fix: cce

README.md

@@ -27,7 +27,6 @@ This repository is the starting point for any information and tools you will nee
     - [Teiler (Frontend)](#teiler-frontend)
     - [Data Exporter Service](#data-exporter-service)
       - [Data Quality Report](#data-quality-report)
-    - [Data Quality Agent](#data-quality-agent)
 4. [Things you should know](#things-you-should-know)
     - [Auto-Updates](#auto-updates)
     - [Auto-Backups](#auto-backups)
@@ -319,12 +318,6 @@ 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:
@@ -332,13 +325,12 @@ 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                                                                                                                                |                                        |
+| DS_DIRECTORY_USER_NAME             | User name for logging in to Directory **Mandatory**                                                                                                                  |                                        |
-| DS_DIRECTORY_USER_PASS             | Password for logging in to Directory                                                                                                                                 |                                        |
+| DS_DIRECTORY_USER_PASS             | Password for logging in to Directory **Mandatory**                                                                                                                   |                                        |
-| 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                                                                                           | 30 22 * * *                            |
+| DS_TIMER_CRON                      | Execution interval for Directory sync, [cron](https://crontab.guru) format                                                                                           | 0 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                                  |
 
@@ -425,32 +417,6 @@ ENABLE_EXPORTER=true
 ```
 [For further information](docs/exporter.md)  
 
-### Data Quality Agent
-
-The Data Quality Agent is an optional module that periodically evaluates the quality of FHIR data stored in Blaze. It generates local data quality reports accessible via the Bridgehead web interface.
-
-To enable the service, set the following variable in your `<PROJECT>.conf` file:
-
-```bash
-ENABLE_DATA_QUALITY_AGENT=true
-```
-
-#### Sharing Data Quality Reports (recommended)
-
-We encourage sharing your data quality reports with the central BBMRI-ERIC quality dashboard. The reports contain only aggregated, non-patient-identifiable statistics and help the network to monitor and improve overall data quality. However, quality reporting is completely optional and opt-in.
-
-To opt in, additionally set the following variables in your `<PROJECT>.conf` file:
-
-```bash
-DATA_QUALITY_SERVER_URL=https://quality-dashboard.bbmri-eric.eu
-DATA_QUALITY_SERVER_NAME=Central Data Quality Server of BBMRI
-```
-
-If these variables are not set, the Data Quality Agent will still run and generate local reports, but no data will be shared externally.
-
-Reports are accessible at `https://<your-host>/bbmri-data-quality-agent` (default credentials are admin:admin, please change it after first login!!).
-
-[Official documentation](https://fdqf.bbmri-eric.eu/user/deployment.html)
 ## Things you should know
 
 ### Auto-Updates

bbmri/modules/data-quality-agent-compose.yml

@@ -1,23 +0,0 @@
-version: "3.7"
-
-services:
-  data-quality-agent:
-    image: ghcr.io/bbmri-cz/data-quality-server:${DATA_QUALITY_AGENT_TAG}
-    container_name: bridgehead-bbmri-data-quality-agent
-    environment:
-      APP_SETTING_FHIR_URL: http://bridgehead-bbmri-blaze:8080/fhir
-      REPORTING_SERVER_URL: ${DATA_QUALITY_SERVER_URL}
-      REPORTING_SERVER_NAME: ${DATA_QUALITY_SERVER_NAME}
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.data_quality_agent_bbmri.rule=PathPrefix(`/bbmri-data-quality-agent`)"
-      - "traefik.http.services.data_quality_agent_bbmri.loadbalancer.server.port=8082"
-      - "traefik.http.routers.data_quality_agent_bbmri.tls=true"
-      - "traefik.http.middlewares.data_quality_agent_bbmri_strip.stripprefix.prefixes=/bbmri-data-quality-agent"
-      - "traefik.http.routers.data_quality_agent_bbmri.middlewares=data_quality_agent_bbmri_strip,auth"
-    depends_on:
-      - "blaze"
-    volumes:
-      - /var/cache/bridgehead/bbmri/agent-db:/app/data
-      - /etc/localtime:/etc/localtime:ro
-      - /etc/timezone:/etc/timezone:ro

bbmri/modules/data-quality-agent-setup.sh

@@ -1,7 +0,0 @@
-#!/bin/bash
-
-if [ "$ENABLE_DATA_QUALITY_AGENT" == "true" ]; then
-    log INFO "Data Quality Agent setup detected -- will start data-quality-agent service."
-    OVERRIDE+=" -f ./$PROJECT/modules/data-quality-agent-compose.yml"
-fi
-

bbmri/modules/directory-sync-compose.yml

@@ -7,8 +7,7 @@ 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_DIRECTORY_USER_TOKEN: ${DS_DIRECTORY_USER_TOKEN}
+      DS_TIMER_CRON: ${DS_TIMER_CRON:-0 22 * * *}
-      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}
@@ -17,6 +16,3 @@ 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 "${DS_DIRECTORY_USER_NAME}" ] || [ -n "${DS_DIRECTORY_USER_TOKEN}" ]; then
+if [ -n "${DS_DIRECTORY_USER_NAME}" ]; then
 	log INFO "Directory sync setup detected -- will start directory sync service."
 	OVERRIDE+=" -f ./$PROJECT/modules/directory-sync-compose.yml"
 fi

bbmri/modules/eric-compose.yml

@@ -11,7 +11,6 @@ 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

@@ -35,9 +35,6 @@ case "$PROJECT" in
 	cce)
 		#nothing extra to do
 		;;
-	pscc)
-		#nothing extra to do
-		;;
 	itcc)
 		#nothing extra to do
 		;;
@@ -47,9 +44,6 @@ case "$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:${FOCUS_TAG}
+    image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}-dktk
     container_name: bridgehead-focus
     environment:
       API_KEY: ${FOCUS_BEAM_SECRET_SHORT}
@@ -34,6 +34,7 @@ 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

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

cce/modules/osiris2fhir-setup.sh

@@ -1,6 +0,0 @@
-#!/bin/bash
-if [ -n "$ENABLE_OSIRIS2FHIR" ]; then
-  log INFO "OSIRIS2FHIR-REST setup detected -- will start osiris2fhir module."
-  OVERRIDE+=" -f ./pscc/modules/osiris2fhir-compose.yml"
-  LOCAL_SALT="$(echo \"local-random-salt\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
-fi

cce/vars

@@ -11,4 +11,4 @@ for module in $PROJECT/modules/*.sh
 do
     log DEBUG "sourcing $module"
     source $module
-done
+done

ccp/modules/dnpm-node-compose.yml

@@ -66,7 +66,6 @@ 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=Host(`${HOST}`) && PathPrefix(`/itcc-localdatamanagement`)"
+      - "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:${FOCUS_TAG}
+    image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}-dktk
     container_name: bridgehead-focus
     environment:
       API_KEY: ${FOCUS_BEAM_SECRET_SHORT}
@@ -34,6 +34,7 @@ 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

@@ -1,6 +0,0 @@
-#!/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

@@ -1,14 +0,0 @@
-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

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

@@ -6,7 +6,6 @@ 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

@@ -12,8 +12,7 @@ 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

@@ -0,0 +1,6 @@
+# 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

@@ -4,41 +4,32 @@ services:
     deploy:
       replicas: 1 #reactivate if lens is in use
     container_name: lens_federated-search
-    image: docker.verbis.dkfz.de/ccp/kr-explorer:main
+    image: docker.verbis.dkfz.de/ccp/lens:${SITE_ID}
-    environment:
-      PUBLIC_SPOT_URL: https://${HOST}/prod
     labels:
-      - "traefik.http.services.lens.loadbalancer.server.port=3000"
       - "traefik.enable=true"
-      - "traefik.http.routers.lens.rule=Host(`${HOST}`)"
+      - "traefik.http.routers.landing.rule=PathPrefix(`/`)"
-      - "traefik.http.routers.lens.tls=true"
+      - "traefik.http.services.landing.loadbalancer.server.port=80"
+      - "traefik.http.routers.landing.tls=true"
 
   spot:
-    image: samply/rustyspot:latest
+    image: docker.verbis.dkfz.de/ccp-private/central-spot
     environment:
       BEAM_SECRET: "${FOCUS_BEAM_SECRET_SHORT}"
-      BEAM_PROXY_URL: http://beam-proxy:8081
+      BEAM_URL: http://beam-proxy:8081
-      BEAM_APP_ID: "spot.${SITE_ID}.${BROKER_ID}"
+      BEAM_PROXY_ID: ${SITE_ID}
-      CORS_ORIGIN: "https://${HOST}"
+      BEAM_BROKER_ID: ${BROKER_ID}
-      SITES: ${SITES}
+      BEAM_APP_ID: "focus"
-      TRANSFORM: LENS
+      PROJECT_METADATA: "kr_supervisors"
-      PROJECT: kr
-      BIND_ADDR: 0.0.0.0:8055
     depends_on:
       - "beam-proxy"
     labels:
       - "traefik.enable=true"
-      - "traefik.http.services.spot.loadbalancer.server.port=8055"
+      - "traefik.http.services.spot.loadbalancer.server.port=8080"
       - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowmethods=GET,OPTIONS,POST"
-      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowheaders=content-type"
       - "traefik.http.middlewares.corsheaders2.headers.accesscontrolalloworiginlist=https://${HOST}"
       - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowcredentials=true"
       - "traefik.http.middlewares.corsheaders2.headers.accesscontrolmaxage=-1"
-      - "traefik.http.routers.spot.rule=Host(`${HOST}`) && PathPrefix(`/prod`)"
+      - "traefik.http.routers.spot.rule=Host(`${HOST}`) && PathPrefix(`/backend`)"
-      - "traefik.http.middlewares.stripprefix_spot.stripprefix.prefixes=/prod"
+      - "traefik.http.middlewares.stripprefix_spot.stripprefix.prefixes=/backend"
       - "traefik.http.routers.spot.tls=true"
-      - "traefik.http.routers.spot.middlewares=corsheaders2,stripprefix_spot,auth"
+      - "traefik.http.routers.spot.middlewares=corsheaders2,stripprefix_spot"
-
-  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/samply/obds2fhir-rest:main
+    image: docker.verbis.dkfz.de/ccp/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=${FOCUS_RETRY_COUNT:-64}
-SUPPORT_EMAIL=p.delpy@dkfz-heidelberg.de
+SUPPORT_EMAIL=arturo.macias@dkfz-heidelberg.de
 PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
 BROKER_URL_FOR_PREREQ=$BROKER_URL
 

lib/functions.sh

@@ -54,7 +54,7 @@ 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|nngm"
+	echo "PROJECTNAME should be one of ccp|bbmri|cce|itcc|kr|dhki"
 }
 
 checkRequirements() {
@@ -327,7 +327,7 @@ function sync_secrets() {
         -e ALL_PROXY=$HTTPS_PROXY_FULL_URL \
         -e PROXY_ID=$proxy_id \
         -e BROKER_URL=$broker_url \
-        -e OIDC_PROVIDER=secret-sync-central.central-secret-sync.$broker_id \
+        -e OIDC_PROVIDER=secret-sync-central.test-secret-sync.$broker_id \
         -e SECRET_DEFINITIONS=$secret_sync_args \
         docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest
 
@@ -337,8 +337,7 @@ function sync_secrets() {
 }
 
 function secret_sync_gitlab_token() {
-    if [[ "$PROJECT" != "ccp" && "$PROJECT" != "bbmri" ]]; then
+    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
@@ -398,7 +397,7 @@ function secret_sync_gitlab_token() {
     else
         log "WARN" "Secret Sync failed"
         # Remove the git credential helper
-        git -C /etc/bridgehead config --unset credential.helper
+        git -C /etc/bridgehead config --unset credential.helpera
     fi
 
     # In the past the git credential helper was also set for /srv/docker/bridgehead but never used.

lib/prepare-system.sh

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

minimal/modules/dnpm-node-compose.yml

@@ -66,7 +66,6 @@ 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

@@ -1,65 +0,0 @@
-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

@@ -1,72 +0,0 @@
-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

@@ -1,8 +0,0 @@
-#!/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

@@ -1,73 +0,0 @@
-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

@@ -1,8 +0,0 @@
-#!/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

@@ -1,20 +0,0 @@
------BEGIN CERTIFICATE-----
-MIIDNTCCAh2gAwIBAgIUWHMDQFPJR5y8RKZ5FC72iOOla4kwDQYJKoZIhvcNAQEL
-BQAwFjEUMBIGA1UEAxMLQnJva2VyLVJvb3QwHhcNMjUxMDI3MTQwMjU1WhcNMzUx
-MDI1MTQwMzI1WjAWMRQwEgYDVQQDEwtCcm9rZXItUm9vdDCCASIwDQYJKoZIhvcN
-AQEBBQADggEPADCCAQoCggEBAKoghRqAo6s9xjDao+ZC9HpZDBgzOgRMRHrl352k
-Y0Gti1p3m8ldwVQV+nlBE6g/Dowo+iaOwUBiHMHOI2BK7vqkGNp0tZ63ZKR4cyOD
-hCDOl71lWxjYD5XmF7l/SbrLFfET0EEorhLDDOMuWrNpxKFfKdvhld6K5BZ3oSfH
-/5W5y5jWRFWEYRzddzil2GOiU2vzAygA0I1nr5oHCgZoteDDXztAYHJ5vnPA9RNQ
-YFoe/5fVOiJo869zYyBwMuY/dV5ff7eIe/HRKzFLZ6iJEOJcBFWx/aWEvj5gSWxS
-x4OzkwoHsZOkRN9wSTXvdO5kPFzmPq8Nq7Hmw4tLVzP1eRECAwEAAaN7MHkwDgYD
-VR0PAQH/BAQDAgEGMA8GA1UdEwEB/wQFMAMBAf8wHQYDVR0OBBYEFP9BHa86rz94
-nvMj2JhM5V3L3TWCMB8GA1UdIwQYMBaAFP9BHa86rz94nvMj2JhM5V3L3TWCMBYG
-A1UdEQQPMA2CC0Jyb2tlci1Sb290MA0GCSqGSIb3DQEBCwUAA4IBAQCkWBXRUGx5
-XFWEEAVbAMcEuXAr6+HtSs+NTORQ01LhNST8Z9HhOaAjfH/dJiLvOjHvOuiOK9y9
-ZGkIIwqkkbhlv1ZcfQBWXh+xDNbq9Q2MaIWY3ZzPTKFgNkxFcEF43MMB+o5pK1Bf
-jJIiSxuEfM0yHg9o+jc3V3XRhU9leXNPkfJezTGfVuWr/B/kTmnQ8zrOCapB+NnX
-vuu1ayNyXflDkj8Gg0X4TarxGhSP6Dpxd9ViEQD9DFG8q42bH0mYveHcAIUN0FJX
-4F2NChiL7dCSFFe6xKdRFDtNe12JrHRjU1rMAcxhYjBRbqt2o2HfDPajSJrhRheY
-T35rRWxDupkP
------END CERTIFICATE-----

nngm/vars

@@ -1,32 +0,0 @@
-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

@@ -1,67 +0,0 @@
-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

@@ -1,40 +0,0 @@
-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

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

pscc/modules/osiris2fhir-compose.yml

@@ -1,15 +0,0 @@
-services:
-  osiris2fhir:
-    container_name: bridgehead-osiris2fhir
-    image: docker.verbis.dkfz.de/ccp/osiris2fhir
-    environment:
-      FHIR_PROFILE: ${PROJECT:-pscc}
-      LOG_LEVEL: ${LOG_LEVEL:-INFO}
-      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

@@ -1,6 +0,0 @@
-#!/bin/bash
-if [ -n "$ENABLE_OSIRIS2FHIR" ]; then
-  log INFO "OSIRIS2FHIR-REST setup detected -- will start osiris2fhir module."
-  OVERRIDE+=" -f ./pscc/modules/osiris2fhir-compose.yml"
-  LOCAL_SALT="$(echo \"local-random-salt\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
-fi

pscc/root.crt.pem

@@ -1,20 +0,0 @@
------BEGIN CERTIFICATE-----
-MIIDNTCCAh2gAwIBAgIUVC1Y1tx0q5PNR33gArAyyBm8PMQwDQYJKoZIhvcNAQEL
-BQAwFjEUMBIGA1UEAxMLQnJva2VyLVJvb3QwHhcNMjUxMTAzMTQxODQ5WhcNMzUx
-MTAxMTQxOTE5WjAWMRQwEgYDVQQDEwtCcm9rZXItUm9vdDCCASIwDQYJKoZIhvcN
-AQEBBQADggEPADCCAQoCggEBAMB1yd7zkh7Io/ReQYindBcAdA1b4ogdVnrdSLRN
-N3zLSh6jN5KIXgs34BdRXx0so0m96q+9xlgacTXGRBn1Tu5SKMRyXdxnCLMzHAYU
-rNKhqF5HeZCYkVyh/tsAyFfDwZDVzsdX64V+0r5+raev2X0gJnlgmF83DIKjkVUS
-2+c+3BnXa9LOdXks0qygJjvaFyi+5MA3DinLnmMLCQ3yAvaZYWyP3xCnGIoVrZFq
-a+YioMCmHrbByuXPoZsXcFY7Z85LQkCtSVt1dH4kkN2/JehXG099nqwMqO8FpLZZ
-xG7/U3P/slX1MMLs97nqRCRoW7Cha2ci1NBYLll+34ekhxMCAwEAAaN7MHkwDgYD
-VR0PAQH/BAQDAgEGMA8GA1UdEwEB/wQFMAMBAf8wHQYDVR0OBBYEFJHTpnuyIGHw
-yvC/mmh+S/JKYVrAMB8GA1UdIwQYMBaAFJHTpnuyIGHwyvC/mmh+S/JKYVrAMBYG
-A1UdEQQPMA2CC0Jyb2tlci1Sb290MA0GCSqGSIb3DQEBCwUAA4IBAQAeDc/k28yb
-I5MLC/LdaA+MKsW2FWF9HT+tsbtltTaQIRnnkwfU/40Ius3gzUU5z+kPqq5+kxhy
-3T646Rbau85Zw24gdNmiVKAAG5ntKoQ7XnyR/06PYyXNGLqnb6aKvbcIPoWtU/+2
-8f5hHdQ/4271aHws7dKcBNWu9V5WmxMZ3YTfnBR5lEda+DhVwHqtmun8EpSbwthD
-aLLIOHJpetr+KWUVFHQdGbO23Qg1Else0Akcn5Gzf/sKkVCVxjHE6jeo4ZwHtstG
-KMoff+ETC+DL5kMZ4CV5VaQ4HxVK7N0qiUxmijWe+EyRZseum1c0s2OEi2L52Q9K
-P4N3yD4ed4p/
------END CERTIFICATE-----

pscc/vars

@@ -1,14 +0,0 @@
-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

@@ -1,7 +1,6 @@
 FOCUS_TAG=develop
 BEAM_TAG=develop
-BLAZE_TAG=0.32
+BLAZE_TAG=main
 POSTGRES_TAG=15.13-alpine
 TEILER_DASHBOARD_TAG=develop
-MTBA_TAG=develop
+MTBA_TAG=develop
-DATA_QUALITY_AGENT_TAG=latest

versions/prod

@@ -3,5 +3,4 @@ BEAM_TAG=main
 BLAZE_TAG=0.32
 POSTGRES_TAG=15.13-alpine
 TEILER_DASHBOARD_TAG=main
-MTBA_TAG=main
+MTBA_TAG=main
-DATA_QUALITY_AGENT_TAG=0.1

versions/test

@@ -1,7 +1,6 @@
 FOCUS_TAG=develop
 BEAM_TAG=develop
-BLAZE_TAG=0.32
+BLAZE_TAG=main
 POSTGRES_TAG=15.13-alpine
 TEILER_DASHBOARD_TAG=develop
-MTBA_TAG=develop
+MTBA_TAG=develop
-DATA_QUALITY_AGENT_TAG=latest