Some more adjustments for dktk

dktk/docker-compose.yml

@@ -52,11 +52,10 @@ services:
 
   connector:
     container_name: bridgehead_dktk_connector
-    image: "samply/share-client:dktk-7"
+    image: "samply/share-client:dktk-pr-148"
     environment:
       STORE_URL: ${STORE_URL}
-      POSTGRES_HOST: ${CONNECTOR_DB_HOST}
+      POSTGRES_PASSWORD: ${CONNECTOR_POSTGRES_PASS}
-      POSTGRES_PASS: ${CONNECTOR_POSTGRES_PASS}
     volumes:
       - "connector_logs:/usr/local/tomcat/logs"
     depends_on:
@@ -66,9 +65,8 @@ services:
       - "traefik.enable=true"
       - "traefik.http.routers.dktk_connector.rule=PathPrefix(`/dktk-connector`)"
       - "traefik.http.services.dktk_connector.loadbalancer.server.port=8080"
-    env_file:
+    ports:
-    ###TODO: Move into Image
+      - 65395:65395
-      - internal.env
 
   connector_db:
     container_name: bridgehead_dktk_connector_db
@@ -88,14 +86,14 @@ services:
     image: docker.verbis.dkfz.de/pseudonymisierung/magicpl:release-0.2.0
     environment:
       TOMCAT_REVERSEPROXY_FQDN: ${HOST}/id-manager
-      MAGICPL_MAINZELLISTE_API_KEY: ${MAGICPL_MAINZELLISTE_API_KEY}
+      MAGICPL_MAINZELLISTE_API_KEY: "123"
-      MAGICPL_API_KEY: ${MAGICPL_API_KEY}
+      MAGICPL_API_KEY: "123"
-      MAGICPL_API_KEY_CONNECTOR: ${MAGICPL_API_KEY_CONNECTOR}
+      MAGICPL_API_KEY_CONNECTOR: "123"
-      MAGICPL_PASSPHRASE: ${MAGICPL_PASSPHRASE}
+      MAGICPL_PASSPHRASE: "123"
-      MAGICPL_MAINZELLISTE_CENTRAL_API_KEY: ${MAGICPL_MAINZELLISTE_CENTRAL_API_KEY}
+      MAGICPL_MAINZELLISTE_CENTRAL_API_KEY: "123"
-      MAGICPL_CENTRAL_API_KEY: ${MAGICPL_CENTRAL_API_KEY}
+      MAGICPL_CENTRAL_API_KEY: "123"
-      MAGICPL_OIDC_CLIENT_ID: ${MAGICPL_OIDC_CLIENT_ID}
+      MAGICPL_OIDC_CLIENT_ID: "123"
-      MAGICPL_OIDC_CLIENT_SECRET: ${MAGICPL_OIDC_CLIENT_SECRET}
+      MAGICPL_OIDC_CLIENT_SECRET: "123"
       TZ: Europe/Berlin
     volumes:
       - "idmanager_logs:/usr/local/tomcat/logs"
@@ -143,9 +141,9 @@ services:
     container_name: bridgehead_dktk_patientlist_db
     image: postgres:13.1-alpine
     environment:
+      POSTGRES_PORT: 5432
+      POSTGRES_DB: mainzelliste
+      POSTGRES_USER: mainzelliste      
       POSTGRES_PASSWORD: ${ML_DB_PASS}
     volumes:
       - "patientlist_db_data:/var/lib/postgresql/data"
-    env_file:
-    ###TODO: Move into Image
-      - internal.env

dktk/internal.env

@@ -6,12 +6,11 @@ CONNECTOR_ENABLE_METRICS=false
 CONNECTOR_MONITOR_INTERVAL=
 CONNECTOR_UPDATE_SERVER=
 
-TOMCAT_REVERSEPROXY_FQDN=${HOST}/dktk-connector
 DEPLOYMENT_CONTEXT=dktk-connector
 
 POSTGRES_PORT=5432
-POSTGRES_DB=samply.connector
+POSTGRES_DB=share_v2
-POSTGRES_USER=samply.connector
+POSTGRES_USER=samplyweb
 
 HTTP_PROXY_HOST=${PROXY_URL}
 HTTP_PROXY_USER=
@@ -28,9 +27,14 @@ 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
+MDR_URL=https://mdr.ccp-it.dktk.dkfz.de/v3/api/mdr
+
 CCP_MONITOR_URL=
 MONITOR_OPTOUT=
 
+PATIENTLIST_URL=http://bridgehead_patientlist:8080/Patientlist
+PROJECTPSEUDONYMISATION_URL=http://bridgehead_patientlist:8080/Patientlist
+
 ## nNGM
 #NNGM_URL=http://bridgeheadstore:8080
 #NNGM_PROFILE=http://uk-koeln.de/fhir/StructureDefinition/Patient/nNGM/pseudonymisiert
@@ -42,9 +46,9 @@ MDR_NAMESPACE=adt,dktk,marker
 MDR_VALIDATION=false
 
 ML_DB_HOST=bridgehead_dktk_patientlist_db
-ML_DB_NAME=samply.connector
+ML_DB_NAME=mainzelliste
 ML_DB_PORT=5432
-ML_DB_USER=samply.connector
+ML_DB_USER=mainzelliste
 
 CENTRAL_CONTROL_NUMBER_GENERATPR_URL=http://e260-serv-03/central/api
 GLOBAL_ID=DKTK
@@ -52,6 +56,8 @@ MAINZELLISTE_URL=https://patientlist-test.ccpit.dktk.dkfz.de/mainzelliste
 ML_DB_DRIVER=org.postgresql.Driver
 ML_DB_TYPE=postgresql
 
+MAGICPL_MAINZELLISTE_URL=http://bridgehead_patientlist:8080
+
 ML_LOG_LEVEL=warning
 ML_SITE=BRIDGEHEAD_DKTK_TEST
 TZ=Europe/Berlin

gbn/docker-compose.yml

@@ -15,11 +15,6 @@ services:
       - --entrypoints.web.address=:80
       - --entrypoints.web-secure.address=:443
       - --providers.docker=true
-    environment:
-      http_proxy: ""
-      HTTP_PROXY: ""
-      https_proxy: ""
-      HTTPS_PROXY: ""      
     ports:
       - 80:80
       - 443:443
@@ -58,31 +53,44 @@ services:
   connector:
     container_name: "bridgehead_gbn_connector"
     image: "samply/share-client:gbn-7"
-    environment:
-      POSTGRES_HOST: "bridgehead_gbn_connector_db"
-      POSTGRES_PASS: ${CONNECTOR_POSTGRES_PASS}
-      POSTGRES_PORT: 5432
-      STORE_URL: "http://bridgehead_gbn_blaze_store:8080/fhir"
-    env_file:
-    ###TODO: Move into Image
-      - internal.env
     labels:
       - "traefik.enable=true"
       - "traefik.http.routers.gbn_connector.rule=PathPrefix(`/gbn-connector`)"
       - "traefik.http.services.gbn_connector.loadbalancer.server.port=8080"
     depends_on:
       - "connector-db"
+    environment:
+      POSTGRES_PASS: ${CONNECTOR_POSTGRES_PASS}
+      POSTGRES_HOST: "bridgehead_gbn_connector_db"
+      MDR_URL: "https://mdr.germanbiobanknode.de/v3/api/mdr"
+      https_proxy: "http://www-int2.inet.dkfz-heidelberg.de:3128"
+      HTTP_PROXY_HOST: "http://www-int2.inet.dkfz-heidelberg.de:3128"
+      HTTPS_PROXY_HOST: "http://www-int2.inet.dkfz-heidelberg.de:3128"
+      HTTPS_PROXY_USER: ""
+      HTTP_PROXY_USER: ""
+      HTTPS_PROXY_PASSWORD: ""
+      HTTP_PROXY_PASSWORD: ""      
+      HTTP_PROXY: "http://www-int2.inet.dkfz-heidelberg.de:3128"
+      HTTPS_PROXY: "http://www-int2.inet.dkfz-heidelberg.de:3128"
+      http_proxy: "http://www-int2.inet.dkfz-heidelberg.de:3128"
+      CATALINA_OPTS: "-agentlib:jdwp=transport=dt_socket,address=65395,server=y,suspend=n"
+    ports:
+    - 65395:65395
     restart: "always"
+    env_file:
+    ###TODO: Move into Image
+      - internal.env
 
   connector-db:
     container_name: "bridgehead_gbn_connector_db"
     image: "postgres:10.17"
     environment:
       POSTGRES_PASSWORD: ${CONNECTOR_POSTGRES_PASS}
+      POSTGRES_USER: "samply"
+      POSTGRES_DB: "samply.connector"
       POSTGRES_PORT: 5432
     volumes:
       - "connector-db-data:/var/lib/postgresql/data"
+    ports:
+    - 5432:5432
     restart: "always"
-    env_file:
-    ###TODO: Move into Image
-      - internal.env

gbn/gbn.env.dev

@@ -1,64 +0,0 @@
-SITE=
-SITEID=
-TESTPROD=
-
-project=gbn
-
-### Bridgehead Operator
-# users may see this contact data for support purposes
-OPERATOR_FIRST_NAME=
-OPERATOR_LAST_NAME=
-OPERATOR_EMAIL=
-OPERATOR_PHONE=
-
-### Proxy configuration
-## ex.: http://my-proxy-host:my-proxy-port
-HTTP_PROXY_HOST=
-HTTP_PROXY_USER=
-HTTP_PROXY_PASSWORD=
-HTTPS_PROXY_HOST=
-HTTPS_PROXY_USER=
-HTTPS_PROXY_PASSWORD=
-
-HTTP_PROXY=
-HTTPS_PROXY=
-http_proxy=
-https_proxy=
-
-NO_PROXY=
-no_proxy=
-
-### SMTP Server
-## ex.: mailhost.intern.klinik.de
-# MAIL_HOST=
-# MAIL_PORT=25
-## ex.: no-reply@bridgehead.intern.klinik.de
-# MAIL_FROM_ADDRESS=
-# MAIL_FROM_NAME=Bridgehead Searchbroker
-
-## Connector 
-CONNECTOR_POSTGRES_HOST=
-CONNECTOR_POSTGRES_PORT=
-CONNECTOR_POSTGRES_DB=
-CONNECTOR_POSTGRES_USER=
-CONNECTOR_SHARE_URL=
-CONNECTOR_ENABLE_METRICS=
-CONNECTOR_MONITOR_INTERVAL=
-CONNECTOR_UPDATE_SERVER=
-CONNECTOR_QUERY_LANGUAGE=
-
-CATALINA_OPTS=
-MDR_URL=
-CENTRAL_SEARCH=
-DECENTRAL_SEARCH=
-MONITOR_URL=
-MONITOR_OPTOUT=
-
-LOG_LEVEL=
-
-feature_BBMRI_DIRECTORY_SYNC=false
-feature_DKTK_CENTRAL_SEARCH=false
-feature_NNGM_CTS=false
-
-LDM_URL=
-ID_MANAGER_URL=

gbn/internal.env

@@ -4,8 +4,6 @@ QUERY_LANGUAGE=CQL
 CONNECTOR_SHARE_URL="http://${HOST}:8080" 
 MDR_URL="https://mdr.germanbiobanknode.de/v3/api/mdr"
 MONITOR_URL=https://ccpit.dktk.dkfz.de/dktk.monitor/rest/info
-no_proxy=bridgehead_gbn_connector,bridgehead_gbn_blaze_store,bridgehead_gbn_connector_db
-TOMCAT_REVERSEPROXY_FQDN=${HOST}/gbn-connector
 DEPLOYMENT_CONTEXT=gbn-connector
 CONNECTOR_MONITOR_INTERVAL=
 CONNECTOR_UPDATE_SERVER=
@@ -13,16 +11,6 @@ feature_BBMRI_DIRECTORY_SYNC=false
 feature_DKTK_CENTRAL_SEARCH=false
 feature_NNGM_CTS=false
 LOG_LEVEL=info
-
+STORE_URL=http://bridgehead_gbn_blaze_store:8080
-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

internal-configuration/magicpl.xml

@@ -40,7 +40,7 @@
                     <iosingle ref="ids" name="ids"/>
                 </output>
                 <switch>
-                    <evaluator name="de.mainzelliste.paths.evaluator.IsConsentedEvaluator">
+                    <evaluator name="de.pseudonymisierung.magicpl.evaluator.IsConsentedEvaluator">
                         <parameters>
                             <parameter name="key">consented</parameter>
                         </parameters>
@@ -79,7 +79,7 @@
                                 <output>
                                     <iosingle ref="tokenId"/>
                                 </output>
-                                <implementation>de.mainzelliste.paths.processor.PathClient</implementation>
+                                <implementation>de.pseudonymisierung.magicpl.processor.PathClient</implementation>
                             </step>
                             <step>
                                 <name>getDktkId</name>
@@ -95,7 +95,7 @@
                                 <output>
                                     <iosingle ref="ids" name="ids"/>
                                 </output>
-                                <implementation>de.mainzelliste.paths.processor.MainzellisteClient</implementation>
+                                <implementation>de.pseudonymisierung.magicpl.processor.MainzellisteClient</implementation>
                             </step>
                             <step>
                                 <name>mapIdStringToExternalId</name>
@@ -108,7 +108,7 @@
                                 <output>
                                     <iosingle ref="extIDs" name="extIDs"/>
                                 </output>
-                                <implementation>de.mainzelliste.paths.processor.InputMapperProcessor</implementation>
+                                <implementation>de.pseudonymisierung.magicpl.processor.InputMapperProcessor</implementation>
                             </step>
                             <step>
                                 <name>getLocalTKTExternalId</name>
@@ -128,7 +128,7 @@
                                 </output>
                                 <!-- TODO: Implementation für Ticket Erzeugung ohne Kontrolnummer -->
                                 <!-- Wird hier eine neue Klasse benötigt oder kann diese hier entsprechend angepasst werden? -->
-                                <implementation>de.mainzelliste.paths.processor.MainzellisteKNTicketClient</implementation>
+                                <implementation>de.pseudonymisierung.magicpl.processor.MainzellisteKNTicketClient</implementation>
                             </step>
                             <step>
                                 <name>generateLocalIdExternalId</name>
@@ -146,7 +146,7 @@
                                 <output>
                                     <iosingle ref="ids" name="ids"/>
                                 </output>
-                                <implementation>de.mainzelliste.paths.processor.MainzellisteClient</implementation>
+                                <implementation>de.pseudonymisierung.magicpl.processor.MainzellisteClient</implementation>
                             </step>
                         </multipath>
                     </case>
@@ -178,7 +178,7 @@
                                     <iosingle ref="tokenId"/>
                                 </output>
                                 <!-- Wird hier eine neue Klasse benötigt oder kann diese hier entsprechend angepasst werden? -->
-                                <implementation>de.mainzelliste.paths.processor.MainzellisteKNTicketClient</implementation>
+                                <implementation>de.pseudonymisierung.magicpl.processor.MainzellisteKNTicketClient</implementation>
                             </step>
                             <step>
                                 <name>generateLocalId</name>
@@ -195,7 +195,7 @@
                                 <output>
                                     <iosingle ref="ids" name="ids"/>
                                 </output>
-                                <implementation>de.mainzelliste.paths.processor.MainzellisteClient</implementation>
+                                <implementation>de.pseudonymisierung.magicpl.processor.MainzellisteClient</implementation>
                             </step>
                         </multipath>
                     </case>
@@ -223,7 +223,7 @@
                     <iosingle ref="patients" name="patients"/>
                 </output>
                 <switch>
-                    <evaluator name="de.mainzelliste.paths.evaluator.RegexEvaluator">
+                    <evaluator name="de.pseudonymisierung.magicpl.evaluator.RegexEvaluator">
                         <parameters>
                             <parameter name="regex">MDS_\*_G-ID</parameter>
                             <parameter name="fieldName">resultIds</parameter>
@@ -255,7 +255,7 @@
                                 <output>
                                     <iosingle ref="tokenId"/>
                                 </output>
-                                <implementation>de.mainzelliste.paths.processor.MainzellisteReadTokenClient</implementation>
+                                <implementation>de.pseudonymisierung.magicpl.processor.MainzellisteReadTokenClient</implementation>
                             </step>
                             <step>
                                 <name>resolveReadTokenCentral</name>
@@ -269,7 +269,7 @@
                                 <output>
                                     <iosingle ref="patients"/>
                                 </output>
-                                <implementation>de.mainzelliste.paths.processor.MainzellisteReadClient</implementation>
+                                <implementation>de.pseudonymisierung.magicpl.processor.MainzellisteReadClient</implementation>
                             </step>
                         </multipath>
                     </case>
@@ -299,7 +299,7 @@
                                 <output>
                                     <iosingle ref="tokenId"/>
                                 </output>
-                                <implementation>de.mainzelliste.paths.processor.MainzellisteReadTokenClient</implementation>
+                                <implementation>de.pseudonymisierung.magicpl.processor.MainzellisteReadTokenClient</implementation>
                             </step>
                             <step>
                                 <name>resolveReadToken</name>
@@ -313,7 +313,7 @@
                                 <output>
                                     <iosingle ref="patients"/>
                                 </output>
-                                <implementation>de.mainzelliste.paths.processor.MainzellisteReadClient</implementation>
+                                <implementation>de.pseudonymisierung.magicpl.processor.MainzellisteReadClient</implementation>
                             </step>
                         </multipath>
                     </case>