Merge branch 'main' into main_directory_sync_extra_attributes_and_star_model

2024-07-25 16:54:47 +02:00 · 2024-07-25 16:54:47 +02:00 · 3f8bb158bc
parent 1a928e6701 c3b770b70f
commit 3f8bb158bc
38 changed files with 935 additions and 93 deletions
--- a/.gitignore
+++ b/.gitignore
@ -1,7 +1,7 @@
 ##Ignore site configuration
 .gitmodules
 site-config/*
-
+.idea
 ## Ignore site configuration
 */docker-compose.override.yml

--- a/README.md
+++ b/README.md
@ -200,7 +200,7 @@ sudo systemctl [enable|disable] bridgehead@<PROJECT>.service
 After starting the Bridgehead, you can watch the initialization process with the following command:

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

 if this exits with something similar to the following:
@ -220,8 +220,9 @@ 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
-journalctl -u bridgehead@bbmri -f
+/srv/docker/bridgehead/bridgehead logs <Project> -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:

@ -235,7 +236,7 @@ You can either do this in a browser or with curl. If you visit the URL in the br
 curl -k https://localhost
 ```

-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.
+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 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.

--- a/bbmri/docker-compose.yml
+++ b/bbmri/docker-compose.yml
@ -4,12 +4,13 @@ version: "3.7"

 services:
  blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:latest
+    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
    container_name: bridgehead-bbmri-blaze
    environment:
      BASE_URL: "http://bridgehead-bbmri-blaze:8080"
-      JAVA_TOOL_OPTIONS: "-Xmx4g"
-      LOG_LEVEL: "debug"
+      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"
--- a/bbmri/modules/directory-sync-compose.yml
+++ b/bbmri/modules/directory-sync-compose.yml
@ -1,3 +1,5 @@
+version: "3.7"
+
 services:
  directory_sync_service:
    image: "docker.verbis.dkfz.de/cache/samply/directory_sync_service"
--- a/bbmri/vars
+++ b/bbmri/vars
@ -4,7 +4,7 @@
 # Makes only sense for German Biobanks
 : ${ENABLE_GBN:=false}

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

 for module in $PROJECT/modules/*.sh
--- a/11
+++ b/11
@ -50,6 +50,8 @@ loadVars() {
 		source /etc/bridgehead/$PROJECT.local.conf || fail_and_report 1 "Found /etc/bridgehead/$PROJECT.local.conf but failed to import"
 	fi
 	fetchVarsFromVaultByFile /etc/bridgehead/$PROJECT.conf || fail_and_report 1 "Unable to fetchVarsFromVaultByFile"
+	setHostname
+	optimizeBlazeMemoryUsage
 	[ -e ./$PROJECT/vars ] && source ./$PROJECT/vars
 	set +a

@ -64,7 +66,6 @@ loadVars() {
 		OVERRIDE+=" -f ./$PROJECT/docker-compose.override.yml"
 	fi
 	detectCompose
-	setHostname
 	setupProxy

 	# Set some project-independent default values
@ -89,11 +90,14 @@ case "$ACTION" in
 		loadVars
 		hc_send log "Bridgehead $PROJECT startup: Checking requirements ..."
 		checkRequirements
+		sync_secrets
 		hc_send log "Bridgehead $PROJECT startup: Requirements checked out. Now starting bridgehead ..."
 		exec $COMPOSE -p $PROJECT -f ./minimal/docker-compose.yml -f ./$PROJECT/docker-compose.yml $OVERRIDE up --abort-on-container-exit
 		;;
 	stop)
 		loadVars
+		# Kill stale secret-sync instances if present
+		docker kill $(docker ps -q --filter ancestor=docker.verbis.dkfz.de/cache/samply/secret-sync-local) 2>/dev/null || true
 		# HACK: This is temporarily to properly shut down false bridgehead instances (bridgehead-ccp instead ccp)
 		$COMPOSE -p bridgehead-$PROJECT -f ./minimal/docker-compose.yml -f ./$PROJECT/docker-compose.yml $OVERRIDE down
 		exec $COMPOSE -p $PROJECT -f ./minimal/docker-compose.yml -f ./$PROJECT/docker-compose.yml $OVERRIDE down
@ -103,6 +107,11 @@ case "$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/ccp/docker-compose.yml
+++ b/ccp/docker-compose.yml
@ -2,11 +2,13 @@ version: "3.7"

 services:
  blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:latest
+    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
    container_name: bridgehead-ccp-blaze
    environment:
      BASE_URL: "http://bridgehead-ccp-blaze:8080"
-      JAVA_TOOL_OPTIONS: "-Xmx4g"
+      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"
@ -19,7 +21,7 @@ services:
      - "traefik.http.routers.blaze_ccp.tls=true"

  focus:
-    image: docker.verbis.dkfz.de/cache/samply/focus:0.4.0
+    image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
    container_name: bridgehead-focus
    environment:
      API_KEY: ${FOCUS_BEAM_SECRET_SHORT}
--- a/ccp/modules/adt2fhir-rest-compose.yml
+++ b/ccp/modules/adt2fhir-rest-compose.yml
@ -1,18 +0,0 @@
-version: "3.7"
-
-services:
-  adt2fhir-rest:
-    container_name: bridgehead-adt2fhir-rest
-    image: docker.verbis.dkfz.de/ccp/adt2fhir-rest:main
-    environment:
-      IDTYPE: BK_${IDMANAGEMENT_FRIENDLY_ID}_L-ID
-      MAINZELLISTE_APIKEY: ${IDMANAGER_LOCAL_PATIENTLIST_APIKEY}
-      SALT: ${LOCAL_SALT}
-    restart: always
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.adt2fhir-rest.rule=PathPrefix(`/adt2fhir-rest`)"
-      - "traefik.http.middlewares.adt2fhir-rest_strip.stripprefix.prefixes=/adt2fhir-rest"
-      - "traefik.http.services.adt2fhir-rest.loadbalancer.server.port=8080"
-      - "traefik.http.routers.adt2fhir-rest.tls=true"
-      - "traefik.http.routers.adt2fhir-rest.middlewares=adt2fhir-rest_strip,auth"
--- a/ccp/modules/adt2fhir-rest-setup.sh
+++ b/ccp/modules/adt2fhir-rest-setup.sh
@ -1,13 +0,0 @@
-#!/bin/bash
-
-function adt2fhirRestSetup() {
-  if [ -n "$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/blaze-secondary-compose.yml
+++ b/ccp/modules/blaze-secondary-compose.yml
@ -0,0 +1,32 @@
+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: ${STORE_PATH:-http://blaze:8080/fhir}
+
+  exporter:
+    environment:
+      BLAZE_HOST: "blaze-secondary"
+
+volumes:
+  blaze-secondary-data:
--- a/ccp/modules/blaze-secondary-setup.sh
+++ b/ccp/modules/blaze-secondary-setup.sh
@ -0,0 +1,11 @@
+#!/bin/bash
+
+function blazeSecondarySetup() {
+  if [ -n "$ENABLE_SECONDARY_BLAZE" ]; then
+    log INFO "Secondary Blaze setup detected -- will start second blaze."
+    OVERRIDE+=" -f ./$PROJECT/modules/blaze-secondary-compose.yml"
+    #make oBDS2FHIR ignore ID-Management and replace target Blaze
+    PATIENTLIST_URL=" "
+    STORE_PATH="http://blaze-secondary:8080/fhir"
+  fi
+}
--- a/ccp/modules/datashield-compose.yml
+++ b/ccp/modules/datashield-compose.yml
@ -0,0 +1,171 @@
+version: "3.7"
+
+services:
+  rstudio:
+    container_name: bridgehead-rstudio
+    image: docker.verbis.dkfz.de/ccp/dktk-rstudio:latest
+    environment:
+      #DEFAULT_USER: "rstudio" # This line is kept for informational purposes
+      PASSWORD: "${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/ccp/modules/datashield-import-template.xml
+++ b/ccp/modules/datashield-import-template.xml
@ -0,0 +1,157 @@
+<template id="opal-ccp" source-id="blaze-store" opal-project="ccp-demo" target-id="opal" >
+
+  <container csv-filename="Patient-${TIMESTAMP}.csv" opal-table="patient" opal-entity-type="Patient">
+    <attribute csv-column="patient-id" opal-value-type="text" primary-key="true" val-fhir-path="Patient.id.value" anonym="Pat" op="EXTRACT_RELATIVE_ID"/>
+    <attribute csv-column="dktk-id-global" opal-value-type="text" val-fhir-path="Patient.identifier.where(type.coding.code = 'Global').value.value"/>
+    <attribute csv-column="dktk-id-lokal" opal-value-type="text" val-fhir-path="Patient.identifier.where(type.coding.code = 'Lokal').value.value" />
+    <attribute csv-column="geburtsdatum" opal-value-type="date" val-fhir-path="Patient.birthDate.value"/>
+    <attribute csv-column="geschlecht" opal-value-type="text" val-fhir-path="Patient.gender.value" />
+    <attribute csv-column="datum_des_letztbekannten_vitalstatus" opal-value-type="date" val-fhir-path="Observation.where(code.coding.code = '75186-7').effective.value" join-fhir-path="/Observation.where(code.coding.code = '75186-7').subject.reference.value"/>
+    <attribute csv-column="vitalstatus" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '75186-7').value.coding.code.value" join-fhir-path="/Observation.where(code.coding.code = '75186-7').subject.reference.value"/>
+    <!--fehlt in ADT2FHIR--><attribute csv-column="tod_tumorbedingt" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '68343-3').value.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.value" join-fhir-path="/Observation.where(code.coding.code = '68343-3').subject.reference.value"/>
+    <!--fehlt in ADT2FHIR--><attribute csv-column="todesursachen" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '68343-3').value.coding.where(system = 'http://dktk.dkfz.de/fhir/onco/core/CodeSystem/JNUCS').code.value" join-fhir-path="/Observation.where(code.coding.code = '68343-3').subject.reference.value"/>
+  </container>
+
+  <container csv-filename="Diagnosis-${TIMESTAMP}.csv" opal-table="diagnosis" opal-entity-type="Diagnosis">
+    <attribute csv-column="diagnosis-id" primary-key="true" opal-value-type="text" val-fhir-path="Condition.id.value" anonym="Dia" op="EXTRACT_RELATIVE_ID"/>
+    <attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="Condition.subject.reference.value" anonym="Pat"/>
+    <attribute csv-column="primaerdiagnose" opal-value-type="text" val-fhir-path="Condition.code.coding.code.value"/>
+    <attribute csv-column="tumor_diagnosedatum" opal-value-type="date" val-fhir-path="Condition.onset.value"/>
+    <attribute csv-column="primaertumor_diagnosetext" opal-value-type="text" val-fhir-path="Condition.code.text.value"/>
+    <attribute csv-column="version_des_icd-10_katalogs" opal-value-type="integer" val-fhir-path="Condition.code.coding.version.value"/>
+    <attribute csv-column="lokalisation" opal-value-type="text" val-fhir-path="Condition.bodySite.coding.where(system = 'urn:oid:2.16.840.1.113883.6.43.1').code.value"/>
+    <attribute csv-column="icd-o_katalog_topographie_version" opal-value-type="text" val-fhir-path="Condition.bodySite.coding.where(system = 'urn:oid:2.16.840.1.113883.6.43.1').version.value"/>
+    <attribute csv-column="seitenlokalisation_nach_adt-gekid" opal-value-type="text" val-fhir-path="Condition.bodySite.coding.where(system = 'http://dktk.dkfz.de/fhir/onco/core/CodeSystem/SeitenlokalisationCS').code.value"/>
+  </container>
+
+  <container csv-filename="Progress-${TIMESTAMP}.csv" opal-table="progress" opal-entity-type="Progress">
+<!--it would be better to generate a an ID, instead of extracting the ClinicalImpression id-->
+    <attribute csv-column="progress-id" primary-key="true" opal-value-type="text" val-fhir-path="ClinicalImpression.id.value" anonym="Pro" op="EXTRACT_RELATIVE_ID"/>
+    <attribute csv-column="diagnosis-id" opal-value-type="text" val-fhir-path="ClinicalImpression.problem.reference.value" anonym="Dia"/>
+    <attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="ClinicalImpression.subject.reference.value" anonym="Pat" />
+    <attribute csv-column="untersuchungs-_befunddatum_im_verlauf" opal-value-type="date" val-fhir-path="ClinicalImpression.effective.value" />
+    <!-- just for evaluation: redundant to Untersuchungs-, Befunddatum im Verlauf-->
+    <attribute csv-column="datum_lokales_oder_regionaeres_rezidiv" opal-value-type="date" val-fhir-path="Observation.where(code.coding.code = 'LA4583-6').effective.value" join-fhir-path="ClinicalImpression.finding.itemReference.reference.value" />
+    <attribute csv-column="gesamtbeurteilung_tumorstatus" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21976-6').value.coding.code.value" join-fhir-path="ClinicalImpression.finding.itemReference.reference.value"/>
+    <attribute csv-column="lokales_oder_regionaeres_rezidiv" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = 'LA4583-6').value.coding.code.value" join-fhir-path="ClinicalImpression.finding.itemReference.reference.value"/>
+    <attribute csv-column="lymphknoten-rezidiv" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = 'LA4370-8').value.coding.code.value" join-fhir-path="ClinicalImpression.finding.itemReference.reference.value" />
+    <attribute csv-column="fernmetastasen" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = 'LA4226-2').value.coding.code.value" join-fhir-path="ClinicalImpression.finding.itemReference.reference.value" />
+  </container>
+
+  <container csv-filename="Histology-${TIMESTAMP}.csv" opal-table="histology" opal-entity-type="Histology" >
+    <attribute csv-column="histology-id" primary-key="true" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '59847-4').id" anonym="His" op="EXTRACT_RELATIVE_ID"/>
+    <attribute csv-column="diagnosis-id" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '59847-4').focus.reference.value" anonym="Dia"/>
+    <attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '59847-4').subject.reference.value" anonym="Pat" />
+    <attribute csv-column="histologie_datum" opal-value-type="date" val-fhir-path="Observation.where(code.coding.code = '59847-4').effective.value"/>
+    <attribute csv-column="icd-o_katalog_morphologie_version" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '59847-4').value.coding.version.value" />
+    <attribute csv-column="morphologie" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '59847-4').value.coding.code.value"/>
+    <attribute csv-column="morphologie-freitext" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '59847-4').value.text.value"/>
+    <attribute csv-column="grading" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '59542-1').value.coding.code.value" join-fhir-path="Observation.where(code.coding.code = '59847-4').hasMember.reference.value"/>
+  </container>
+
+
+  <container csv-filename="Metastasis-${TIMESTAMP}.csv" opal-table="metastasis" opal-entity-type="Metastasis" >
+    <attribute csv-column="metastasis-id" primary-key="true" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21907-1').id" anonym="Met" op="EXTRACT_RELATIVE_ID"/>
+    <attribute csv-column="diagnosis-id" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21907-1').focus.reference.value" anonym="Dia"/>
+    <attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21907-1').subject.reference.value" anonym="Pat" />
+    <attribute csv-column="datum_fernmetastasen" opal-value-type="date" val-fhir-path="Observation.where(code.coding.code = '21907-1').effective.value"/>
+    <attribute csv-column="fernmetastasen_vorhanden" opal-value-type="boolean" val-fhir-path="Observation.where(code.coding.code = '21907-1').value.coding.code.value"/>
+    <attribute csv-column="lokalisation_fernmetastasen" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21907-1').bodySite.coding.code.value"/>
+  </container>
+
+  <container csv-filename="TNM-${TIMESTAMP}.csv" opal-table="tnm" opal-entity-type="TNM">
+    <attribute csv-column="tnm-id" primary-key="true" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').id" anonym="TNM" op="EXTRACT_RELATIVE_ID"/>
+    <attribute csv-column="diagnosis-id" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').focus.reference.value" anonym="Dia"/>
+    <attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').subject.reference.value" anonym="Pat" />
+    <attribute csv-column="datum_der_tnm_dokumentation_datum_befund" opal-value-type="date" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').effective.value"/>
+    <attribute csv-column="uicc_stadium" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').value.coding.code.value"/>
+    <attribute csv-column="tnm-t" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').component.where(code.coding.code = '21905-5' or code.coding.code = '21899-0').value.coding.code.value"/>
+    <attribute csv-column="tnm-n" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').component.where(code.coding.code = '21906-3' or code.coding.code = '21900-6').value.coding.code.value"/>
+    <attribute csv-column="tnm-m" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').component.where(code.coding.code = '21907-1' or code.coding.code = '21901-4').value.coding.code.value"/>
+    <attribute csv-column="c_p_u_preefix_t" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').component.where(code.coding.code = '21905-5' or code.coding.code = '21899-0').extension('http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Extension-TNMcpuPraefix').value.coding.code.value"/>
+    <attribute csv-column="c_p_u_preefix_n" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').component.where(code.coding.code = '21906-3' or code.coding.code = '21900-6').extension('http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Extension-TNMcpuPraefix').value.coding.code.value"/>
+    <attribute csv-column="c_p_u_preefix_m" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').component.where(code.coding.code = '21907-1' or code.coding.code = '21901-4').extension('http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Extension-TNMcpuPraefix').value.coding.code.value"/>
+    <attribute csv-column="tnm-y-symbol" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').component.where(code.coding.code = '59479-6' or code.coding.code = '59479-6').value.coding.code.value"/>
+    <attribute csv-column="tnm-r-symbol" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').component.where(code.coding.code = '21983-2' or code.coding.code = '21983-2').value.coding.code.value"/>
+    <attribute csv-column="tnm-m-symbol" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').component.where(code.coding.code = '42030-7' or code.coding.code = '42030-7').value.coding.code.value"/>
+    <!--nur bei UICC, nicht in ADT2FHIR--><attribute csv-column="tnm-version" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').value.coding.version.value"/>
+  </container>
+
+
+  <container csv-filename="System-Therapy-${TIMESTAMP}.csv" opal-table="system-therapy" opal-entity-type="SystemTherapy">
+    <attribute csv-column="system-therapy-id" primary-key="true" opal-value-type="text" val-fhir-path="MedicationStatement.id" anonym="Sys" op="EXTRACT_RELATIVE_ID"/>
+    <attribute csv-column="diagnosis-id" opal-value-type="text" val-fhir-path="MedicationStatement.reasonReference.reference.value" anonym="Dia"/>
+    <attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="MedicationStatement.subject.reference.value" anonym="Pat" />
+    <attribute csv-column="systemische_therapie_stellung_zu_operativer_therapie" opal-value-type="text" val-fhir-path="MedicationStatement.extension('http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Extension-StellungZurOp').value.coding.code.value"/>
+    <attribute csv-column="intention_chemotherapie" opal-value-type="text" val-fhir-path="MedicationStatement.extension('http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Extension-SYSTIntention').value.coding.code.value"/>
+    <attribute csv-column="therapieart" opal-value-type="text" val-fhir-path="MedicationStatement.category.coding.code.value"/>
+    <attribute csv-column="systemische_therapie_beginn" opal-value-type="date" val-fhir-path="MedicationStatement.effective.start.value"/>
+    <attribute csv-column="systemische_therapie_ende" opal-value-type="date" val-fhir-path="MedicationStatement.effective.end.value"/>
+    <attribute csv-column="systemische_therapie_protokoll" opal-value-type="text" val-fhir-path="MedicationStatement.extension('http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Extension-SystemischeTherapieProtokoll').value.text.value"/>
+    <attribute csv-column="systemische_therapie_substanzen" opal-value-type="text" val-fhir-path="MedicationStatement.medication.text.value"/>
+    <attribute csv-column="chemotherapie" opal-value-type="boolean" val-fhir-path="MedicationStatement.where(category.coding.code = 'CH').exists().value" />
+    <attribute csv-column="hormontherapie" opal-value-type="boolean" val-fhir-path="MedicationStatement.where(category.coding.code = 'HO').exists().value" />
+    <attribute csv-column="immuntherapie" opal-value-type="boolean" val-fhir-path="MedicationStatement.where(category.coding.code = 'IM').exists().value" />
+    <attribute csv-column="knochenmarktransplantation" opal-value-type="boolean" val-fhir-path="MedicationStatement.where(category.coding.code = 'KM').exists().value" />
+    <attribute csv-column="abwartende_strategie" opal-value-type="boolean" val-fhir-path="MedicationStatement.where(category.coding.code = 'WS').exists().value" />
+  </container>
+
+
+  <container csv-filename="Surgery-${TIMESTAMP}.csv" opal-table="surgery" opal-entity-type="Surgery">
+    <attribute csv-column="surgery-id" primary-key="true" opal-value-type="text" val-fhir-path="Procedure.where(category.coding.code = 'OP').id" anonym="Sur" op="EXTRACT_RELATIVE_ID"/>
+    <attribute csv-column="diagnosis-id" opal-value-type="text" val-fhir-path="Procedure.where(category.coding.code = 'OP').reasonReference.reference.value" anonym="Dia"/>
+    <attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="Procedure.where(category.coding.code = 'OP').subject.reference.value" anonym="Pat" />
+    <attribute csv-column="ops-code" opal-value-type="text" val-fhir-path="Procedure.where(category.coding.code = 'OP').code.coding.code.value"/>
+    <attribute csv-column="datum_der_op" opal-value-type="date" val-fhir-path="Procedure.where(category.coding.code = 'OP').performed.value"/>
+    <attribute csv-column="intention_op" opal-value-type="text" val-fhir-path="Procedure.extension('http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Extension-OPIntention').value.coding.code.value"/>
+    <attribute csv-column="lokale_beurteilung_resttumor" opal-value-type="text" val-fhir-path="Procedure.where(category.coding.code = 'OP').outcome.coding.where(system = 'http://dktk.dkfz.de/fhir/onco/core/CodeSystem/LokaleBeurteilungResidualstatusCS').code.value" />
+    <attribute csv-column="gesamtbeurteilung_resttumor" opal-value-type="text" val-fhir-path="Procedure.where(category.coding.code = 'OP').outcome.coding.where(system = 'http://dktk.dkfz.de/fhir/onco/core/CodeSystem/GesamtbeurteilungResidualstatusCS').code.value"  />
+  </container>
+
+
+  <container csv-filename="Radiation-Therapy-${TIMESTAMP}.csv" opal-table="radiation-therapy" opal-entity-type="RadiationTherapy">
+    <attribute csv-column="radiation-therapy-id" primary-key="true" opal-value-type="text" val-fhir-path="Procedure.where(category.coding.code = 'ST').id" anonym="Rad" op="EXTRACT_RELATIVE_ID"/>
+    <attribute csv-column="diagnosis-id" opal-value-type="text" val-fhir-path="Procedure.where(category.coding.code = 'ST').reasonReference.reference.value" anonym="Dia"/>
+    <attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="Procedure.where(category.coding.code = 'ST').subject.reference.value" anonym="Pat" />
+    <attribute csv-column="strahlentherapie_stellung_zu_operativer_therapie" opal-value-type="text" val-fhir-path="Procedure.extension('http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Extension-StellungZurOp').value.coding.code.value"/>
+    <attribute csv-column="intention_strahlentherapie" opal-value-type="text" val-fhir-path="Procedure.extension('http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Extension-SYSTIntention').value.coding.code.value" />
+    <attribute csv-column="strahlentherapie_beginn" opal-value-type="date" val-fhir-path="Procedure.where(category.coding.code = 'ST').performed.start.value"/>
+    <attribute csv-column="strahlentherapie_ende" opal-value-type="date" val-fhir-path="Procedure.where(category.coding.code = 'ST').performed.end.value"/>
+  </container>
+
+
+  <container csv-filename="Molecular-Marker-${TIMESTAMP}.csv" opal-table="molecular-marker" opal-entity-type="MolecularMarker">
+    <attribute csv-column="mol-marker-id" primary-key="true" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '69548-6').id" anonym="Mol" op="EXTRACT_RELATIVE_ID"/>
+    <attribute csv-column="diagnosis-id" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '69548-6').focus.reference.value" anonym="Dia" />
+    <attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '69548-6').subject.reference.value" anonym="Pat" />
+    <attribute csv-column="datum_der_datenerhebung" opal-value-type="date" val-fhir-path="Observation.where(code.coding.code = '69548-6').effective.value"/>
+    <attribute csv-column="marker" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '69548-6').component.value.coding.code.value"/>
+    <attribute csv-column="status_des_molekularen_markers" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '69548-6').value.coding.code.value" />
+    <attribute csv-column="zusaetzliche_alternative_dokumentation" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '69548-6').value.text.value"/>
+  </container>
+
+
+  <container csv-filename="Sample-${TIMESTAMP}.csv" opal-table="sample" opal-entity-type="Sample">
+    <attribute csv-column="sample-id" primary-key="true" opal-value-type="text" val-fhir-path="Specimen.id" anonym="Sam" op="EXTRACT_RELATIVE_ID"/>
+    <attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="Specimen.subject.reference.value" anonym="Pat" />
+    <attribute csv-column="entnahmedatum" opal-value-type="date" val-fhir-path="Specimen.collection.collectedDateTime.value"/>
+    <attribute csv-column="probenart" opal-value-type="text" val-fhir-path="Specimen.type.coding.code.value"/>
+    <attribute csv-column="status" opal-value-type="text" val-fhir-path="Specimen.status.code.value"/>
+    <attribute csv-column="projekt" opal-value-type="text" val-fhir-path="Specimen.identifier.system.value"/>
+   <!-- @TODO: it is still necessary to clarify whether it would not be better to take the quantity of collection.quantity -->
+    <attribute csv-column="menge" opal-value-type="integer" val-fhir-path="Specimen.container.specimenQuantity.value.value"/>
+    <attribute csv-column="einheit" opal-value-type="text" val-fhir-path="Specimen.container.specimenQuantity.unit.value"/>
+    <attribute csv-column="aliquot" opal-value-type="text" val-fhir-path="Specimen.parent.reference.exists().value" />
+  </container>
+
+
+
+
+  <fhir-rev-include>Observation:patient</fhir-rev-include>
+  <fhir-rev-include>Condition:patient</fhir-rev-include>
+  <fhir-rev-include>ClinicalImpression:patient</fhir-rev-include>
+  <fhir-rev-include>MedicationStatement:patient</fhir-rev-include>
+  <fhir-rev-include>Procedure:patient</fhir-rev-include>
+  <fhir-rev-include>Specimen:patient</fhir-rev-include>
+
+</template>
--- a/ccp/modules/datashield-setup.sh
+++ b/ccp/modules/datashield-setup.sh
@ -0,0 +1,44 @@
+#!/bin/bash -e
+
+if [ "$ENABLE_DATASHIELD" == true ]; then
+  # HACK: This only works because exporter-setup.sh and teiler-setup.sh are sourced after datashield-setup.sh
+  if [ -z "${ENABLE_EXPORTER}" ] || [ "${ENABLE_EXPORTER}" != "true" ]; then
+    log WARN "The ENABLE_EXPORTER variable is either not set or not set to 'true'."
+  fi
+  OAUTH2_CALLBACK=/oauth2/callback
+  OAUTH2_PROXY_SECRET="$(echo \"This is a salt string to generate one consistent encryption key for the oauth2_proxy. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 32)"
+  add_private_oidc_redirect_url "${OAUTH2_CALLBACK}"
+
+  log INFO "DataSHIELD setup detected -- will start DataSHIELD services."
+  OVERRIDE+=" -f ./$PROJECT/modules/datashield-compose.yml"
+  EXPORTER_OPAL_PASSWORD="$(generate_password \"exporter in Opal\")"
+  TOKEN_MANAGER_OPAL_PASSWORD="$(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="$(echo \"Token Manager\" | generate_simple_password)"
+  if [ ! -e /tmp/bridgehead/opal-cert.pem ]; then
+    mkdir -p /tmp/bridgehead/
+    openssl req -x509 -newkey rsa:4096 -nodes -keyout /tmp/bridgehead/opal-key.pem -out /tmp/bridgehead/opal-cert.pem -days 3650 -subj "/CN=opal/C=DE"
+  fi
+  mkdir -p /tmp/bridgehead/opal-map
+  sites="$(cat ./$PROJECT/modules/datashield-sites.json)"
+  echo "$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",
+    "internal": "opal:8443",
+    "allowed": input | map("datashield-connect.\(.).'"$BROKER_ID"'")
+  }]' >/tmp/bridgehead/opal-map/local.json
+  if [ "$USER" == "root" ]; then
+    chown -R bridgehead:docker /tmp/bridgehead
+    chmod g+wr /tmp/bridgehead/opal-map/*
+    chmod g+r /tmp/bridgehead/opal-key.pem
+  fi
+  add_private_oidc_redirect_url "/opal/*"
+fi
--- a/ccp/modules/datashield-sites.json
+++ b/ccp/modules/datashield-sites.json
@ -0,0 +1,14 @@
+[
+    "berlin",
+    "muenchen-lmu",
+    "dresden",
+    "freiburg",
+    "muenchen-tum",
+    "tuebingen",
+    "mainz",
+    "frankfurt",
+    "essen",
+    "dktk-datashield-test",
+    "dktk-test",
+    "mannheim"
+]
--- a/ccp/modules/datashield.md
+++ b/ccp/modules/datashield.md
@ -0,0 +1,28 @@
+# DataSHIELD
+This module constitutes the infrastructure to run DataSHIELD within the bridgehead. 
+For more information about DataSHIELD, please visit https://www.datashield.org/
+
+## R-Studio
+To connect to the different bridgeheads of the CCP through DataSHIELD, you can use your own R-Studio environment.
+However, this R-Studio has already installed the DataSHIELD libraries and is integrated within the bridgehead.
+This can save you some time for extra configuration of your R-Studio environment.
+
+## Opal
+This is the core of DataSHIELD. It is made up of Opal, a Postgres database and an R-server.
+For more information about Opal, please visit https://opaldoc.obiba.org
+
+### Opal
+Opal is OBiBa’s core database application for biobanks. 
+
+### Opal-DB
+Opal requires a database to import the data for DataSHIELD. We use a Postgres instance as database. 
+The data is imported within the bridgehead through the exporter.
+
+### Opal-R-Server
+R-Server to execute R scripts in DataSHIELD.
+
+## Beam
+### Beam-Connect
+Beam-Connect is used to route http(s) traffic through beam to enable R-Studio to access data from other bridgeheads that have datashield enabled.
+### Beam-Proxy
+The usual beam proxy used for communication.
--- a/ccp/modules/dnpm-setup.sh
+++ b/ccp/modules/dnpm-setup.sh
@ -1,4 +1,4 @@
-#!/bin/bash
+#!/bin/bash -e

 if [ -n "${ENABLE_DNPM}" ]; then
 	log INFO "DNPM setup detected (Beam.Connect) -- will start Beam.Connect for DNPM."
--- a/ccp/modules/export-and-qb.curl-templates
+++ b/ccp/modules/export-and-qb.curl-templates
@ -0,0 +1,6 @@
+# Full Excel Export
+curl --location --request POST 'https://${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'
--- a/ccp/modules/exporter-compose.yml
+++ b/ccp/modules/exporter-compose.yml
@ -0,0 +1,67 @@
+version: "3.7"
+
+services:
+  exporter:
+    image: docker.verbis.dkfz.de/ccp/dktk-exporter:latest
+    container_name: bridgehead-ccp-exporter
+    environment:
+      JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
+      LOG_LEVEL: "INFO"
+      EXPORTER_API_KEY: "${EXPORTER_API_KEY}" # Set in exporter-setup.sh
+      CROSS_ORIGINS: "https://${HOST}"
+      EXPORTER_DB_USER: "exporter"
+      EXPORTER_DB_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
+      EXPORTER_DB_URL: "jdbc:postgresql://exporter-db:5432/exporter"
+      HTTP_RELATIVE_PATH: "/ccp-exporter"
+      SITE: "${SITE_ID}"
+      HTTP_SERVLET_REQUEST_SCHEME: "https"
+      OPAL_PASSWORD: "${EXPORTER_OPAL_PASSWORD}"
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.exporter_ccp.rule=PathPrefix(`/ccp-exporter`)"
+      - "traefik.http.services.exporter_ccp.loadbalancer.server.port=8092"
+      - "traefik.http.routers.exporter_ccp.tls=true"
+      - "traefik.http.middlewares.exporter_ccp_strip.stripprefix.prefixes=/ccp-exporter"
+      - "traefik.http.routers.exporter_ccp.middlewares=exporter_ccp_strip"
+    volumes:
+      - "/var/cache/bridgehead/ccp/exporter-files:/app/exporter-files/output"
+
+  exporter-db:
+    image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
+    container_name: bridgehead-ccp-exporter-db
+    environment:
+      POSTGRES_USER: "exporter"
+      POSTGRES_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
+      POSTGRES_DB: "exporter"
+    volumes:
+      # Consider removing this volume once we find a solution to save Lens-queries to be executed in the explorer.
+      - "/var/cache/bridgehead/ccp/exporter-db:/var/lib/postgresql/data"
+
+  reporter:
+    image: docker.verbis.dkfz.de/ccp/dktk-reporter:latest
+    container_name: bridgehead-ccp-reporter
+    environment:
+      JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
+      LOG_LEVEL: "INFO"
+      CROSS_ORIGINS: "https://${HOST}"
+      HTTP_RELATIVE_PATH: "/ccp-reporter"
+      SITE: "${SITE_ID}"
+      EXPORTER_API_KEY: "${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/ccp/reporter-files:/app/reports"
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.reporter_ccp.rule=PathPrefix(`/ccp-reporter`)"
+      - "traefik.http.services.reporter_ccp.loadbalancer.server.port=8095"
+      - "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"
--- a/ccp/modules/exporter-setup.sh
+++ b/ccp/modules/exporter-setup.sh
@ -0,0 +1,8 @@
+#!/bin/bash -e
+
+if [ "$ENABLE_EXPORTER" == true ]; then
+  log INFO "Exporter setup detected -- will start Exporter service."
+  OVERRIDE+=" -f ./$PROJECT/modules/exporter-compose.yml"
+  EXPORTER_DB_PASSWORD="$(echo \"This is a salt string to generate one consistent password for the exporter. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
+  EXPORTER_API_KEY="$(echo \"This is a salt string to generate one consistent API KEY for the exporter. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 64)"
+fi
--- a/ccp/modules/exporter.md
+++ b/ccp/modules/exporter.md
@ -0,0 +1,15 @@
+# Exporter and Reporter
+
+
+## Exporter
+The exporter is a REST API that exports the data of the different databases of the bridgehead in a set of tables.
+It can accept different output formats as CSV, Excel, JSON or XML. It can also export data into Opal.
+
+## Exporter-DB
+It is a database to save queries for its execution in the exporter. 
+The exporter manages also the different executions of the same query in through the database.
+
+## Reporter
+This component is a plugin of the exporter that allows to create more complex Excel reports described in templates.
+It is compatible with different template engines as Groovy, Thymeleaf,...
+It is perfect to generate a document as our traditional CCP quality report.
--- a/ccp/modules/id-management-compose.yml
+++ b/ccp/modules/id-management-compose.yml
@ -1,4 +1,5 @@
 version: "3.7"
+
 services:
  id-manager:
    image: docker.verbis.dkfz.de/bridgehead/magicpl
@ -28,6 +29,7 @@ services:
    container_name: bridgehead-patientlist
    environment:
      - TOMCAT_REVERSEPROXY_FQDN=${HOST}
+      - TOMCAT_REVERSEPROXY_SSL=true
      - ML_SITE=${IDMANAGEMENT_FRIENDLY_ID}
      - ML_DB_PASS=${PATIENTLIST_POSTGRES_PASSWORD}
      - ML_API_KEY=${IDMANAGER_LOCAL_PATIENTLIST_APIKEY}
@ -43,7 +45,7 @@ services:
      - patientlist-db

  patientlist-db:
-    image: docker.verbis.dkfz.de/cache/postgres:15.6-alpine
+    image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
    container_name: bridgehead-patientlist-db
    environment:
      POSTGRES_USER: "mainzelliste"
--- a/ccp/modules/id-management-setup.sh
+++ b/ccp/modules/id-management-setup.sh
@ -1,4 +1,4 @@
-#!/bin/bash
+#!/bin/bash -e

 function idManagementSetup() {
 	if [ -n "$IDMANAGER_UPLOAD_APIKEY" ]; then
--- a/ccp/modules/mtba-compose.yml
+++ b/ccp/modules/mtba-compose.yml
@ -2,7 +2,7 @@ version: "3.7"

 services:
  mtba:
-    image: docker.verbis.dkfz.de/cache/samply/mtba:1.0.0
+    image: docker.verbis.dkfz.de/cache/samply/mtba:develop
    container_name: bridgehead-mtba
    environment:
      BLAZE_STORE_URL: http://blaze:8080
@ -11,22 +11,30 @@ services:
      ID_MANAGER_API_KEY: ${IDMANAGER_UPLOAD_APIKEY}
      ID_MANAGER_PSEUDONYM_ID_TYPE: BK_${IDMANAGEMENT_FRIENDLY_ID}_L-ID
      ID_MANAGER_URL: http://id-manager:8080/id-manager
-      PATIENT_CSV_FIRST_NAME_HEADER: ${MTBA_PATIENT_CSV_FIRST_NAME_HEADER}
-      PATIENT_CSV_LAST_NAME_HEADER: ${MTBA_PATIENT_CSV_LAST_NAME_HEADER}
-      PATIENT_CSV_GENDER_HEADER: ${MTBA_PATIENT_CSV_GENDER_HEADER}
-      PATIENT_CSV_BIRTHDAY_HEADER: ${MTBA_PATIENT_CSV_BIRTHDAY_HEADER}
+      PATIENT_CSV_FIRST_NAME_HEADER: ${MTBA_PATIENT_CSV_FIRST_NAME_HEADER:-FIRST_NAME}
+      PATIENT_CSV_LAST_NAME_HEADER: ${MTBA_PATIENT_CSV_LAST_NAME_HEADER:-LAST_NAME}
+      PATIENT_CSV_GENDER_HEADER: ${MTBA_PATIENT_CSV_GENDER_HEADER:-GENDER}
+      PATIENT_CSV_BIRTHDAY_HEADER: ${MTBA_PATIENT_CSV_BIRTHDAY_HEADER:-BIRTHDAY}
      CBIOPORTAL_URL:  http://cbioportal:8080
-      FILE_CHARSET: ${MTBA_FILE_CHARSET}
-      FILE_END_OF_LINE: ${MTBA_FILE_END_OF_LINE}
-      CSV_DELIMITER: ${MTBA_CSV_DELIMITER}
+      FILE_CHARSET: ${MTBA_FILE_CHARSET:-UTF-8}
+      FILE_END_OF_LINE: ${MTBA_FILE_END_OF_LINE:-LF}
+      CSV_DELIMITER: ${MTBA_CSV_DELIMITER:-TAB}
+      HTTP_RELATIVE_PATH: "/mtba"
+      OIDC_ADMIN_GROUP: "${OIDC_ADMIN_GROUP}"
+      OIDC_CLIENT_ID: "${OIDC_PRIVATE_CLIENT_ID}"
+      OIDC_CLIENT_SECRET: "${OIDC_CLIENT_SECRET}"
+      OIDC_REALM: "${OIDC_REALM}"
+      OIDC_URL: "${OIDC_URL}"
+
    labels:
      - "traefik.enable=true"
-      - "traefik.http.routers.mtba.rule=PathPrefix(`/`)"
-      - "traefik.http.services.mtba.loadbalancer.server.port=80"
-      - "traefik.http.routers.mtba.tls=true"
+      - "traefik.http.routers.mtba_ccp.rule=PathPrefix(`/mtba`)"
+      - "traefik.http.services.mtba_ccp.loadbalancer.server.port=8480"
+      - "traefik.http.routers.mtba_ccp.tls=true"
+
    volumes:
-      - /tmp/bridgehead/mtba/input:/app/input
-      - /tmp/bridgehead/mtba/persist:/app/persist
+      - /var/cache/bridgehead/ccp/mtba/input:/app/input
+      - /var/cache/bridgehead/ccp/mtba/persist:/app/persist

  # TODO: Include CBioPortal in Deployment ...
  # NOTE: CBioPortal can't load data while the system is running. So after import of data bridgehead needs to be restarted!
--- a/ccp/modules/mtba-setup.sh
+++ b/ccp/modules/mtba-setup.sh
@ -1,12 +1,12 @@
-#!/bin/bash
+#!/bin/bash -e

 function mtbaSetup() {
  if [ -n "$ENABLE_MTBA" ];then
    log INFO "MTBA setup detected -- will start MTBA Service and CBioPortal."
    if [ ! -n "$IDMANAGER_UPLOAD_APIKEY" ]; then
      log ERROR "Missing ID-Management Module! Fix this by setting up ID Management:"
-      exit 1;
    fi
    OVERRIDE+=" -f ./$PROJECT/modules/mtba-compose.yml"
+    add_private_oidc_redirect_url "/mtba/*"
  fi
 }
--- a/ccp/modules/mtba.md
+++ b/ccp/modules/mtba.md
@ -0,0 +1,6 @@
+# Molecular Tumor Board Alliance (MTBA)
+
+In this module, the genetic data to import is stored in a directory (/tmp/bridgehead/mtba/input). A process checks
+regularly if there are files in the directory. The files are pseudonomized when the IDAT is provided. The files are
+combined with clinical data of the blaze and imported in cBioPortal. On the other hand, this files are also imported in
+Blaze.
--- a/ccp/modules/nngm-compose.yml
+++ b/ccp/modules/nngm-compose.yml
@ -1,4 +1,5 @@
 version: "3.7"
+
 volumes:
  nngm-rest:

@ -21,9 +22,6 @@ services:
      - "traefik.http.routers.connector.middlewares=connector_strip,auth-nngm"
    volumes:
      - nngm-rest:/var/log
-
  traefik:
    labels:
      - "traefik.http.middlewares.auth-nngm.basicauth.users=${NNGM_AUTH}"
-
-
--- a/ccp/modules/nngm-setup.sh
+++ b/ccp/modules/nngm-setup.sh
@ -1,4 +1,4 @@
-#!/bin/bash
+#!/bin/bash -e

 if [ -n "$NNGM_CTS_APIKEY" ]; then
  log INFO "nNGM setup detected -- will start nNGM Connector."
--- a/ccp/modules/obds2fhir-rest-compose.yml
+++ b/ccp/modules/obds2fhir-rest-compose.yml
@ -0,0 +1,20 @@
+version: "3.7"
+
+services:
+  obds2fhir-rest:
+    container_name: bridgehead-obds2fhir-rest
+    image: docker.verbis.dkfz.de/ccp/obds2fhir-rest:main
+    environment:
+      IDTYPE: BK_${IDMANAGEMENT_FRIENDLY_ID}_L-ID
+      MAINZELLISTE_APIKEY: ${IDMANAGER_LOCAL_PATIENTLIST_APIKEY}
+      SALT: ${LOCAL_SALT}
+      KEEP_INTERNAL_ID: ${KEEP_INTERNAL_ID:-false}
+      MAINZELLISTE_URL: ${PATIENTLIST_URL:-http://patientlist:8080/patientlist}
+    restart: always
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.obds2fhir-rest.rule=PathPrefix(`/obds2fhir-rest`) || PathPrefix(`/adt2fhir-rest`)"
+      - "traefik.http.middlewares.obds2fhir-rest_strip.stripprefix.prefixes=/obds2fhir-rest,/adt2fhir-rest"
+      - "traefik.http.services.obds2fhir-rest.loadbalancer.server.port=8080"
+      - "traefik.http.routers.obds2fhir-rest.tls=true"
+      - "traefik.http.routers.obds2fhir-rest.middlewares=obds2fhir-rest_strip,auth"
--- a/ccp/modules/obds2fhir-rest-setup.sh
+++ b/ccp/modules/obds2fhir-rest-setup.sh
@ -0,0 +1,13 @@
+#!/bin/bash
+
+function obds2fhirRestSetup() {
+  if [ -n "$ENABLE_OBDS2FHIR_REST" ]; then
+    log INFO "oBDS2FHIR-REST setup detected -- will start obds2fhir-rest module."
+    if [ ! -n "$IDMANAGER_UPLOAD_APIKEY" ]; then
+      log ERROR "Missing ID-Management Module! Fix this by setting up ID Management:"
+      PATIENTLIST_URL=" "
+    fi
+    OVERRIDE+=" -f ./$PROJECT/modules/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/ccp/modules/teiler-compose.yml
+++ b/ccp/modules/teiler-compose.yml
@ -0,0 +1,81 @@
+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_ccp.rule=PathPrefix(`/ccp-teiler`)"
+      - "traefik.http.services.teiler_orchestrator_ccp.loadbalancer.server.port=9000"
+      - "traefik.http.routers.teiler_orchestrator_ccp.tls=true"
+      - "traefik.http.middlewares.teiler_orchestrator_ccp_strip.stripprefix.prefixes=/ccp-teiler"
+      - "traefik.http.routers.teiler_orchestrator_ccp.middlewares=teiler_orchestrator_ccp_strip"
+    environment:
+      TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend"
+      TEILER_DASHBOARD_URL: "https://${HOST}/ccp-teiler-dashboard"
+      DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE_LOWER_CASE}"
+      HTTP_RELATIVE_PATH: "/ccp-teiler"
+
+  teiler-dashboard:
+    image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:develop
+    container_name: bridgehead-teiler-dashboard
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.teiler_dashboard_ccp.rule=PathPrefix(`/ccp-teiler-dashboard`)"
+      - "traefik.http.services.teiler_dashboard_ccp.loadbalancer.server.port=80"
+      - "traefik.http.routers.teiler_dashboard_ccp.tls=true"
+      - "traefik.http.middlewares.teiler_dashboard_ccp_strip.stripprefix.prefixes=/ccp-teiler-dashboard"
+      - "traefik.http.routers.teiler_dashboard_ccp.middlewares=teiler_dashboard_ccp_strip"
+    environment:
+      DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
+      TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend"
+      OIDC_URL: "${OIDC_URL}"
+      OIDC_REALM: "${OIDC_REALM}"
+      OIDC_CLIENT_ID: "${OIDC_PUBLIC_CLIENT_ID}"
+      OIDC_TOKEN_GROUP: "${OIDC_GROUP_CLAIM}"
+      TEILER_ADMIN_NAME: "${OPERATOR_FIRST_NAME} ${OPERATOR_LAST_NAME}"
+      TEILER_ADMIN_EMAIL: "${OPERATOR_EMAIL}"
+      TEILER_ADMIN_PHONE: "${OPERATOR_PHONE}"
+      TEILER_PROJECT: "${PROJECT}"
+      EXPORTER_API_KEY: "${EXPORTER_API_KEY}"
+      TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler"
+      TEILER_DASHBOARD_HTTP_RELATIVE_PATH: "/ccp-teiler-dashboard"
+      TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler"
+      TEILER_USER: "${OIDC_USER_GROUP}"
+      TEILER_ADMIN: "${OIDC_ADMIN_GROUP}"
+      REPORTER_DEFAULT_TEMPLATE_ID: "ccp-qb"
+      EXPORTER_DEFAULT_TEMPLATE_ID: "ccp"
+
+
+  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_ccp.rule=PathPrefix(`/ccp-teiler-backend`)"
+      - "traefik.http.services.teiler_backend_ccp.loadbalancer.server.port=8085"
+      - "traefik.http.routers.teiler_backend_ccp.tls=true"
+      - "traefik.http.middlewares.teiler_backend_ccp_strip.stripprefix.prefixes=/ccp-teiler-backend"
+      - "traefik.http.routers.teiler_backend_ccp.middlewares=teiler_backend_ccp_strip"
+    environment:
+      LOG_LEVEL: "INFO"
+      APPLICATION_PORT: "8085"
+      APPLICATION_ADDRESS: "${HOST}"
+      DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
+      CONFIG_ENV_VAR_PATH: "/run/secrets/ccp.conf"
+      TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler"
+      TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler"
+      TEILER_DASHBOARD_DE_URL: "https://${HOST}/ccp-teiler-dashboard/de"
+      TEILER_DASHBOARD_EN_URL: "https://${HOST}/ccp-teiler-dashboard/en"
+      CENTRAX_URL: "${CENTRAXX_URL}"
+      HTTP_PROXY: "http://forward_proxy:3128"
+      ENABLE_MTBA: "${ENABLE_MTBA}"
+      ENABLE_DATASHIELD: "${ENABLE_DATASHIELD}"
+    secrets:
+      - ccp.conf
+
+secrets:
+  ccp.conf:
+    file: /etc/bridgehead/ccp.conf
--- a/ccp/modules/teiler-setup.sh
+++ b/ccp/modules/teiler-setup.sh
@ -0,0 +1,9 @@
+#!/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=${TEILER_DEFAULT_LANGUAGE,,}
+  add_public_oidc_redirect_url "/ccp-teiler/*"
+fi
--- a/ccp/modules/teiler.md
+++ b/ccp/modules/teiler.md
@ -0,0 +1,19 @@
+# Teiler
+This module orchestrates the different microfrontends of the bridgehead as a single page application.  
+
+## Teiler Orchestrator
+Single SPA component that consists on the root HTML site of the single page application and a javascript code that
+gets the information about the microfrontend calling the teiler backend and is responsible for registering them. With the
+resulting mapping, it can initialize, mount and unmount the required microfrontends on the fly. 
+
+The microfrontends run independently in different containers and can be based on different frameworks (Angular, Vue, React,...)
+This microfrontends can run as single alone but need an extension with Single-SPA (https://single-spa.js.org/docs/ecosystem).
+There are also available three templates (Angular, Vue, React) to be directly extended to be used directly in the teiler.
+
+## Teiler Dashboard
+It consists on the main dashboard and a set of embedded services.
+### Login
+user and password in ccp.local.conf
+
+## Teiler Backend
+In this component, the microfrontends are configured.
--- a/ccp/vars
+++ b/ccp/vars
@ -2,12 +2,23 @@ BROKER_ID=broker.ccp-it.dktk.dkfz.de
 BROKER_URL=https://${BROKER_ID}
 PROXY_ID=${SITE_ID}.${BROKER_ID}
 FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
-FOCUS_RETRY_COUNT=32
+FOCUS_RETRY_COUNT=${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

+OIDC_USER_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})"
+OIDC_ADMIN_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})_Verwalter"
+OIDC_PRIVATE_CLIENT_ID=${SITE_ID}-private
+OIDC_PUBLIC_CLIENT_ID=${SITE_ID}-public
+# Use "test-realm-01" for testing
+OIDC_REALM="${OIDC_REALM:-master}"
+OIDC_URL="https://login.verbis.dkfz.de"
+OIDC_ISSUER_URL="${OIDC_URL}/realms/${OIDC_REALM}"
+OIDC_GROUP_CLAIM="groups"
+
+POSTGRES_TAG=15.6-alpine

 for module in $PROJECT/modules/*.sh
 do
@ -17,4 +28,5 @@ done

 idManagementSetup
 mtbaSetup
-adt2fhirRestSetup
+obds2fhirRestSetup
+blazeSecondarySetup
--- a/lib/functions.sh
+++ b/lib/functions.sh
@ -53,7 +53,7 @@ checkOwner(){
 }

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

@ -155,6 +155,28 @@ setHostname() {
 	fi
 }

+# This function optimizes the usage of memory through blaze, according to the official performance tuning guide:
+#   https://github.com/samply/blaze/blob/master/docs/tuning-guide.md
+# Short summary of the adjustments made:
+# - set blaze memory cap to a quarter of the system memory
+# - set db block cache size to a quarter of the system memory
+# - limit resource count allowed in blaze to 1,25M per 4GB available system memory
+optimizeBlazeMemoryUsage() {
+	if [ -z "$BLAZE_MEMORY_CAP" ]; then
+	   system_memory_in_mb=$(LC_ALL=C free -m | grep 'Mem:' | awk '{print $2}');
+	   export BLAZE_MEMORY_CAP=$(($system_memory_in_mb/4));
+	fi
+	if [ -z "$BLAZE_RESOURCE_CACHE_CAP" ]; then
+		available_system_memory_chunks=$((BLAZE_MEMORY_CAP / 1000))
+		if [ $available_system_memory_chunks -eq 0 ]; then
+			log WARN "Only ${BLAZE_MEMORY_CAP} system memory available for Blaze. If your Blaze stores more than 128000 fhir ressources it will run significally slower."
+			export BLAZE_RESOURCE_CACHE_CAP=128000;
+		else
+			export BLAZE_RESOURCE_CACHE_CAP=$((available_system_memory_chunks * 312500))
+		fi
+	fi
+}
+
 # Takes 1) The Backup Directory Path 2) The name of the Service to be backuped
 # Creates 3 Backups: 1) For the past seven days 2) For the current month and 3) for each calendar week
 createEncryptedPostgresBackup(){
@ -239,3 +261,113 @@ add_basic_auth_user() {
 	log DEBUG "Saving clear text credentials in $FILE. If wanted, delete them manually."
   sed -i "/^$NAME/ s|$|\n# User: $USER\n# Password: $PASSWORD|" $FILE
 }
+
+OIDC_PUBLIC_REDIRECT_URLS=${OIDC_PUBLIC_REDIRECT_URLS:-""}
+OIDC_PRIVATE_REDIRECT_URLS=${OIDC_PRIVATE_REDIRECT_URLS:-""}
+
+# Add a redirect url to the public oidc client of the bridgehead
+function add_public_oidc_redirect_url() {
+    if [[ $OIDC_PUBLIC_REDIRECT_URLS == "" ]]; then
+        OIDC_PUBLIC_REDIRECT_URLS+="$(generate_redirect_urls $1)"
+    else 
+        OIDC_PUBLIC_REDIRECT_URLS+=",$(generate_redirect_urls $1)"
+    fi
+}
+
+# Add a redirect url to the private oidc client of the bridgehead
+function add_private_oidc_redirect_url() {
+    if [[ $OIDC_PRIVATE_REDIRECT_URLS == "" ]]; then
+        OIDC_PRIVATE_REDIRECT_URLS+="$(generate_redirect_urls $1)"
+    else 
+        OIDC_PRIVATE_REDIRECT_URLS+=",$(generate_redirect_urls $1)"
+    fi
+}
+
+function sync_secrets() {
+    local delimiter=$'\x1E'
+    local secret_sync_args=""
+    if [[ $OIDC_PRIVATE_REDIRECT_URLS != "" ]]; then
+        secret_sync_args="OIDC:OIDC_CLIENT_SECRET:private;$OIDC_PRIVATE_REDIRECT_URLS"
+    fi
+    if [[ $OIDC_PUBLIC_REDIRECT_URLS != "" ]]; then
+        if [[ $secret_sync_args == "" ]]; then
+            secret_sync_args="OIDC:OIDC_PUBLIC:public;$OIDC_PUBLIC_REDIRECT_URLS"
+        else
+            secret_sync_args+="${delimiter}OIDC:OIDC_PUBLIC:public;$OIDC_PUBLIC_REDIRECT_URLS"
+        fi
+    fi
+    if [[ $secret_sync_args == "" ]]; then
+        return
+    fi
+    mkdir -p /var/cache/bridgehead/secrets/ || fail_and_report 1 "Failed to create '/var/cache/bridgehead/secrets/'. Please run sudo './bridgehead install $PROJECT' again."
+    touch /var/cache/bridgehead/secrets/oidc
+    docker run --rm \
+        -v /var/cache/bridgehead/secrets/oidc:/usr/local/cache \
+        -v $PRIVATEKEYFILENAME:/run/secrets/privkey.pem:ro \
+        -v /srv/docker/bridgehead/$PROJECT/root.crt.pem:/run/secrets/root.crt.pem:ro \
+        -v /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro \
+        -e TLS_CA_CERTIFICATES_DIR=/conf/trusted-ca-certs \
+        -e NO_PROXY=localhost,127.0.0.1 \
+        -e ALL_PROXY=$HTTPS_PROXY_FULL_URL \
+        -e PROXY_ID=$PROXY_ID \
+        -e BROKER_URL=$BROKER_URL \
+        -e OIDC_PROVIDER=secret-sync-central.oidc-client-enrollment.$BROKER_ID \
+        -e SECRET_DEFINITIONS=$secret_sync_args \
+        docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest
+
+    set -a # Export variables as environment variables
+    source /var/cache/bridgehead/secrets/*
+    set +a # Export variables in the regular way
+}
+
+capitalize_first_letter() {
+    input="$1"
+    capitalized="$(tr '[:lower:]' '[:upper:]' <<< ${input:0:1})${input:1}"
+    echo "$capitalized"
+}
+
+# Generate a string of ',' separated string of redirect urls relative to $HOST.
+# $1 will be appended to the url
+# If the host looks like dev-jan.inet.dkfz-heidelberg.de it will generate urls with dev-jan and the original $HOST as url Authorities
+function generate_redirect_urls(){
+    local redirect_urls="https://${HOST}$1"
+    local host_without_proxy="$(echo "$HOST" | cut -d '.' -f1)"
+    # Only append second url if its different and the host is not an ip address
+    if [[ "$HOST" != "$host_without_proxy" && ! "$HOST" =~ ^[0-9]+\.[0-9]+\.[0-9]+\.[0-9]+$ ]]; then
+        redirect_urls+=",https://$host_without_proxy$1"
+    fi
+    echo "$redirect_urls"
+}
+
+# This password contains at least one special char, a random number and a random upper and lower case letter
+generate_password(){
+  local seed_text="$1"
+  local seed_num=$(awk 'BEGIN{FS=""} NR==1{print $10}' /etc/bridgehead/pki/${SITE_ID}.priv.pem | od -An -tuC)
+  local nums="1234567890"
+  local n=$(echo "$seed_num" | awk '{print $1 % 10}')
+  local random_digit=${nums:$n:1}
+  local n=$(echo "$seed_num" | awk '{print $1 % 26}')
+  local upper="ABCDEFGHIJKLMNOPQRSTUVWXYZ"
+  local lower="abcdefghijklmnopqrstuvwxyz"
+  local random_upper=${upper:$n:1}
+  local random_lower=${lower:$n:1}
+  local n=$(echo "$seed_num" | awk '{print $1 % 8}')
+  local special='@#$%^&+='
+  local random_special=${special:$n:1}
+
+  local combined_text="This is a salt string to generate one consistent password for ${seed_text}. It is not required to be secret."
+  local main_password=$(echo "${combined_text}" | sha1sum | openssl pkeyutl -sign -inkey "/etc/bridgehead/pki/${SITE_ID}.priv.pem" 2> /dev/null | base64 | head -c 26 | sed 's/\//A/g')
+
+  echo "${main_password}${random_digit}${random_upper}${random_lower}${random_special}"
+}
+
+# This password only contains alphanumeric characters
+generate_simple_password(){
+  local seed_text="$1"
+  local combined_text="This is a salt string to generate one consistent password for ${seed_text}. It is not required to be secret."
+  echo "${combined_text}" | sha1sum | openssl pkeyutl -sign -inkey "/etc/bridgehead/pki/${SITE_ID}.priv.pem" 2> /dev/null | base64 | head -c 26 | sed 's/[+\/]/A/g'
+}
+
+docker_jq() {
+    docker run --rm -i docker.verbis.dkfz.de/cache/jqlang/jq:latest "$@"
+}
--- a/lib/prepare-system.sh
+++ b/lib/prepare-system.sh
@ -89,6 +89,9 @@ elif [[ "$DEV_MODE" == "DEV" ]]; then
 fi

 chown -R bridgehead /etc/bridgehead /srv/docker/bridgehead
+mkdir -p /tmp/bridgehead /var/cache/bridgehead
+chown -R bridgehead:docker /tmp/bridgehead /var/cache/bridgehead
+chmod -R g+wr /var/cache/bridgehead /tmp/bridgehead

 log INFO "System preparation is completed and configuration is present."

--- a/lib/prerequisites.sh
+++ b/lib/prerequisites.sh
@ -67,29 +67,30 @@ log INFO "Checking network access ($BROKER_URL_FOR_PREREQ) ..."
 source /etc/bridgehead/${PROJECT}.conf
 source ${PROJECT}/vars

-set +e
-SERVERTIME="$(https_proxy=$HTTPS_PROXY_FULL_URL curl -m 5 -s -I $BROKER_URL_FOR_PREREQ 2>&1 | grep -i -e '^Date: ' | sed -e 's/^Date: //i')"
-RET=$?
-set -e
-if [ $RET -ne 0 ]; then
-	log WARN "Unable to connect to Samply.Beam broker at $BROKER_URL_FOR_PREREQ. Please check your proxy settings.\nThe currently configured proxy was \"$HTTPS_PROXY_URL\". This error is normal when using proxy authentication."
-	log WARN "Unable to check clock skew due to previous error."
-else
-	log INFO "Checking clock skew ..."
+if [ "${PROJECT}" != "minimal" ]; then
+  set +e
+  SERVERTIME="$(https_proxy=$HTTPS_PROXY_FULL_URL curl -m 5 -s -I $BROKER_URL_FOR_PREREQ 2>&1 | grep -i -e '^Date: ' | sed -e 's/^Date: //i')"
+  RET=$?
+  set -e
+  if [ $RET -ne 0 ]; then
+	  log WARN "Unable to connect to Samply.Beam broker at $BROKER_URL_FOR_PREREQ. Please check your proxy settings.\nThe currently configured proxy was \"$HTTPS_PROXY_URL\". This error is normal when using proxy authentication."
+  	log WARN "Unable to check clock skew due to previous error."
+  else
+	  log INFO "Checking clock skew ..."

-	SERVERTIME_AS_TIMESTAMP=$(date --date="$SERVERTIME" +%s)
-	MYTIME=$(date +%s)
-	SKEW=$(($SERVERTIME_AS_TIMESTAMP - $MYTIME))
-	SKEW=$(echo $SKEW | awk -F- '{print $NF}')
-	SYNCTEXT="For example, consider entering a correct NTP server (e.g. your institution's Active Directory Domain Controller in /etc/systemd/timesyncd.conf (option NTP=) and restart systemd-timesyncd."
-	if [ $SKEW -ge 300 ]; then
-		report_error 5 "Your clock is not synchronized (${SKEW}s off). This will cause Samply.Beam's certificate will fail. Please setup time synchronization. $SYNCTEXT"
-		exit 1
-	elif [ $SKEW -ge 60 ]; then
-		log WARN "Your clock is more than a minute off (${SKEW}s). Consider syncing to a time server. $SYNCTEXT"
-	fi
+    SERVERTIME_AS_TIMESTAMP=$(date --date="$SERVERTIME" +%s)
+	  MYTIME=$(date +%s)
+	  SKEW=$(($SERVERTIME_AS_TIMESTAMP - $MYTIME))
+	  SKEW=$(echo $SKEW | awk -F- '{print $NF}')
+	  SYNCTEXT="For example, consider entering a correct NTP server (e.g. your institution's Active Directory Domain Controller in /etc/systemd/timesyncd.conf (option NTP=) and restart systemd-timesyncd."
+	  if [ $SKEW -ge 300 ]; then
+		  report_error 5 "Your clock is not synchronized (${SKEW}s off). This will cause Samply.Beam's certificate will fail. Please setup time synchronization. $SYNCTEXT"
+		  exit 1
+	  elif [ $SKEW -ge 60 ]; then
+		  log WARN "Your clock is more than a minute off (${SKEW}s). Consider syncing to a time server. $SYNCTEXT"
+	  fi
+  fi
 fi
-
 checkPrivKey() {
  if [ -e /etc/bridgehead/pki/${SITE_ID}.priv.pem ]; then
    log INFO "Success - private key found."
@ -100,7 +101,7 @@ checkPrivKey() {
  return 0
 }

-if [[ "$@" =~ "noprivkey" ]]; then
+if [[ "$@" =~ "noprivkey" ||  "${PROJECT}" != "minimal" ]]; then
  log INFO "Skipping check for private key for now."
 else
  checkPrivKey || exit 1
--- a/minimal/docker-compose.yml
+++ b/minimal/docker-compose.yml
@ -42,6 +42,9 @@ 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
@ -55,5 +58,3 @@ services:
      HOST: ${HOST}
      PROJECT: ${PROJECT}
      SITE_NAME: ${SITE_NAME}
-
-