Changed: image used for cbioportal and teiler backend

- used image for cbioportal in cbioportal-compose to the Harbor image

- Ran tests to make sure cbioportal and cbioportal API work in Teiler backend.

bbmri/docker-compose.yml

@@ -8,9 +8,8 @@ services:
     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
+      JAVA_TOOL_OPTIONS: "-Xmx4g"
+      LOG_LEVEL: "debug"
       ENFORCE_REFERENTIAL_INTEGRITY: "false"
     volumes:
       - "blaze-data:/app/data"

bbmri/modules/dnpm-compose.yml

@@ -0,0 +1,53 @@
+version: "3.7"
+
+services:
+  dnpm-beam-proxy:
+    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
+    container_name: bridgehead-dnpm-beam-proxy
+    environment:
+      BROKER_URL: ${DNPM_BROKER_URL}
+      PROXY_ID: ${DNPM_PROXY_ID}
+      APP_dnpm-connect_KEY: ${DNPM_BEAM_SECRET_SHORT}
+      PRIVKEY_FILE: /run/secrets/proxy.pem
+      ALL_PROXY: http://forward_proxy:3128
+      TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
+      ROOTCERT_FILE: /conf/root.crt.pem
+    secrets:
+      - proxy.pem
+    depends_on:
+      - "forward_proxy"
+    volumes:
+      - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
+      - /srv/docker/bridgehead/ccp/root.crt.pem:/conf/root.crt.pem:ro
+
+  dnpm-beam-connect:
+    depends_on: [ dnpm-beam-proxy ]
+    image: docker.verbis.dkfz.de/cache/samply/beam-connect:develop
+    container_name: bridgehead-dnpm-beam-connect
+    environment:
+      PROXY_URL: http://dnpm-beam-proxy:8081
+      PROXY_APIKEY: ${DNPM_BEAM_SECRET_SHORT}
+      APP_ID: dnpm-connect.${DNPM_PROXY_ID}
+      DISCOVERY_URL: "./conf/central_targets.json"
+      LOCAL_TARGETS_FILE: "./conf/connect_targets.json"
+      HTTP_PROXY: http://forward_proxy:3128
+      HTTPS_PROXY: http://forward_proxy:3128
+      NO_PROXY: dnpm-beam-proxy,dnpm-backend, host.docker.internal
+      RUST_LOG: ${RUST_LOG:-info}
+      NO_AUTH: "true"
+    extra_host:
+      - "host.docker.internal:host-gateway"
+    volumes:
+      - /etc/bridgehead/dnpm/local_targets.json:/conf/connect_targets.json:ro
+      - /etc/bridgehead/dnpm/central_targets.json:/conf/central_targets.json:ro
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.dnpm-connect.rule=PathPrefix(`/dnpm-connect`)"
+      - "traefik.http.middlewares.dnpm-connect-strip.stripprefix.prefixes=/dnpm-connect"
+      - "traefik.http.routers.dnpm-connect.middlewares=dnpm-connect-strip"
+      - "traefik.http.services.dnpm-connect.loadbalancer.server.port=8062"
+      - "traefik.http.routers.dnpm-connect.tls=true"
+
+secrets:
+  proxy.pem:
+    file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

bbmri/modules/dnpm-node-compose.yml

@@ -0,0 +1,33 @@
+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}
+    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"

bbmri/modules/dnpm-node-setup.sh

@@ -0,0 +1,27 @@
+#!/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
+			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

bbmri/modules/dnpm-setup.sh

@@ -0,0 +1,12 @@
+#!/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_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

bridgehead

@@ -41,6 +41,7 @@ case "$PROJECT" in
 		;;
 esac
 
+# TODO: Please add proper documentation for variable priorities (1. secrets, 2. vars, 3. PROJECT.local.conf, 4. PROJECT.conf, 5. ???
 loadVars() {
 	# Load variables from /etc/bridgehead and /srv/docker/bridgehead
 	set -a
@@ -51,7 +52,6 @@ loadVars() {
 	fi
 	fetchVarsFromVaultByFile /etc/bridgehead/$PROJECT.conf || fail_and_report 1 "Unable to fetchVarsFromVaultByFile"
 	setHostname
-	optimizeBlazeMemoryUsage
 	[ -e ./$PROJECT/vars ] && source ./$PROJECT/vars
 	set +a
 
@@ -90,14 +90,12 @@ case "$ACTION" in
 		loadVars
 		hc_send log "Bridgehead $PROJECT startup: Checking requirements ..."
 		checkRequirements
-		sync_secrets
+        sync_secrets
 		hc_send log "Bridgehead $PROJECT startup: Requirements checked out. Now starting bridgehead ..."
 		exec $COMPOSE -p $PROJECT -f ./minimal/docker-compose.yml -f ./$PROJECT/docker-compose.yml $OVERRIDE up --abort-on-container-exit
 		;;
 	stop)
 		loadVars
-		# Kill stale secret-sync instances if present
-		docker kill $(docker ps -q --filter ancestor=docker.verbis.dkfz.de/cache/samply/secret-sync-local) 2>/dev/null || true
 		# HACK: This is temporarily to properly shut down false bridgehead instances (bridgehead-ccp instead ccp)
 		$COMPOSE -p bridgehead-$PROJECT -f ./minimal/docker-compose.yml -f ./$PROJECT/docker-compose.yml $OVERRIDE down
 		exec $COMPOSE -p $PROJECT -f ./minimal/docker-compose.yml -f ./$PROJECT/docker-compose.yml $OVERRIDE down
@@ -106,11 +104,6 @@ case "$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

@@ -6,9 +6,7 @@ services:
     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: $BLAZE_MEMORY_CAP
+      JAVA_TOOL_OPTIONS: "-Xmx4g"
       ENFORCE_REFERENTIAL_INTEGRITY: "false"
     volumes:
       - "blaze-data:/app/data"
@@ -19,30 +17,9 @@ services:
       - "traefik.http.services.blaze_ccp.loadbalancer.server.port=8080"
       - "traefik.http.routers.blaze_ccp.middlewares=ccp_b_strip,auth"
       - "traefik.http.routers.blaze_ccp.tls=true"
-    
-  frontend:
-    image: "samply/blaze-frontend:latest"
-    environment:
-      ORIGIN: "https://${HOST}/ccp-blaze-frontend"
-      BACKEND_BASE_URL: "https://${HOST}/ccp-localdatamanagement"
-      AUTH_CLIENT_ID: "${OIDC_PRIVATE_CLIENT_ID}"
-      AUTH_CLIENT_SECRET: "${OIDC_CLIENT_SECRET}"
-      AUTH_ISSUER: "${OIDC_URL}"
-      AUTH_SECRET: "666df42c74ce1f4728fe2ffe99b146e0f2e4b4f9810594fcf68c0330495bca0f" # TODO: Generate
-      PROTOCOL_HEADER: "x-forwarded-proto"
-      HOST_HEADER: "x-forwarded-host"
-    depends_on:
-      - blaze
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.blaze_frontend.rule=PathPrefix(`/ccp-blaze-frontend`)"
-      - "traefik.http.middlewares.ccp_blaze_frontend_strip.stripprefix.prefixes=/ccp-blaze-frontend"
-      - "traefik.http.routers.blaze_ccp.middlewares=ccp_blaze_frontend_strip"
-      - "traefik.http.services.blaze_frontend.loadbalancer.server.port=3000"
-      - "traefik.http.routers.blaze_frontend.tls=true"
 
   focus:
-    image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
+    image: docker.verbis.dkfz.de/cache/samply/focus:main
     container_name: bridgehead-focus
     environment:
       API_KEY: ${FOCUS_BEAM_SECRET_SHORT}
@@ -75,6 +52,12 @@ services:
       - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
       - /srv/docker/bridgehead/ccp/root.crt.pem:/conf/root.crt.pem:ro
 
+  traefik:
+    labels:
+      - "traefik.http.middlewares.oidcAuth.forwardAuth.address=http://oauth2_proxy:4180/"
+      - "traefik.http.middlewares.oidcAuth.forwardAuth.trustForwardHeader=true"
+      - "traefik.http.middlewares.oidcAuth.forwardAuth.authResponseHeaders=X-Auth-Request-Access-Token,Authorization"
+
 
 volumes:
   blaze-data:

ccp/modules/cbioportal-compose.yml

@@ -0,0 +1,53 @@
+version: '3.7'
+
+services:
+  cbioportal:
+    # image: docker.verbis.dkfz.de/ccp/dktk-cbioportal:latest
+    image: dktk-cbioportal
+    container_name: bridgehead-cbioportal
+    environment:
+      DB_PASSWORD: ${CBIOPORTAL_DB_PASSWORD}
+      HTTP_RELATIVE_PATH: "/cbioportal"
+      UPLOAD_HTTP_RELATIVE_PATH: "/cbioportal-upload"
+    depends_on:
+      - cbioportal-database
+      - cbioportal-session
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.cbioportal.rule=PathPrefix(`/cbioportal`)"
+      - "traefik.http.routers.cbioportal.service=cbioportal"
+      - "traefik.http.services.cbioportal.loadbalancer.server.port=8080"
+      - "traefik.http.routers.cbioportal.tls=true"
+      - "traefik.http.routers.cbioportal-upload.rule=PathPrefix(`/cbioportal-upload`)"    
+      - "traefik.http.routers.cbioportal-upload.service=cbioportal-upload"
+      - "traefik.http.routers.cbioportal-upload.tls=true"
+      - "traefik.http.services.cbioportal-upload.loadbalancer.server.port=8001"
+      
+
+  cbioportal-database:
+    image: docker.verbis.dkfz.de/ccp/dktk-cbioportal-database:latest
+    container_name: bridgehead-cbioportal-database
+    environment:
+      MYSQL_DATABASE: cbioportal
+      MYSQL_USER: cbio_user
+      MYSQL_PASSWORD: ${CBIOPORTAL_DB_PASSWORD}
+      MYSQL_ROOT_PASSWORD: ${CBIOPORTAL_DB_ROOT_PASSWORD}
+    volumes:
+      - /var/cache/bridgehead/ccp/cbioportal_db_data:/var/lib/mysql
+
+  cbioportal-session:
+    image: cbioportal/session-service:0.6.1
+    container_name: bridgehead-cbioportal-session
+    environment:
+      SERVER_PORT: 5000
+      JAVA_OPTS: -Dspring.data.mongodb.uri=mongodb://cbioportal-session-database:27017/session-service
+    depends_on:
+      - cbioportal-session-database
+
+  cbioportal-session-database:
+    image: mongo:4.2
+    container_name: bridgehead-cbioportal-session-database
+    environment:
+      MONGO_INITDB_DATABASE: session_service
+    volumes:
+      - /var/cache/bridgehead/ccp/cbioportal_session_db_data:/data/db

ccp/modules/cbioportal-setup.sh

@@ -0,0 +1,8 @@
+#!/bin/bash -e
+
+ if [ "$ENABLE_CBIOPORTAL" == true ]; then
+  log INFO "cBioPortal setup detected -- will start cBioPortal service."
+  OVERRIDE+=" -f ./$PROJECT/modules/cbioportal-compose.yml"
+  CBIOPORTAL_DB_PASSWORD="$(echo \"This is a salt string to generate one consistent password for the cbioportal database. It is not required to be secret.\" | openssl rsautl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
+  CBIOPORTAL_DB_ROOT_PASSWORD="$(echo \"This is a salt string to generate one consistent root password for the cbioportal database. It is not required to be secret.\" | openssl rsautl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 64)" 
+ fi

ccp/modules/cbioportal.md

@@ -0,0 +1,10 @@
+# CBioPortal Data uploader
+
+
+## Usage
+
+We have integrated an API that allows you to upload data directly to cbioportal without the need to have cbioportal installed in your system.
+
+## Tech stack
+
+We used Flask to add this feature

ccp/modules/datashield-compose.yml

@@ -44,11 +44,11 @@ services:
       APP_CONTEXT_PATH: "/opal"
       OPAL_PRIVATE_KEY: "/run/secrets/opal-key.pem"
       OPAL_CERTIFICATE: "/run/secrets/opal-cert.pem"
-      OIDC_URL: "${OIDC_URL}"
-      OIDC_REALM: "${OIDC_REALM}"
-      OIDC_CLIENT_ID: "${OIDC_PRIVATE_CLIENT_ID}"
-      OIDC_CLIENT_SECRET: "${OIDC_CLIENT_SECRET}"
-      OIDC_ADMIN_GROUP: "${OIDC_ADMIN_GROUP}"
+      KEYCLOAK_URL: "${KEYCLOAK_URL}"
+      KEYCLOAK_REALM: "${KEYCLOAK_REALM}"
+      KEYCLOAK_CLIENT_ID: "${KEYCLOAK_PRIVATE_CLIENT_ID}"
+      KEYCLOAK_CLIENT_SECRET: "${OIDC_CLIENT_SECRET}"
+      KEYCLOAK_ADMIN_GROUP: "${KEYCLOAK_ADMIN_GROUP}"
       TOKEN_MANAGER_PASSWORD: "${TOKEN_MANAGER_OPAL_PASSWORD}"
       EXPORTER_PASSWORD: "${EXPORTER_OPAL_PASSWORD}"
       BEAM_APP_ID: token-manager.${PROXY_ID}
@@ -62,7 +62,7 @@ services:
 
   opal-db:
     container_name: bridgehead-opal-db
-    image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
+    image: docker.verbis.dkfz.de/cache/postgres:15.4-alpine
     environment:
       POSTGRES_PASSWORD: "${OPAL_DB_PASSWORD}" # Set in datashield-setup.sh
       POSTGRES_USER: "opal"
@@ -96,12 +96,8 @@ services:
     networks:
       - default
       - rstudio
-
+  
   traefik:
-    labels:
-      - "traefik.http.middlewares.oidcAuth.forwardAuth.address=http://oauth2-proxy:4180/"
-      - "traefik.http.middlewares.oidcAuth.forwardAuth.trustForwardHeader=true"
-      - "traefik.http.middlewares.oidcAuth.forwardAuth.authResponseHeaders=X-Auth-Request-Access-Token,Authorization"
     networks:
       - default
       - rstudio
@@ -115,15 +111,15 @@ services:
       APP_datashield-connect_KEY: ${DATASHIELD_CONNECT_SECRET}
       APP_token-manager_KEY: ${TOKEN_MANAGER_SECRET}
 
-  # TODO: Allow users of group /DataSHIELD and OIDC_USER_GROUP at the same time:
-  # Maybe a solution would be (https://oauth2-proxy.github.io/oauth2-proxy/configuration/oauth_provider):
-  # --allowed-groups=/DataSHIELD,OIDC_USER_GROUP
-  oauth2-proxy:
-    image: docker.verbis.dkfz.de/cache/oauth2-proxy/oauth2-proxy:latest
-    container_name: bridgehead-oauth2proxy
+  # TODO: Allow users of group /DataSHIELD and KEYCLOAK_USER_GROUP at the same time:
+  # Maybe a solution would be (https://oauth2-proxy.github.io/oauth2-proxy/docs/configuration/overview/):
+  # --allowed-groups=/DataSHIELD,KEYCLOAK_USER_GROUP
+  oauth2_proxy:
+    image: quay.io/oauth2-proxy/oauth2-proxy
+    container_name: bridgehead_oauth2_proxy
     command: >-
-      --allowed-group=DataSHIELD
-      --oidc-groups-claim=${OIDC_GROUP_CLAIM}
+      --allowed-group=/DataSHIELD
+      --oidc-groups-claim=${KEYCLOAK_GROUP_CLAIM}
       --auth-logging=true
       --whitelist-domain=${HOST}
       --http-address="0.0.0.0:4180"
@@ -138,10 +134,10 @@ services:
       #OIDC settings
       --provider="keycloak-oidc"
       --provider-display-name="VerbIS Login"
-      --client-id="${OIDC_PRIVATE_CLIENT_ID}"
+      --client-id="${KEYCLOAK_PRIVATE_CLIENT_ID}"
       --client-secret="${OIDC_CLIENT_SECRET}"
       --redirect-url="https://${HOST}${OAUTH2_CALLBACK}"
-      --oidc-issuer-url="${OIDC_ISSUER_URL}"
+      --oidc-issuer-url="${KEYCLOAK_ISSUER_URL}"
       --scope="openid email profile"
       --code-challenge-method="S256"
       --skip-provider-button=true
@@ -154,12 +150,6 @@ services:
       - "traefik.http.routers.oauth2_proxy.rule=Host(`${HOST}`) && PathPrefix(`/oauth2`, `/oauth2/callback`)"
       - "traefik.http.services.oauth2_proxy.loadbalancer.server.port=4180"
       - "traefik.http.routers.oauth2_proxy.tls=true"
-    environment:
-      http_proxy: "http://forward_proxy:3128"
-      https_proxy: "http://forward_proxy:3128"
-    depends_on:
-      forward_proxy:
-        condition: service_healthy
 
 secrets:
   opal-cert.pem:

ccp/modules/datashield-mappings.json

@@ -9,6 +9,5 @@
     "frankfurt",
     "essen",
     "dktk-datashield-test",
-    "dktk-test",
-    "mannheim"
+    "dktk-test"
 ]

ccp/modules/datashield-setup.sh

@@ -1,14 +1,6 @@
 #!/bin/bash -e
 
 if [ "$ENABLE_DATASHIELD" == true ]; then
-  # HACK: This only works because exporter-setup.sh and teiler-setup.sh are sourced after datashield-setup.sh
-  if [ -z "${ENABLE_EXPORTER}" ] || [ "${ENABLE_EXPORTER}" != "true" ]; then
-    log WARN "The ENABLE_EXPORTER variable is either not set or not set to 'true'."
-  fi
-  OAUTH2_CALLBACK=/oauth2/callback
-  OAUTH2_PROXY_SECRET="$(echo \"This is a salt string to generate one consistent encryption key for the oauth2_proxy. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 32)"
-  add_private_oidc_redirect_url "${OAUTH2_CALLBACK}"
-
   log INFO "DataSHIELD setup detected -- will start DataSHIELD services."
   OVERRIDE+=" -f ./$PROJECT/modules/datashield-compose.yml"
   EXPORTER_OPAL_PASSWORD="$(generate_password \"exporter in Opal\")"
@@ -20,25 +12,22 @@ if [ "$ENABLE_DATASHIELD" == true ]; then
   TOKEN_MANAGER_SECRET="$(echo \"Token Manager\" | generate_simple_password)"
   if [ ! -e /tmp/bridgehead/opal-cert.pem ]; then
     mkdir -p /tmp/bridgehead/
+    chown -R bridgehead:docker /tmp/bridgehead/
     openssl req -x509 -newkey rsa:4096 -nodes -keyout /tmp/bridgehead/opal-key.pem -out /tmp/bridgehead/opal-cert.pem -days 3650 -subj "/CN=opal/C=DE"
+    chmod g+r /tmp/bridgehead/opal-key.pem
   fi
   mkdir -p /tmp/bridgehead/opal-map
-  sites="$(cat ./$PROJECT/modules/datashield-sites.json)"
-  echo "$sites" | docker_jq -n --args '{"sites": input | map({
+  jq -n '{"sites": input | map({
     "name": .,
     "id": .,
     "virtualhost": "\(.):443",
     "beamconnect": "datashield-connect.\(.).'"$BROKER_ID"'"
-  })}' $sites >/tmp/bridgehead/opal-map/central.json
-  echo "$sites" | docker_jq -n --args '[{
+  })}' ./$PROJECT/modules/datashield-mappings.json > /tmp/bridgehead/opal-map/central.json
+  jq -n '[{
     "external": "'"$SITE_ID"':443",
     "internal": "opal:8443",
     "allowed": input | map("datashield-connect.\(.).'"$BROKER_ID"'")
-  }]' >/tmp/bridgehead/opal-map/local.json
-  if [ "$USER" == "root" ]; then
-    chown -R bridgehead:docker /tmp/bridgehead
-    chmod g+wr /tmp/bridgehead/opal-map/*
-    chmod g+r /tmp/bridgehead/opal-key.pem
-  fi
+  }]' ./$PROJECT/modules/datashield-mappings.json > /tmp/bridgehead/opal-map/local.json
+  chown -R bridgehead:docker /tmp/bridgehead/
   add_private_oidc_redirect_url "/opal/*"
 fi

ccp/modules/dnpm-compose.yml

@@ -16,14 +16,12 @@ 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,host.docker.internal${DNPM_ADDITIONAL_NO_PROXY}
+      NO_PROXY: beam-proxy,dnpm-backend,host.docker.internal
       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:
@@ -33,7 +31,3 @@ 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

@@ -6,7 +6,6 @@ services:
     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

ccp/modules/dnpm-node-setup.sh

@@ -14,15 +14,14 @@ if [ -n "${ENABLE_DNPM_NODE}" ]; then
 		log ERROR "Mandatory variable DNPM_DATA_DIR not defined!"
 		exit 1
 	fi
-	DNPM_SYNTH_NUM=${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
+			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

@@ -6,10 +6,4 @@ if [ -n "${ENABLE_DNPM}" ]; then
 
 	# Set variables required for Beam-Connect
 	DNPM_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
-	# If the DNPM_NO_PROXY variable is set, prefix it with a comma (as it gets added to a comma separated list)
-	if [ -n "${DNPM_NO_PROXY}" ]; then
-		DNPM_ADDITIONAL_NO_PROXY=",${DNPM_NO_PROXY}"
-	else
-		DNPM_ADDITIONAL_NO_PROXY=""
-	fi
 fi

ccp/modules/exporter-compose.yml

@@ -27,7 +27,7 @@ services:
       - "/var/cache/bridgehead/ccp/exporter-files:/app/exporter-files/output"
 
   exporter-db:
-    image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
+    image: docker.verbis.dkfz.de/cache/postgres:15.4-alpine
     container_name: bridgehead-ccp-exporter-db
     environment:
       POSTGRES_USER: "exporter"

ccp/modules/exporter-setup.sh

@@ -3,6 +3,6 @@
 if [ "$ENABLE_EXPORTER" == true ]; then
   log INFO "Exporter setup detected -- will start Exporter service."
   OVERRIDE+=" -f ./$PROJECT/modules/exporter-compose.yml"
-  EXPORTER_DB_PASSWORD="$(echo \"This is a salt string to generate one consistent password for the exporter. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
-  EXPORTER_API_KEY="$(echo \"This is a salt string to generate one consistent API KEY for the exporter. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 64)"
+  EXPORTER_DB_PASSWORD="$(echo \"This is a salt string to generate one consistent password for the exporter. It is not required to be secret.\" | openssl rsautl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
+  EXPORTER_API_KEY="$(echo \"This is a salt string to generate one consistent API KEY for the exporter. It is not required to be secret.\" | openssl rsautl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 64)"
 fi

ccp/modules/id-management-compose.yml

@@ -29,7 +29,6 @@ services:
     container_name: bridgehead-patientlist
     environment:
       - TOMCAT_REVERSEPROXY_FQDN=${HOST}
-      - TOMCAT_REVERSEPROXY_SSL=true
       - ML_SITE=${IDMANAGEMENT_FRIENDLY_ID}
       - ML_DB_PASS=${PATIENTLIST_POSTGRES_PASSWORD}
       - ML_API_KEY=${IDMANAGER_LOCAL_PATIENTLIST_APIKEY}
@@ -45,7 +44,7 @@ services:
       - patientlist-db
 
   patientlist-db:
-    image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
+    image: docker.verbis.dkfz.de/cache/postgres:15.6-alpine
     container_name: bridgehead-patientlist-db
     environment:
       POSTGRES_USER: "mainzelliste"

ccp/modules/login-compose.yml

@@ -0,0 +1,47 @@
+version: "3.7"
+
+services:
+
+  login-db:
+    image: docker.verbis.dkfz.de/cache/postgres:15.4-alpine
+    container_name: bridgehead-login-db
+    environment:
+      POSTGRES_USER: "keycloak"
+      POSTGRES_PASSWORD: "${KEYCLOAK_DB_PASSWORD}" # Set in login-setup.sh
+      POSTGRES_DB: "keycloak"
+    tmpfs:
+      - /var/lib/postgresql/data
+# Consider removing this comment once we have collected experience in production.
+#    volumes:
+#      - "bridgehead-login-db:/var/lib/postgresql/data"
+
+  login:
+    image: docker.verbis.dkfz.de/ccp/dktk-keycloak:latest
+    container_name: bridgehead-login
+    environment:
+      KEYCLOAK_ADMIN: "admin"
+      KEYCLOAK_ADMIN_PASSWORD: "${LDM_AUTH}"
+      TEILER_ADMIN: "${PROJECT}"
+      TEILER_ADMIN_PASSWORD: "${LDM_AUTH}"
+      TEILER_ADMIN_FIRST_NAME: "${OPERATOR_FIRST_NAME}"
+      TEILER_ADMIN_LAST_NAME: "${OPERATOR_LAST_NAME}"
+      TEILER_ADMIN_EMAIL: "${OPERATOR_EMAIL}"
+      KC_DB_PASSWORD: "${KEYCLOAK_DB_PASSWORD}" # Set in login-setup.sh
+      KC_HOSTNAME_URL: "https://${HOST}/login"
+      KC_HOSTNAME_STRICT: "false"
+      KC_PROXY_ADDRESS_FORWARDING: "true"
+      TEILER_ORCHESTRATOR_EXTERN_URL: "https://${HOST}/ccp-teiler"
+    command:
+      - start-dev --import-realm --proxy edge --http-relative-path=/login
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.login.rule=PathPrefix(`/login`)"
+      - "traefik.http.services.login.loadbalancer.server.port=8080"
+      - "traefik.http.routers.login.tls=true"
+    depends_on:
+      - login-db
+
+# Consider removing this comment once we have collected experience in production.
+#volumes:
+#  bridgehead-login-db:
+#    name: "bridgehead-login-db"

ccp/modules/login-setup.sh

@@ -0,0 +1,7 @@
+#!/bin/bash -e
+
+if [ "$ENABLE_LOGIN" == true ]; then
+  log INFO "Login setup detected -- will start Login services."
+  OVERRIDE+=" -f ./$PROJECT/modules/login-compose.yml"
+  KEYCLOAK_DB_PASSWORD="$(generate_password \"local Keycloak\")"
+fi

ccp/modules/login.md

@@ -0,0 +1,13 @@
+# Login
+The login component is a local Keycloak instance. In the future will be replaced by the central keycloak instance
+or maybe can be used to add local identity providers to the bridgehead or just to simplify the configuration of
+the central keycloak instance for the integration of every new bridgehead.
+The basic configuration of our Keycloak instance is contained in a small json file.
+
+### Teiler User
+Currently, the local keycloak is used by the teiler. There is a basic admin user in the basic configuration of keycloak.
+The user can be configured with the environment variables TEILER_ADMIN_XXX.
+
+## Login-DB
+Keycloak requires a local database for its configuration. However, as we use an initial json configuration file, if no
+local identity provider is configured nor any local user, theoretically we don't need a volume for the login.

ccp/modules/mtba-compose.yml

@@ -2,6 +2,7 @@ version: "3.7"
 
 services:
   mtba:
+    #image: docker.verbis.dkfz.de/cache/samply/mtba:latest
     image: docker.verbis.dkfz.de/cache/samply/mtba:develop
     container_name: bridgehead-mtba
     environment:
@@ -20,11 +21,11 @@ services:
       FILE_END_OF_LINE: ${MTBA_FILE_END_OF_LINE:-LF}
       CSV_DELIMITER: ${MTBA_CSV_DELIMITER:-TAB}
       HTTP_RELATIVE_PATH: "/mtba"
-      OIDC_ADMIN_GROUP: "${OIDC_ADMIN_GROUP}"
-      OIDC_CLIENT_ID: "${OIDC_PRIVATE_CLIENT_ID}"
-      OIDC_CLIENT_SECRET: "${OIDC_CLIENT_SECRET}"
-      OIDC_REALM: "${OIDC_REALM}"
-      OIDC_URL: "${OIDC_URL}"
+      KEYCLOAK_ADMIN_GROUP: "${KEYCLOAK_ADMIN_GROUP}"
+      KEYCLOAK_CLIENT_ID: "${KEYCLOAK_PRIVATE_CLIENT_ID}"
+      KEYCLOAK_CLIENT_SECRET: "${OIDC_CLIENT_SECRET}"
+      KEYCLOAK_REALM: "${KEYCLOAK_REALM}"
+      KEYCLOAK_URL: "${KEYCLOAK_URL}"
 
     labels:
       - "traefik.enable=true"

ccp/modules/teiler-compose.yml

@@ -15,11 +15,11 @@ services:
     environment:
       TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend"
       TEILER_DASHBOARD_URL: "https://${HOST}/ccp-teiler-dashboard"
-      DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE_LOWER_CASE}"
+      DEFAULT_LANGUAGE: "${DEFAULT_LANGUAGE_LOWER_CASE}"
       HTTP_RELATIVE_PATH: "/ccp-teiler"
 
   teiler-dashboard:
-    image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:develop
+    image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:latest
     container_name: bridgehead-teiler-dashboard
     labels:
       - "traefik.enable=true"
@@ -29,12 +29,12 @@ services:
       - "traefik.http.middlewares.teiler_dashboard_ccp_strip.stripprefix.prefixes=/ccp-teiler-dashboard"
       - "traefik.http.routers.teiler_dashboard_ccp.middlewares=teiler_dashboard_ccp_strip"
     environment:
-      DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
+      DEFAULT_LANGUAGE: "${DEFAULT_LANGUAGE}"
       TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend"
-      OIDC_URL: "${OIDC_URL}"
-      OIDC_REALM: "${OIDC_REALM}"
-      OIDC_CLIENT_ID: "${OIDC_PUBLIC_CLIENT_ID}"
-      OIDC_TOKEN_GROUP: "${OIDC_GROUP_CLAIM}"
+      KEYCLOAK_URL: "${KEYCLOAK_URL}"
+      KEYCLOAK_REALM: "${KEYCLOAK_REALM}"
+      KEYCLOAK_CLIENT_ID: "${KEYCLOAK_PUBLIC_CLIENT_ID}"
+      KEYCLOAK_TOKEN_GROUP: "${KEYCLOAK_GROUP_CLAIM}"
       TEILER_ADMIN_NAME: "${OPERATOR_FIRST_NAME} ${OPERATOR_LAST_NAME}"
       TEILER_ADMIN_EMAIL: "${OPERATOR_EMAIL}"
       TEILER_ADMIN_PHONE: "${OPERATOR_PHONE}"
@@ -43,14 +43,15 @@ services:
       TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler"
       TEILER_DASHBOARD_HTTP_RELATIVE_PATH: "/ccp-teiler-dashboard"
       TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler"
-      TEILER_USER: "${OIDC_USER_GROUP}"
-      TEILER_ADMIN: "${OIDC_ADMIN_GROUP}"
+      TEILER_USER: "${KEYCLOAK_USER_GROUP}"
+      TEILER_ADMIN: "${KEYCLOAK_ADMIN_GROUP}"
       REPORTER_DEFAULT_TEMPLATE_ID: "ccp-qb"
       EXPORTER_DEFAULT_TEMPLATE_ID: "ccp"
 
 
   teiler-backend:
-    image: docker.verbis.dkfz.de/ccp/dktk-teiler-backend:latest
+    # image: docker.verbis.dkfz.de/ccp/dktk-teiler-backend:latest
+    image: dktk-teiler-backend
     container_name: bridgehead-teiler-backend
     labels:
       - "traefik.enable=true"
@@ -63,7 +64,7 @@ services:
       LOG_LEVEL: "INFO"
       APPLICATION_PORT: "8085"
       APPLICATION_ADDRESS: "${HOST}"
-      DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
+      DEFAULT_LANGUAGE: "${DEFAULT_LANGUAGE}"
       CONFIG_ENV_VAR_PATH: "/run/secrets/ccp.conf"
       TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler"
       TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler"

ccp/modules/teiler-setup.sh

@@ -3,7 +3,5 @@
 if [ "$ENABLE_TEILER" == true ];then
   log INFO "Teiler setup detected -- will start Teiler services."
   OVERRIDE+=" -f ./$PROJECT/modules/teiler-compose.yml"
-  TEILER_DEFAULT_LANGUAGE=DE
-  TEILER_DEFAULT_LANGUAGE_LOWER_CASE=${TEILER_DEFAULT_LANGUAGE,,}
   add_public_oidc_redirect_url "/ccp-teiler/*"
 fi

ccp/vars

@@ -7,19 +7,25 @@ SUPPORT_EMAIL=support-ccp@dkfz-heidelberg.de
 PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
 
 BROKER_URL_FOR_PREREQ=$BROKER_URL
+DEFAULT_LANGUAGE=DE
+DEFAULT_LANGUAGE_LOWER_CASE=${DEFAULT_LANGUAGE,,}
+ENABLE_EXPORTER=true
+ENABLE_TEILER=true
+#ENABLE_DATASHIELD=true
 
-OIDC_USER_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})"
-OIDC_ADMIN_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})_Verwalter"
-OIDC_PRIVATE_CLIENT_ID=${SITE_ID}-private
-OIDC_PUBLIC_CLIENT_ID=${SITE_ID}-public
-# Use "test-realm-01" for testing
-OIDC_REALM="${OIDC_REALM:-master}"
-OIDC_URL="https://login.verbis.dkfz.de"
-OIDC_ISSUER_URL="${OIDC_URL}/realms/${OIDC_REALM}"
-OIDC_GROUP_CLAIM="groups"
-add_private_oidc_redirect_url "/ccp-localdatamanagement"
+KEYCLOAK_USER_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})"
+KEYCLOAK_ADMIN_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})_Verwalter"
+KEYCLOAK_PRIVATE_CLIENT_ID=${SITE_ID}-private
+KEYCLOAK_PUBLIC_CLIENT_ID=${SITE_ID}-public
+# TODO: Change Keycloak Realm to productive. "test-realm-01" is only for testing
+KEYCLOAK_REALM="${KEYCLOAK_REALM:-test-realm-01}"
+KEYCLOAK_URL="https://login.verbis.dkfz.de"
+KEYCLOAK_ISSUER_URL="${KEYCLOAK_URL}/realms/${KEYCLOAK_REALM}"
+KEYCLOAK_GROUP_CLAIM="groups"
+OAUTH2_CALLBACK=/oauth2/callback
+OAUTH2_PROXY_SECRET="$(echo \"This is a salt string to generate one consistent encryption key for the oauth2_proxy. It is not required to be secret.\" | openssl rsautl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 32)"
 
-POSTGRES_TAG=15.6-alpine
+add_private_oidc_redirect_url "${OAUTH2_CALLBACK}"
 
 for module in $PROJECT/modules/*.sh
 do

lib/functions.sh

@@ -53,7 +53,7 @@ checkOwner(){
 }
 
 printUsage() {
-	echo "Usage: bridgehead start|stop|logs|is-running|update|install|uninstall|adduser|enroll PROJECTNAME"
+	echo "Usage: bridgehead start|stop|is-running|update|install|uninstall|adduser|enroll PROJECTNAME"
 	echo "PROJECTNAME should be one of ccp|bbmri"
 }
 
@@ -155,28 +155,6 @@ setHostname() {
 	fi
 }
 
-# This function optimizes the usage of memory through blaze, according to the official performance tuning guide:
-#   https://github.com/samply/blaze/blob/master/docs/tuning-guide.md
-# Short summary of the adjustments made:
-# - set blaze memory cap to a quarter of the system memory
-# - set db block cache size to a quarter of the system memory
-# - limit resource count allowed in blaze to 1,25M per 4GB available system memory
-optimizeBlazeMemoryUsage() {
-	if [ -z "$BLAZE_MEMORY_CAP" ]; then
-	   system_memory_in_mb=$(LC_ALL=C free -m | grep 'Mem:' | awk '{print $2}');
-	   export BLAZE_MEMORY_CAP=$(($system_memory_in_mb/4));
-	fi
-	if [ -z "$BLAZE_RESOURCE_CACHE_CAP" ]; then
-		available_system_memory_chunks=$((BLAZE_MEMORY_CAP / 1000))
-		if [ $available_system_memory_chunks -eq 0 ]; then
-			log WARN "Only ${BLAZE_MEMORY_CAP} system memory available for Blaze. If your Blaze stores more than 128000 fhir ressources it will run significally slower."
-			export BLAZE_RESOURCE_CACHE_CAP=128000;
-		else
-			export BLAZE_RESOURCE_CACHE_CAP=$((available_system_memory_chunks * 312500))
-		fi
-	fi
-}
-
 # Takes 1) The Backup Directory Path 2) The name of the Service to be backuped
 # Creates 3 Backups: 1) For the past seven days 2) For the current month and 3) for each calendar week
 createEncryptedPostgresBackup(){
@@ -289,32 +267,32 @@ function sync_secrets() {
     if [[ $OIDC_PRIVATE_REDIRECT_URLS != "" ]]; then
         secret_sync_args="OIDC:OIDC_CLIENT_SECRET:private;$OIDC_PRIVATE_REDIRECT_URLS"
     fi
-    if [[ $OIDC_PUBLIC_REDIRECT_URLS != "" ]]; then
+    if [[ $OIDC_PRIVATE_REDIRECT_URLS != "" ]]; then
         if [[ $secret_sync_args == "" ]]; then
             secret_sync_args="OIDC:OIDC_PUBLIC:public;$OIDC_PUBLIC_REDIRECT_URLS"
-        else
+        else 
             secret_sync_args+="${delimiter}OIDC:OIDC_PUBLIC:public;$OIDC_PUBLIC_REDIRECT_URLS"
         fi
     fi
     if [[ $secret_sync_args == "" ]]; then
         return
     fi
-    mkdir -p /var/cache/bridgehead/secrets/ || fail_and_report 1 "Failed to create '/var/cache/bridgehead/secrets/'. Please run sudo './bridgehead install $PROJECT' again."
+    mkdir -p /var/cache/bridgehead/secrets/
     touch /var/cache/bridgehead/secrets/oidc
+    chown -R bridgehead:docker /var/cache/bridgehead/secrets
+    # The oidc provider will need to be switched based on the project at some point I guess
     docker run --rm \
         -v /var/cache/bridgehead/secrets/oidc:/usr/local/cache \
         -v $PRIVATEKEYFILENAME:/run/secrets/privkey.pem:ro \
         -v /srv/docker/bridgehead/$PROJECT/root.crt.pem:/run/secrets/root.crt.pem:ro \
         -v /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro \
         -e TLS_CA_CERTIFICATES_DIR=/conf/trusted-ca-certs \
-        -e NO_PROXY=localhost,127.0.0.1 \
-        -e ALL_PROXY=$HTTPS_PROXY_FULL_URL \
+        -e HTTPS_PROXY=$HTTPS_PROXY_FULL_URL \
         -e PROXY_ID=$PROXY_ID \
         -e BROKER_URL=$BROKER_URL \
         -e OIDC_PROVIDER=secret-sync-central.oidc-client-enrollment.$BROKER_ID \
         -e SECRET_DEFINITIONS=$secret_sync_args \
         docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest
-
     set -a # Export variables as environment variables
     source /var/cache/bridgehead/secrets/*
     set +a # Export variables in the regular way
@@ -356,7 +334,7 @@ generate_password(){
   local random_special=${special:$n:1}
 
   local combined_text="This is a salt string to generate one consistent password for ${seed_text}. It is not required to be secret."
-  local main_password=$(echo "${combined_text}" | sha1sum | openssl pkeyutl -sign -inkey "/etc/bridgehead/pki/${SITE_ID}.priv.pem" 2> /dev/null | base64 | head -c 26 | sed 's/\//A/g')
+  local main_password=$(echo "${combined_text}" | openssl rsautl -sign -inkey "/etc/bridgehead/pki/${SITE_ID}.priv.pem" 2> /dev/null | base64 | head -c 26 | sed 's/\//A/g')
 
   echo "${main_password}${random_digit}${random_upper}${random_lower}${random_special}"
 }
@@ -365,9 +343,5 @@ generate_password(){
 generate_simple_password(){
   local seed_text="$1"
   local combined_text="This is a salt string to generate one consistent password for ${seed_text}. It is not required to be secret."
-  echo "${combined_text}" | sha1sum | openssl pkeyutl -sign -inkey "/etc/bridgehead/pki/${SITE_ID}.priv.pem" 2> /dev/null | base64 | head -c 26 | sed 's/[+\/]/A/g'
-}
-
-docker_jq() {
-    docker run --rm -i docker.verbis.dkfz.de/cache/jqlang/jq:latest "$@"
+  echo "${combined_text}" | openssl rsautl -sign -inkey "/etc/bridgehead/pki/${SITE_ID}.priv.pem" 2> /dev/null | base64 | head -c 26 | sed 's/[+\/]/A/g'
 }

lib/prepare-system.sh

@@ -89,9 +89,6 @@ elif [[ "$DEV_MODE" == "DEV" ]]; then
 fi
 
 chown -R bridgehead /etc/bridgehead /srv/docker/bridgehead
-mkdir -p /tmp/bridgehead /var/cache/bridgehead
-chown -R bridgehead:docker /tmp/bridgehead /var/cache/bridgehead
-chmod -R g+wr /var/cache/bridgehead /tmp/bridgehead
 
 log INFO "System preparation is completed and configuration is present."
 

lib/prerequisites.sh

@@ -67,30 +67,29 @@ log INFO "Checking network access ($BROKER_URL_FOR_PREREQ) ..."
 source /etc/bridgehead/${PROJECT}.conf
 source ${PROJECT}/vars
 
-if [ "${PROJECT}" != "minimal" ]; then
-  set +e
-  SERVERTIME="$(https_proxy=$HTTPS_PROXY_FULL_URL curl -m 5 -s -I $BROKER_URL_FOR_PREREQ 2>&1 | grep -i -e '^Date: ' | sed -e 's/^Date: //i')"
-  RET=$?
-  set -e
-  if [ $RET -ne 0 ]; then
-	  log WARN "Unable to connect to Samply.Beam broker at $BROKER_URL_FOR_PREREQ. Please check your proxy settings.\nThe currently configured proxy was \"$HTTPS_PROXY_URL\". This error is normal when using proxy authentication."
-  	log WARN "Unable to check clock skew due to previous error."
-  else
-	  log INFO "Checking clock skew ..."
+set +e
+SERVERTIME="$(https_proxy=$HTTPS_PROXY_FULL_URL curl -m 5 -s -I $BROKER_URL_FOR_PREREQ 2>&1 | grep -i -e '^Date: ' | sed -e 's/^Date: //i')"
+RET=$?
+set -e
+if [ $RET -ne 0 ]; then
+	log WARN "Unable to connect to Samply.Beam broker at $BROKER_URL_FOR_PREREQ. Please check your proxy settings.\nThe currently configured proxy was \"$HTTPS_PROXY_URL\". This error is normal when using proxy authentication."
+	log WARN "Unable to check clock skew due to previous error."
+else
+	log INFO "Checking clock skew ..."
 
-    SERVERTIME_AS_TIMESTAMP=$(date --date="$SERVERTIME" +%s)
-	  MYTIME=$(date +%s)
-	  SKEW=$(($SERVERTIME_AS_TIMESTAMP - $MYTIME))
-	  SKEW=$(echo $SKEW | awk -F- '{print $NF}')
-	  SYNCTEXT="For example, consider entering a correct NTP server (e.g. your institution's Active Directory Domain Controller in /etc/systemd/timesyncd.conf (option NTP=) and restart systemd-timesyncd."
-	  if [ $SKEW -ge 300 ]; then
-		  report_error 5 "Your clock is not synchronized (${SKEW}s off). This will cause Samply.Beam's certificate will fail. Please setup time synchronization. $SYNCTEXT"
-		  exit 1
-	  elif [ $SKEW -ge 60 ]; then
-		  log WARN "Your clock is more than a minute off (${SKEW}s). Consider syncing to a time server. $SYNCTEXT"
-	  fi
-  fi
+	SERVERTIME_AS_TIMESTAMP=$(date --date="$SERVERTIME" +%s)
+	MYTIME=$(date +%s)
+	SKEW=$(($SERVERTIME_AS_TIMESTAMP - $MYTIME))
+	SKEW=$(echo $SKEW | awk -F- '{print $NF}')
+	SYNCTEXT="For example, consider entering a correct NTP server (e.g. your institution's Active Directory Domain Controller in /etc/systemd/timesyncd.conf (option NTP=) and restart systemd-timesyncd."
+	if [ $SKEW -ge 300 ]; then
+		report_error 5 "Your clock is not synchronized (${SKEW}s off). This will cause Samply.Beam's certificate will fail. Please setup time synchronization. $SYNCTEXT"
+		exit 1
+	elif [ $SKEW -ge 60 ]; then
+		log WARN "Your clock is more than a minute off (${SKEW}s). Consider syncing to a time server. $SYNCTEXT"
+	fi
 fi
+
 checkPrivKey() {
   if [ -e /etc/bridgehead/pki/${SITE_ID}.priv.pem ]; then
     log INFO "Success - private key found."
@@ -101,7 +100,7 @@ checkPrivKey() {
   return 0
 }
 
-if [[ "$@" =~ "noprivkey" ||  "${PROJECT}" != "minimal" ]]; then
+if [[ "$@" =~ "noprivkey" ]]; then
   log INFO "Skipping check for private key for now."
 else
   checkPrivKey || exit 1

lib/update-bridgehead.sh

@@ -86,7 +86,7 @@ done
 # Check docker updates
 log "INFO" "Checking for updates to running docker images ..."
 docker_updated="false"
-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
+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
   log "INFO" "Checking for Updates of Image: $IMAGE"
   if docker pull $IMAGE | grep "Downloaded newer image"; then
     CHANGE="Image $IMAGE updated."

minimal/docker-compose.yml

@@ -42,9 +42,6 @@ services:
       - /var/spool/squid
     volumes:
       - /etc/bridgehead/trusted-ca-certs:/docker/custom-certs/:ro
-    healthcheck:
-      # Wait 1s before marking this service healthy. Required for the oauth2-proxy to talk to the OIDC provider on startup which will fail if the forward proxy is not started yet.
-      test: ["CMD", "sleep", "1"]
 
   landing:
     container_name: bridgehead-landingpage
@@ -58,3 +55,5 @@ services:
       HOST: ${HOST}
       PROJECT: ${PROJECT}
       SITE_NAME: ${SITE_NAME}
+
+

minimal/modules/dnpm-compose.yml

@@ -32,14 +32,12 @@ 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, host.docker.internal${DNPM_ADDITIONAL_NO_PROXY}
+      NO_PROXY: dnpm-beam-proxy,dnpm-backend, host.docker.internal
       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:
@@ -50,10 +48,6 @@ 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

@@ -6,7 +6,6 @@ services:
     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

minimal/modules/dnpm-node-setup.sh

@@ -14,15 +14,14 @@ if [ -n "${ENABLE_DNPM_NODE}" ]; then
 		log ERROR "Mandatory variable DNPM_DATA_DIR not defined!"
 		exit 1
 	fi
-	DNPM_SYNTH_NUM=${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
+			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

@@ -13,10 +13,4 @@ if [ -n "${ENABLE_DNPM}" ]; then
 		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