minor fix

fix: deactivate landingpage for KR project

bbmri/docker-compose.yml

@@ -4,13 +4,14 @@ version: "3.7"
 
 services:
   blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
+    image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
     container_name: bridgehead-bbmri-blaze
     environment:
       BASE_URL: "http://bridgehead-bbmri-blaze:8080"
       JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
       DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
-      DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP
+      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"

bbmri/vars

@@ -7,6 +7,7 @@
 FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64}
 PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
 
+source versions
 for module in $PROJECT/modules/*.sh
 do
     log DEBUG "sourcing $module"

bridgehead

@@ -64,7 +64,7 @@ loadVars() {
 	fetchVarsFromVaultByFile /etc/bridgehead/$PROJECT.conf || fail_and_report 1 "Unable to fetchVarsFromVaultByFile"
 	setHostname
 	optimizeBlazeMemoryUsage
-	[ -e ./$PROJECT/vars ] && source ./$PROJECT/vars
+	[ -e ./$PROJECT/vars ] && source ./versions ./$PROJECT/vars
 	set +a
 
 	OVERRIDE=${OVERRIDE:=""}

cce/docker-compose.yml

@@ -2,7 +2,7 @@ version: "3.7"
 
 services:
   blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
+    image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
     container_name: bridgehead-cce-blaze
     environment:
       BASE_URL: "http://bridgehead-cce-blaze:8080"

cce/modules/lens-compose.yml

@@ -0,0 +1,33 @@
+version: "3.7"
+services:
+  landing:
+    container_name: lens_federated-search
+    image: docker.verbis.dkfz.de/ccp/lens:${SITE_ID}
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.landing.rule=PathPrefix(`/`)"
+      - "traefik.http.services.landing.loadbalancer.server.port=80"
+      - "traefik.http.routers.landing.tls=true"
+
+  spot:
+    image: docker.verbis.dkfz.de/ccp-private/central-spot
+    environment:
+      BEAM_SECRET: "${FOCUS_BEAM_SECRET_SHORT}"
+      BEAM_URL: http://beam-proxy:8081
+      BEAM_PROXY_ID: ${SITE_ID}
+      BEAM_BROKER_ID: ${BROKER_ID}
+      BEAM_APP_ID: "focus"
+      PROJECT_METADATA: "cce_supervisors"
+    depends_on:
+      - "beam-proxy"
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.services.spot.loadbalancer.server.port=8080"
+      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowmethods=GET,OPTIONS,POST"
+      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolalloworiginlist=https://${HOST}"
+      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowcredentials=true"
+      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolmaxage=-1"
+      - "traefik.http.routers.spot.rule=Host(`${HOST}`) && PathPrefix(`/backend`)"
+      - "traefik.http.middlewares.stripprefix_spot.stripprefix.prefixes=/backend"
+      - "traefik.http.routers.spot.tls=true"
+      - "traefik.http.routers.spot.middlewares=corsheaders2,stripprefix_spot"

cce/modules/lens-setup.sh

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

cce/vars

@@ -7,7 +7,8 @@ SUPPORT_EMAIL=manoj.waikar@dkfz-heidelberg.de
 PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
 BROKER_URL_FOR_PREREQ=$BROKER_URL
 
-for module in common/*.sh
+source versions
+for module in $PROJECT/modules/*.sh
 do
     log DEBUG "sourcing $module"
     source $module

ccp/docker-compose.yml

@@ -2,13 +2,14 @@ version: "3.7"
 
 services:
   blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
+    image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
     container_name: bridgehead-ccp-blaze
     environment:
       BASE_URL: "http://bridgehead-ccp-blaze:8080"
       JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
       DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
-      DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP
+      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"

ccp/modules/blaze-secondary-compose.yml

@@ -2,13 +2,14 @@ version: "3.7"
 
 services:
   blaze-secondary:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
+    image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
     container_name: bridgehead-ccp-blaze-secondary
     environment:
       BASE_URL: "http://bridgehead-ccp-blaze-secondary:8080"
       JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
       DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
-      DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP
+      DB_BLOCK_CACHE_SIZE: ${BLAZE_MEMORY_CAP}
+      CQL_EXPR_CACHE_SIZE: ${BLAZE_CQL_CACHE_CAP:-32}
       ENFORCE_REFERENTIAL_INTEGRITY: "false"
     volumes:
       - "blaze-secondary-data:/app/data"

ccp/modules/blaze-secondary-setup.sh

@@ -3,7 +3,7 @@
 function blazeSecondarySetup() {
   if [ -n "$ENABLE_SECONDARY_BLAZE" ]; then
     log INFO "Secondary Blaze setup detected -- will start second blaze."
-    OVERRIDE+=" -f ./common/blaze-secondary-compose.yml"
+    OVERRIDE+=" -f ./$PROJECT/modules/blaze-secondary-compose.yml"
     #make oBDS2FHIR ignore ID-Management and replace target Blaze
     PATIENTLIST_URL=" "
     STORE_PATH="http://blaze-secondary:8080/fhir"

ccp/modules/datashield-compose.yml

@@ -151,7 +151,7 @@ services:
       --pass-access-token=false
     labels:
       - "traefik.enable=true"
-      - "traefik.http.routers.oauth2_proxy.rule=Host(`${HOST}`) && PathPrefix(`/oauth2`)"
+      - "traefik.http.routers.oauth2_proxy.rule=PathPrefix(`/oauth2`)"
       - "traefik.http.services.oauth2_proxy.loadbalancer.server.port=4180"
       - "traefik.http.routers.oauth2_proxy.tls=true"
     environment:

ccp/modules/datashield-setup.sh

@@ -10,7 +10,7 @@ if [ "$ENABLE_DATASHIELD" == true ]; then
   add_private_oidc_redirect_url "${OAUTH2_CALLBACK}"
 
   log INFO "DataSHIELD setup detected -- will start DataSHIELD services."
-  OVERRIDE+=" -f ./common/datashield-compose.yml"
+  OVERRIDE+=" -f ./$PROJECT/modules/datashield-compose.yml"
   EXPORTER_OPAL_PASSWORD="$(generate_password \"exporter in Opal\")"
   TOKEN_MANAGER_OPAL_PASSWORD="$(generate_password \"Token Manager in Opal\")"
   OPAL_DB_PASSWORD="$(echo \"Opal DB\" | generate_simple_password)"
@@ -23,7 +23,7 @@ if [ "$ENABLE_DATASHIELD" == true ]; then
     openssl req -x509 -newkey rsa:4096 -nodes -keyout /tmp/bridgehead/opal-key.pem -out /tmp/bridgehead/opal-cert.pem -days 3650 -subj "/CN=opal/C=DE"
   fi
   mkdir -p /tmp/bridgehead/opal-map
-  sites="$(cat ./common/datashield-sites.json)"
+  sites="$(cat ./$PROJECT/modules/datashield-sites.json)"
   echo "$sites" | docker_jq -n --args '{"sites": input | map({
     "name": .,
     "id": .,

ccp/modules/dnpm-node-setup.sh

@@ -2,7 +2,7 @@
 
 if [ -n "${ENABLE_DNPM_NODE}" ]; then
 	log INFO "DNPM setup detected (BwHC Node) -- will start BwHC node."
-	OVERRIDE+=" -f ./common/dnpm-node-compose.yml"
+	OVERRIDE+=" -f ./$PROJECT/modules/dnpm-node-compose.yml"
 
 	# Set variables required for BwHC Node. ZPM_SITE is assumed to be set in /etc/bridgehead/<project>.conf
 	DNPM_APPLICATION_SECRET="$(echo \"This is a salt string to generate one consistent password for DNPM. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"

ccp/modules/dnpm-setup.sh

@@ -2,7 +2,7 @@
 
 if [ -n "${ENABLE_DNPM}" ]; then
 	log INFO "DNPM setup detected (Beam.Connect) -- will start Beam.Connect for DNPM."
-	OVERRIDE+=" -f ./common/dnpm-compose.yml"
+	OVERRIDE+=" -f ./$PROJECT/modules/dnpm-compose.yml"
 
 	# Set variables required for Beam-Connect
 	DNPM_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"

ccp/modules/exporter-setup.sh

@@ -2,7 +2,7 @@
 
 if [ "$ENABLE_EXPORTER" == true ]; then
   log INFO "Exporter setup detected -- will start Exporter service."
-  OVERRIDE+=" -f ./common/exporter-compose.yml"
+  OVERRIDE+=" -f ./$PROJECT/modules/exporter-compose.yml"
   EXPORTER_DB_PASSWORD="$(echo \"This is a salt string to generate one consistent password for the exporter. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
   EXPORTER_API_KEY="$(echo \"This is a salt string to generate one consistent API KEY for the exporter. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 64)"
 fi

ccp/modules/fhir2sql-setup.sh

@@ -2,6 +2,6 @@
 
 if [ "$ENABLE_FHIR2SQL" == true ]; then
   log INFO "Dashboard setup detected -- will start Dashboard backend and FHIR2SQL service."
-  OVERRIDE+=" -f ./common/fhir2sql-compose.yml"
+  OVERRIDE+=" -f ./$PROJECT/modules/fhir2sql-compose.yml"
   DASHBOARD_DB_PASSWORD="$(generate_simple_password 'fhir2sql')"
 fi

ccp/modules/id-management-compose.yml

@@ -19,10 +19,18 @@ services:
       - traefik-forward-auth
     labels:
       - "traefik.enable=true"
+      # Router with Authentication
       - "traefik.http.routers.id-manager.rule=PathPrefix(`/id-manager`)"
-      - "traefik.http.services.id-manager.loadbalancer.server.port=8080"
       - "traefik.http.routers.id-manager.tls=true"
       - "traefik.http.routers.id-manager.middlewares=traefik-forward-auth-idm"
+      - "traefik.http.routers.id-manager.service=id-manager-service"
+      # Router without Authentication
+      - "traefik.http.routers.id-manager-compatibility.rule=PathPrefix(`/id-manager/paths/translator/getIds`)"
+      - "traefik.http.routers.id-manager-compatibility.tls=true"
+      - "traefik.http.routers.id-manager-compatibility.service=id-manager-service"
+      # Definition of Service
+      - "traefik.http.services.id-manager-service.loadbalancer.server.port=8080"
+      - "traefik.http.services.id-manager-service.loadbalancer.server.scheme=http"
 
   patientlist:
     image: docker.verbis.dkfz.de/bridgehead/mainzelliste
@@ -57,7 +65,7 @@ services:
       - "/tmp/bridgehead/patientlist/:/docker-entrypoint-initdb.d/"
 
   traefik-forward-auth:
-    image: docker.verbis.dkfz.de/cache/oauth2-proxy/oauth2-proxy:v7.6.0
+    image: docker.verbis.dkfz.de/cache/oauth2-proxy/oauth2-proxy:latest
     environment:
       - http_proxy=http://forward_proxy:3128
       - https_proxy=http://forward_proxy:3128
@@ -67,6 +75,7 @@ services:
       - OAUTH2_PROXY_CLIENT_ID=bridgehead-${SITE_ID}
       - OAUTH2_PROXY_CLIENT_SECRET=${IDMANAGER_AUTH_CLIENT_SECRET}
       - OAUTH2_PROXY_COOKIE_SECRET=${IDMANAGER_AUTH_COOKIE_SECRET}
+      - OAUTH2_PROXY_COOKIE_NAME=_BRIDGEHEAD_oauth2_idm
       - OAUTH2_PROXY_COOKIE_DOMAINS=.${HOST}
       - OAUTH2_PROXY_HTTP_ADDRESS=:4180
       - OAUTH2_PROXY_REVERSE_PROXY=true

ccp/modules/id-management-setup.sh

@@ -3,7 +3,7 @@
 function idManagementSetup() {
 	if [ -n "$IDMANAGER_UPLOAD_APIKEY" ]; then
 		log INFO "id-management setup detected -- will start id-management (mainzelliste & magicpl)."
-		OVERRIDE+=" -f ./common/id-management-compose.yml"
+		OVERRIDE+=" -f ./ccp/modules/id-management-compose.yml"
 
 		# Auto Generate local Passwords
 		PATIENTLIST_POSTGRES_PASSWORD="$(echo \"id-management-module-db-password-salt\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"

ccp/modules/mtba-setup.sh

@@ -6,7 +6,7 @@ function mtbaSetup() {
     if [ ! -n "$IDMANAGER_UPLOAD_APIKEY" ]; then
       log ERROR "Missing ID-Management Module! Fix this by setting up ID Management:"
     fi
-    OVERRIDE+=" -f ./common/mtba-compose.yml"
+    OVERRIDE+=" -f ./$PROJECT/modules/mtba-compose.yml"
     add_private_oidc_redirect_url "/mtba/*"
   fi
 }

ccp/modules/nngm-setup.sh

@@ -2,5 +2,5 @@
 
 if [ -n "$NNGM_CTS_APIKEY" ]; then
   log INFO "nNGM setup detected -- will start nNGM Connector."
-  OVERRIDE+=" -f ./common/nngm-compose.yml"
+  OVERRIDE+=" -f ./$PROJECT/modules/nngm-compose.yml"
 fi

ccp/modules/obds2fhir-rest-setup.sh

@@ -7,7 +7,7 @@ function obds2fhirRestSetup() {
       log ERROR "Missing ID-Management Module! Fix this by setting up ID Management:"
       PATIENTLIST_URL=" "
     fi
-    OVERRIDE+=" -f ./common/obds2fhir-rest-compose.yml"
+    OVERRIDE+=" -f ./ccp/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
 }

ccp/modules/teiler-setup.sh

@@ -2,7 +2,7 @@
 
 if [ "$ENABLE_TEILER" == true ];then
   log INFO "Teiler setup detected -- will start Teiler services."
-  OVERRIDE+=" -f ./common/teiler-compose.yml"
+  OVERRIDE+=" -f ./$PROJECT/modules/teiler-compose.yml"
   TEILER_DEFAULT_LANGUAGE=DE
   TEILER_DEFAULT_LANGUAGE_LOWER_CASE=${TEILER_DEFAULT_LANGUAGE,,}
   add_public_oidc_redirect_url "/ccp-teiler/*"

ccp/vars

@@ -18,9 +18,8 @@ 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 common/*.sh
+source versions
+for module in $PROJECT/modules/*.sh
 do
     log DEBUG "sourcing $module"
     source $module

common/datashield-sites.json

@@ -1,15 +0,0 @@
-[
-    "berlin",
-    "muenchen-lmu",
-    "dresden",
-    "freiburg",
-    "muenchen-tum",
-    "tuebingen",
-    "mainz",
-    "frankfurt",
-    "essen",
-    "dktk-datashield-test",
-    "dktk-test",
-    "mannheim",
-    "central-ds-orchestrator"
-]

common/lens-setup.sh

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

dhki/docker-compose.yml

@@ -2,7 +2,7 @@ version: "3.7"
 
 services:
   blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
+    image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
     container_name: bridgehead-dhki-blaze
     environment:
       BASE_URL: "http://bridgehead-dhki-blaze:8080"
@@ -39,7 +39,7 @@ services:
       - "blaze"
 
   beam-proxy:
-    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
+    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${BEAM_TAG}
     container_name: bridgehead-beam-proxy
     environment:
       BROKER_URL: ${BROKER_URL}

dhki/vars

@@ -8,9 +8,8 @@ PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
 
 BROKER_URL_FOR_PREREQ=$BROKER_URL
 
-POSTGRES_TAG=15.6-alpine
-
-for module in common/*.sh
+source versions
+for module in ccp/modules/*.sh
 do
     log DEBUG "sourcing $module"
     source $module

itcc/docker-compose.yml

@@ -2,7 +2,7 @@ version: "3.7"
 
 services:
   blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
+    image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
     container_name: bridgehead-itcc-blaze
     environment:
       BASE_URL: "http://bridgehead-itcc-blaze:8080"

itcc/modules/lens-setup.sh

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

itcc/vars

@@ -7,7 +7,8 @@ SUPPORT_EMAIL=arturo.macias@dkfz-heidelberg.de
 PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
 BROKER_URL_FOR_PREREQ=$BROKER_URL
 
-for module in common/*.sh
+source versions
+for module in $PROJECT/modules/*.sh
 do
     log DEBUG "sourcing $module"
     source $module

kr/docker-compose.yml

@@ -1,8 +1,12 @@
 version: "3.7"
 
 services:
+  landing:
+    deploy:
+      replicas: 0 #deactivate landing page
+
   blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
+    image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
     container_name: bridgehead-kr-blaze
     environment:
       BASE_URL: "http://bridgehead-kr-blaze:8080"
@@ -36,7 +40,7 @@ services:
       - "blaze"
 
   beam-proxy:
-    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
+    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${BEAM_TAG}
     container_name: bridgehead-beam-proxy
     environment:
       BROKER_URL: ${BROKER_URL}

kr/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"

kr/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

kr/modules/lens-compose.yml

@@ -0,0 +1,35 @@
+version: "3.7"
+services:
+  landing:
+    deploy:
+      replicas: 1 #reactivate if lens is in use
+    container_name: lens_federated-search
+    image: docker.verbis.dkfz.de/ccp/lens:${SITE_ID}
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.landing.rule=PathPrefix(`/`)"
+      - "traefik.http.services.landing.loadbalancer.server.port=80"
+      - "traefik.http.routers.landing.tls=true"
+
+  spot:
+    image: docker.verbis.dkfz.de/ccp-private/central-spot
+    environment:
+      BEAM_SECRET: "${FOCUS_BEAM_SECRET_SHORT}"
+      BEAM_URL: http://beam-proxy:8081
+      BEAM_PROXY_ID: ${SITE_ID}
+      BEAM_BROKER_ID: ${BROKER_ID}
+      BEAM_APP_ID: "focus"
+      PROJECT_METADATA: "kr_supervisors"
+    depends_on:
+      - "beam-proxy"
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.services.spot.loadbalancer.server.port=8080"
+      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowmethods=GET,OPTIONS,POST"
+      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolalloworiginlist=https://${HOST}"
+      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowcredentials=true"
+      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolmaxage=-1"
+      - "traefik.http.routers.spot.rule=Host(`${HOST}`) && PathPrefix(`/backend`)"
+      - "traefik.http.middlewares.stripprefix_spot.stripprefix.prefixes=/backend"
+      - "traefik.http.routers.spot.tls=true"
+      - "traefik.http.routers.spot.middlewares=corsheaders2,stripprefix_spot"

kr/modules/lens-setup.sh

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

kr/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"

kr/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
+}

kr/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

kr/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

kr/vars

@@ -7,7 +7,8 @@ SUPPORT_EMAIL=arturo.macias@dkfz-heidelberg.de
 PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
 BROKER_URL_FOR_PREREQ=$BROKER_URL
 
-for module in common/*.sh
+source versions
+for module in $PROJECT/modules/*.sh
 do
     log DEBUG "sourcing $module"
     source $module

lib/functions.sh

@@ -170,9 +170,11 @@ optimizeBlazeMemoryUsage() {
 		available_system_memory_chunks=$((BLAZE_MEMORY_CAP / 1000))
 		if [ $available_system_memory_chunks -eq 0 ]; then
 			log WARN "Only ${BLAZE_MEMORY_CAP} system memory available for Blaze. If your Blaze stores more than 128000 fhir ressources it will run significally slower."
-			export BLAZE_RESOURCE_CACHE_CAP=128000;
+			export BLAZE_RESOURCE_CACHE_CAP=128000
+			export BLAZE_CQL_CACHE_CAP=32
 		else
 			export BLAZE_RESOURCE_CACHE_CAP=$((available_system_memory_chunks * 312500))
+			export BLAZE_CQL_CACHE_CAP=$((($system_memory_in_mb/4)/16))
 		fi
 	fi
 }

lib/prepare-system.sh

@@ -57,9 +57,9 @@ case "$PROJECT" in
 		;;
 	itcc)
 		site_configuration_repository_middle="git.verbis.dkfz.de/itcc-sites/"
-        ;;
-    dhki)
-        site_configuration_repository_middle="git.verbis.dkfz.de/dhki/"
+    ;;
+  dhki)
+    site_configuration_repository_middle="git.verbis.dkfz.de/dhki/"
 		;;
 	kr)
 		site_configuration_repository_middle="git.verbis.dkfz.de/krebsregister-sites/"

lib/prerequisites.sh

@@ -3,14 +3,16 @@
 source lib/functions.sh
 
 detectCompose
+CONFIG_DIR="/etc/bridgehead/"
+COMPONENT_DIR="/srv/docker/bridgehead/"
 
 if ! id "bridgehead" &>/dev/null; then
   log ERROR "User bridgehead does not exist. Please run bridgehead install $PROJECT"
   exit 1
 fi
 
-checkOwner /srv/docker/bridgehead bridgehead || exit 1
-checkOwner /etc/bridgehead bridgehead || exit 1
+checkOwner "${CONFIG_DIR}" bridgehead || exit 1
+checkOwner "${COMPONENT_DIR}" bridgehead || exit 1
 
 ## Check if user is a su
 log INFO "Checking if all prerequisites are met ..."
@@ -32,31 +34,31 @@ fi
 log INFO "Checking configuration ..."
 
 ## Download submodule
-if [ ! -d "/etc/bridgehead/" ]; then
-  fail_and_report 1 "Please set up the config folder at /etc/bridgehead. Instruction are in the readme."
+if [ ! -d "${CONFIG_DIR}" ]; then
+  fail_and_report 1 "Please set up the config folder at ${CONFIG_DIR}. Instruction are in the readme."
 fi
 
 # TODO: Check all required variables here in a generic loop
 
 #check if project env is present
-if [ -d "/etc/bridgehead/${PROJECT}.conf" ]; then
-   fail_and_report 1 "Project config not found. Please copy the template from ${PROJECT} and put it under /etc/bridgehead-config/${PROJECT}.conf."
+if [ -d "${CONFIG_DIR}${PROJECT}.conf" ]; then
+   fail_and_report 1 "Project config not found. Please copy the template from ${PROJECT} and put it under ${CONFIG_DIR}${PROJECT}.conf."
 fi
 
 # TODO: Make sure you're in the right directory, or, even better, be independent from the working directory.
 
 log INFO "Checking ssl cert for accessing bridgehead via https"
 
-if [ ! -d "/etc/bridgehead/traefik-tls" ]; then
+if [ ! -d "${CONFIG_DIR}traefik-tls" ]; then
   log WARN "TLS certs for accessing bridgehead via https missing, we'll now create a self-signed one. Please consider getting an officially signed one (e.g. via Let's Encrypt ...) and put into /etc/bridgehead/traefik-tls"
   mkdir -p /etc/bridgehead/traefik-tls
 fi
 
-if [ ! -e "/etc/bridgehead/traefik-tls/fullchain.pem" ]; then
+if [ ! -e "${CONFIG_DIR}traefik-tls/fullchain.pem" ]; then
   openssl req -x509 -newkey rsa:4096 -nodes -keyout /etc/bridgehead/traefik-tls/privkey.pem -out /etc/bridgehead/traefik-tls/fullchain.pem -days 3650 -subj "/CN=$HOST"
 fi
 
-if [ -e /etc/bridgehead/vault.conf ]; then
+if [ -e "${CONFIG_DIR}"vault.conf ]; then
   if [ "$(stat -c "%a %U" /etc/bridgehead/vault.conf)" != "600 bridgehead" ]; then
     fail_and_report 1 "/etc/bridgehead/vault.conf has wrong owner/permissions. To correct this issue, run chmod 600 /etc/bridgehead/vault.conf && chown bridgehead /etc/bridgehead/vault.conf."
   fi
@@ -64,8 +66,8 @@ fi
 
 log INFO "Checking network access ($BROKER_URL_FOR_PREREQ) ..."
 
-source /etc/bridgehead/${PROJECT}.conf
-source ${PROJECT}/vars
+source "${CONFIG_DIR}${PROJECT}".conf
+source ${PROJECT}/vars vars
 
 if [ "${PROJECT}" != "minimal" ]; then
   set +e
@@ -92,10 +94,10 @@ if [ "${PROJECT}" != "minimal" ]; then
   fi
 fi
 checkPrivKey() {
-  if [ -e /etc/bridgehead/pki/${SITE_ID}.priv.pem ]; then
+  if [ -e "${CONFIG_DIR}pki/${SITE_ID}.priv.pem" ]; then
     log INFO "Success - private key found."
   else
-    log ERROR "Unable to find private key at /etc/bridgehead/pki/${SITE_ID}.priv.pem. To fix, please run\n  bridgehead enroll ${PROJECT}\nand follow the instructions."
+    log ERROR "Unable to find private key at ${CONFIG_DIR}pki/${SITE_ID}.priv.pem. To fix, please run\n  bridgehead enroll ${PROJECT}\nand follow the instructions."
     return 1
   fi
   return 0
@@ -107,6 +109,11 @@ else
   checkPrivKey || exit 1
 fi
 
+for dir in  "${CONFIG_DIR}" "${COMPONENT_DIR}"; do
+  log INFO "Checking branch: $(cd $dir && echo "$dir $(git branch --show-current)")"
+  hc_send log "Checking branch: $(cd $dir && echo "$dir $(git branch --show-current)")"
+done
+
 log INFO "Success - all prerequisites are met!"
 hc_send log "Success - all prerequisites are met!"
 

minimal/docker-compose.yml

@@ -10,13 +10,13 @@ services:
       - --providers.docker=true
       - --providers.docker.exposedbydefault=false
       - --providers.file.directory=/configuration/
-      - --api.dashboard=true
+      - --api.dashboard=false
       - --accesslog=true
       - --entrypoints.web.http.redirections.entrypoint.to=websecure
       - --entrypoints.web.http.redirections.entrypoint.scheme=https
     labels:
       - "traefik.enable=true"
-      - "traefik.http.routers.dashboard.rule=PathPrefix(`/api`) || PathPrefix(`/dashboard`)"
+      - "traefik.http.routers.dashboard.rule=PathPrefix(`/api`) || PathPrefix(`/dashboard/`)"
       - "traefik.http.routers.dashboard.entrypoints=websecure"
       - "traefik.http.routers.dashboard.service=api@internal"
       - "traefik.http.routers.dashboard.tls=true"

minimal/vars

@@ -1,3 +1,5 @@
+
+source versions
 for module in $PROJECT/modules/*.sh
 do
     log DEBUG "sourcing $module"

versions

@@ -0,0 +1,2 @@
+BLAZE_TAG=0.28
+POSTGRES_TAG=15.6-alpine