add additional credential encoding for curl

Curl seems not to like full percent-encoding of all characters which might be related to https://github.com/curl/curl/issues/5448#event-3371269895. The version in this PR escapes a lot and strictly follows RFC3986 section 2.3 for unescaped characters

README.md

@@ -318,6 +318,12 @@ To enable it, you will need to explicitly set the username and password variable
 DS_DIRECTORY_USER_NAME=your_directory_username
 DS_DIRECTORY_USER_PASS=your_directory_password
 ```
+Alternatively, if you have obtained a token from the Directory, you can insert the following into the configuration file:
+```
+DS_DIRECTORY_USER_TOKEN=your_directory_token
+```
+If you don't supply any authentification information (either login credentials or a token), Directory sync will not start.
+
 Please contact your National Node or Directory support (directory-dev@helpdesk.bbmri-eric.eu) to obtain these credentials.
 
 The following environment variables can be used from within your config file to control the behavior of Directory sync:
@@ -325,12 +331,13 @@ The following environment variables can be used from within your config file to
 | Variable                           | Purpose                                                                                                                                                              | Default if not specified               |
 |:-----------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------|
 | DS_DIRECTORY_URL                   | Base URL of the Directory                                                                                                                                            | https://directory-backend.molgenis.net |
-| DS_DIRECTORY_USER_NAME             | User name for logging in to Directory **Mandatory**                                                                                                                  |                                        |
+| DS_DIRECTORY_USER_NAME             | User name for logging in to Directory                                                                                                                                |                                        |
-| DS_DIRECTORY_USER_PASS             | Password for logging in to Directory **Mandatory**                                                                                                                   |                                        |
+| DS_DIRECTORY_USER_PASS             | Password for logging in to Directory                                                                                                                                 |                                        |
+| DS_DIRECTORY_USER_TOKEN            | Token for logging in to Directory                                                                                                                                    |                                        |
 | DS_DIRECTORY_DEFAULT_COLLECTION_ID | ID of collection to be used if not in samples                                                                                                                        |                                        |
 | DS_DIRECTORY_ALLOW_STAR_MODEL      | Set to 'True' to send star model info to Directory                                                                                                                   | True                                  |
 | DS_FHIR_STORE_URL                  | URL for FHIR store                                                                                                                                                   | http://bridgehead-bbmri-blaze:8080     |
-| DS_TIMER_CRON                      | Execution interval for Directory sync, [cron](https://crontab.guru) format                                                                                           | 0 22 * * *                             |
+| DS_TIMER_CRON                      | Execution interval for Directory sync, [cron](https://crontab.guru) format                                                                                           | 30 22 * * *                            |
 | DS_IMPORT_BIOBANKS                 | Set to 'True' to import biobank metadata from Directory                                                                                                              | True                                  |
 | DS_IMPORT_COLLECTIONS              | Set to 'True' to import collection metadata from Directory                                                                                                           | True                                  |
 

bbmri/modules/directory-sync-compose.yml

@@ -7,7 +7,8 @@ services:
       DS_DIRECTORY_URL: ${DS_DIRECTORY_URL:-https://directory.bbmri-eric.eu}
       DS_DIRECTORY_USER_NAME: ${DS_DIRECTORY_USER_NAME}
       DS_DIRECTORY_USER_PASS: ${DS_DIRECTORY_USER_PASS}
-      DS_TIMER_CRON: ${DS_TIMER_CRON:-0 22 * * *}
+      DS_DIRECTORY_USER_TOKEN: ${DS_DIRECTORY_USER_TOKEN}
+      DS_TIMER_CRON: ${DS_TIMER_CRON:-30 22 * * *}
       DS_DIRECTORY_ALLOW_STAR_MODEL: ${DS_DIRECTORY_ALLOW_STAR_MODEL:-true}
       DS_DIRECTORY_MOCK: ${DS_DIRECTORY_MOCK}
       DS_DIRECTORY_DEFAULT_COLLECTION_ID: ${DS_DIRECTORY_DEFAULT_COLLECTION_ID}
@@ -16,3 +17,6 @@ services:
       DS_IMPORT_COLLECTIONS: ${DS_IMPORT_COLLECTIONS:-true}
     depends_on:
       - "blaze"
+    volumes:
+      - /etc/localtime:/etc/localtime:ro # inherit host timezone
+      - /etc/timezone:/etc/timezone:ro   # inherit host timezone name

bbmri/modules/directory-sync.sh

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

bbmri/modules/eric-compose.yml

@@ -11,6 +11,7 @@ services:
       BLAZE_URL: "http://blaze:8080/fhir/"
       BEAM_PROXY_URL: http://beam-proxy-eric:8081
       RETRY_COUNT: ${FOCUS_RETRY_COUNT}
+      OBFUSCATE_BBMRI_ERIC_WAY: "true"
     depends_on:
       - "beam-proxy-eric"
       - "blaze"

bridgehead

@@ -35,6 +35,9 @@ case "$PROJECT" in
 	cce)
 		#nothing extra to do
 		;;
+	pscc)
+		#nothing extra to do
+		;;
 	itcc)
 		#nothing extra to do
 		;;
@@ -44,6 +47,9 @@ case "$PROJECT" in
 	dhki)
 		#nothing extra to do
 		;;
+	nngm)
+		#nothing extra to do
+		;;
 	minimal)
 		#nothing extra to do
 		;;

cce/docker-compose.yml

@@ -22,7 +22,7 @@ services:
       - "traefik.http.routers.blaze_cce.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}
@@ -34,7 +34,6 @@ services:
       EPSILON: 0.28
       QUERIES_TO_CACHE: '/queries_to_cache.conf'
       ENDPOINT_TYPE: ${FOCUS_ENDPOINT_TYPE:-blaze}
-      CQL_PROJECTS_ENABLED: "cce"
     volumes:
       - /srv/docker/bridgehead/cce/queries_to_cache.conf:/queries_to_cache.conf:ro
     depends_on:

cce/modules/lens-compose.yml

@@ -1,33 +1,46 @@
 version: "3.7"
 services:
-  landing:
+  lens:
     container_name: lens_federated-search
-    image: docker.verbis.dkfz.de/ccp/lens:${SITE_ID}
+    image: samply/cce-explorer:main
+    environment:
+      PUBLIC_SPOT_URL: https://${HOST}/prod
     labels:
+      - "traefik.http.services.lens.loadbalancer.server.port=3000"
       - "traefik.enable=true"
-      - "traefik.http.routers.landing.rule=PathPrefix(`/`)"
+      - "traefik.http.routers.lens.rule=Host(`${HOST}`)"
-      - "traefik.http.services.landing.loadbalancer.server.port=80"
+      - "traefik.http.routers.lens.tls=true"
-      - "traefik.http.routers.landing.tls=true"
 
   spot:
-    image: docker.verbis.dkfz.de/ccp-private/central-spot
+    image: samply/rustyspot:latest
     environment:
+      HTTP_PROXY: ${HTTP_PROXY_URL}
+      HTTPS_PROXY: ${HTTPS_PROXY_URL}
+      NO_PROXY: beam-proxy
       BEAM_SECRET: "${FOCUS_BEAM_SECRET_SHORT}"
-      BEAM_URL: http://beam-proxy:8081
+      BEAM_PROXY_URL: http://beam-proxy:8081
-      BEAM_PROXY_ID: ${SITE_ID}
+      BEAM_APP_ID: "spot.${SITE_ID}.${BROKER_ID}"
-      BEAM_BROKER_ID: ${BROKER_ID}
+      CORS_ORIGIN: "https://${HOST}"
-      BEAM_APP_ID: "focus"
+      SITES: ${SITES}
-      PROJECT_METADATA: "cce"
+      TRANSFORM: LENS
+      PROJECT: cce
+      BIND_ADDR: 0.0.0.0:8055
     depends_on:
       - "beam-proxy"
     labels:
       - "traefik.enable=true"
-      - "traefik.http.services.spot.loadbalancer.server.port=8080"
+      - "traefik.http.services.spot.loadbalancer.server.port=8055"
       - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowmethods=GET,OPTIONS,POST"
+      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowheaders=content-type"
       - "traefik.http.middlewares.corsheaders2.headers.accesscontrolalloworiginlist=https://${HOST}"
       - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowcredentials=true"
       - "traefik.http.middlewares.corsheaders2.headers.accesscontrolmaxage=-1"
-      - "traefik.http.routers.spot.rule=Host(`${HOST}`) && PathPrefix(`/backend`)"
+      - "traefik.http.routers.spot.rule=Host(`${HOST}`) && PathPrefix(`/prod`)"
-      - "traefik.http.middlewares.stripprefix_spot.stripprefix.prefixes=/backend"
+      - "traefik.http.middlewares.stripprefix_spot.stripprefix.prefixes=/prod"
       - "traefik.http.routers.spot.tls=true"
       - "traefik.http.routers.spot.middlewares=corsheaders2,stripprefix_spot,auth"
+
+  beam-proxy:
+    environment:
+      APP_spot_KEY: ${FOCUS_BEAM_SECRET_SHORT}
+      

ccp/modules/dnpm-node-compose.yml

@@ -66,6 +66,7 @@ services:
       - HATEOAS_HOST=https://${HOST}
       - CONNECTOR_TYPE=broker
       - AUTHUP_URL=robot://system:${DNPM_AUTHUP_SECRET}@http://dnpm-authup:3000
+      - TZ=Europe/Berlin
     volumes:
       - /etc/bridgehead/dnpm/config:/dnpm_config
       - /var/cache/bridgehead/dnpm/backend-data:/dnpm_data

itcc/docker-compose.yml

@@ -15,14 +15,14 @@ services:
       - "blaze-data:/app/data"
     labels:
       - "traefik.enable=true"
-      - "traefik.http.routers.blaze_itcc.rule=PathPrefix(`/itcc-localdatamanagement`)"
+      - "traefik.http.routers.blaze_itcc.rule=Host(`${HOST}`) && PathPrefix(`/itcc-localdatamanagement`)"
       - "traefik.http.middlewares.itcc_b_strip.stripprefix.prefixes=/itcc-localdatamanagement"
       - "traefik.http.services.blaze_itcc.loadbalancer.server.port=8080"
       - "traefik.http.routers.blaze_itcc.middlewares=itcc_b_strip,auth"
       - "traefik.http.routers.blaze_itcc.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}
@@ -34,7 +34,6 @@ services:
       EPSILON: 0.28
       QUERIES_TO_CACHE: '/queries_to_cache.conf'
       ENDPOINT_TYPE: ${FOCUS_ENDPOINT_TYPE:-blaze}
-      CQL_PROJECTS_ENABLED: "itcc"
     volumes:
       - /srv/docker/bridgehead/itcc/queries_to_cache.conf:/queries_to_cache.conf:ro
     depends_on:

itcc/modules/itcc-omics-ingest.sh

@@ -0,0 +1,6 @@
+#!/bin/bash
+
+if [ -n "$ENABLE_OMICS" ];then
+  OVERRIDE+=" -f ./$PROJECT/modules/itcc-omics-ingest.yaml"
+  GENERATE_API_KEY="$(generate_simple_password 'omics')"
+fi

itcc/modules/itcc-omics-ingest.yaml

@@ -0,0 +1,14 @@
+services:
+  omics-endpoint:
+    image: ghcr.io/samply/itcc-omics-ingest:main
+    environment:
+      - API_KEY=${GENERATE_API_KEY}
+    volumes:
+      - /var/cache/bridgehead/omics/data:/data/uploads
+    labels:
+      - "traefik.http.routers.omics.rule=Host(`${HOST}`) && PathPrefix(`/api/omics`)"
+      - "traefik.enable=true"
+      - "traefik.http.services.omics.loadbalancer.server.port=6080"
+      - "traefik.http.routers.omics.tls=true"
+      - "traefik.http.middlewares.omics-stripprefix.stripprefix.prefixes=/api"
+      - "traefik.http.routers.omics.middlewares=omics-stripprefix"

itcc/modules/lens-compose.yml

@@ -1,33 +1,47 @@
 version: "3.7"
 services:
-  landing:
+  itcc-explorer:
-    container_name: lens_federated-search
+    container_name: lens_itcc_explorer
-    image: docker.verbis.dkfz.de/ccp/lens:${SITE_ID}
+    image: samply/itcc-explorer:main
+    environment:
+      HOST: "0.0.0.0"
+      BIND_ADDR: "0.0.0.0:3000"
+      PUBLIC_ENVIRONMENT: ${PUBLIC_ENVIRONMENT}
     labels:
       - "traefik.enable=true"
-      - "traefik.http.routers.landing.rule=PathPrefix(`/`)"
+      - "traefik.http.routers.itcc.rule=Host(`${HOST}`) && PathPrefix(`/`)"
-      - "traefik.http.services.landing.loadbalancer.server.port=80"
+      - "traefik.http.routers.itcc.entrypoints=websecure"
-      - "traefik.http.routers.landing.tls=true"
+      - "traefik.http.services.itcc.loadbalancer.server.port=3000"
+      - "traefik.http.routers.itcc.tls=true"
 
   spot:
-    image: docker.verbis.dkfz.de/ccp-private/central-spot
+    image: samply/rustyspot:latest
     environment:
       BEAM_SECRET: "${FOCUS_BEAM_SECRET_SHORT}"
-      BEAM_URL: http://beam-proxy:8081
+      BEAM_PROXY_URL: http://beam-proxy:8081
       BEAM_PROXY_ID: ${SITE_ID}
       BEAM_BROKER_ID: ${BROKER_ID}
-      BEAM_APP_ID: "focus"
+      BEAM_APP_ID: "spot.${SITE_ID}.${BROKER_ID}"
-      PROJECT_METADATA: "itcc"
+      CORS_ORIGIN: "https://${HOST}"
+      SITES: ${SITES}
+      TRANSFORM: LENS
+      PROJECT: "itcc"
+      BIND_ADDR: 0.0.0.0:8055
     depends_on:
       - "beam-proxy"
     labels:
       - "traefik.enable=true"
-      - "traefik.http.services.spot.loadbalancer.server.port=8080"
+      - "traefik.http.services.spot.loadbalancer.server.port=8055"
       - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowmethods=GET,OPTIONS,POST"
+      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowheaders=content-type"
       - "traefik.http.middlewares.corsheaders2.headers.accesscontrolalloworiginlist=https://${HOST}"
       - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowcredentials=true"
       - "traefik.http.middlewares.corsheaders2.headers.accesscontrolmaxage=-1"
-      - "traefik.http.routers.spot.rule=Host(`${HOST}`) && PathPrefix(`/backend`)"
+      - "traefik.http.routers.spot.rule=Host(`${HOST}`) && PathPrefix(`/prod`)"
-      - "traefik.http.middlewares.stripprefix_spot.stripprefix.prefixes=/backend"
+      - "traefik.http.middlewares.stripprefix_spot.stripprefix.prefixes=/prod"
       - "traefik.http.routers.spot.tls=true"
       - "traefik.http.routers.spot.middlewares=corsheaders2,stripprefix_spot,auth"
+
+  beam-proxy:
+    environment:
+      APP_spot_KEY: ${FOCUS_BEAM_SECRET_SHORT}

itcc/vars

@@ -6,6 +6,7 @@ FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64}
 SUPPORT_EMAIL=arturo.macias@dkfz-heidelberg.de
 PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
 BROKER_URL_FOR_PREREQ=$BROKER_URL
+PUBLIC_ENVIRONMENT=prod
 
 for module in $PROJECT/modules/*.sh
 do

kr/docker-compose.yml

@@ -12,7 +12,8 @@ services:
       BASE_URL: "http://bridgehead-kr-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"

kr/modules/export-and-qb.curl-templates

@@ -1,6 +0,0 @@
-# Full Excel Export
-curl --location --request POST 'https://${HOST}/ccp-exporter/request?query=Patient&query-format=FHIR_PATH&template-id=ccp&output-format=EXCEL' \
---header 'x-api-key: ${EXPORT_API_KEY}'
-
-# QB
-curl --location --request POST 'https://${HOST}/ccp-reporter/generate?template-id=ccp'

kr/modules/lens-compose.yml

@@ -4,32 +4,41 @@ services:
     deploy:
       replicas: 1 #reactivate if lens is in use
     container_name: lens_federated-search
-    image: docker.verbis.dkfz.de/ccp/lens:${SITE_ID}
+    image: docker.verbis.dkfz.de/ccp/kr-explorer:main
+    environment:
+      PUBLIC_SPOT_URL: https://${HOST}/prod
     labels:
+      - "traefik.http.services.lens.loadbalancer.server.port=3000"
       - "traefik.enable=true"
-      - "traefik.http.routers.landing.rule=PathPrefix(`/`)"
+      - "traefik.http.routers.lens.rule=Host(`${HOST}`)"
-      - "traefik.http.services.landing.loadbalancer.server.port=80"
+      - "traefik.http.routers.lens.tls=true"
-      - "traefik.http.routers.landing.tls=true"
 
   spot:
-    image: docker.verbis.dkfz.de/ccp-private/central-spot
+    image: samply/rustyspot:latest
     environment:
       BEAM_SECRET: "${FOCUS_BEAM_SECRET_SHORT}"
-      BEAM_URL: http://beam-proxy:8081
+      BEAM_PROXY_URL: http://beam-proxy:8081
-      BEAM_PROXY_ID: ${SITE_ID}
+      BEAM_APP_ID: "spot.${SITE_ID}.${BROKER_ID}"
-      BEAM_BROKER_ID: ${BROKER_ID}
+      CORS_ORIGIN: "https://${HOST}"
-      BEAM_APP_ID: "focus"
+      SITES: ${SITES}
-      PROJECT_METADATA: "kr_supervisors"
+      TRANSFORM: LENS
+      PROJECT: kr
+      BIND_ADDR: 0.0.0.0:8055
     depends_on:
       - "beam-proxy"
     labels:
       - "traefik.enable=true"
-      - "traefik.http.services.spot.loadbalancer.server.port=8080"
+      - "traefik.http.services.spot.loadbalancer.server.port=8055"
       - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowmethods=GET,OPTIONS,POST"
+      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowheaders=content-type"
       - "traefik.http.middlewares.corsheaders2.headers.accesscontrolalloworiginlist=https://${HOST}"
       - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowcredentials=true"
       - "traefik.http.middlewares.corsheaders2.headers.accesscontrolmaxage=-1"
-      - "traefik.http.routers.spot.rule=Host(`${HOST}`) && PathPrefix(`/backend`)"
+      - "traefik.http.routers.spot.rule=Host(`${HOST}`) && PathPrefix(`/prod`)"
-      - "traefik.http.middlewares.stripprefix_spot.stripprefix.prefixes=/backend"
+      - "traefik.http.middlewares.stripprefix_spot.stripprefix.prefixes=/prod"
       - "traefik.http.routers.spot.tls=true"
-      - "traefik.http.routers.spot.middlewares=corsheaders2,stripprefix_spot"
+      - "traefik.http.routers.spot.middlewares=corsheaders2,stripprefix_spot,auth"
+
+  beam-proxy:
+    environment:
+      APP_spot_KEY: ${FOCUS_BEAM_SECRET_SHORT}

kr/modules/obds2fhir-rest-compose.yml

@@ -3,7 +3,7 @@ version: "3.7"
 services:
   obds2fhir-rest:
     container_name: bridgehead-obds2fhir-rest
-    image: docker.verbis.dkfz.de/ccp/obds2fhir-rest:main
+    image: docker.verbis.dkfz.de/samply/obds2fhir-rest:main
     environment:
       IDTYPE: BK_${IDMANAGEMENT_FRIENDLY_ID}_L-ID
       MAINZELLISTE_APIKEY: ${IDMANAGER_LOCAL_PATIENTLIST_APIKEY}

kr/vars

@@ -3,7 +3,7 @@ BROKER_URL=https://${BROKER_ID}
 PROXY_ID=${SITE_ID}.${BROKER_ID}
 FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
 FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64}
-SUPPORT_EMAIL=arturo.macias@dkfz-heidelberg.de
+SUPPORT_EMAIL=p.delpy@dkfz-heidelberg.de
 PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
 BROKER_URL_FOR_PREREQ=$BROKER_URL
 

lib/functions.sh

@@ -9,6 +9,15 @@ detectCompose() {
 	fi
 }
 
+# Encodes all characters not in unrestricted character set of RFC3986 Section 2.3
+urlencode() {
+  for ((i=0;i<${#1};i++)); do
+    local c=${1:i:1}
+    [[ "$c" =~ [a-zA-Z0-9._~-] ]] && printf '%s' "$c" || printf '%%%02X' "'$c"
+  done
+  echo
+}
+
 setupProxy() {
 	### Note: As the current data protection concepts do not allow communication via HTTP,
 	### we are not setting a proxy for HTTP requests.
@@ -22,9 +31,12 @@ setupProxy() {
 		HTTPS_PROXY_HOST="$(echo $hostport | sed -e 's,:.*,,g')"
 		HTTPS_PROXY_PORT="$(echo $hostport | sed -e 's,^.*:,:,g' -e 's,.*:\([0-9]*\).*,\1,g' -e 's,[^0-9],,g')"
 		if [[ ! -z "$HTTPS_PROXY_USERNAME" && ! -z "$HTTPS_PROXY_PASSWORD" ]]; then
+			local ESCAPED_PASSWORD="$(echo $HTTPS_PROXY_PASSWORD | od -An -v -t x1 | sed -e 's/[[:space:]]//g' -e 's/\([0-9a-f][0-9a-f]\)/%\1/g' | tr -d '\n')"
+			local CURL_ESCAPED_PW="$(urlencode $HTTPS_PROXY_PASSWORD)"
 			local proto="$(echo $HTTPS_PROXY_URL | grep :// | sed -e 's,^\(.*://\).*,\1,g')"
 			local fqdn="$(echo ${HTTPS_PROXY_URL/$proto/})"
-			HTTPS_PROXY_FULL_URL="$(echo $proto$HTTPS_PROXY_USERNAME:$HTTPS_PROXY_PASSWORD@$fqdn)"
+			HTTPS_PROXY_FULL_URL="$(echo $proto$HTTPS_PROXY_USERNAME:$ESCAPED_PASSWORD@$fqdn)"
+			CURL_HTTPS_PROXY_FULL_URL="$(echo $proto$HTTPS_PROXY_USERNAME:$CURL_ESCAPED_PW@$fqdn)"
 			https="authenticated"
 		else
 			HTTPS_PROXY_FULL_URL=$HTTPS_PROXY_URL
@@ -33,7 +45,7 @@ setupProxy() {
 	fi
 
 	log INFO "Configuring proxy servers: $http http proxy (we're not supporting unencrypted comms), $https https proxy"
-	export HTTPS_PROXY_HOST HTTPS_PROXY_PORT HTTPS_PROXY_FULL_URL
+	export HTTPS_PROXY_HOST HTTPS_PROXY_PORT HTTPS_PROXY_FULL_URL CURL_HTTPS_PROXY_FULL_URL
 }
 
 exitIfNotRoot() {
@@ -54,7 +66,7 @@ checkOwner(){
 
 printUsage() {
 	echo "Usage: bridgehead start|stop|logs|docker-logs|is-running|update|check|install|uninstall|adduser|enroll PROJECTNAME"
-	echo "PROJECTNAME should be one of ccp|bbmri|cce|itcc|kr|dhki"
+	echo "PROJECTNAME should be one of ccp|bbmri|cce|itcc|kr|dhki|nngm"
 }
 
 checkRequirements() {
@@ -327,7 +339,7 @@ function sync_secrets() {
         -e ALL_PROXY=$HTTPS_PROXY_FULL_URL \
         -e PROXY_ID=$proxy_id \
         -e BROKER_URL=$broker_url \
-        -e OIDC_PROVIDER=secret-sync-central.test-secret-sync.$broker_id \
+        -e OIDC_PROVIDER=secret-sync-central.central-secret-sync.$broker_id \
         -e SECRET_DEFINITIONS=$secret_sync_args \
         docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest
 
@@ -338,6 +350,7 @@ function sync_secrets() {
 
 function secret_sync_gitlab_token() {
     if [[ "$PROJECT" != "dktk" && "$PROJECT" != "bbmri" ]]; then
+        log "INFO" "Not running Secret Sync for project minimal"
         return
     fi
     # Map the origin of the git repository /etc/bridgehead to the prefix recognized by Secret Sync
@@ -397,7 +410,7 @@ function secret_sync_gitlab_token() {
     else
         log "WARN" "Secret Sync failed"
         # Remove the git credential helper
-        git -C /etc/bridgehead config --unset credential.helpera
+        git -C /etc/bridgehead config --unset credential.helper
     fi
 
     # In the past the git credential helper was also set for /srv/docker/bridgehead but never used.

lib/monitoring.sh

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

lib/prepare-system.sh

@@ -55,6 +55,9 @@ case "$PROJECT" in
 	cce)
 		site_configuration_repository_middle="git.verbis.dkfz.de/cce-sites/"
 		;;
+	pscc)
+		site_configuration_repository_middle="git.verbis.dkfz.de/pscc-sites/"
+		;;
 	itcc)
 		site_configuration_repository_middle="git.verbis.dkfz.de/itcc-sites/"
         ;;
@@ -67,6 +70,9 @@ case "$PROJECT" in
 	dhki)
 		site_configuration_repository_middle="git.verbis.dkfz.de/dhki/"
 		;;
+	nngm)
+		site_configuration_repository_middle="git.verbis.dkfz.de/nngm/"
+		;;
 	minimal)
 		site_configuration_repository_middle="git.verbis.dkfz.de/minimal-bridgehead-configs/"
 		;;

lib/prerequisites.sh

@@ -71,7 +71,7 @@ source ${PROJECT}/vars
 
 if [ "${PROJECT}" != "minimal" ]; then
   set +e
-  SERVERTIME="$(https_proxy=$HTTPS_PROXY_FULL_URL curl -m 5 -s -I $BROKER_URL_FOR_PREREQ 2>&1 | grep -i -e '^Date: ' | sed -e 's/^Date: //i')"
+  SERVERTIME="$(https_proxy=$CURL_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

lib/tests/test_proxyparsing.sh

@@ -0,0 +1,123 @@
+source ../functions.sh
+
+test_setupProxy() {
+  # simple logger for tests
+  log() { :; }
+
+  local failures=0
+  local total=0
+
+  assert_eq() {
+    local label="$1" got="$2" expected="$3"
+    total=$((total + 1))
+    if [[ "$got" != "$expected" ]]; then
+      failures=$((failures + 1))
+      printf 'FAIL: %s\n  got:      %q\n  expected: %q\n\n' "$label" "$got" "$expected"
+    else
+      printf 'ok: %s\n' "$label"
+    fi
+  }
+
+  run_case() {
+    local name="$1"
+    local url="$2"
+    local u="$3"
+    local p="$4"
+    local exp_host="$5"
+    local exp_port="$6"
+    local exp_full="$7"
+
+    HTTPS_PROXY_URL="$url"
+    HTTPS_PROXY_USERNAME="$u"
+    HTTPS_PROXY_PASSWORD="$p"
+
+    setupProxy >/dev/null 2>&1
+
+    assert_eq "$name host" "$HTTPS_PROXY_HOST" "$exp_host"
+    assert_eq "$name port" "$HTTPS_PROXY_PORT" "$exp_port"
+    assert_eq "$name full" "$HTTPS_PROXY_FULL_URL" "$exp_full"
+  }
+
+  echo "Running setupProxy tests..."
+  echo
+
+  # 1) Basic https host:port
+  run_case "basic https" \
+    "https://proxy.example.org:8443" "" "" \
+    "proxy.example.org" "8443" \
+    "https://proxy.example.org:8443"
+
+  # 2) https without port -> default 443
+  run_case "https no port" \
+    "https://proxy.example.org" "" "" \
+    "proxy.example.org" "443" \
+    "https://proxy.example.org"
+
+  # 3) no scheme, host:port -> defaults scheme=https
+  run_case "no scheme hostport" \
+    "proxy.example.org:3128" "" "" \
+    "proxy.example.org" "3128" \
+    "https://proxy.example.org:3128"
+
+  # 4) URL with path/query/fragment
+  run_case "ignores path" \
+    "https://proxy.example.org:8443/some/path?x=1#y" "" "" \
+    "proxy.example.org" "8443" \
+    "https://proxy.example.org:8443"
+
+  # 5) explicit env creds inserted
+  run_case "env creds override" \
+    "https://proxy.example.org:8443" "alice" "secret" \
+    "proxy.example.org" "8443" \
+    "https://alice:secret@proxy.example.org:8443"
+
+  # 6) embedded creds used if env creds absent
+  run_case "embedded creds" \
+    "https://bob:pw@proxy.example.org:8443" "" "" \
+    "proxy.example.org" "8443" \
+    "https://bob:pw@proxy.example.org:8443"
+
+  # 7) env creds override embedded creds
+  run_case "env overrides embedded" \
+    "https://bob:pw@proxy.example.org:8443" "alice" "secret" \
+    "proxy.example.org" "8443" \
+    "https://alice:secret@proxy.example.org:8443"
+
+  # 8) IPv6 literal with port
+  run_case "ipv6 with port" \
+    "https://[2001:db8::1]:8080" "" "" \
+    "2001:db8::1" "8080" \
+    "https://[2001:db8::1]:8080"
+
+  # 9) IPv6 literal without port -> default 443
+  run_case "ipv6 no port" \
+    "https://[2001:db8::1]" "" "" \
+    "2001:db8::1" "443" \
+    "https://[2001:db8::1]"
+
+  # 10) http scheme rejected -> outputs empty
+  HTTPS_PROXY_URL="http://proxy.example.org:8080"
+  HTTPS_PROXY_USERNAME=""
+  HTTPS_PROXY_PASSWORD=""
+  setupProxy >/dev/null 2>&1
+  assert_eq "http rejected host" "${HTTPS_PROXY_HOST:-}" ""
+  assert_eq "http rejected port" "${HTTPS_PROXY_PORT:-}" ""
+  assert_eq "http rejected full" "${HTTPS_PROXY_FULL_URL:-}" ""
+
+  # 11) empty URL -> outputs empty but no failure
+  HTTPS_PROXY_URL=""
+  setupProxy >/dev/null 2>&1
+  assert_eq "empty url host" "${HTTPS_PROXY_HOST:-}" ""
+  assert_eq "empty url port" "${HTTPS_PROXY_PORT:-}" ""
+  assert_eq "empty url full" "${HTTPS_PROXY_FULL_URL:-}" ""
+
+  echo
+  echo "Tests complete: $((total - failures))/$total passed."
+  if (( failures > 0 )); then
+    echo "Some tests failed."
+    return 1
+  fi
+  return 0
+}
+
+test_setupProxy

minimal/docker-compose.yml

@@ -32,7 +32,7 @@ services:
 
   forward_proxy:
     container_name: bridgehead-forward-proxy
-    image: docker.verbis.dkfz.de/cache/samply/bridgehead-forward-proxy:latest
+    image: samply/bridgehead-forward-proxy:pr-16
     environment:
       HTTPS_PROXY: ${HTTPS_PROXY_URL}
       HTTPS_PROXY_USERNAME: ${HTTPS_PROXY_USERNAME}

minimal/modules/dnpm-node-compose.yml

@@ -66,6 +66,7 @@ services:
       - HATEOAS_HOST=https://${HOST}
       - CONNECTOR_TYPE=broker
       - AUTHUP_URL=robot://system:${DNPM_AUTHUP_SECRET}@http://dnpm-authup:3000
+      - TZ=Europe/Berlin
     volumes:
       - /etc/bridgehead/dnpm/config:/dnpm_config
       - /var/cache/bridgehead/dnpm/backend-data:/dnpm_data

nngm/docker-compose.yml

@@ -0,0 +1,65 @@
+version: "3.7"
+
+services:
+  blaze:
+    image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
+    container_name: bridgehead-nngm-blaze
+    environment:
+      BASE_URL: "http://bridgehead-nngm-blaze:8080"
+      JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
+      DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
+      DB_BLOCK_CACHE_SIZE: ${BLAZE_MEMORY_CAP}
+      CQL_EXPR_CACHE_SIZE: ${BLAZE_CQL_CACHE_CAP:-32}
+      ENFORCE_REFERENTIAL_INTEGRITY: "false"
+    volumes:
+      - "blaze-data:/app/data"
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.blaze_nngm.rule=PathPrefix(`/nngm-localdatamanagement`)"
+      - "traefik.http.middlewares.nngm_b_strip.stripprefix.prefixes=/nngm-localdatamanagement"
+      - "traefik.http.services.blaze_nngm.loadbalancer.server.port=8080"
+      - "traefik.http.routers.blaze_nngm.middlewares=nngm_b_strip,auth"
+      - "traefik.http.routers.blaze_nngm.tls=true"
+
+  focus:
+    image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
+    container_name: bridgehead-focus
+    environment:
+    - API_KEY=${FOCUS_BEAM_SECRET_SHORT}
+    - BEAM_APP_ID_LONG=focus.${PROXY_ID}
+    - PROXY_ID=${PROXY_ID}
+    - BLAZE_URL=http://bridgehead-nngm-blaze:8080/fhir/
+    - BEAM_PROXY_URL=http://beam-proxy:8081
+    - RETRY_COUNT=${FOCUS_RETRY_COUNT}
+    - EPSILON=0.28
+    - ENDPOINT_TYPE=${FOCUS_ENDPOINT_TYPE:-blaze}
+    - CQL_PROJECTS_ENABLED
+    depends_on:
+      - "beam-proxy"
+      - "blaze"
+
+  beam-proxy:
+    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${BEAM_TAG}
+    container_name: bridgehead-beam-proxy
+    environment:
+      BROKER_URL: ${BROKER_URL}
+      PROXY_ID: ${PROXY_ID}
+      APP_focus_KEY: ${FOCUS_BEAM_SECRET_SHORT}
+      PRIVKEY_FILE: /run/secrets/proxy.pem
+      ALL_PROXY: http://forward_proxy:3128
+      TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
+      ROOTCERT_FILE: /conf/root.crt.pem
+    secrets:
+      - proxy.pem
+    depends_on:
+      - "forward_proxy"
+    volumes:
+      - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
+      - /srv/docker/bridgehead/nngm/root.crt.pem:/conf/root.crt.pem:ro
+
+volumes:
+  blaze-data:
+
+secrets:
+  proxy.pem:
+    file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

nngm/modules/exporter-compose.yml

@@ -0,0 +1,72 @@
+version: "3.7"
+
+services:
+  exporter:
+    image: docker.verbis.dkfz.de/ccp/dktk-exporter:latest
+    container_name: bridgehead-nngm-exporter
+    environment:
+      JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
+      LOG_LEVEL: "INFO"
+      EXPORTER_API_KEY: "${EXPORTER_API_KEY}" # Set in exporter-setup.sh
+      CROSS_ORIGINS: "https://${HOST}"
+      EXPORTER_DB_USER: "exporter"
+      EXPORTER_DB_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
+      EXPORTER_DB_URL: "jdbc:postgresql://exporter-db:5432/exporter"
+      HTTP_RELATIVE_PATH: "/nngm-exporter"
+      SITE: "${SITE_ID}"
+      HTTP_SERVLET_REQUEST_SCHEME: "https"
+      OPAL_PASSWORD: "${EXPORTER_OPAL_PASSWORD}"
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.exporter_nngm.rule=PathPrefix(`/nngm-exporter`)"
+      - "traefik.http.services.exporter_nngm.loadbalancer.server.port=8092"
+      - "traefik.http.routers.exporter_nngm.tls=true"
+      - "traefik.http.middlewares.exporter_nngm_strip.stripprefix.prefixes=/nngm-exporter"
+      - "traefik.http.routers.exporter_nngm.middlewares=exporter_nngm_strip"
+    volumes:
+      - "/var/cache/bridgehead/nngm/exporter-files:/app/exporter-files/output"
+
+  exporter-db:
+    image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
+    container_name: bridgehead-nngm-exporter-db
+    environment:
+      POSTGRES_USER: "exporter"
+      POSTGRES_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
+      POSTGRES_DB: "exporter"
+    volumes:
+      # Consider removing this volume once we find a solution to save Lens-queries to be executed in the explorer.
+      - "/var/cache/bridgehead/nngm/exporter-db:/var/lib/postgresql/data"
+
+  reporter:
+    image: docker.verbis.dkfz.de/ccp/dktk-reporter:latest
+    container_name: bridgehead-nngm-reporter
+    environment:
+      JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
+      LOG_LEVEL: "INFO"
+      CROSS_ORIGINS: "https://${HOST}"
+      HTTP_RELATIVE_PATH: "/nngm-reporter"
+      SITE: "${SITE_ID}"
+      EXPORTER_API_KEY: "${EXPORTER_API_KEY}" # Set in exporter-setup.sh
+      EXPORTER_URL: "http://exporter:8092"
+      LOG_FHIR_VALIDATION: "false"
+      HTTP_SERVLET_REQUEST_SCHEME: "https"
+
+    # In this initial development state of the bridgehead, we are trying to have so many volumes as possible.
+    # However, in the first executions in the CCP sites, this volume seems to be very important. A report is
+    # a process that can take several hours, because it depends on the exporter.
+    # There is a risk that the bridgehead restarts, losing the already created export.
+
+    volumes:
+      - "/var/cache/bridgehead/nngm/reporter-files:/app/reports"
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.reporter_nngm.rule=PathPrefix(`/nngm-reporter`)"
+      - "traefik.http.services.reporter_nngm.loadbalancer.server.port=8095"
+      - "traefik.http.routers.reporter_nngm.tls=true"
+      - "traefik.http.middlewares.reporter_nngm_strip.stripprefix.prefixes=/nngm-reporter"
+      - "traefik.http.routers.reporter_nngm.middlewares=reporter_nngm_strip"
+
+  focus:
+    environment:
+      EXPORTER_URL: "http://exporter:8092"
+      EXPORTER_API_KEY: "${EXPORTER_API_KEY}"

nngm/modules/exporter-setup.sh

@@ -0,0 +1,8 @@
+#!/bin/bash -e
+
+if [ "$ENABLE_EXPORTER" == true ]; then
+  log INFO "Exporter setup detected -- will start Exporter service."
+  OVERRIDE+=" -f ./$PROJECT/modules/exporter-compose.yml"
+  EXPORTER_DB_PASSWORD="$(echo \"This is a salt string to generate one consistent password for the exporter. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
+  EXPORTER_API_KEY="$(echo \"This is a salt string to generate one consistent API KEY for the exporter. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 64)"
+fi

nngm/modules/teiler-compose.yml

@@ -0,0 +1,73 @@
+version: "3.7"
+
+services:
+
+  teiler-orchestrator:
+    image: docker.verbis.dkfz.de/cache/samply/teiler-orchestrator:latest
+    container_name: bridgehead-teiler-orchestrator
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.teiler_orchestrator_nngm.rule=PathPrefix(`/nngm-teiler`)"
+      - "traefik.http.services.teiler_orchestrator_nngm.loadbalancer.server.port=9000"
+      - "traefik.http.routers.teiler_orchestrator_nngm.tls=true"
+      - "traefik.http.middlewares.teiler_orchestrator_nngm_strip.stripprefix.prefixes=/nngm-teiler"
+      - "traefik.http.routers.teiler_orchestrator_nngm.middlewares=teiler_orchestrator_nngm_strip"
+    environment:
+      TEILER_BACKEND_URL: "/nngm-teiler-backend"
+      TEILER_DASHBOARD_URL: "/nngm-teiler-dashboard"
+      DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE_LOWER_CASE}"
+      HTTP_RELATIVE_PATH: "/nngm-teiler"
+
+  teiler-dashboard:
+    image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:${TEILER_DASHBOARD_TAG}
+    container_name: bridgehead-teiler-dashboard
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.teiler_dashboard_nngm.rule=PathPrefix(`/nngm-teiler-dashboard`)"
+      - "traefik.http.services.teiler_dashboard_nngm.loadbalancer.server.port=80"
+      - "traefik.http.routers.teiler_dashboard_nngm.tls=true"
+      - "traefik.http.middlewares.teiler_dashboard_nngm_strip.stripprefix.prefixes=/nngm-teiler-dashboard"
+      - "traefik.http.routers.teiler_dashboard_nngm.middlewares=teiler_dashboard_nngm_strip"
+    environment:
+      DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
+      TEILER_BACKEND_URL: "/nngm-teiler-backend"
+      TEILER_DASHBOARD_URL: "/nngm-teiler-dashboard"
+      OIDC_URL: "${OIDC_URL}"
+      OIDC_CLIENT_ID: "${OIDC_PUBLIC_CLIENT_ID}"
+      OIDC_TOKEN_GROUP: "${OIDC_GROUP_CLAIM}"
+      TEILER_ADMIN_NAME: "${OPERATOR_FIRST_NAME} ${OPERATOR_LAST_NAME}"
+      TEILER_ADMIN_EMAIL: "${OPERATOR_EMAIL}"
+      TEILER_ADMIN_PHONE: "${OPERATOR_PHONE}"
+      TEILER_PROJECT: "${PROJECT}"
+      EXPORTER_API_KEY: "${EXPORTER_API_KEY}"
+      TEILER_ORCHESTRATOR_URL: "/nngm-teiler"
+      TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/nngm-teiler"
+      TEILER_USER: "${OIDC_USER_GROUP}"
+      TEILER_ADMIN: "${OIDC_ADMIN_GROUP}"
+      REPORTER_DEFAULT_TEMPLATE_ID: "ccp-qb"
+      EXPORTER_DEFAULT_TEMPLATE_ID: "ccp"
+
+
+# TODO: Replace dktk-teiler-backend with nngm-teiler-backend
+  teiler-backend:
+    image: docker.verbis.dkfz.de/ccp/dktk-teiler-backend:latest
+    container_name: bridgehead-teiler-backend
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.teiler_backend_nngm.rule=PathPrefix(`/nngm-teiler-backend`)"
+      - "traefik.http.services.teiler_backend_nngm.loadbalancer.server.port=8085"
+      - "traefik.http.routers.teiler_backend_nngm.tls=true"
+      - "traefik.http.middlewares.teiler_backend_nngm_strip.stripprefix.prefixes=/nngm-teiler-backend"
+      - "traefik.http.routers.teiler_backend_nngm.middlewares=teiler_backend_nngm_strip"
+    environment:
+      LOG_LEVEL: "INFO"
+      APPLICATION_PORT: "8085"
+      DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
+      TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/nngm-teiler"
+      TEILER_ORCHESTRATOR_URL: "/nngm-teiler"
+      TEILER_DASHBOARD_DE_URL: "/nngm-teiler-dashboard/de"
+      TEILER_DASHBOARD_EN_URL: "/nngm-teiler-dashboard/en"
+      HTTP_PROXY: "http://forward_proxy:3128"
+      ENABLE_MTBA: "${ENABLE_MTBA}"
+      ENABLE_DATASHIELD: "${ENABLE_DATASHIELD}"
+      IDMANAGER_UPLOAD_APIKEY: "${IDMANAGER_UPLOAD_APIKEY}" # Only used to check if the ID Manager is active

nngm/modules/teiler-setup.sh

@@ -0,0 +1,8 @@
+#!/bin/bash -e
+
+if [ "$ENABLE_TEILER" == true ];then
+  log INFO "Teiler setup detected -- will start Teiler services."
+  OVERRIDE+=" -f ./$PROJECT/modules/teiler-compose.yml"
+  TEILER_DEFAULT_LANGUAGE=DE
+  TEILER_DEFAULT_LANGUAGE_LOWER_CASE=${TEILER_DEFAULT_LANGUAGE,,}
+fi

nngm/root.crt.pem

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

nngm/vars

@@ -0,0 +1,32 @@
+BROKER_ID=broker.nngm.dkfz.de
+BROKER_URL=https://${BROKER_ID}
+PROXY_ID=${SITE_ID}.${BROKER_ID}
+FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
+FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64}
+# TODO: Add real nNGM-Support email
+SUPPORT_EMAIL=support-nngm@dkfz-heidelberg.de
+PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
+
+BROKER_URL_FOR_PREREQ=$BROKER_URL
+
+# TODO: Replace with nNGM OIDC Server
+OIDC_USER_GROUP="NNGM_$(capitalize_first_letter ${SITE_ID})"
+OIDC_ADMIN_GROUP="NNGM_$(capitalize_first_letter ${SITE_ID})_Verwalter"
+OIDC_PSP_GROUP="NNGM_$(capitalize_first_letter ${SITE_ID})_PSP"
+OIDC_PRIVATE_CLIENT_ID=${SITE_ID}-private
+OIDC_PUBLIC_CLIENT_ID=${SITE_ID}-public
+OIDC_URL="https://sso.verbis.dkfz.de/application/o/${OIDC_PUBLIC_CLIENT_ID}/"
+OIDC_PRIVATE_URL="https://sso.verbis.dkfz.de/application/o/${OIDC_PRIVATE_CLIENT_ID}/"
+OIDC_GROUP_CLAIM="groups"
+
+for module in $PROJECT/modules/*.sh
+do
+    log DEBUG "sourcing $module"
+    source $module
+done
+
+for module in modules/*.sh
+do
+    log DEBUG "sourcing $module"
+    source $module
+done

pscc/docker-compose.yml

@@ -0,0 +1,67 @@
+version: "3.7"
+
+services:
+  blaze:
+    image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
+    container_name: bridgehead-pscc-blaze
+    environment:
+      BASE_URL: "http://bridgehead-pscc-blaze:8080"
+      JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
+      DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
+      DB_BLOCK_CACHE_SIZE: ${BLAZE_MEMORY_CAP}
+      CQL_EXPR_CACHE_SIZE: ${BLAZE_CQL_CACHE_CAP:-32}
+      ENFORCE_REFERENTIAL_INTEGRITY: "false"
+    volumes:
+      - "blaze-data:/app/data"
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.blaze_pscc.rule=PathPrefix(`/pscc-localdatamanagement`)"
+      - "traefik.http.middlewares.pscc_b_strip.stripprefix.prefixes=/pscc-localdatamanagement"
+      - "traefik.http.services.blaze_pscc.loadbalancer.server.port=8080"
+      - "traefik.http.routers.blaze_pscc.middlewares=pscc_b_strip,auth"
+      - "traefik.http.routers.blaze_pscc.tls=true"
+
+  focus:
+    image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
+    container_name: bridgehead-focus
+    environment:
+      API_KEY: ${FOCUS_BEAM_SECRET_SHORT}
+      BEAM_APP_ID_LONG: focus.${PROXY_ID}
+      PROXY_ID: ${PROXY_ID}
+      BLAZE_URL: "http://bridgehead-pscc-blaze:8080/fhir/"
+      BEAM_PROXY_URL: http://beam-proxy:8081
+      RETRY_COUNT: ${FOCUS_RETRY_COUNT}
+      EPSILON: 0.28
+      ENDPOINT_TYPE: ${FOCUS_ENDPOINT_TYPE:-blaze}
+    depends_on:
+      - "beam-proxy"
+      - "blaze"
+
+  beam-proxy:
+    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${BEAM_TAG}
+    container_name: bridgehead-beam-proxy
+    environment:
+      BROKER_URL: ${BROKER_URL}
+      PROXY_ID: ${PROXY_ID}
+      APP_focus_KEY: ${FOCUS_BEAM_SECRET_SHORT}
+      PRIVKEY_FILE: /run/secrets/proxy.pem
+      ALL_PROXY: http://forward_proxy:3128
+      TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
+      ROOTCERT_FILE: /conf/root.crt.pem
+    secrets:
+      - proxy.pem
+    depends_on:
+      - "forward_proxy"
+    volumes:
+      - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
+      - /srv/docker/bridgehead/pscc/root.crt.pem:/conf/root.crt.pem:ro
+
+  landing:
+    profiles: [deactivated]
+
+volumes:
+  blaze-data:
+
+secrets:
+  proxy.pem:
+    file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

pscc/modules/lens-compose.yml

@@ -0,0 +1,40 @@
+version: "3.7"
+services:
+  lens:
+    container_name: lens-federated-search
+    image: docker.verbis.dkfz.de/ccp/lens:${SITE_ID}
+    labels:
+      - "traefik.http.services.lens.loadbalancer.server.port=3000"
+      - "traefik.enable=true"
+      - "traefik.http.routers.lens.rule=Host(`${HOST}`)"
+      - "traefik.http.routers.lens.tls=true"
+
+  spot:
+    image: samply/rustyspot:latest
+    platform: linux/amd64
+    environment:
+      HTTP_PROXY: ${HTTP_PROXY_URL}
+      HTTPS_PROXY: ${HTTPS_PROXY_URL}
+      NO_PROXY: beam-proxy
+      BEAM_SECRET: "${FOCUS_BEAM_SECRET_SHORT}"
+      BEAM_PROXY_URL: http://beam-proxy:8081
+      BEAM_APP_ID: "spot.${SITE_ID}.${BROKER_ID}"
+      CORS_ORIGIN: "https://${HOST}"
+      SITES: ${SITES}
+      TRANSFORM: LENS
+      PROJECT: pscc
+      BIND_ADDR: 0.0.0.0:8055
+    depends_on:
+      - "beam-proxy"
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.services.spot.loadbalancer.server.port=8055"
+      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowmethods=GET,OPTIONS,POST"
+      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowheaders=content-type"
+      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolalloworiginlist=https://${HOST}"
+      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowcredentials=true"
+      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolmaxage=-1"
+      - "traefik.http.routers.spot.rule=Host(`${HOST}`) && PathPrefix(`/prod`)"
+      - "traefik.http.middlewares.stripprefix_spot.stripprefix.prefixes=/prod"
+      - "traefik.http.routers.spot.tls=true"
+      - "traefik.http.routers.spot.middlewares=corsheaders2,stripprefix_spot,auth"

pscc/modules/lens-setup.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+
+if [ -n "$ENABLE_LENS" ];then
+  OVERRIDE+=" -f ./$PROJECT/modules/lens-compose.yml"
+fi

pscc/modules/osiris2fhir-compose.yml

@@ -0,0 +1,13 @@
+services:
+  osiris2fhir:
+    container_name: bridgehead-osiris2fhir
+    image: docker.verbis.dkfz.de/ccp/osiris2fhir:${SITE_ID}
+    environment:
+      SALT: ${LOCAL_SALT}
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.osiris2fhir.rule=PathPrefix(`/osiris2fhir`)"
+      - "traefik.http.middlewares.osiris2fhir_strip.stripprefix.prefixes=/osiris2fhir"
+      - "traefik.http.services.osiris2fhir.loadbalancer.server.port=8080"
+      - "traefik.http.routers.osiris2fhir.tls=true"
+      - "traefik.http.routers.osiris2fhir.middlewares=osiris2fhir_strip,auth"

pscc/modules/osiris2fhir-setup.sh

@@ -0,0 +1,6 @@
+#!/bin/bash
+if [ -n "$ENABLE_OSIRIS2FHIR" ]; then
+  log INFO "oBDS2FHIR-REST setup detected -- will start osiris2fhir module."
+  OVERRIDE+=" -f ./pscc/modules/osiris2fhir-compose.yml"
+  LOCAL_SALT="$(echo \"local-random-salt\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
+fi

pscc/root.crt.pem

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

pscc/vars

@@ -0,0 +1,14 @@
+BROKER_ID=broker.pscc.org
+BROKER_URL=https://${BROKER_ID}
+PROXY_ID=${SITE_ID}.${BROKER_ID}
+FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
+FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64}
+SUPPORT_EMAIL=denis.koether@dkfz-heidelberg.de
+PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
+BROKER_URL_FOR_PREREQ=$BROKER_URL
+
+for module in $PROJECT/modules/*.sh
+do
+    log DEBUG "sourcing $module"
+    source $module
+done

versions/acceptance

@@ -1,6 +1,6 @@
 FOCUS_TAG=develop
 BEAM_TAG=develop
-BLAZE_TAG=main
+BLAZE_TAG=0.32
 POSTGRES_TAG=15.13-alpine
 TEILER_DASHBOARD_TAG=develop
 MTBA_TAG=develop

versions/test

@@ -1,6 +1,6 @@
 FOCUS_TAG=develop
 BEAM_TAG=develop
-BLAZE_TAG=main
+BLAZE_TAG=0.32
 POSTGRES_TAG=15.13-alpine
 TEILER_DASHBOARD_TAG=develop
 MTBA_TAG=develop