chore: update datashield beam-connect mappings

feat: Add file-dispatcher to exporter compose
feat: Move to central rstudio
2025-06-16 17:20:15 +02:00 · 2024-05-23 09:55:22 +02:00 · 2024-05-23 09:38:37 +02:00 · 2024-04-17 14:25:59 +02:00
64 changed files with 176 additions and 941 deletions
--- a/README.md
+++ b/README.md
@ -34,7 +34,7 @@ This repository is the starting point for any information and tools you will nee

 ## Requirements

-The data protection officer at your site will probably want to know exactly what our software does with patient data, and you may need to get their approval before you are allowed to install a Bridgehead. To help you with this, we have provided some data protection concepts:
+The data protection group at your site will probably want to know exactly what our software does with patient data, and you may need to get their approval before you are allowed to install a Bridgehead. To help you with this, we have provided some data protection concepts:

 - [Germany](https://www.bbmri.de/biobanking/it/infrastruktur/datenschutzkonzept/)

@ -46,8 +46,6 @@ Hardware requirements strongly depend on the specific use-cases of your network
 - 32 GB RAM
 - 160GB Hard Drive, SSD recommended

-We recommend using a dedicated VM for the Bridgehead, with no other applications running on it. While the Bridgehead can, in principle, run on a shared VM, you might run into surprising problems such as resource conflicts (e.g., two apps using tcp port 443).
-
 ### Software

 You are strongly recommended to install the Bridgehead under a Linux operating system (but see the section [Non-Linux OS](#non-linux-os)). You will need root (administrator) priveleges on this machine in order to perform the deployment. We recommend the newest Ubuntu LTS server release.
@ -202,7 +200,7 @@ sudo systemctl [enable|disable] bridgehead@<PROJECT>.service
 After starting the Bridgehead, you can watch the initialization process with the following command:

 ```shell
-/srv/docker/bridgehead/bridgehead logs <project> -f
+journalctl -u bridgehead@bbmri -f
 ```

 if this exits with something similar to the following:
@ -222,9 +220,8 @@ docker ps
 There should be 6 - 10 Docker proceses. If there are fewer, then you know that something has gone wrong. To see what is going on, run:

 ```shell
-/srv/docker/bridgehead/bridgehead logs <Project> -f
+journalctl -u bridgehead@bbmri -f
 ```
-This translates to a journalctl command so all the regular journalctl flags can be used.

 Once the Bridgehead has passed these checks, take a look at the landing page:

@ -238,7 +235,7 @@ You can either do this in a browser or with curl. If you visit the URL in the br
 curl -k https://localhost
 ```

-Should the landing page not show anything, you can inspect the logs of the containers to determine what is going wrong. To do this you can use `./bridgehead docker-logs <Project> -f` to follow the logs of the container. This transaltes to a docker compose logs command meaning all the ususal docker logs flags work.
+If you get errors when you do this, you need to use ```docker logs``` to examine your landing page container in order to determine what is going wrong.

 If you have chosen to take part in our monitoring program (by setting the ```MONITOR_APIKEY``` variable in the configuration), you will be informed by email when problems are detected in your Bridgehead.

@ -301,19 +298,19 @@ Once you have added your biobank to the Directory you got persistent identifier

 The Bridgehead's **Directory Sync** is an optional feature that keeps the Directory up to date with your local data, e.g. number of samples. Conversely, it also updates the local FHIR store with the latest contact details etc. from the Directory. You must explicitly set your country specific directory URL, username and password to enable this feature.

-You should talk with your local data protection group regarding the information that is published by Directory sync.
-
 Full details can be found in [directory_sync_service](https://github.com/samply/directory_sync_service).

 To enable it, you will need to set these variables to the ```bbmri.conf``` file of your GitLab repository. Here is an example config:

 ```
+DS_DIRECTORY_URL=https://directory.bbmri-eric.eu
 DS_DIRECTORY_USER_NAME=your_directory_username
-DS_DIRECTORY_USER_PASS=your_directory_password
+DS_DIRECTORY_USER_PASS=qwdnqwswdvqHBVGFR9887
+DS_TIMER_CRON="0 22 * * *"
 ```
-Please contact your National Node to obtain this information.
+You must contact the Directory team for your national node to find the URL, and to register as a user.

-Optionally, you **may** change when you want Directory sync to run by specifying a [cron](https://crontab.guru) expression, e.g. `DS_TIMER_CRON="0 22 * * *"` for 10 pm every evening.
+Additionally, you should choose when you want Directory sync to run. In the example above, this is set to happen at 10 pm every evening. You can modify this to suit your requirements. The timer specification should follow the [cron](https://crontab.guru) convention.

 Once you edited the gitlab config, the bridgehead will autoupdate the config with the values and will sync the data.

--- a/bbmri/docker-compose.yml
+++ b/bbmri/docker-compose.yml
@ -4,7 +4,7 @@ version: "3.7"

 services:
  blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
+    image: docker.verbis.dkfz.de/cache/samply/blaze:latest
    container_name: bridgehead-bbmri-blaze
    environment:
      BASE_URL: "http://bridgehead-bbmri-blaze:8080"
--- a/bbmri/modules/directory-sync-compose.yml
+++ b/bbmri/modules/directory-sync-compose.yml
@ -4,13 +4,7 @@ services:
  directory_sync_service:
    image: "docker.verbis.dkfz.de/cache/samply/directory_sync_service"
    environment:
-      DS_DIRECTORY_URL: ${DS_DIRECTORY_URL:-https://directory.bbmri-eric.eu}
+      DS_DIRECTORY_URL: ${DS_DIRECTORY_URL}
      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_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}
-      DS_DIRECTORY_COUNTRY: ${DS_DIRECTORY_COUNTRY}
-    depends_on:
-      - "blaze"
+      DS_DIRECTORY_PASS_CODE: ${DS_DIRECTORY_PASS_CODE}
+      DS_TIMER_CRON: ${DS_TIMER_CRON}
--- a/bbmri/modules/eric-compose.yml
+++ b/bbmri/modules/eric-compose.yml
@ -16,7 +16,7 @@ services:
      - "blaze"

  beam-proxy-eric:
-    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${BEAM_TAG}
+    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
    container_name: bridgehead-beam-proxy-eric
    environment:
      BROKER_URL: ${ERIC_BROKER_URL}
--- a/bbmri/modules/gbn-compose.yml
+++ b/bbmri/modules/gbn-compose.yml
@ -16,7 +16,7 @@ services:
      - "blaze"

  beam-proxy-gbn:
-    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${BEAM_TAG}
+    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
    container_name: bridgehead-beam-proxy-gbn
    environment:
      BROKER_URL: ${GBN_BROKER_URL}
--- a/bbmri/vars
+++ b/bbmri/vars
@ -4,7 +4,7 @@
 # Makes only sense for German Biobanks
 : ${ENABLE_GBN:=false}

-FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64}
+FOCUS_RETRY_COUNT=32
 PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem

 for module in $PROJECT/modules/*.sh
--- a/21
+++ b/21
@ -32,18 +32,6 @@ case "$PROJECT" in
 	bbmri)
 		#nothing extra to do
 		;;
-	cce)
-		#nothing extra to do
-		;;
-	itcc)
-		#nothing extra to do
-		;;
-	kr)
-		#nothing extra to do
-		;;
-	dhki)
-		#nothing extra to do
-		;;
 	minimal)
 		#nothing extra to do
 		;;
@ -82,21 +70,17 @@ loadVars() {

 	# Set some project-independent default values
 	: ${ENVIRONMENT:=production}
-	export ENVIRONMENT

 	case "$ENVIRONMENT" in
 		"production")
 			export FOCUS_TAG=main
-			export BEAM_TAG=main
 			;;
 		"test")
 			export FOCUS_TAG=develop
-			export BEAM_TAG=develop
 			;;
 		*)
 			report_error 7 "Environment \"$ENVIRONMENT\" is unknown. Assuming production. FIX THIS!"
 			export FOCUS_TAG=main
-			export BEAM_TAG=main
 			;;
 	esac
 }
@ -123,11 +107,6 @@ case "$ACTION" in
 		exit $?
 		;;
 	logs)
-		loadVars
-		shift 2
-		exec journalctl -u bridgehead@$PROJECT -u bridgehead-update@$PROJECT -a $@
-		;;
-	docker-logs)
 		loadVars
 		shift 2
 		exec $COMPOSE -p $PROJECT -f ./minimal/docker-compose.yml -f ./$PROJECT/docker-compose.yml $OVERRIDE logs -f $@
--- a/cce/docker-compose.yml
+++ b/cce/docker-compose.yml
@ -1,63 +0,0 @@
-version: "3.7"
-
-services:
-  blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
-    container_name: bridgehead-cce-blaze
-    environment:
-      BASE_URL: "http://bridgehead-cce-blaze:8080"
-      JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
-      DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
-      DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP
-      ENFORCE_REFERENTIAL_INTEGRITY: "false"
-    volumes:
-      - "blaze-data:/app/data"
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.blaze_cce.rule=PathPrefix(`/cce-localdatamanagement`)"
-      - "traefik.http.middlewares.cce_b_strip.stripprefix.prefixes=/cce-localdatamanagement"
-      - "traefik.http.services.blaze_cce.loadbalancer.server.port=8080"
-      - "traefik.http.routers.blaze_cce.middlewares=cce_b_strip,auth"
-      - "traefik.http.routers.blaze_cce.tls=true"
-
-  focus:
-    image: docker.verbis.dkfz.de/cache/samply/focus:${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-cce-blaze:8080/fhir/"
-      BEAM_PROXY_URL: http://beam-proxy:8081
-      RETRY_COUNT: ${FOCUS_RETRY_COUNT}
-      EPSILON: 0.28
-    depends_on:
-      - "beam-proxy"
-      - "blaze"
-
-  beam-proxy:
-    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${BEAM_TAG}
-    container_name: bridgehead-beam-proxy
-    environment:
-      BROKER_URL: ${BROKER_URL}
-      PROXY_ID: ${PROXY_ID}
-      APP_focus_KEY: ${FOCUS_BEAM_SECRET_SHORT}
-      PRIVKEY_FILE: /run/secrets/proxy.pem
-      ALL_PROXY: http://forward_proxy:3128
-      TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
-      ROOTCERT_FILE: /conf/root.crt.pem
-    secrets:
-      - proxy.pem
-    depends_on:
-      - "forward_proxy"
-    volumes:
-      - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
-      - /srv/docker/bridgehead/cce/root.crt.pem:/conf/root.crt.pem:ro
-
-
-volumes:
-  blaze-data:
-
-secrets:
-  proxy.pem:
-    file: /etc/bridgehead/pki/${SITE_ID}.priv.pem
--- a/cce/root.crt.pem
+++ b/cce/root.crt.pem
@ -1,20 +0,0 @@
-----BEGIN CERTIFICATE-----
-MIIDNTCCAh2gAwIBAgIUW34NEb7bl0+Ywx+I1VKtY5vpAOowDQYJKoZIhvcNAQEL
-BQAwFjEUMBIGA1UEAxMLQnJva2VyLVJvb3QwHhcNMjQwMTIyMTMzNzEzWhcNMzQw
-MTE5MTMzNzQzWjAWMRQwEgYDVQQDEwtCcm9rZXItUm9vdDCCASIwDQYJKoZIhvcN
-AQEBBQADggEPADCCAQoCggEBAL5UegLXTlq3XRRj8LyFs3aF0tpRPVoW9RXp5kFI
-TnBvyO6qjNbMDT/xK+4iDtEX4QQUvsxAKxfXbe9i1jpdwjgH7JHaSGm2IjAiKLqO
-OXQQtguWwfNmmp96Ql13ArLj458YH08xMO/w2NFWGwB/hfARa4z/T0afFuc/tKJf
-XbGCG9xzJ9tmcG45QN8NChGhVvaTweNdVxGWlpHxmi0Mn8OM9CEuB7nPtTTiBuiu
-pRC2zVVmNjVp4ktkAqL7IHOz+/F5nhiz6tOika9oD3376Xj055lPznLcTQn2+4d7
-K7ZrBopCFxIQPjkgmYRLfPejbpdUjK1UVJw7hbWkqWqH7JMCAwEAAaN7MHkwDgYD
-VR0PAQH/BAQDAgEGMA8GA1UdEwEB/wQFMAMBAf8wHQYDVR0OBBYEFGjvRcaIP4HM
-poIguUAK9YL2n7fbMB8GA1UdIwQYMBaAFGjvRcaIP4HMpoIguUAK9YL2n7fbMBYG
-A1UdEQQPMA2CC0Jyb2tlci1Sb290MA0GCSqGSIb3DQEBCwUAA4IBAQCbzycJSaDm
-AXXNJqQ88djrKs5MDXS8RIjS/cu2ayuLaYDe+BzVmUXNA0Vt9nZGdaz63SLLcjpU
-fNSxBfKbwmf7s30AK8Cnfj9q4W/BlBeVizUHQsg1+RQpDIdMrRQrwkXv8mfLw+w5
-3oaXNW6W/8KpBp/H8TBZ6myl6jCbeR3T8EMXBwipMGop/1zkbF01i98Xpqmhx2+l
-n+80ofPsSspOo5XmgCZym8CD/m/oFHmjcvOfpOCvDh4PZ+i37pmbSlCYoMpla3u/
-7MJMP5lugfLBYNDN2p+V4KbHP/cApCDT5UWLOeAWjgiZQtHH5ilDeYqEc1oPjyJt
-Rtup0MTxSJtN
-----END CERTIFICATE-----
--- a/cce/vars
+++ b/cce/vars
@ -1,14 +0,0 @@
-BROKER_ID=test-no-real-data.broker.samply.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=${FOCUS_RETRY_COUNT:-64}
-SUPPORT_EMAIL=manoj.waikar@dkfz-heidelberg.de
-PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
-BROKER_URL_FOR_PREREQ=$BROKER_URL
-
-for module in common/*.sh
-do
-    log DEBUG "sourcing $module"
-    source $module
-done
--- a/ccp/docker-compose.yml
+++ b/ccp/docker-compose.yml
@ -2,7 +2,7 @@ version: "3.7"

 services:
  blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
+    image: docker.verbis.dkfz.de/cache/samply/blaze:latest
    container_name: bridgehead-ccp-blaze
    environment:
      BASE_URL: "http://bridgehead-ccp-blaze:8080"
@ -21,7 +21,7 @@ services:
      - "traefik.http.routers.blaze_ccp.tls=true"

  focus:
-    image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
+    image: docker.verbis.dkfz.de/cache/samply/focus:0.4.4
    container_name: bridgehead-focus
    environment:
      API_KEY: ${FOCUS_BEAM_SECRET_SHORT}
@ -31,15 +31,12 @@ services:
      BEAM_PROXY_URL: http://beam-proxy:8081
      RETRY_COUNT: ${FOCUS_RETRY_COUNT}
      EPSILON: 0.28
-      QUERIES_TO_CACHE: '/queries_to_cache.conf'
-    volumes:
-      - /srv/docker/bridgehead/ccp/queries_to_cache.conf:/queries_to_cache.conf
    depends_on:
      - "beam-proxy"
      - "blaze"

  beam-proxy:
-    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${BEAM_TAG}
+    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
    container_name: bridgehead-beam-proxy
    environment:
      BROKER_URL: ${BROKER_URL}
--- a/ccp/modules/adt2fhir-rest-compose.yml
+++ b/ccp/modules/adt2fhir-rest-compose.yml
@ -0,0 +1,18 @@
+version: "3.7"
+
+services:
+  adt2fhir-rest:
+    container_name: bridgehead-adt2fhir-rest
+    image: docker.verbis.dkfz.de/ccp/adt2fhir-rest:main
+    environment:
+      IDTYPE: BK_${IDMANAGEMENT_FRIENDLY_ID}_L-ID
+      MAINZELLISTE_APIKEY: ${IDMANAGER_LOCAL_PATIENTLIST_APIKEY}
+      SALT: ${LOCAL_SALT}
+    restart: always
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.adt2fhir-rest.rule=PathPrefix(`/adt2fhir-rest`)"
+      - "traefik.http.middlewares.adt2fhir-rest_strip.stripprefix.prefixes=/adt2fhir-rest"
+      - "traefik.http.services.adt2fhir-rest.loadbalancer.server.port=8080"
+      - "traefik.http.routers.adt2fhir-rest.tls=true"
+      - "traefik.http.routers.adt2fhir-rest.middlewares=adt2fhir-rest_strip,auth"
--- a/ccp/modules/adt2fhir-rest-setup.sh
+++ b/ccp/modules/adt2fhir-rest-setup.sh
@ -0,0 +1,13 @@
+#!/bin/bash
+
+function adt2fhirRestSetup() {
+  if [ -n "$ENABLE_ADT2FHIR_REST" ]; then
+    log INFO "ADT2FHIR-REST setup detected -- will start adt2fhir-rest API."
+    if [ ! -n "$IDMANAGER_LOCAL_PATIENTLIST_APIKEY" ]; then
+      log ERROR "Missing ID-Management Module! Fix this by setting up ID Management:"
+      exit 1;
+    fi
+    OVERRIDE+=" -f ./$PROJECT/modules/adt2fhir-rest-compose.yml"
+    LOCAL_SALT="$(echo \"local-random-salt\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
+  fi
+}
--- a/ccp/modules/datashield-compose.yml
+++ b/ccp/modules/datashield-compose.yml
@ -0,0 +1,87 @@
+version: "3.7"
+
+services:
+  opal:
+    container_name: bridgehead-opal
+    image: docker.verbis.dkfz.de/ccp/dktk-opal:latest
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.opal_ccp.rule=PathPrefix(`/opal`)"
+      - "traefik.http.services.opal_ccp.loadbalancer.server.port=8080"
+      - "traefik.http.routers.opal_ccp.tls=true"
+    links:
+      - opal-rserver
+      - opal-db
+    environment:
+      JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC -Dhttps.proxyHost=forward_proxy -Dhttps.proxyPort=3128"
+      # OPAL_ADMINISTRATOR_USER: "administrator" # This line is kept for informational purposes
+      OPAL_ADMINISTRATOR_PASSWORD: "${OPAL_ADMIN_PASSWORD}"
+      POSTGRESDATA_HOST: "opal-db"
+      POSTGRESDATA_DATABASE: "opal"
+      POSTGRESDATA_USER: "opal"
+      POSTGRESDATA_PASSWORD: "${OPAL_DB_PASSWORD}"
+      ROCK_HOSTS: "opal-rserver:8085"
+      APP_URL: "https://${HOST}/opal"
+      APP_CONTEXT_PATH: "/opal"
+      OPAL_PRIVATE_KEY: "/run/secrets/opal-key.pem"
+      OPAL_CERTIFICATE: "/run/secrets/opal-cert.pem"
+      OIDC_URL: "${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}"
+      TOKEN_MANAGER_PASSWORD: "${TOKEN_MANAGER_OPAL_PASSWORD}"
+      EXPORTER_PASSWORD: "${EXPORTER_OPAL_PASSWORD}"
+      BEAM_APP_ID: token-manager.${PROXY_ID}
+      BEAM_SECRET: ${TOKEN_MANAGER_SECRET}
+      BEAM_DATASHIELD_PROXY: request-manager
+    volumes:
+      - "/var/cache/bridgehead/ccp/opal-metadata-db:/srv" # Opal metadata
+    secrets:
+      - opal-cert.pem
+      - opal-key.pem
+
+  opal-db:
+    container_name: bridgehead-opal-db
+    image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
+    environment:
+      POSTGRES_PASSWORD: "${OPAL_DB_PASSWORD}" # Set in datashield-setup.sh
+      POSTGRES_USER: "opal"
+      POSTGRES_DB: "opal"
+    volumes:
+      - "/var/cache/bridgehead/ccp/opal-db:/var/lib/postgresql/data" # Opal project data (imported from exporter)
+
+  opal-rserver:
+    container_name: bridgehead-opal-rserver
+    image: docker.verbis.dkfz.de/ccp/dktk-rserver # datashield/rock-base + dsCCPhos
+    tmpfs:
+      - /srv
+
+  beam-connect:
+    image: docker.verbis.dkfz.de/cache/samply/beam-connect:develop
+    container_name: bridgehead-datashield-connect
+    environment:
+      PROXY_URL: "http://beam-proxy:8081"
+      TLS_CA_CERTIFICATES_DIR: /run/secrets
+      APP_ID: datashield-connect.${SITE_ID}.${BROKER_ID}
+      PROXY_APIKEY: ${DATASHIELD_CONNECT_SECRET}
+      DISCOVERY_URL: "./map/central.json"
+      LOCAL_TARGETS_FILE: "./map/local.json"
+      NO_AUTH: "true"
+    secrets:
+      - opal-cert.pem
+    depends_on:
+      - beam-proxy
+    volumes:
+      - /tmp/bridgehead/opal-map/:/map/:ro
+
+  beam-proxy:
+    environment:
+      APP_datashield-connect_KEY: ${DATASHIELD_CONNECT_SECRET}
+      APP_token-manager_KEY: ${TOKEN_MANAGER_SECRET}
+
+secrets:
+  opal-cert.pem:
+    file: /tmp/bridgehead/opal-cert.pem
+  opal-key.pem:
+    file: /tmp/bridgehead/opal-key.pem
--- a/ccp/modules/datashield-setup.sh
+++ b/ccp/modules/datashield-setup.sh
@ -5,17 +5,12 @@ if [ "$ENABLE_DATASHIELD" == true ]; then
  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 "${OAUTH2_CALLBACK}"
-
  log INFO "DataSHIELD setup detected -- will start DataSHIELD services."
-  OVERRIDE+=" -f ./common/datashield-compose.yml"
+  OVERRIDE+=" -f ./$PROJECT/modules/datashield-compose.yml"
  EXPORTER_OPAL_PASSWORD="$(generate_password \"exporter in Opal\")"
  TOKEN_MANAGER_OPAL_PASSWORD="$(generate_password \"Token Manager in Opal\")"
  OPAL_DB_PASSWORD="$(echo \"Opal DB\" | generate_simple_password)"
  OPAL_ADMIN_PASSWORD="$(generate_password \"admin password for Opal\")"
-  RSTUDIO_ADMIN_PASSWORD="$(generate_password \"admin password for R-Studio\")"
  DATASHIELD_CONNECT_SECRET="$(echo \"DataShield Connect\" | generate_simple_password)"
  TOKEN_MANAGER_SECRET="$(echo \"Token Manager\" | generate_simple_password)"
  if [ ! -e /tmp/bridgehead/opal-cert.pem ]; then
@ -23,17 +18,11 @@ if [ "$ENABLE_DATASHIELD" == true ]; then
    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"
  fi
  mkdir -p /tmp/bridgehead/opal-map
-  sites="$(cat ./common/datashield-sites.json)"
-  echo "$sites" | docker_jq -n --args '{"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 '[{
-    "external": "'"$SITE_ID"':443",
+  echo '{"sites": []}' >/tmp/bridgehead/opal-map/central.json
+  echo '[{
+    "external": "'$SITE_ID':443",
    "internal": "opal:8443",
-    "allowed": input | map("\(.).'"$BROKER_ID"'")
+    "allowed": ["central-ds-orchestrator.'$BROKER_ID'"]
  }]' > /tmp/bridgehead/opal-map/local.json
  if [ "$USER" == "root" ]; then
    chown -R bridgehead:docker /tmp/bridgehead
--- a/ccp/modules/datashield-sites.json
+++ b/ccp/modules/datashield-sites.json
@ -1,15 +0,0 @@
-[
-    "berlin",
-    "muenchen-lmu",
-    "dresden",
-    "freiburg",
-    "muenchen-tum",
-    "tuebingen",
-    "mainz",
-    "frankfurt",
-    "essen",
-    "dktk-datashield-test",
-    "dktk-test",
-    "mannheim",
-    "central-ds-orchestrator"
-]
--- a/ccp/modules/datashield.md
+++ b/ccp/modules/datashield.md
@ -1,5 +1,5 @@
 # DataSHIELD
-This module constitutes the infrastructure to run DataSHIELD within the bridgehead. 
+This module constitutes the infrastructure to run DataSHIELD within the bridghead. 
 For more information about DataSHIELD, please visit https://www.datashield.org/

 ## R-Studio
--- a/ccp/modules/dnpm-compose.yml
+++ b/ccp/modules/dnpm-compose.yml
--- a/ccp/modules/dnpm-node-compose.yml
+++ b/ccp/modules/dnpm-node-compose.yml
--- a/ccp/modules/dnpm-node-setup.sh
+++ b/ccp/modules/dnpm-node-setup.sh
@ -2,7 +2,7 @@

 if [ -n "${ENABLE_DNPM_NODE}" ]; then
 	log INFO "DNPM setup detected (BwHC Node) -- will start BwHC node."
-	OVERRIDE+=" -f ./common/dnpm-node-compose.yml"
+	OVERRIDE+=" -f ./$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)"
--- a/ccp/modules/dnpm-setup.sh
+++ b/ccp/modules/dnpm-setup.sh
@ -2,7 +2,7 @@

 if [ -n "${ENABLE_DNPM}" ]; then
 	log INFO "DNPM setup detected (Beam.Connect) -- will start Beam.Connect for DNPM."
-	OVERRIDE+=" -f ./common/dnpm-compose.yml"
+	OVERRIDE+=" -f ./$PROJECT/modules/dnpm-compose.yml"

 	# Set variables required for Beam-Connect
 	DNPM_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
--- a/ccp/modules/exporter-compose.yml
+++ b/ccp/modules/exporter-compose.yml
@ -65,3 +65,16 @@ services:
      - "traefik.http.routers.reporter_ccp.tls=true"
      - "traefik.http.middlewares.reporter_ccp_strip.stripprefix.prefixes=/ccp-reporter"
      - "traefik.http.routers.reporter_ccp.middlewares=reporter_ccp_strip"
+
+  file-dispatcher:
+    image: docker.verbis.dkfz.de/cache/samply/file-dispatcher:latest
+    environment:
+      - BEAM_ID=file-dispatcher.${PROXY_ID}
+      - PROJECT_MANAGER_ID=project-manager.request-manager.${BROKER_ID}
+      - BEAM_SECRET=${FILE_DISPATCHER_BEAM_SECRET} # Generated in exporter-setup.sh
+      - BEAM_URL=http://beam-proxy:8081
+      - EXPORTER_URL=http://exporter:8092
+  
+  beam-proxy:
+    environment:
+      - APP_file-dispatcher_KEY=${FILE_DISPATCHER_BEAM_SECRET}
--- a/ccp/modules/exporter-setup.sh
+++ b/ccp/modules/exporter-setup.sh
@ -2,7 +2,8 @@

 if [ "$ENABLE_EXPORTER" == true ]; then
  log INFO "Exporter setup detected -- will start Exporter service."
-  OVERRIDE+=" -f ./common/exporter-compose.yml"
+  OVERRIDE+=" -f ./$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)"
+  FILE_DISPATCHER_BEAM_SECRET="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
 fi
--- a/ccp/modules/exporter.md
+++ b/ccp/modules/exporter.md
--- a/ccp/modules/id-management-compose.yml
+++ b/ccp/modules/id-management-compose.yml
@ -14,22 +14,21 @@ services:
      MAGICPL_CONNECTOR_APIKEY: ${IDMANAGER_READ_APIKEY}
      MAGICPL_CENTRAL_PATIENTLIST_APIKEY: ${IDMANAGER_CENTRAL_PATIENTLIST_APIKEY}
      MAGICPL_CONTROLNUMBERGENERATOR_APIKEY: ${IDMANAGER_CONTROLNUMBERGENERATOR_APIKEY}
+      MAGICPL_OIDC_CLIENT_ID: ${IDMANAGER_AUTH_CLIENT_ID}
+      MAGICPL_OIDC_CLIENT_SECRET: ${IDMANAGER_AUTH_CLIENT_SECRET}
    depends_on:
      - patientlist
-      - traefik-forward-auth
    labels:
      - "traefik.enable=true"
      - "traefik.http.routers.id-manager.rule=PathPrefix(`/id-manager`)"
      - "traefik.http.services.id-manager.loadbalancer.server.port=8080"
      - "traefik.http.routers.id-manager.tls=true"
-      - "traefik.http.routers.id-manager.middlewares=traefik-forward-auth-idm"

  patientlist:
    image: docker.verbis.dkfz.de/bridgehead/mainzelliste
    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}
@ -56,41 +55,5 @@ services:
      # NOTE: Add backups here. This is only imported if /var/lib/bridgehead/data/patientlist/ is empty!!!
      - "/tmp/bridgehead/patientlist/:/docker-entrypoint-initdb.d/"

-  traefik-forward-auth:
-    image: docker.verbis.dkfz.de/cache/oauth2-proxy/oauth2-proxy:v7.6.0
-    environment:
-      - http_proxy=http://forward_proxy:3128
-      - https_proxy=http://forward_proxy:3128
-      - OAUTH2_PROXY_PROVIDER=oidc
-      - OAUTH2_PROXY_SKIP_PROVIDER_BUTTON=true
-      - OAUTH2_PROXY_OIDC_ISSUER_URL=https://login.verbis.dkfz.de/realms/master
-      - OAUTH2_PROXY_CLIENT_ID=bridgehead-${SITE_ID}
-      - OAUTH2_PROXY_CLIENT_SECRET=${IDMANAGER_AUTH_CLIENT_SECRET}
-      - OAUTH2_PROXY_COOKIE_SECRET=${IDMANAGER_AUTH_COOKIE_SECRET}
-      - OAUTH2_PROXY_COOKIE_DOMAINS=.${HOST}
-      - OAUTH2_PROXY_HTTP_ADDRESS=:4180
-      - OAUTH2_PROXY_REVERSE_PROXY=true
-      - OAUTH2_PROXY_WHITELIST_DOMAINS=.${HOST}
-      - OAUTH2_PROXY_UPSTREAMS=static://202
-      - OAUTH2_PROXY_EMAIL_DOMAINS=*
-      - OAUTH2_PROXY_SCOPE=openid profile email
-      # Pass Authorization Header and some user information to backend services
-      - OAUTH2_PROXY_SET_AUTHORIZATION_HEADER=true
-      - OAUTH2_PROXY_SET_XAUTHREQUEST=true
-      # Keycloak has an expiration time of 60s therefore oauth2-proxy needs to refresh after that
-      - OAUTH2_PROXY_COOKIE_REFRESH=60s
-      - OAUTH2_PROXY_ALLOWED_GROUPS=DKTK-CCP-PPSN
-      - OAUTH2_PROXY_PROXY_PREFIX=/oauth2-idm
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.services.traefik-forward-auth.loadbalancer.server.port=4180"
-      - "traefik.http.routers.traefik-forward-auth.rule=Host(`${HOST}`) && PathPrefix(`/oauth2-idm`)"
-      - "traefik.http.routers.traefik-forward-auth.tls=true"
-      - "traefik.http.middlewares.traefik-forward-auth-idm.forwardauth.address=http://traefik-forward-auth:4180"
-      - "traefik.http.middlewares.traefik-forward-auth-idm.forwardauth.authResponseHeaders=Authorization"
-    depends_on:
-      forward_proxy:
-        condition: service_healthy
-
 volumes:
  patientlist-db-data:
--- a/ccp/modules/id-management-setup.sh
+++ b/ccp/modules/id-management-setup.sh
@ -3,7 +3,7 @@
 function idManagementSetup() {
 	if [ -n "$IDMANAGER_UPLOAD_APIKEY" ]; then
 		log INFO "id-management setup detected -- will start id-management (mainzelliste & magicpl)."
-		OVERRIDE+=" -f ./common/id-management-compose.yml"
+		OVERRIDE+=" -f ./$PROJECT/modules/id-management-compose.yml"

 		# Auto Generate local Passwords
 		PATIENTLIST_POSTGRES_PASSWORD="$(echo \"id-management-module-db-password-salt\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
--- a/ccp/modules/id-management.md
+++ b/ccp/modules/id-management.md
--- a/ccp/modules/mtba-compose.yml
+++ b/ccp/modules/mtba-compose.yml
--- a/ccp/modules/mtba-setup.sh
+++ b/ccp/modules/mtba-setup.sh
@ -5,8 +5,9 @@ function mtbaSetup() {
    log INFO "MTBA setup detected -- will start MTBA Service and CBioPortal."
    if [ ! -n "$IDMANAGER_UPLOAD_APIKEY" ]; then
      log ERROR "Missing ID-Management Module! Fix this by setting up ID Management:"
+      exit 1;
    fi
-    OVERRIDE+=" -f ./common/mtba-compose.yml"
+    OVERRIDE+=" -f ./$PROJECT/modules/mtba-compose.yml"
    add_private_oidc_redirect_url "/mtba/*"
  fi
 }
--- a/ccp/modules/mtba.md
+++ b/ccp/modules/mtba.md
--- a/ccp/modules/nngm-compose.yml
+++ b/ccp/modules/nngm-compose.yml
--- a/ccp/modules/nngm-setup.sh
+++ b/ccp/modules/nngm-setup.sh
@ -2,5 +2,5 @@

 if [ -n "$NNGM_CTS_APIKEY" ]; then
  log INFO "nNGM setup detected -- will start nNGM Connector."
-  OVERRIDE+=" -f ./common/nngm-compose.yml"
+  OVERRIDE+=" -f ./$PROJECT/modules/nngm-compose.yml"
 fi
--- a/ccp/modules/teiler-compose.yml
+++ b/ccp/modules/teiler-compose.yml
--- a/ccp/modules/teiler-setup.sh
+++ b/ccp/modules/teiler-setup.sh
@ -2,7 +2,7 @@

 if [ "$ENABLE_TEILER" == true ];then
  log INFO "Teiler setup detected -- will start Teiler services."
-  OVERRIDE+=" -f ./common/teiler-compose.yml"
+  OVERRIDE+=" -f ./$PROJECT/modules/teiler-compose.yml"
  TEILER_DEFAULT_LANGUAGE=DE
  TEILER_DEFAULT_LANGUAGE_LOWER_CASE=${TEILER_DEFAULT_LANGUAGE,,}
  add_public_oidc_redirect_url "/ccp-teiler/*"
--- a/ccp/modules/teiler.md
+++ b/ccp/modules/teiler.md
--- a/ccp/queries_to_cache.conf
+++ b/ccp/queries_to_cache.conf
@ -1,2 +0,0 @@
-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
-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
--- a/ccp/vars
+++ b/ccp/vars
@ -2,7 +2,7 @@ BROKER_ID=broker.ccp-it.dktk.dkfz.de
 BROKER_URL=https://${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}
+FOCUS_RETRY_COUNT=32
 SUPPORT_EMAIL=support-ccp@dkfz-heidelberg.de
 PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem

@ -20,7 +20,7 @@ OIDC_GROUP_CLAIM="groups"

 POSTGRES_TAG=15.6-alpine

-for module in common/*.sh
+for module in $PROJECT/modules/*.sh
 do
    log DEBUG "sourcing $module"
    source $module
@ -28,5 +28,4 @@ done

 idManagementSetup
 mtbaSetup
-obds2fhirRestSetup
-blazeSecondarySetup
+adt2fhirRestSetup
--- a/common/blaze-secondary-compose.yml
+++ b/common/blaze-secondary-compose.yml
@ -1,32 +0,0 @@
-version: "3.7"
-
-services:
-  blaze-secondary:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
-    container_name: bridgehead-ccp-blaze-secondary
-    environment:
-      BASE_URL: "http://bridgehead-ccp-blaze-secondary:8080"
-      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
-      ENFORCE_REFERENTIAL_INTEGRITY: "false"
-    volumes:
-      - "blaze-secondary-data:/app/data"
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.blaze-secondary_ccp.rule=PathPrefix(`/ccp-localdatamanagement-secondary`)"
-      - "traefik.http.middlewares.ccp_b-secondary_strip.stripprefix.prefixes=/ccp-localdatamanagement-secondary"
-      - "traefik.http.services.blaze-secondary_ccp.loadbalancer.server.port=8080"
-      - "traefik.http.routers.blaze-secondary_ccp.middlewares=ccp_b-secondary_strip,auth"
-      - "traefik.http.routers.blaze-secondary_ccp.tls=true"
-
-  obds2fhir-rest:
-    environment:
-      STORE_PATH: ${STORE_PATH:-http://blaze:8080/fhir}
-
-  exporter:
-    environment:
-      BLAZE_HOST: "blaze-secondary"
-
-volumes:
-  blaze-secondary-data:
--- a/common/blaze-secondary-setup.sh
+++ b/common/blaze-secondary-setup.sh
@ -1,11 +0,0 @@
-#!/bin/bash
-
-function blazeSecondarySetup() {
-  if [ -n "$ENABLE_SECONDARY_BLAZE" ]; then
-    log INFO "Secondary Blaze setup detected -- will start second blaze."
-    OVERRIDE+=" -f ./common/blaze-secondary-compose.yml"
-    #make oBDS2FHIR ignore ID-Management and replace target Blaze
-    PATIENTLIST_URL=" "
-    STORE_PATH="http://blaze-secondary:8080/fhir"
-  fi
-}
--- a/common/datashield-compose.yml
+++ b/common/datashield-compose.yml
@ -1,171 +0,0 @@
-version: "3.7"
-
-services:
-  rstudio:
-    container_name: bridgehead-rstudio
-    image: docker.verbis.dkfz.de/ccp/dktk-rstudio:latest
-    environment:
-      #DEFAULT_USER: "rstudio" # This line is kept for informational purposes
-      PASSWORD: "${RSTUDIO_ADMIN_PASSWORD}" # It is required, even if the authentication is disabled
-      DISABLE_AUTH: "true" # https://rocker-project.org/images/versioned/rstudio.html#how-to-use
-      HTTP_RELATIVE_PATH: "/rstudio"
-      ALL_PROXY: "http://forward_proxy:3128" # https://rocker-project.org/use/networking.html
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.rstudio_ccp.rule=PathPrefix(`/rstudio`)"
-      - "traefik.http.services.rstudio_ccp.loadbalancer.server.port=8787"
-      - "traefik.http.middlewares.rstudio_ccp_strip.stripprefix.prefixes=/rstudio"
-      - "traefik.http.routers.rstudio_ccp.tls=true"
-      - "traefik.http.routers.rstudio_ccp.middlewares=oidcAuth,rstudio_ccp_strip"
-    networks:
-      - rstudio
-
-  opal:
-    container_name: bridgehead-opal
-    image: docker.verbis.dkfz.de/ccp/dktk-opal:latest
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.opal_ccp.rule=PathPrefix(`/opal`)"
-      - "traefik.http.services.opal_ccp.loadbalancer.server.port=8080"
-      - "traefik.http.routers.opal_ccp.tls=true"
-    links:
-      - opal-rserver
-      - opal-db
-    environment:
-      JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC -Dhttps.proxyHost=forward_proxy -Dhttps.proxyPort=3128"
-      # OPAL_ADMINISTRATOR_USER: "administrator" # This line is kept for informational purposes
-      OPAL_ADMINISTRATOR_PASSWORD: "${OPAL_ADMIN_PASSWORD}"
-      POSTGRESDATA_HOST: "opal-db"
-      POSTGRESDATA_DATABASE: "opal"
-      POSTGRESDATA_USER: "opal"
-      POSTGRESDATA_PASSWORD: "${OPAL_DB_PASSWORD}"
-      ROCK_HOSTS: "opal-rserver:8085"
-      APP_URL: "https://${HOST}/opal"
-      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: "${OIDC_ADMIN_GROUP}"
-      TOKEN_MANAGER_PASSWORD: "${TOKEN_MANAGER_OPAL_PASSWORD}"
-      EXPORTER_PASSWORD: "${EXPORTER_OPAL_PASSWORD}"
-      BEAM_APP_ID: token-manager.${PROXY_ID}
-      BEAM_SECRET: ${TOKEN_MANAGER_SECRET}
-      BEAM_DATASHIELD_PROXY: request-manager
-    volumes:
-      - "/var/cache/bridgehead/ccp/opal-metadata-db:/srv" # Opal metadata
-    secrets:
-      - opal-cert.pem
-      - opal-key.pem
-
-  opal-db:
-    container_name: bridgehead-opal-db
-    image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
-    environment:
-      POSTGRES_PASSWORD: "${OPAL_DB_PASSWORD}" # Set in datashield-setup.sh
-      POSTGRES_USER: "opal"
-      POSTGRES_DB: "opal"
-    volumes:
-      - "/var/cache/bridgehead/ccp/opal-db:/var/lib/postgresql/data" # Opal project data (imported from exporter)
-
-  opal-rserver:
-    container_name: bridgehead-opal-rserver
-    image: docker.verbis.dkfz.de/ccp/dktk-rserver # datashield/rock-base + dsCCPhos
-    tmpfs:
-      - /srv
-
-  beam-connect:
-    image: docker.verbis.dkfz.de/cache/samply/beam-connect:develop
-    container_name: bridgehead-datashield-connect
-    environment:
-      PROXY_URL: "http://beam-proxy:8081"
-      TLS_CA_CERTIFICATES_DIR: /run/secrets
-      APP_ID: datashield-connect.${SITE_ID}.${BROKER_ID}
-      PROXY_APIKEY: ${DATASHIELD_CONNECT_SECRET}
-      DISCOVERY_URL: "./map/central.json"
-      LOCAL_TARGETS_FILE: "./map/local.json"
-      NO_AUTH: "true"
-    secrets:
-      - opal-cert.pem
-    depends_on:
-      - beam-proxy
-    volumes:
-      - /tmp/bridgehead/opal-map/:/map/:ro
-    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
-  forward_proxy:
-    networks:
-      - default
-      - rstudio
-
-  beam-proxy:
-    environment:
-      APP_datashield-connect_KEY: ${DATASHIELD_CONNECT_SECRET}
-      APP_token-manager_KEY: ${TOKEN_MANAGER_SECRET}
-
-  # TODO: Allow users of group /DataSHIELD and OIDC_USER_GROUP at the same time:
-  # Maybe a solution would be (https://oauth2-proxy.github.io/oauth2-proxy/configuration/oauth_provider):
-  # --allowed-groups=/DataSHIELD,OIDC_USER_GROUP
-  oauth2-proxy:
-    image: docker.verbis.dkfz.de/cache/oauth2-proxy/oauth2-proxy:latest
-    container_name: bridgehead-oauth2proxy
-    command: >-
-      --allowed-group=DataSHIELD
-      --oidc-groups-claim=${OIDC_GROUP_CLAIM}
-      --auth-logging=true
-      --whitelist-domain=${HOST}
-      --http-address="0.0.0.0:4180"
-      --reverse-proxy=true
-      --upstream="static://202"
-      --email-domain="*"
-      --cookie-name="_BRIDGEHEAD_oauth2"
-      --cookie-secret="${OAUTH2_PROXY_SECRET}"
-      --cookie-expire="12h"
-      --cookie-secure="true"
-      --cookie-httponly="true"
-      #OIDC settings
-      --provider="keycloak-oidc"
-      --provider-display-name="VerbIS Login"
-      --client-id="${OIDC_PRIVATE_CLIENT_ID}"
-      --client-secret="${OIDC_CLIENT_SECRET}"
-      --redirect-url="https://${HOST}${OAUTH2_CALLBACK}"
-      --oidc-issuer-url="${OIDC_ISSUER_URL}"
-      --scope="openid email profile"
-      --code-challenge-method="S256"
-      --skip-provider-button=true
-      #X-Forwarded-Header settings - true/false depending on your needs
-      --pass-basic-auth=true
-      --pass-user-headers=false
-      --pass-access-token=false
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.oauth2_proxy.rule=Host(`${HOST}`) && PathPrefix(`/oauth2`)"
-      - "traefik.http.services.oauth2_proxy.loadbalancer.server.port=4180"
-      - "traefik.http.routers.oauth2_proxy.tls=true"
-    environment:
-      http_proxy: "http://forward_proxy:3128"
-      https_proxy: "http://forward_proxy:3128"
-    depends_on:
-      forward_proxy:
-        condition: service_healthy
-
-secrets:
-  opal-cert.pem:
-    file: /tmp/bridgehead/opal-cert.pem
-  opal-key.pem:
-    file: /tmp/bridgehead/opal-key.pem
-
-networks:
-  rstudio:
--- a/common/datashield-sites.json
+++ b/common/datashield-sites.json
@ -1,15 +0,0 @@
-[
-    "berlin",
-    "muenchen-lmu",
-    "dresden",
-    "freiburg",
-    "muenchen-tum",
-    "tuebingen",
-    "mainz",
-    "frankfurt",
-    "essen",
-    "dktk-datashield-test",
-    "dktk-test",
-    "mannheim",
-    "central-ds-orchestrator"
-]
--- a/common/export-and-qb.curl-templates
+++ b/common/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'
--- a/common/fhir2sql-compose.yml
+++ b/common/fhir2sql-compose.yml
@ -1,25 +0,0 @@
-version: "3.7"
-
-services:
-  fhir2sql:
-    depends_on:
-      - "dashboard-db"
-      - "blaze"
-    image: docker.verbis.dkfz.de/cache/samply/fhir2sql:latest
-    container_name: bridgehead-ccp-dashboard-fhir2sql
-    environment:
-      BLAZE_BASE_URL: "http://bridgehead-ccp-blaze:8080"
-      PG_HOST: "dashboard-db"
-      PG_USERNAME: "dashboard"
-      PG_PASSWORD: "${DASHBOARD_DB_PASSWORD}" # Set in dashboard-setup.sh
-      PG_DBNAME: "dashboard"
-
-  dashboard-db:
-    image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
-    container_name: bridgehead-ccp-dashboard-db
-    environment:
-      POSTGRES_USER: "dashboard"
-      POSTGRES_PASSWORD: "${DASHBOARD_DB_PASSWORD}" # Set in dashboard-setup.sh
-      POSTGRES_DB: "dashboard"
-    volumes:
-      - "/var/cache/bridgehead/ccp/dashboard-db:/var/lib/postgresql/data"
--- a/common/fhir2sql-setup.sh
+++ b/common/fhir2sql-setup.sh
@ -1,7 +0,0 @@
-#!/bin/bash -e
-
-if [ "$ENABLE_FHIR2SQL" == true ]; then
-  log INFO "Dashboard setup detected -- will start Dashboard backend and FHIR2SQL service."
-  OVERRIDE+=" -f ./common/fhir2sql-compose.yml"
-  DASHBOARD_DB_PASSWORD="$(generate_simple_password 'fhir2sql')"
-fi
--- a/common/fhir2sql.md
+++ b/common/fhir2sql.md
@ -1,36 +0,0 @@
-# fhir2sql
-fhir2sql connects to Blaze, retrieves data, and syncs it with a PostgreSQL database. The application is designed to run continuously, syncing data at regular intervals.
-The Dashboard module is a optional component of the Bridgehead CCP setup. When enabled, it starts two Docker services: **fhir2sql** and **dashboard-db**. Data held in PostgreSQL is only stored temporarily and Blaze is considered to be the 'leading system' or 'source of truth'.
-
-## Services
-### fhir2sql
-* Image: docker.verbis.dkfz.de/cache/samply/fhir2sql:latest
-* Container name: bridgehead-ccp-dashboard-fhir2sql
-* Depends on: dashboard-db
-* Environment variables:
-  - BLAZE_BASE_URL: The base URL of the Blaze FHIR server (set to http://blaze:8080/fhir/)
-  - PG_HOST: The hostname of the PostgreSQL database (set to dashboard-db)
-  - PG_USERNAME: The username for the PostgreSQL database (set to dashboard)
-  - PG_PASSWORD: The password for the PostgreSQL database (set to the value of DASHBOARD_DB_PASSWORD)
-  - PG_DBNAME: The name of the PostgreSQL database (set to dashboard)
-
-### dashboard-db
-
-* Image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
-* Container name: bridgehead-ccp-dashboard-db
-* Environment variables:
-  - POSTGRES_USER: The username for the PostgreSQL database (set to dashboard)
-  - POSTGRES_PASSWORD: The password for the PostgreSQL database (set to the value of DASHBOARD_DB_PASSWORD)
-  - POSTGRES_DB: The name of the PostgreSQL database (set to dashboard)
-* Volumes:
-  - /var/cache/bridgehead/ccp/dashboard-db:/var/lib/postgresql/data
-
-The volume used by dashboard-db can be removed safely and should be restored to a working order by re-importing data from Blaze.
-
-### Environment Variables
-* DASHBOARD_DB_PASSWORD: A generated password for the PostgreSQL database, created using a salt string and the SHA1 hash function.
-* POSTGRES_TAG: The tag of the PostgreSQL image to use (not set in this module, but required by the dashboard-db service).
-
-
-### Setup
-To enable the Dashboard module, set the ENABLE_FHIR2SQL environment variable to true. The dashboard-setup.sh script will then start the fhir2sql and dashboard-db services, using the environment variables and volumes defined above.
--- a/common/lens-compose.yml
+++ b/common/lens-compose.yml
@ -1,33 +0,0 @@
-version: "3.7"
-services:
-  landing:
-    container_name: lens_federated-search
-    image: docker.verbis.dkfz.de/ccp/lens:${SITE_ID}
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.landing.rule=PathPrefix(`/`)"
-      - "traefik.http.services.landing.loadbalancer.server.port=80"
-      - "traefik.http.routers.landing.tls=true"
-
-  spot:
-    image: docker.verbis.dkfz.de/ccp-private/central-spot
-    environment:
-      BEAM_SECRET: "${FOCUS_BEAM_SECRET_SHORT}"
-      BEAM_URL: http://beam-proxy:8081
-      BEAM_PROXY_ID: ${SITE_ID}
-      BEAM_BROKER_ID: ${BROKER_ID}
-      BEAM_APP_ID: "focus"
-      PROJECT_METADATA: "dktk_supervisors"
-    depends_on:
-      - "beam-proxy"
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.services.spot.loadbalancer.server.port=8080"
-      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowmethods=GET,OPTIONS,POST"
-      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolalloworiginlist=https://${HOST}"
-      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowcredentials=true"
-      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolmaxage=-1"
-      - "traefik.http.routers.spot.rule=Host(`${HOST}`) && PathPrefix(`/backend`)"
-      - "traefik.http.middlewares.stripprefix_spot.stripprefix.prefixes=/backend"
-      - "traefik.http.routers.spot.tls=true"
-      - "traefik.http.routers.spot.middlewares=corsheaders2,stripprefix_spot"
--- a/common/lens-setup.sh
+++ b/common/lens-setup.sh
@ -1,5 +0,0 @@
-#!/bin/bash
-
-if [ -n "$ENABLE_LENS" ];then
-  OVERRIDE+=" -f ./common/lens-compose.yml"
-fi
--- a/common/obds2fhir-rest-compose.yml
+++ b/common/obds2fhir-rest-compose.yml
@ -1,20 +0,0 @@
-version: "3.7"
-
-services:
-  obds2fhir-rest:
-    container_name: bridgehead-obds2fhir-rest
-    image: docker.verbis.dkfz.de/ccp/obds2fhir-rest:main
-    environment:
-      IDTYPE: BK_${IDMANAGEMENT_FRIENDLY_ID}_L-ID
-      MAINZELLISTE_APIKEY: ${IDMANAGER_LOCAL_PATIENTLIST_APIKEY}
-      SALT: ${LOCAL_SALT}
-      KEEP_INTERNAL_ID: ${KEEP_INTERNAL_ID:-false}
-      MAINZELLISTE_URL: ${PATIENTLIST_URL:-http://patientlist:8080/patientlist}
-    restart: always
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.obds2fhir-rest.rule=PathPrefix(`/obds2fhir-rest`) || PathPrefix(`/adt2fhir-rest`)"
-      - "traefik.http.middlewares.obds2fhir-rest_strip.stripprefix.prefixes=/obds2fhir-rest,/adt2fhir-rest"
-      - "traefik.http.services.obds2fhir-rest.loadbalancer.server.port=8080"
-      - "traefik.http.routers.obds2fhir-rest.tls=true"
-      - "traefik.http.routers.obds2fhir-rest.middlewares=obds2fhir-rest_strip,auth"
--- a/common/obds2fhir-rest-setup.sh
+++ b/common/obds2fhir-rest-setup.sh
@ -1,13 +0,0 @@
-#!/bin/bash
-
-function obds2fhirRestSetup() {
-  if [ -n "$ENABLE_OBDS2FHIR_REST" ]; then
-    log INFO "oBDS2FHIR-REST setup detected -- will start obds2fhir-rest module."
-    if [ ! -n "$IDMANAGER_UPLOAD_APIKEY" ]; then
-      log ERROR "Missing ID-Management Module! Fix this by setting up ID Management:"
-      PATIENTLIST_URL=" "
-    fi
-    OVERRIDE+=" -f ./common/obds2fhir-rest-compose.yml"
-    LOCAL_SALT="$(echo \"local-random-salt\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
-  fi
-}
--- a/dhki/docker-compose.yml
+++ b/dhki/docker-compose.yml
@ -1,66 +0,0 @@
-version: "3.7"
-
-services:
-  blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
-    container_name: bridgehead-dhki-blaze
-    environment:
-      BASE_URL: "http://bridgehead-dhki-blaze:8080"
-      JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
-      DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
-      DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP
-      ENFORCE_REFERENTIAL_INTEGRITY: "false"
-    volumes:
-      - "blaze-data:/app/data"
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.blaze_dhki.rule=PathPrefix(`/dhki-localdatamanagement`)"
-      - "traefik.http.middlewares.dhki_b_strip.stripprefix.prefixes=/dhki-localdatamanagement"
-      - "traefik.http.services.blaze_dhki.loadbalancer.server.port=8080"
-      - "traefik.http.routers.blaze_dhki.middlewares=dhki_b_strip,auth"
-      - "traefik.http.routers.blaze_dhki.tls=true"
-
-  focus:
-    image: docker.verbis.dkfz.de/cache/samply/focus:${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-dhki-blaze:8080/fhir/"
-      BEAM_PROXY_URL: http://beam-proxy:8081
-      RETRY_COUNT: ${FOCUS_RETRY_COUNT}
-      EPSILON: 0.28
-      QUERIES_TO_CACHE: '/queries_to_cache.conf'
-    volumes:
-      - /srv/docker/bridgehead/dhki/queries_to_cache.conf:/queries_to_cache.conf
-    depends_on:
-      - "beam-proxy"
-      - "blaze"
-
-  beam-proxy:
-    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
-    container_name: bridgehead-beam-proxy
-    environment:
-      BROKER_URL: ${BROKER_URL}
-      PROXY_ID: ${PROXY_ID}
-      APP_focus_KEY: ${FOCUS_BEAM_SECRET_SHORT}
-      PRIVKEY_FILE: /run/secrets/proxy.pem
-      ALL_PROXY: http://forward_proxy:3128
-      TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
-      ROOTCERT_FILE: /conf/root.crt.pem
-    secrets:
-      - proxy.pem
-    depends_on:
-      - "forward_proxy"
-    volumes:
-      - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
-      - /srv/docker/bridgehead/dhki/root.crt.pem:/conf/root.crt.pem:ro
-
-
-volumes:
-  blaze-data:
-
-secrets:
-  proxy.pem:
-    file: /etc/bridgehead/pki/${SITE_ID}.priv.pem
--- a/dhki/queries_to_cache.conf
+++ b/dhki/queries_to_cache.conf
@ -1,2 +0,0 @@
-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
-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
--- a/dhki/root.crt.pem
+++ b/dhki/root.crt.pem
@ -1,20 +0,0 @@
-----BEGIN CERTIFICATE-----
-MIIDNTCCAh2gAwIBAgIUSWUPebUMNfJvPKMjdgX+WiH+OXgwDQYJKoZIhvcNAQEL
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-eG0eKFUS0REJ
-----END CERTIFICATE-----
--- a/dhki/vars
+++ b/dhki/vars
@ -1,20 +0,0 @@
-BROKER_ID=broker.hector.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=${FOCUS_RETRY_COUNT:-64}
-SUPPORT_EMAIL=support-ccp@dkfz-heidelberg.de
-PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
-
-BROKER_URL_FOR_PREREQ=$BROKER_URL
-
-POSTGRES_TAG=15.6-alpine
-
-for module in common/*.sh
-do
-    log DEBUG "sourcing $module"
-    source $module
-done
-
-idManagementSetup
-obds2fhirRestSetup
--- a/itcc/docker-compose.yml
+++ b/itcc/docker-compose.yml
@ -1,63 +0,0 @@
-version: "3.7"
-
-services:
-  blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
-    container_name: bridgehead-itcc-blaze
-    environment:
-      BASE_URL: "http://bridgehead-itcc-blaze:8080"
-      JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
-      DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
-      DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP
-      ENFORCE_REFERENTIAL_INTEGRITY: "false"
-    volumes:
-      - "blaze-data:/app/data"
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.blaze_itcc.rule=PathPrefix(`/itcc-localdatamanagement`)"
-      - "traefik.http.middlewares.itcc_b_strip.stripprefix.prefixes=/itcc-localdatamanagement"
-      - "traefik.http.services.blaze_itcc.loadbalancer.server.port=8080"
-      - "traefik.http.routers.blaze_itcc.middlewares=itcc_b_strip,auth"
-      - "traefik.http.routers.blaze_itcc.tls=true"
-
-  focus:
-    image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
-    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-itcc-blaze:8080/fhir/"
-      BEAM_PROXY_URL: http://beam-proxy:8081
-      RETRY_COUNT: ${FOCUS_RETRY_COUNT}
-      EPSILON: 0.28
-    depends_on:
-      - "beam-proxy"
-      - "blaze"
-
-  beam-proxy:
-    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${BEAM_TAG}
-    container_name: bridgehead-beam-proxy
-    environment:
-      BROKER_URL: ${BROKER_URL}
-      PROXY_ID: ${PROXY_ID}
-      APP_focus_KEY: ${FOCUS_BEAM_SECRET_SHORT}
-      PRIVKEY_FILE: /run/secrets/proxy.pem
-      ALL_PROXY: http://forward_proxy:3128
-      TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
-      ROOTCERT_FILE: /conf/root.crt.pem
-    secrets:
-      - proxy.pem
-    depends_on:
-      - "forward_proxy"
-    volumes:
-      - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
-      - /srv/docker/bridgehead/itcc/root.crt.pem:/conf/root.crt.pem:ro
-
-
-volumes:
-  blaze-data:
-
-secrets:
-  proxy.pem:
-    file: /etc/bridgehead/pki/${SITE_ID}.priv.pem
--- a/itcc/root.crt.pem
+++ b/itcc/root.crt.pem
@ -1,20 +0,0 @@
-----BEGIN CERTIFICATE-----
-MIIDNTCCAh2gAwIBAgIUW34NEb7bl0+Ywx+I1VKtY5vpAOowDQYJKoZIhvcNAQEL
-BQAwFjEUMBIGA1UEAxMLQnJva2VyLVJvb3QwHhcNMjQwMTIyMTMzNzEzWhcNMzQw
-MTE5MTMzNzQzWjAWMRQwEgYDVQQDEwtCcm9rZXItUm9vdDCCASIwDQYJKoZIhvcN
-AQEBBQADggEPADCCAQoCggEBAL5UegLXTlq3XRRj8LyFs3aF0tpRPVoW9RXp5kFI
-TnBvyO6qjNbMDT/xK+4iDtEX4QQUvsxAKxfXbe9i1jpdwjgH7JHaSGm2IjAiKLqO
-OXQQtguWwfNmmp96Ql13ArLj458YH08xMO/w2NFWGwB/hfARa4z/T0afFuc/tKJf
-XbGCG9xzJ9tmcG45QN8NChGhVvaTweNdVxGWlpHxmi0Mn8OM9CEuB7nPtTTiBuiu
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-n+80ofPsSspOo5XmgCZym8CD/m/oFHmjcvOfpOCvDh4PZ+i37pmbSlCYoMpla3u/
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-Rtup0MTxSJtN
-----END CERTIFICATE-----
--- a/itcc/vars
+++ b/itcc/vars
@ -1,14 +0,0 @@
-BROKER_ID=test-no-real-data.broker.samply.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=${FOCUS_RETRY_COUNT:-64}
-SUPPORT_EMAIL=arturo.macias@dkfz-heidelberg.de
-PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
-BROKER_URL_FOR_PREREQ=$BROKER_URL
-
-for module in common/*.sh
-do
-    log DEBUG "sourcing $module"
-    source $module
-done
--- a/kr/docker-compose.yml
+++ b/kr/docker-compose.yml
@ -1,63 +0,0 @@
-version: "3.7"
-
-services:
-  blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
-    container_name: bridgehead-kr-blaze
-    environment:
-      BASE_URL: "http://bridgehead-kr-blaze:8080"
-      JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
-      DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
-      DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP
-      ENFORCE_REFERENTIAL_INTEGRITY: "false"
-    volumes:
-      - "blaze-data:/app/data"
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.blaze_kr.rule=PathPrefix(`/kr-localdatamanagement`)"
-      - "traefik.http.middlewares.kr_b_strip.stripprefix.prefixes=/kr-localdatamanagement"
-      - "traefik.http.services.blaze_kr.loadbalancer.server.port=8080"
-      - "traefik.http.routers.blaze_kr.middlewares=kr_b_strip,auth"
-      - "traefik.http.routers.blaze_kr.tls=true"
-
-  focus:
-    image: docker.verbis.dkfz.de/cache/samply/focus:${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-kr-blaze:8080/fhir/"
-      BEAM_PROXY_URL: http://beam-proxy:8081
-      RETRY_COUNT: ${FOCUS_RETRY_COUNT}
-      EPSILON: 0.28
-    depends_on:
-      - "beam-proxy"
-      - "blaze"
-
-  beam-proxy:
-    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
-    container_name: bridgehead-beam-proxy
-    environment:
-      BROKER_URL: ${BROKER_URL}
-      PROXY_ID: ${PROXY_ID}
-      APP_focus_KEY: ${FOCUS_BEAM_SECRET_SHORT}
-      PRIVKEY_FILE: /run/secrets/proxy.pem
-      ALL_PROXY: http://forward_proxy:3128
-      TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
-      ROOTCERT_FILE: /conf/root.crt.pem
-    secrets:
-      - proxy.pem
-    depends_on:
-      - "forward_proxy"
-    volumes:
-      - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
-      - /srv/docker/bridgehead/kr/root.crt.pem:/conf/root.crt.pem:ro
-
-
-volumes:
-  blaze-data:
-
-secrets:
-  proxy.pem:
-    file: /etc/bridgehead/pki/${SITE_ID}.priv.pem
--- a/kr/root.crt.pem
+++ b/kr/root.crt.pem
@ -1,20 +0,0 @@
-----BEGIN CERTIFICATE-----
-MIIDNTCCAh2gAwIBAgIUW34NEb7bl0+Ywx+I1VKtY5vpAOowDQYJKoZIhvcNAQEL
-BQAwFjEUMBIGA1UEAxMLQnJva2VyLVJvb3QwHhcNMjQwMTIyMTMzNzEzWhcNMzQw
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-poIguUAK9YL2n7fbMB8GA1UdIwQYMBaAFGjvRcaIP4HMpoIguUAK9YL2n7fbMBYG
-A1UdEQQPMA2CC0Jyb2tlci1Sb290MA0GCSqGSIb3DQEBCwUAA4IBAQCbzycJSaDm
-AXXNJqQ88djrKs5MDXS8RIjS/cu2ayuLaYDe+BzVmUXNA0Vt9nZGdaz63SLLcjpU
-fNSxBfKbwmf7s30AK8Cnfj9q4W/BlBeVizUHQsg1+RQpDIdMrRQrwkXv8mfLw+w5
-3oaXNW6W/8KpBp/H8TBZ6myl6jCbeR3T8EMXBwipMGop/1zkbF01i98Xpqmhx2+l
-n+80ofPsSspOo5XmgCZym8CD/m/oFHmjcvOfpOCvDh4PZ+i37pmbSlCYoMpla3u/
-7MJMP5lugfLBYNDN2p+V4KbHP/cApCDT5UWLOeAWjgiZQtHH5ilDeYqEc1oPjyJt
-Rtup0MTxSJtN
-----END CERTIFICATE-----
--- a/kr/vars
+++ b/kr/vars
@ -1,16 +0,0 @@
-BROKER_ID=test-no-real-data.broker.samply.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=${FOCUS_RETRY_COUNT:-64}
-SUPPORT_EMAIL=arturo.macias@dkfz-heidelberg.de
-PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
-BROKER_URL_FOR_PREREQ=$BROKER_URL
-
-for module in common/*.sh
-do
-    log DEBUG "sourcing $module"
-    source $module
-done
-
-obds2fhirRestSetup
--- a/lib/functions.sh
+++ b/lib/functions.sh
@ -53,8 +53,8 @@ checkOwner(){
 }

 printUsage() {
-	echo "Usage: bridgehead start|stop|logs|docker-logs|is-running|update|install|uninstall|adduser|enroll PROJECTNAME"
-	echo "PROJECTNAME should be one of ccp|bbmri|cce|itcc|kr|dhki"
+	echo "Usage: bridgehead start|stop|logs|is-running|update|install|uninstall|adduser|enroll PROJECTNAME"
+	echo "PROJECTNAME should be one of ccp|bbmri"
 }

 checkRequirements() {
@ -367,7 +367,3 @@ generate_simple_password(){
  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/${SITE_ID}.priv.pem" 2> /dev/null | base64 | head -c 26 | sed 's/[+\/]/A/g'
 }
-
-docker_jq() {
-    docker run --rm -i docker.verbis.dkfz.de/cache/jqlang/jq:latest "$@"
-}
--- a/lib/prepare-system.sh
+++ b/lib/prepare-system.sh
@ -52,21 +52,6 @@ case "$PROJECT" in
 	bbmri)
 		site_configuration_repository_middle="git.verbis.dkfz.de/bbmri-bridgehead-configs/"
 		;;
-	cce)
-		site_configuration_repository_middle="git.verbis.dkfz.de/cce-sites/"
-		;;
-	itcc)
-		site_configuration_repository_middle="git.verbis.dkfz.de/itcc-sites/"
-        ;;
-    dhki)
-        site_configuration_repository_middle="git.verbis.dkfz.de/dhki/"
-		;;
-	kr)
-		site_configuration_repository_middle="git.verbis.dkfz.de/krebsregister-sites/"
-		;;
-	dhki)
-		site_configuration_repository_middle="git.verbis.dkfz.de/dhki/"
-		;;
 	minimal)
 		site_configuration_repository_middle="git.verbis.dkfz.de/minimal-bridgehead-configs/"
 		;;
--- a/lib/systemd/bridgehead-update@.timer
+++ b/lib/systemd/bridgehead-update@.timer
@ -1,9 +1,8 @@
 [Unit]
-Description=Daily Updates at 6am of Bridgehead (%i)
+Description=Hourly Updates of Bridgehead (%i)

 [Timer]
-OnCalendar=*-*-* 06:00:00
-Persistent=true
+OnCalendar=*-*-* *:00:00

 [Install]
 WantedBy=basic.target
--- a/minimal/docker-compose.yml
+++ b/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
@ -58,4 +55,3 @@ services:
      HOST: ${HOST}
      PROJECT: ${PROJECT}
      SITE_NAME: ${SITE_NAME}
-      ENVIRONMENT: ${ENVIRONMENT}
--- a/minimal/modules/dnpm-compose.yml
+++ b/minimal/modules/dnpm-compose.yml
@ -2,7 +2,7 @@ version: "3.7"

 services:
  dnpm-beam-proxy:
-    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${BEAM_TAG}
+    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
    container_name: bridgehead-dnpm-beam-proxy
    environment:
      BROKER_URL: ${DNPM_BROKER_URL}
Author	SHA1	Message	Date
janskiba	96c1b8ede5	chore: update datashield beam-connect mappings	2024-05-23 09:55:22 +02:00
janskiba	eac9374815	feat: Add file-dispatcher to exporter compose	2024-05-23 09:38:37 +02:00
janskiba	8b33912fee	feat: Move to central rstudio	2024-04-17 14:25:59 +02:00