diff --git a/dktk/docker-compose.yml b/dktk/docker-compose.yml
index c8b748a..b45e434 100644
--- a/dktk/docker-compose.yml
+++ b/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_PASS: ${CONNECTOR_POSTGRES_PASS}
+ POSTGRES_PASSWORD: ${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:
- ###TODO: Move into Image
- - internal.env
+ ports:
+ - 65395:65395
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_API_KEY: ${MAGICPL_API_KEY}
- MAGICPL_API_KEY_CONNECTOR: ${MAGICPL_API_KEY_CONNECTOR}
- MAGICPL_PASSPHRASE: ${MAGICPL_PASSPHRASE}
- MAGICPL_MAINZELLISTE_CENTRAL_API_KEY: ${MAGICPL_MAINZELLISTE_CENTRAL_API_KEY}
- MAGICPL_CENTRAL_API_KEY: ${MAGICPL_CENTRAL_API_KEY}
- MAGICPL_OIDC_CLIENT_ID: ${MAGICPL_OIDC_CLIENT_ID}
- MAGICPL_OIDC_CLIENT_SECRET: ${MAGICPL_OIDC_CLIENT_SECRET}
+ MAGICPL_MAINZELLISTE_API_KEY: "123"
+ MAGICPL_API_KEY: "123"
+ MAGICPL_API_KEY_CONNECTOR: "123"
+ MAGICPL_PASSPHRASE: "123"
+ MAGICPL_MAINZELLISTE_CENTRAL_API_KEY: "123"
+ MAGICPL_CENTRAL_API_KEY: "123"
+ MAGICPL_OIDC_CLIENT_ID: "123"
+ 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: ${ML_DB_PASS}
volumes:
- "patientlist_db_data:/var/lib/postgresql/data"
- env_file:
- ###TODO: Move into Image
- - internal.env
\ No newline at end of file
diff --git a/dktk/internal.env b/dktk/internal.env
index c2cab6d..ca7ec08 100644
--- a/dktk/internal.env
+++ b/dktk/internal.env
@@ -6,12 +6,11 @@ CONNECTOR_ENABLE_METRICS=false
CONNECTOR_MONITOR_INTERVAL=
CONNECTOR_UPDATE_SERVER=
-TOMCAT_REVERSEPROXY_FQDN=${HOST}/dktk-connector
DEPLOYMENT_CONTEXT=dktk-connector
POSTGRES_PORT=5432
-POSTGRES_DB=samply.connector
-POSTGRES_USER=samply.connector
+POSTGRES_DB=share_v2
+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
diff --git a/gbn/docker-compose.yml b/gbn/docker-compose.yml
index e3b7b54..276b68a 100644
--- a/gbn/docker-compose.yml
+++ b/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: ${CONNECTOR_POSTGRES_PASS}
+ POSTGRES_USER: "samply"
+ POSTGRES_DB: "samply.connector"
POSTGRES_PORT: 5432
volumes:
- "connector-db-data:/var/lib/postgresql/data"
- restart: "always"
- env_file:
- ###TODO: Move into Image
- - internal.env
\ No newline at end of file
+ ports:
+ - 5432:5432
+ restart: "always"
\ No newline at end of file
diff --git a/gbn/gbn.env.dev b/gbn/gbn.env.dev
index 04cc72e..e69de29 100644
--- a/gbn/gbn.env.dev
+++ b/gbn/gbn.env.dev
@@ -1,64 +0,0 @@
-SITE=
-SITEID=
-TESTPROD=
-
-project=gbn
-
-### Bridgehead Operator
-# users may see this contact data for support purposes
-OPERATOR_FIRST_NAME=
-OPERATOR_LAST_NAME=
-OPERATOR_EMAIL=
-OPERATOR_PHONE=
-
-### Proxy configuration
-## ex.: http://my-proxy-host:my-proxy-port
-HTTP_PROXY_HOST=
-HTTP_PROXY_USER=
-HTTP_PROXY_PASSWORD=
-HTTPS_PROXY_HOST=
-HTTPS_PROXY_USER=
-HTTPS_PROXY_PASSWORD=
-
-HTTP_PROXY=
-HTTPS_PROXY=
-http_proxy=
-https_proxy=
-
-NO_PROXY=
-no_proxy=
-
-### SMTP Server
-## ex.: mailhost.intern.klinik.de
-# MAIL_HOST=
-# MAIL_PORT=25
-## ex.: no-reply@bridgehead.intern.klinik.de
-# MAIL_FROM_ADDRESS=
-# MAIL_FROM_NAME=Bridgehead Searchbroker
-
-## Connector
-CONNECTOR_POSTGRES_HOST=
-CONNECTOR_POSTGRES_PORT=
-CONNECTOR_POSTGRES_DB=
-CONNECTOR_POSTGRES_USER=
-CONNECTOR_SHARE_URL=
-CONNECTOR_ENABLE_METRICS=
-CONNECTOR_MONITOR_INTERVAL=
-CONNECTOR_UPDATE_SERVER=
-CONNECTOR_QUERY_LANGUAGE=
-
-CATALINA_OPTS=
-MDR_URL=
-CENTRAL_SEARCH=
-DECENTRAL_SEARCH=
-MONITOR_URL=
-MONITOR_OPTOUT=
-
-LOG_LEVEL=
-
-feature_BBMRI_DIRECTORY_SYNC=false
-feature_DKTK_CENTRAL_SEARCH=false
-feature_NNGM_CTS=false
-
-LDM_URL=
-ID_MANAGER_URL=
\ No newline at end of file
diff --git a/gbn/internal.env b/gbn/internal.env
index 57806f0..a6fc63f 100644
--- a/gbn/internal.env
+++ b/gbn/internal.env
@@ -4,8 +4,6 @@ QUERY_LANGUAGE=CQL
CONNECTOR_SHARE_URL="http://${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=${HOST}/gbn-connector
DEPLOYMENT_CONTEXT=gbn-connector
CONNECTOR_MONITOR_INTERVAL=
CONNECTOR_UPDATE_SERVER=
@@ -13,16 +11,6 @@ feature_BBMRI_DIRECTORY_SYNC=false
feature_DKTK_CENTRAL_SEARCH=false
feature_NNGM_CTS=false
LOG_LEVEL=info
-
-HTTP_PROXY_HOST=${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}
+STORE_URL=http://bridgehead_gbn_blaze_store:8080
CONNECTOR_ENABLE_METRICS=false
diff --git a/internal-configuration/magicpl.xml b/internal-configuration/magicpl.xml
index 7208e34..7d5d4d4 100644
--- a/internal-configuration/magicpl.xml
+++ b/internal-configuration/magicpl.xml
@@ -40,7 +40,7 @@
-
+
consented
@@ -79,7 +79,7 @@
- de.mainzelliste.paths.processor.PathClient
+ de.pseudonymisierung.magicpl.processor.PathClient
getDktkId
@@ -95,7 +95,7 @@
- de.mainzelliste.paths.processor.MainzellisteClient
+ de.pseudonymisierung.magicpl.processor.MainzellisteClient
mapIdStringToExternalId
@@ -108,7 +108,7 @@
- de.mainzelliste.paths.processor.InputMapperProcessor
+ de.pseudonymisierung.magicpl.processor.InputMapperProcessor
getLocalTKTExternalId
@@ -128,7 +128,7 @@
- de.mainzelliste.paths.processor.MainzellisteKNTicketClient
+ de.pseudonymisierung.magicpl.processor.MainzellisteKNTicketClient
generateLocalIdExternalId
@@ -146,7 +146,7 @@
- de.mainzelliste.paths.processor.MainzellisteClient
+ de.pseudonymisierung.magicpl.processor.MainzellisteClient
@@ -178,7 +178,7 @@
- de.mainzelliste.paths.processor.MainzellisteKNTicketClient
+ de.pseudonymisierung.magicpl.processor.MainzellisteKNTicketClient
generateLocalId
@@ -195,7 +195,7 @@
- de.mainzelliste.paths.processor.MainzellisteClient
+ de.pseudonymisierung.magicpl.processor.MainzellisteClient
@@ -223,7 +223,7 @@
-
+
MDS_\*_G-ID
resultIds
@@ -255,7 +255,7 @@
- de.mainzelliste.paths.processor.MainzellisteReadTokenClient
+ de.pseudonymisierung.magicpl.processor.MainzellisteReadTokenClient
resolveReadTokenCentral
@@ -269,7 +269,7 @@
- de.mainzelliste.paths.processor.MainzellisteReadClient
+ de.pseudonymisierung.magicpl.processor.MainzellisteReadClient
@@ -299,7 +299,7 @@
- de.mainzelliste.paths.processor.MainzellisteReadTokenClient
+ de.pseudonymisierung.magicpl.processor.MainzellisteReadTokenClient
resolveReadToken
@@ -313,7 +313,7 @@
- de.mainzelliste.paths.processor.MainzellisteReadClient
+ de.pseudonymisierung.magicpl.processor.MainzellisteReadClient