Manges changes and moving vars to the correct file

c4/internal.env

@@ -0,0 +1,47 @@
+SITE=bridgehead_test
+SITEID=BRIDGEHEAD_TEST
+
+CONNECTOR_SHARE_URL="http://${HOST}:8080" 
+CONNECTOR_ENABLE_METRICS=false
+CONNECTOR_MONITOR_INTERVAL=
+CONNECTOR_UPDATE_SERVER=
+
+CONNECTOR_POSTGRES_PORT=5432
+CONNECTOR_POSTGRES_DB=samply.connector
+CONNECTOR_POSTGRES_USER=samply.connector
+
+HTTP_PROXY_HOST=${PROXY_URL}
+HTTP_PROXY_USER=
+HTTP_PROXY_PASSWORD=
+HTTPS_PROXY_HOST=${PROXY_URL}
+HTTPS_PROXY_USER=
+HTTPS_PROXY_PASSWORD=
+HTTP_PROXY=${PROXY_URL}
+HTTPS_PROXY=${PROXY_URL}
+http_proxy=${PROXY_URL}
+https_proxy=${PROXY_URL}
+
+CCP_CENTRALSEARCH_URL=https://centralsearch-test.dktk.dkfz.de/
+CCP_DECENTRALSEARCH_URL=https://decentralsearch-test.ccp-it.dktk.dkfz.de/
+
+CCP_MDR_URL=https://mdr.ccp-it.dktk.dkfz.de/v3/api/mdr
+CCP_MONITOR_URL=
+MONITOR_OPTOUT=
+
+## nNGM
+#NNGM_URL=http://bridgeheadstore:8080
+#NNGM_PROFILE=http://uk-koeln.de/fhir/StructureDefinition/Patient/nNGM/pseudonymisiert
+#NNGM_MAINZELLISTE_URL=https://test.verbis.dkfz.de/mpl
+
+##MDR
+MDR_NAMESPACE=adt,dktk,marker
+#MDR_MAP=
+MDR_VALIDATION=false
+
+ML_DB_NAME=mainzelliste
+ML_DB_PORT=5432
+ML_DB_USER=mainzelliste
+
+CENTRAL_CONTROL_NUMBER_GENERATPR_URL=http://e260-serv-03/central/api
+GLOBAL_ID=DKTK
+MAINZELLISTE_URL=https://patientlist-test.ccpit.dktk.dkfz.de/mainzelliste

dktk/docker-compose.yml

@@ -24,30 +24,9 @@ services:
     container_name: bridgehead_dktk_connector
     image: "samply/share-client:dktk-7"
     environment:
-      SITE: ${SITE}
+      STORE_URL: ${STORE_URL}
-      SITEID: ${SITEID}
-      CENTRAL_SEARCH: ${CCP_CENTRALSEARCH_URL}
-      DECENTRAL_SEARCH: ${CCP_DECENTRALSEARCH_URL}
-      MDR_URL: ${CCP_MDR_URL}
-      MONITOR_URL: ${CCP_MONITOR_URL}
-      SHARE_URL: "${PROTOCOL}://${HOST}:${PORT}"
-      ID_MANAGER_URL: ${ID_MANAGER_URL}
-      PROJECTPSEUDONYMISATION_URL: ${PROJECTPSEUDONYMISATION_URL}
-      PATIENTLIST_URL: ${PATIENTLIST_URL}
-      STORE_URL: ${LDM_URL}
       POSTGRES_HOST: ${CONNECTOR_DB_HOST}
-      POSTGRES_PORT: ${CONNECTOR_POSTGRES_PORT}
-      POSTGRES_DB: ${CONNECTOR_POSTGRES_DB}
-      POSTGRES_USER: ${CONNECTOR_POSTGRES_USER}
       POSTGRES_PASS: ${CONNECTOR_POSTGRES_PASS}
-      HTTP_PROXY_URL: ${HTTP_PROXY_URL}
-      HTTP_PROXY_USERNAME: ${HTTP_PROXY_USER}
-      HTTP_PROXY_PASSWORD: ${HTTP_PROXY_PASSWORD}
-      HTTPS_PROXY_URL: ${HTTPS_PROXY_URL}
-      HTTPS_PROXY_USERNAME: ${HTTPS_PROXY_USER}
-      HTTPS_PROXY_PASSWORD: ${HTTPS_PROXY_PASSWORD}
-      NO_PROXY: ${NO_PROXY}
-      TZ: Europe/Berlin
     volumes:
       - "connector_logs:/usr/local/tomcat/logs"
     depends_on:
@@ -55,6 +34,9 @@ services:
     ports:
       - "8080:8080"
     restart: always
+    env_file:
+    ###TODO: Move into Image
+      - internal.env
     networks:
       - "samply"
       - "connector-db"
@@ -64,20 +46,20 @@ services:
     image: postgres:10.17
     environment:
       POSTGRES_HOST: ${CONNECTOR_DB_HOST}
-      POSTGRES_DB: ${CONNECTOR_POSTGRES_DB}
-      POSTGRES_USER: ${CONNECTOR_POSTGRES_USER}
       POSTGRES_PASSWORD: ${CONNECTOR_POSTGRES_PASS}
-      TZ: Europe/Berlin
     volumes:
       - "connector_db_data:/var/lib/postgresql/data"
     restart: always
+    env_file:
+    ###TODO: Move into Image
+      - internal.env
     networks:
       - "connector-db"
 
 
   idmanager:
     container_name: bridgehead_dktk_idmanager
-    image: docker.verbis.dkfz.de/pseudonymisierung/magicpl:0.2.0-RC23
+    image: docker.verbis.dkfz.de/pseudonymisierung/magicpl:release-0.2.0
     environment:
       MAGICPL_MAINZELLISTE_URL: ${MAGICPL_MAINZELLISTE_URL}
       MAGICPL_MAINZELLISTE_API_KEY: ${MAGICPL_MAINZELLISTE_API_KEY}
@@ -91,8 +73,7 @@ services:
       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
       TZ: Europe/Berlin
     volumes:
       - "idmanager_logs:/usr/local/tomcat/logs"
@@ -102,6 +83,9 @@ services:
       - proxy.docker.xml
     depends_on:
       - patientlist
+    env_file:
+    ###TODO: Move into Image
+      - internal.env
     ports:
       - "8085:8080"
     networks:
@@ -111,19 +95,12 @@ services:
     container_name: bridgehead_dktk_patientlist
     image: medicalinformatics/mainzelliste:develop
     environment:
-      ML_DB_DRIVER: org.postgresql.Driver
+      ML_DB_HOST: bridgehead_dktk_patientlist_db
-      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
+      - internal.env
     volumes:
       - "patientlist_logs:/usr/local/tomcat/logs"
     secrets:
@@ -140,12 +117,12 @@ services:
     container_name: bridgehead_dktk_patientlist_db
     image: postgres:13.1-alpine
     environment:
-      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"
+    env_file:
+    ###TODO: Move into Image
+      - internal.env
     networks:
       - "samply"
       

dktk/internal.env

@@ -0,0 +1,56 @@
+SITE=bridgehead_dktk_test
+SITEID=BRIDGEHEAD_DKTK_TEST
+
+CONNECTOR_SHARE_URL="http://${HOST}:8080" 
+CONNECTOR_ENABLE_METRICS=false
+CONNECTOR_MONITOR_INTERVAL=
+CONNECTOR_UPDATE_SERVER=
+
+POSTGRES_PORT=5432
+POSTGRES_DB=samply.connector
+POSTGRES_USER=samply.connector
+
+HTTP_PROXY_HOST=${PROXY_URL}
+HTTP_PROXY_USER=
+HTTP_PROXY_PASSWORD=
+HTTPS_PROXY_HOST=${PROXY_URL}
+HTTPS_PROXY_USER=
+HTTPS_PROXY_PASSWORD=
+HTTP_PROXY=${PROXY_URL}
+HTTPS_PROXY=${PROXY_URL}
+http_proxy=${PROXY_URL}
+https_proxy=${PROXY_URL}
+
+CCP_CENTRALSEARCH_URL=https://centralsearch-test.dktk.dkfz.de/
+CCP_DECENTRALSEARCH_URL=https://decentralsearch-test.ccp-it.dktk.dkfz.de/
+
+CCP_MDR_URL=https://mdr.ccp-it.dktk.dkfz.de/v3/api/mdr
+CCP_MONITOR_URL=
+MONITOR_OPTOUT=
+
+## nNGM
+#NNGM_URL=http://bridgeheadstore:8080
+#NNGM_PROFILE=http://uk-koeln.de/fhir/StructureDefinition/Patient/nNGM/pseudonymisiert
+#NNGM_MAINZELLISTE_URL=https://test.verbis.dkfz.de/mpl
+
+##MDR
+MDR_NAMESPACE=adt,dktk,marker
+#MDR_MAP=
+MDR_VALIDATION=false
+
+ML_DB_NAME=samply.connector
+ML_DB_PORT=5432
+ML_DB_USER=samply.connector
+
+CENTRAL_CONTROL_NUMBER_GENERATPR_URL=http://e260-serv-03/central/api
+GLOBAL_ID=DKTK
+MAINZELLISTE_URL=https://patientlist-test.ccpit.dktk.dkfz.de/mainzelliste
+ML_DB_DRIVER=org.postgresql.Driver
+ML_DB_TYPE=postgresql
+
+ML_LOG_LEVEL=warning
+ML_SITE=BRIDGEHEAD_DKTK_TEST
+TZ=Europe/Berlin
+
+MAGICPL_SITE=adt
+MAGICPL_LOG_LEVEL=info

gbn/docker-compose.yml

@@ -1,6 +1,17 @@
 version: '3.4'
-services:
+networks:
+  samply:
+    driver: "bridge"
+  connector-db:
+    driver: "bridge"
 
+volumes:
+  store-db-data:
+    name: "store-db-data"
+  connector-db-data:
+    name: "connector-db-data"
+
+services:
   store:
     container_name: "bridgehead_gbn_blaze_store"
     image: "samply/blaze:0.15"
@@ -20,12 +31,12 @@ services:
     image: "samply/share-client:gbn-7"
     environment:
       POSTGRES_HOST: "bridgehead_gbn_connector_db"
-      POSTGRES_DB: "samply.connector"
-      POSTGRES_USER: "samply"
       POSTGRES_PASS: ${CONNECTOR_POSTGRES_PASS}
-      STORE_URL: "http://bridgehead_store:8080/fhir"
+      POSTGRES_PORT: 5432
-      QUERY_LANGUAGE: "CQL"
+      STORE_URL: "http://bridgehead_gbn_blaze_store:8080/fhir"
-      MDR_URL: "https://mdr.germanbiobanknode.de/v3/api/mdr"
+    env_file:
+    ###TODO: Move into Image
+      - internal.env
     networks:
       - "samply"
       - "connector-db"
@@ -39,23 +50,13 @@ services:
     container_name: "bridgehead_gbn_connector_db"
     image: "postgres:10.17"
     environment:
-      POSTGRES_USER: "samply"
       POSTGRES_PASSWORD: ${CONNECTOR_POSTGRES_PASS}
-      POSTGRES_DB: "samply.connector"
+      POSTGRES_PORT: 5432
     networks:
       - "connector-db"
     volumes:
       - "connector-db-data:/var/lib/postgresql/data"
     restart: "always"
-
+    env_file:
-networks:
+    ###TODO: Move into Image
-  samply:
+      - internal.env
-    driver: "bridge"
-  connector-db:
-    driver: "bridge"
-
-volumes:
-  store-db-data:
-    name: "store-db-data"
-  connector-db-data:
-    name: "connector-db-data"

gbn/internal.env

@@ -0,0 +1,26 @@
+POSTGRES_DB=samply.connector
+POSTGRES_USER=samply
+QUERY_LANGUAGE=CQL
+CONNECTOR_SHARE_URL="http://${HOST}:8080" 
+MDR_URL="https://mdr.germanbiobanknode.de/v3/api/mdr"
+MONITOR_URL=https://ccpit.dktk.dkfz.de/dktk.monitor/rest/info
+no_proxy=bridgehead_gbn_connector,bridgehead_gbn_blaze_store,bridgehead_gbn_connector_db
+CONNECTOR_MONITOR_INTERVAL=
+CONNECTOR_UPDATE_SERVER=
+feature_BBMRI_DIRECTORY_SYNC=false
+feature_DKTK_CENTRAL_SEARCH=false
+feature_NNGM_CTS=false
+LOG_LEVEL=info
+
+HTTP_PROXY_HOST=${PROXY_URL}
+HTTP_PROXY_USER=
+HTTP_PROXY_PASSWORD=
+HTTPS_PROXY_HOST=${PROXY_URL}
+HTTPS_PROXY_USER=
+HTTPS_PROXY_PASSWORD=
+HTTP_PROXY=${PROXY_URL}
+HTTPS_PROXY=${PROXY_URL}
+http_proxy=${PROXY_URL}
+https_proxy=${PROXY_URL}
+
+CONNECTOR_ENABLE_METRICS=false

install-bridgehead.sh

@@ -11,7 +11,7 @@ if ! ./lib/prerequisites.sh; then
 fi
 source site.conf
 
-log -e "\nInstalling systemd units ..."
+echo -e "\nInstalling systemd units ..."
 cp -v \
     lib/systemd/bridgehead\@.service \
     lib/systemd/bridgehead-update\@.service \
@@ -23,12 +23,12 @@ systemctl daemon-reload
 echo
 
 if ! systemctl is-active --quiet bridgehead@"${project}"; then
-    log "Enabling autostart of bridgehead@${project}.service"
+    echo "Enabling autostart of bridgehead@${project}.service"
     systemctl enable bridgehead@"${project}"
-    log "Enabling nightly updates for bridgehead@${project}.service ..."
+    echo "Enabling nightly updates for bridgehead@${project}.service ..."
     systemctl enable --now bridgehead-update@"${project}".timer
 fi
 
-log -e "\nDone - now start your bridgehead by running\n\tsystemctl start bridgehead@${project}.service\nor by rebooting your machine."
+echo -e "\nDone - now start your bridgehead by running\n\tsystemctl start bridgehead@${project}.service\nor by rebooting your machine."
 
 # TODO: Configuration of the different modules

site.dev.conf

@@ -4,9 +4,17 @@
 ##Setting Network properties
 export HOSTIP=$(MSYS_NO_PATHCONV=1 docker run --rm --add-host=host.docker.internal:host-gateway ubuntu cat /etc/hosts | grep 'host.docker.internal' | awk '{print $1}');
 export HOST=
+export PROXY_URL=
 
 export site_name=
 ### Write the Project you want to start with the brigdehead
 ##Exmaple project=gbn
-project=c4
+project=
 
+###secrets
+## Connector Password
+export CONNECTOR_POSTGRES_PASS=
+
+##ID-Manager
+#This needs to be set if the project is either c4 or dktk
+export 

update-bridgehead.sh

@@ -3,7 +3,7 @@ service="bridgehead"
 
 source lib/functions.sh
 
-if ! ./prerequisites.sh; then
+if ! lib/prerequisites.sh; then
     log "Prerequisites failed, exiting"
     exit
 fi