Added setting bridgehead path to enviroment

c4/docker-compose.yml

@@ -28,7 +28,7 @@ services:
       SITEID: ${SITEID}
       CENTRAL_SEARCH: ${CCP_CENTRALSEARCH_URL}
       DECENTRAL_SEARCH: ${CCP_DECENTRALSEARCH_URL}
-      MDR_URL: ${MDR_URL}
+      MDR_URL: ${CCP_MDR_URL}
       MONITOR_URL: ${CCP_MONITOR_URL}
       SHARE_URL: "${PROTOCOL}://${HOST}:${PORT}"
       ID_MANAGER_URL: ${ID_MANAGER_URL}
@@ -39,8 +39,7 @@ services:
       POSTGRES_PORT: ${CONNECTOR_DB_PORT}
       POSTGRES_DB: ${CONNECTOR_POSTGRES_DB}
       POSTGRES_USER: ${CONNECTOR_POSTGRES_USER}
-      POSTGRES_PASS: ${C4_CONNECTOR_POSTGRES_PASSWORD}
+      POSTGRES_PASS: ${CONNECTOR_POSTGRES_PASS}
-      DEPLOYMENT_CONTEXT: ${COMPOSE_PROJECT_NAME}-connector
       HTTP_PROXY_URL: ${HTTP_PROXY_URL}
       HTTP_PROXY_USERNAME: ${HTTP_PROXY_USERNAME}
       HTTP_PROXY_PASSWORD: ${HTTP_PROXY_PASSWORD}
@@ -53,54 +52,104 @@ services:
     depends_on:
       - connector_db
     ports:
-      - "8082:8080"
+      - "8080:8080"
-      - "65496:65395"
     restart: always
  
   connector_db:
     container_name: bridgehead_connector_db
     image: postgres:10.17
     environment:
+      POSTGRES_HOST: ${CONNECTOR_POSTGRES_HOST}
       POSTGRES_DB: ${CONNECTOR_POSTGRES_DB}
       POSTGRES_USER: ${CONNECTOR_POSTGRES_USER}
-      POSTGRES_PASSWORD: ${C4_CONNECTOR_POSTGRES_PASSWORD}
+      POSTGRES_PASSWORD: ${CONNECTOR_POSTGRES_PASS}
       TZ: Europe/Berlin
     volumes:
       - "connector_db_data:/var/lib/postgresql/data"
     restart: always
 
-  ## ID-Management
+
   idmanager:
     container_name: bridgehead_idmanager
-    image: docker.verbis.dkfz.de/ccp/idmanager:deploy-c4
+    image: docker.verbis.dkfz.de/pseudonymisierung/magicpl:0.2.0-RC23
     environment:
-      MAGICPL_MAINZELLISTE_CENTRAL_URL: ${CCP_PATIENTLIST_URL}
+      MAGICPL_MAINZELLISTE_URL: ${MAGICPL_MAINZELLISTE_URL}
-      MAGICPL_CENTRAL_URL: ${CCP_CONTROLLNUMBERGENERATOR_URL}
+      MAGICPL_MAINZELLISTE_API_KEY: ${MAGICPL_MAINZELLISTE_API_KEY}
-      MAGICPL_SITE: ${SITEID}
+      MAGICPL_API_KEY: ${MAGICPL_API_KEY}
+      MAGICPL_API_KEY_CONNECTOR: ${MAGICPL_API_KEY_CONNECTOR}
+      MAGICPL_PASSPHRASE: ${MAGICPL_PASSPHRASE}
+      MAGICPL_MAINZELLISTE_CENTRAL_URL: ${MAGICPL_MAINZELLISTE_CENTRAL_URL}
+      MAGICPL_MAINZELLISTE_CENTRAL_API_KEY: ${MAGICPL_MAINZELLISTE_CENTRAL_API_KEY}
+      MAGICPL_CENTRAL_URL: ${MAGICPL_CENTRAL_URL}
+      MAGICPL_CENTRAL_API_KEY: ${MAGICPL_CENTRAL_API_KEY}
+      MAGICPL_OIDC_PROVIDER: ${MAGICPL_OIDC_PROVIDER}
+      MAGICPL_OIDC_CLIENT_ID: ${MAGICPL_OIDC_CLIENT_ID}
+      MAGICPL_OIDC_CLIENT_SECRET: ${MAGICPL_OIDC_CLIENT_SECRET}
+      MAGICPL_SITE: adt
       MAGICPL_LOG_LEVEL: info
-      GLOBAL_ID: DKTK
       TZ: Europe/Berlin
     volumes:
       - "idmanager_logs:/usr/local/tomcat/logs"
-    ports:
-      - "8084:8080"
     secrets:
       - magicpl.docker.xml
       - dktk_bridgehead_info.docker.xml
       - proxy.docker.xml
+    depends_on:
+      - patientlist
+    ports:
+      - "8085:8080"
+  
+  patientlist:
+    container_name: bridgehead_patientlist
+    image: medicalinformatics/mainzelliste:develop
+    environment:
+      ML_DB_DRIVER: org.postgresql.Driver
+      ML_DB_TYPE: postgresql
+      ML_DB_HOST: ${ML_DB_HOST}
+      ML_DB_PORT: ${ML_DB_PORT}
+      ML_DB_NAME: ${ML_DB_NAME}
+      ML_DB_USER: ${ML_DB_USER}
+      ML_DB_PASS: ${ML_DB_PASS}
+      ML_API_KEY: ${ML_API_KEY}
+      ML_LOG_LEVEL: warning
+      ML_SITE: adt
+      TZ: Europe/Berlin
+    env_file:
+      - ./site-config/patientlist.env
+    volumes:
+      - "patientlist_logs:/usr/local/tomcat/logs"
+    secrets:
+      - mainzelliste.docker.conf
+      - centralSearchPublicKey
+    depends_on:
+      - patientlist_db
+    ports:
+      - "8086:8080"
+
+  patientlist_db:
+    container_name: bridgehead_patientlist_db
+    image: postgres:13.1-alpine
+    environment:
+      POSTGRES_HOST: ${ML_DB_HOST}
+      POSTGRES_DB: ${ML_DB_NAME}
+      POSTGRES_USER: ${ML_DB_USER}
+      POSTGRES_PASSWORD: ${ML_DB_PASS}
+      TZ: Europe/Berlin
+    volumes:
+      - "patientlist_db_data:/var/lib/postgresql/data"
 
   store:
     container_name: bridgehead_store
     image: docker.verbis.dkfz.de/ccp/samply.store:release-5.1.2
     environment:
       MDR_URL: ${CCP_MDR_URL}
-      MDR_NAMESPACE: adt,dktk,marker
+      MDR_NAMESPACE: ${MDR_NAMESPACE}
-      MDR_VALIDATION: "false"
+      MDR_VALIDATION: ${MDR_VALIDATION}
-      POSTGRES_HOST: bridgehead_store_db
+      POSTGRES_HOST: ${STORE_POSTGRES_HOST}
-      POSTGRES_PORT: 5432
+      POSTGRES_PORT: ${STORE_POSTGRES_PORT}
-      POSTGRES_DB: samplystore
+      POSTGRES_DB: ${STORE_POSTGRES_DB}
-      POSTGRES_USER: samplystore
+      POSTGRES_USER: ${STORE_POSTGRES_USER}
-      POSTGRES_PASSWORD: ${C4_SAMPLY_STORE_PASS}
+      POSTGRES_PASSWORD: ${STORE_POSTGRES_PASS}
       TZ: Europe/Berlin
     volumes:
       - "store_logs:/usr/local/tomcat/logs"
@@ -108,7 +157,6 @@ services:
       - store_db
     ports:
       - "8083:8080"
-      - "65495:65395"
     restart: always
 
   store_db:
@@ -116,11 +164,11 @@ services:
     image: postgres:10.17
     command: postgres -c datestyle='iso, dmy'
     environment:
-      POSTGRES_HOST: store_db
+      POSTGRES_HOST: ${STORE_POSTGRES_HOST}
-      POSTGRES_PORT: 5432
+      POSTGRES_PORT: ${STORE_POSTGRES_PORT}
-      POSTGRES_DB: samplystore
+      POSTGRES_DB: ${STORE_POSTGRES_DB}
-      POSTGRES_USER: samplystore
+      POSTGRES_USER: ${STORE_POSTGRES_USER}
-      POSTGRES_PASSWORD: ${C4_SAMPLY_STORE_PASS}
+      POSTGRES_PASSWORD: ${STORE_POSTGRES_PASS}
       TZ: Europe/Berlin
     volumes:
       - "store_db_data:/var/lib/postgresql/data"

dktk/docker-compose.yml

@@ -1,10 +1,12 @@
 version: "3.7"
 volumes:
-  connector_db_data: 
+  connector_db_data: null
-  connector_logs: 
+  connector_logs: null
-  patientlist_db_data: 
+  patientlist_db_data: null
-  patientlist_logs: 
+  patientlist_logs: null
-  idmanager_logs: 
+  idmanager_logs: null
+  store_db_data: null
+  store_logs: null
 secrets:
   mainzelliste.docker.conf:
     file: ../internal-configuration/mainzelliste.conf
@@ -19,12 +21,11 @@ secrets:
 
 services:
   connector:
-    container_name: bridgehead_dktk_connector
+    container_name: bridgehead_c4_connector
-    image: samply/share-client:dktk-develop
+    image: "samply/share-client:c4-7"
     environment:
       SITE: ${SITE}
       SITEID: ${SITEID}
-      TOMCAT_REVERSEPROXY_FQDN: ${HOST}/${COMPOSE_PROJECT_NAME}-connector
       CENTRAL_SEARCH: ${CCP_CENTRALSEARCH_URL}
       DECENTRAL_SEARCH: ${CCP_DECENTRALSEARCH_URL}
       MDR_URL: ${CCP_MDR_URL}
@@ -35,11 +36,10 @@ services:
       PATIENTLIST_URL: ${PATIENTLIST_URL}
       STORE_URL: ${LDM_URL}
       POSTGRES_HOST: ${CONNECTOR_DB_HOST}
-      POSTGRES_PORT: 5432
+      POSTGRES_PORT: ${CONNECTOR_DB_PORT}
       POSTGRES_DB: ${CONNECTOR_POSTGRES_DB}
       POSTGRES_USER: ${CONNECTOR_POSTGRES_USER}
-      POSTGRES_PASS: ${DKTK_CONNECTOR_POSTGRES_PASSWORD}
+      POSTGRES_PASS: ${CONNECTOR_POSTGRES_PASS}
-      DEPLOYMENT_CONTEXT: ${COMPOSE_PROJECT_NAME}-connector
       HTTP_PROXY_URL: ${HTTP_PROXY_URL}
       HTTP_PROXY_USERNAME: ${HTTP_PROXY_USERNAME}
       HTTP_PROXY_PASSWORD: ${HTTP_PROXY_PASSWORD}
@@ -51,48 +51,41 @@ services:
       - "connector_logs:/usr/local/tomcat/logs"
     depends_on:
       - connector_db
+    ports:
+      - "8080:8080"
     restart: always
-    extra_hosts:
-      - "host.docker.internal:host-gateway"
-      - "${HOST}:${HOSTIP}"
  
   connector_db:
-    container_name: bridgead_connector_db
+    container_name: bridgehead_connector_db
     image: postgres:10.17
     environment:
+      POSTGRES_HOST: ${CONNECTOR_POSTGRES_HOST}
       POSTGRES_DB: ${CONNECTOR_POSTGRES_DB}
       POSTGRES_USER: ${CONNECTOR_POSTGRES_USER}
-      POSTGRES_PASSWORD: ${DKTK_CONNECTOR_POSTGRES_PASSWORD}
+      POSTGRES_PASSWORD: ${CONNECTOR_POSTGRES_PASS}
       TZ: Europe/Berlin
     volumes:
       - "connector_db_data:/var/lib/postgresql/data"
     restart: always
-    extra_hosts:
-      - "host.docker.internal:host-gateway"
-      - "${HOST}:${HOSTIP}"
 
-  ## ID-Management
+
   idmanager:
     container_name: bridgehead_idmanager
-    image: docker.verbis.dkfz.de/pseudonymisierung/magicpl:release-0.2.0
+    image: docker.verbis.dkfz.de/pseudonymisierung/magicpl:0.2.0-RC23
     environment:
-      TOMCAT_REVERSEPROXY_FQDN: ${HOST}/ID-Manager
+      MAGICPL_MAINZELLISTE_URL: ${MAGICPL_MAINZELLISTE_URL}
-      TOMCAT_REVERSEPROXY_SCHEME: ${PROTOCOL}
+      MAGICPL_MAINZELLISTE_API_KEY: ${MAGICPL_MAINZELLISTE_API_KEY}
-      TOMCAT_REVERSEPROXY_PORT: ${PORT}
+      MAGICPL_API_KEY: ${MAGICPL_API_KEY}
-      MAGICPL_MAINZELLISTE_URL: http://patientlist:8080/Patientlist
+      MAGICPL_API_KEY_CONNECTOR: ${MAGICPL_API_KEY_CONNECTOR}
-      MAGICPL_MAINZELLISTE_API_KEY: ${LOCAL_IDMANAGER_MAINZELLISTE_APIKEY}
+      MAGICPL_PASSPHRASE: ${MAGICPL_PASSPHRASE}
-      MAGICPL_API_KEY: ${LOCAL_IDMANAGER_LDM_APIKEY}
+      MAGICPL_MAINZELLISTE_CENTRAL_URL: ${MAGICPL_MAINZELLISTE_CENTRAL_URL}
-      MAGICPL_API_KEY_CONNECTOR: ${LOCAL_IDMANAGER_CONNECTOR_APIKEY}
+      MAGICPL_MAINZELLISTE_CENTRAL_API_KEY: ${MAGICPL_MAINZELLISTE_CENTRAL_API_KEY}
-      MAGICPL_PASSPHRASE: notUsedInThisConfigurationButMandatory
+      MAGICPL_CENTRAL_URL: ${MAGICPL_CENTRAL_URL}
-      ### Configuration for communication with central identity management
+      MAGICPL_CENTRAL_API_KEY: ${MAGICPL_CENTRAL_API_KEY}
-      MAGICPL_MAINZELLISTE_CENTRAL_URL: ${CCP_PATIENTLIST_URL}
+      MAGICPL_OIDC_PROVIDER: ${MAGICPL_OIDC_PROVIDER}
-      MAGICPL_MAINZELLISTE_CENTRAL_API_KEY: ${CCP_PATIENTLISTE_APIKEY}
+      MAGICPL_OIDC_CLIENT_ID: ${MAGICPL_OIDC_CLIENT_ID}
-      MAGICPL_CENTRAL_URL: ${CCP_CONTROLLNUMBERGENERATOR_URL}
+      MAGICPL_OIDC_CLIENT_SECRET: ${MAGICPL_OIDC_CLIENT_SECRET}
-      MAGICPL_CENTRAL_API_KEY: ${CCP_CONTROLLNUMBERGENERATOR_APIKEY}
+      MAGICPL_SITE: adt
-      MAGICPL_OIDC_PROVIDER: ${CCP_OIDC_PROVIDER_URL}/oauth2
-      MAGICPL_OIDC_CLIENT_ID: ${CCP_OIDC_CLIENT_ID}
-      MAGICPL_OIDC_CLIENT_SECRET: ${CCP_OIDC_CLIENT_SECRET}
-      MAGICPL_SITE: ${SITEID}
       MAGICPL_LOG_LEVEL: info
       TZ: Europe/Berlin
     volumes:
@@ -103,24 +96,23 @@ services:
       - proxy.docker.xml
     depends_on:
       - patientlist
+    ports:
+      - "8085:8080"
   
   patientlist:
     container_name: bridgehead_patientlist
     image: medicalinformatics/mainzelliste:develop
     environment:
-      TOMCAT_REVERSEPROXY_FQDN: ${HOST}/Patientlist
-      TOMCAT_REVERSEPROXY_SCHEME: ${PROTOCOL}
-      TOMCAT_REVERSEPROXY_PORT: ${PORT}
       ML_DB_DRIVER: org.postgresql.Driver
       ML_DB_TYPE: postgresql
-      ML_DB_HOST: patientlist_db
+      ML_DB_HOST: ${ML_DB_HOST}
-      ML_DB_PORT: 5432
+      ML_DB_PORT: ${ML_DB_PORT}
       ML_DB_NAME: ${ML_DB_NAME}
       ML_DB_USER: ${ML_DB_USER}
-      ML_DB_PASS: ${DKTK_PATIENTLIST_DBPASS}
+      ML_DB_PASS: ${ML_DB_PASS}
-      ML_API_KEY: ${DKTK_IDMANAGER_MAINZELLISTE_APIKEY}
+      ML_API_KEY: ${ML_API_KEY}
       ML_LOG_LEVEL: warning
-      ML_SITE: ${SITEID}
+      ML_SITE: adt
       TZ: Europe/Berlin
     env_file:
       - ./site-config/patientlist.env
@@ -131,15 +123,17 @@ services:
       - centralSearchPublicKey
     depends_on:
       - patientlist_db
+    ports:
+      - "8086:8080"
 
   patientlist_db:
     container_name: bridgehead_patientlist_db
     image: postgres:13.1-alpine
     environment:
+      POSTGRES_HOST: ${ML_DB_HOST}
       POSTGRES_DB: ${ML_DB_NAME}
       POSTGRES_USER: ${ML_DB_USER}
-      POSTGRES_PASSWORD: ${DKTK_PATIENTLIST_DBPASS}
+      POSTGRES_PASSWORD: ${ML_DB_PASS}
       TZ: Europe/Berlin
     volumes:
       - "patientlist_db_data:/var/lib/postgresql/data"
-

gbn/docker-compose.yml

@@ -5,7 +5,7 @@ services:
     container_name: "bridgehead_blaze_store"
     image: "samply/blaze:0.15"
     environment:
-      BASE_URL: "http://store:8080"
+      BASE_URL: "http://bridgehead_blzae_store:8080"
       JAVA_TOOL_OPTIONS: "-Xmx4g"
     networks:
       - "samply"
@@ -16,14 +16,14 @@ services:
     restart: "always"
 
   connector:
-    container_name: "bridgehead_connector"
+    container_name: "bridgehead_gbn_connector"
     image: "samply/share-client:gbn-7"
     environment:
-      POSTGRES_HOST: "connector-db"
+      POSTGRES_HOST: "bridgehead_connector_db"
       POSTGRES_DB: "samply.connector"
       POSTGRES_USER: "samply"
-      POSTGRES_PASS: ${GBN_CONNECTOR_POSTGRES_PASS}
+      POSTGRES_PASS: ${CONNECTOR_POSTGRES_PASS}
-      STORE_URL: "http://store:8080/fhir"
+      STORE_URL: "http://bridgehead_store:8080/fhir"
       QUERY_LANGUAGE: "CQL"
       MDR_URL: "https://mdr.germanbiobanknode.de/v3/api/mdr"
     networks:
@@ -36,11 +36,11 @@ services:
     restart: "always"
 
   connector-db:
-    container_name: "bridgehead_connector-db"
+    container_name: "bridgehead_connector_db"
     image: "postgres:10.17"
     environment:
       POSTGRES_USER: "samply"
-      POSTGRES_PASSWORD: "samply"
+      POSTGRES_PASSWORD: ${CONNECTOR_POSTGRES_PASS}
       POSTGRES_DB: "samply.connector"
     networks:
       - "connector-db"

install-bridgehead.sh

@@ -1,18 +1,29 @@
 #!/bin/bash
 ### Note: Currently not complete, needs some features before useable for production
 
-./prerequisites.sh
+if ! ./prerequisites.sh; then
+    echo "Prerequisites failed, exiting"
+    exiting
+fi
 source site.conf
 
 echo "Installing bridgehead"
 
+if ! grep -E 'BRIDGEHEAD_PATH=' /etc/environment; then  
+  echo "BRIDGEHEAD_PATH=${PWD}" >> /etc/environment
+  echo "Please reboot the system to properly set the enviroment"
+  exit
+fi
+
+sed -i -e "s|\BRIDGEHEAD_PATH=.*|\BRIDGEHEAD_PATH=${PWD}|" environment
+
 cd /etc/systemd/system/
 
 echo "Installing bridgehead\@.service in systemd ..."
-sudo cp /srv/docker/bridgehead/convenience/bridgehead\@.service ./
+sudo cp ${BRIDGEHEAD_PATH}/convenience/bridgehead\@.service ./
 echo "Installing bridgehead\@.update.service in systemd ..."
-sudo cp /srv/docker/bridgehead/convenience/bridgehead-update\@.service ./
+sudo cp ${BRIDGEHEAD_PATH}/convenience/bridgehead-update\@.service ./
-sudo cp /srv/docker/bridgehead/convenience/bridgehead-update\@.timer ./
+sudo cp ${BRIDGEHEAD_PATH}/convenience/bridgehead-update\@.timer ./
 
 echo "Loading the bridgehead definitions in systemd"
 sudo systemctl daemon-reload

start-bridgehead.sh

@@ -1,7 +1,10 @@
 #!/bin/bash
 ### Note: Currently not complete, needs some features before useable for production
 
-./prerequisites.sh
+if ! ./prerequisites.sh; then
+    echo "Prerequisites failed, exiting"
+    exiting
+fi
 source site.conf
 
 echo "Starting bridgehead"

uninstall-bridgehead.sh

@@ -6,6 +6,9 @@ systemctl stop bridgehead@"${project}".service
 systemctl stop bridgehead-update@"${project}".timer
 systemctl stop bridgehead-update@"${project}".service
 
+sed -i -e "s|BRIDGEHEAD_PATH=.*||" /etc/environment
+
+
 cd /etc/systemd/system/
 rm bridgehead\@.service
 rm bridgehead-update\@.timer