOG_LEVEL_MTBA:-WARN}
 
     labels:
       - "traefik.enable=true"

ccp/modules/nngm-compose.yml

@@ -12,8 +12,6 @@ services:
       CTS_API_KEY: ${NNGM_CTS_APIKEY}
       CRYPT_KEY: ${NNGM_CRYPTKEY}
       #CTS_MAGICPL_SITE: ${SITE_ID}TODO
-      LOG_LEVEL: ${LOG_LEVEL_NNGM:-WARN}
-    restart: always
     labels:
       - "traefik.enable=true"
       - "traefik.http.routers.connector.rule=PathPrefix(`/nngm-connector`)"

ccp/modules/obds2fhir-rest-compose.yml

@@ -10,8 +10,6 @@ services:
       SALT: ${LOCAL_SALT}
       KEEP_INTERNAL_ID: ${KEEP_INTERNAL_ID:-false}
       MAINZELLISTE_URL: ${PATIENTLIST_URL:-http://patientlist:8080/patientlist}
-      LOG_LEVEL: ${LOG_LEVEL_REPORTER:-WARN}
-    restart: always
     labels:
       - "traefik.enable=true"
       - "traefik.http.routers.obds2fhir-rest.rule=PathPrefix(`/obds2fhir-rest`) || PathPrefix(`/adt2fhir-rest`)"

ccp/modules/teiler-compose.yml

@@ -17,7 +17,6 @@ services:
       TEILER_DASHBOARD_URL: "https://${HOST}/ccp-teiler-dashboard"
       DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE_LOWER_CASE}"
       HTTP_RELATIVE_PATH: "/ccp-teiler"
-      LOG_LEVEL: ${LOG_LEVEL_TEILER:-WARN}
 
   teiler-dashboard:
     image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:develop
@@ -48,7 +47,6 @@ services:
       TEILER_ADMIN: "${OIDC_ADMIN_GROUP}"
       REPORTER_DEFAULT_TEMPLATE_ID: "ccp-qb"
       EXPORTER_DEFAULT_TEMPLATE_ID: "ccp"
-      LOG_LEVEL: ${LOG_LEVEL_TEILER:-WARN}
 
 
   teiler-backend:
@@ -62,6 +60,7 @@ services:
       - "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}"
@@ -74,7 +73,6 @@ services:
       HTTP_PROXY: "http://forward_proxy:3128"
       ENABLE_MTBA: "${ENABLE_MTBA}"
       ENABLE_DATASHIELD: "${ENABLE_DATASHIELD}"
-      LOG_LEVEL: ${LOG_LEVEL_TEILER:-WARN}
     secrets:
       - ccp.conf
 

dhki/docker-compose.yml

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

docs/update-access-token.md

@@ -0,0 +1,42 @@
+## 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:0.28
+    image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
     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:0.28
+    image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
     container_name: bridgehead-kr-blaze
     environment:
       BASE_URL: "http://bridgehead-kr-blaze:8080"

kr/modules/obds2fhir-rest-compose.yml

@@ -10,7 +10,6 @@ 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/update-bridgehead.sh

@@ -58,7 +58,8 @@ 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
-    report_error log "Unable to update git $DIR: $OUT"
+    OUT_SAN=$(echo $OUT | sed -E 's|://[^:]+:[^@]+@|://credentials@|g')
+    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(`/api`) || PathPrefix(`/dashboard/`)"
+      - "traefik.http.routers.dashboard.rule=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

@@ -0,0 +1,142 @@
+{
+    "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
-      - /etc/bridgehead/dnpm/central_targets.json:/conf/central_targets.json:ro
+      - /srv/docker/bridgehead/minimal/modules/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

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

minimal/modules/dnpm-node-setup.sh

@@ -1,28 +1,16 @@
 #!/bin/bash
 
 if [ -n "${ENABLE_DNPM_NODE}" ]; then
-	log INFO "DNPM setup detected (BwHC Node) -- will start BwHC node."
+	log INFO "DNPM setup detected -- will start DNPM:DIP node."
 	OVERRIDE+=" -f ./$PROJECT/modules/dnpm-node-compose.yml"
 
 	# Set variables required for BwHC Node. ZPM_SITE is assumed to be set in /etc/bridgehead/<project>.conf
-	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
+    mkdir -p /var/cache/bridgehead/dnpm/ || fail_and_report 1 "Failed to create '/var/cache/bridgehead/dnpm/'. Please run sudo './bridgehead install $PROJECT' again to fix the permissions."
-		log ERROR "Mandatory variable DNPM_DATA_DIR not defined!"
+    DNPM_SYNTH_NUM=${DNPM_SYNTH_NUM:--1}
-		exit 1
+    DNPM_MYSQL_ROOT_PASSWORD="$(generate_simple_password 'dnpm mysql')"
-	fi
+    DNPM_AUTHUP_SECRET="$(generate_simple_password 'dnpm authup')"
-	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

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