refactor: Resorted environment and prepared special images for dktk

c4/docker-compose.yml

@@ -7,21 +7,10 @@ volumes:
   idmanager_logs:
   store_db_data:
   store_logs:
-secrets:
-  mainzelliste.docker.conf:
-    file: ../internal-configuration/mainzelliste.conf
-  magicpl.docker.xml:
-    file: ../internal-configuration/magicpl.xml
-  dktk_bridgehead_info.docker.xml:
-    file: ../internal-configuration/bridgehead-common.xml
-  centralSearchPublicKey:
-    file: ../internal-configuration/centralSearchPublicKey.der
-  proxy.docker.xml:
-    file: ../internal-configuration/proxy.xml
 
 services:
   traefik:
-    container_name: bridgehead_traefik
+    container_name: traefik
     image: traefik:2.4
     command:
       - --api.insecure=true
@@ -41,7 +30,7 @@ services:
       - /var/run/docker.sock:/var/run/docker.sock:ro
 
   landing:
-    container_name: bridgehead_landingpage
+    container_name: landingpage
     image: nginx:stable
     volumes:
       - ../landing/:/usr/share/nginx/html
@@ -51,15 +40,12 @@ services:
       - "traefik.http.services.landing.loadbalancer.server.port=80"
 
   connector:
-    container_name: bridgehead_c4_connector
+    container_name: c4-connector
-    image: docker.verbis.dkfz.de/ccp/connector:3
+    image: "samply/share-client:c4-feature-environmentPreconfigurationTorben"
     environment:
-      STORE_URL: http://bridgehead_c4_store:8080
+      STORE_URL: http://store:8080
-      LDM_URL: http://bridgehead_c4_store:8080
+      LDM_URL: http://store:8080
-      POSTGRES_HOST: ${CONNECTOR_DB_HOST}
       POSTGRES_PASSWORD: ${CONNECTOR_POSTGRES_PASS}
-      NNGM_PASSWORD: ${NNGM_PASSWORD}
-      NNGM_MAINZELLISTE_APIKEY: ${NNGM_MAINZELLISTE_APIKEY}
     volumes:
       - "connector_logs:/usr/local/tomcat/logs"
     labels:
@@ -67,53 +53,69 @@ services:
       - "traefik.http.routers.c4_connector.rule=PathPrefix(`/c4-connector`)"
       - "traefik.http.services.c4_connector.loadbalancer.server.port=8080"
     depends_on:
-      - connector_db
+      - connector-db
     restart: always
-    env_file:
-    ###TODO: Move into Image
-      - internal.env
 
-  connector_db:
+  connector-db:
-    container_name: bridgehead_c4_connector_db
+    container_name: connector-db
     image: postgres:10.17
     environment:
-      POSTGRES_HOST: ${CONNECTOR_DB_HOST}
+      POSTGRES_DB: "share_v2"
+      POSTGRES_USER: "samplyweb"
       POSTGRES_PASSWORD: ${CONNECTOR_POSTGRES_PASS}
     volumes:
       - "connector_db_data:/var/lib/postgresql/data"
     restart: always
-    env_file:
-    ###TODO: Move into Image
-      - internal.env
 
   idmanager:
-    container_name: bridgehead_idmanager
+    container_name: idmanager
-    image: docker.verbis.dkfz.de/ccp/idmanager:deploy-c4
+    image: docker.verbis.dkfz.de/ccp/idmanager:bridgehead-develop
     environment:
-      TOMCAT_REVERSEPROXY_FQDN: ${HOST}/id-manager
+      TOMCAT_REVERSEPROXY_FQDN: ${HOST}
+      MAGICPL_SITE: ${SITE}
       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}
     volumes:
       - "idmanager_logs:/usr/local/tomcat/logs"
-    secrets:
+    depends_on:
-      - magicpl.docker.xml
+      - patientlist
-      - dktk_bridgehead_info.docker.xml
-      - proxy.docker.xml
     labels:
-      - "traefik.http.routers.idmanager.rule=PathPrefix(`/id-manager`)"
+      - "traefik.http.routers.idmanager.rule=PathPrefix(`/ID-Manager`)"
-      - "traefik.http.middlewares.idmanager_strip.stripprefix.prefixes=/id-mana\
-        ger"
-      - "traefik.http.routers.idmanager.middlewares=idmanager_strip"
       - "traefik.http.services.idmanager.loadbalancer.server.port=8080"
+
+  patientlist:
+    container_name: patientlist
+    image: docker.verbis.dkfz.de/ccp/patientlist:bridgehead-develop
+    environment:
+      ML_SITE: ${SITE}
+      ML_API_KEY: ${ML_API_KEY}
+      TOMCAT_REVERSEPROXY_FQDN: ${HOST}
     env_file:
-    ###TODO: Move into Image
+      # TODO: Implement automatic seed generation in mainzelliste
-      - internal.env
+      - ../site-config/patientlist.env
+    volumes:
+      - "patientlist_logs:/usr/local/tomcat/logs"
+    labels:
+      - "traefik.http.routers.patientlist.rule=PathPrefix(`/Patientlist`)"
+      - "traefik.http.services.patientlist.loadbalancer.server.port=8080"
+    depends_on:
+      - patientlist-db
+
+  patientlist-db:
+    container_name: patientlist-db
+    image: postgres:13.1-alpine
+    environment:
+      POSTGRES_DB: mainzelliste
+      POSTGRES_USER: mainzelliste
+      POSTGRES_PASSWORD: ${ML_DB_PASS}
+      TZ: "Europe/Berlin"
+    volumes:
+      - "patientlist_db_data:/var/lib/postgresql/data"
 
   store:
     container_name: bridgehead_c4_store

c4/internal.env

@@ -1,57 +0,0 @@
-SITE=bridgehead_test
-SITEID=BRIDGEHEAD_TEST
-
-TOMCAT_REVERSEPROXY_FQDN=${HOST}/c4-connector
-DEPLOYMENT_CONTEXT=c4-connector
-
-CONNECTOR_SHARE_URL="http://${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/
-CENTRAL_SEARCH=https://centralsearch-test.dktk.dkfz.de/
-CCP_DECENTRALSEARCH_URL=https://decentralsearch-test.ccp-it.dktk.dkfz.de/
-DECENTRAL_SEARCH=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=
-
-## 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
-
-NNGM_URL=https://test.anforderung.nngm.de/trial/nNGMv09/import-fb
-NNGM_PROFILE=http://uk-koeln.de/fhir/StructureDefinition/Patient/nNGM/pseudonymisiert
-NNGM_MAINZELLISTE_URL=https://test.verbis.dkfz.de/mpl

dktk/docker-compose.yml

@@ -7,32 +7,16 @@ volumes:
   idmanager_logs:
   store_db_data:
   store_logs:
-secrets:
-  mainzelliste.docker.conf:
-    file: ../internal-configuration/mainzelliste.conf
-  magicpl.docker.xml:
-    file: ../internal-configuration/magicpl.xml
-  dktk_bridgehead_info.docker.xml:
-    file: ../internal-configuration/bridgehead-common.xml
-  centralSearchPublicKey:
-    file: ../internal-configuration/centralSearchPublicKey.der
-  proxy.docker.xml:
-    file: ../internal-configuration/proxy.xml
 
 services:
   traefik:
-    container_name: bridgehead_traefik
+    container_name: traefik
     image: traefik:2.4
     command:
       - --api.insecure=true
       - --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
@@ -41,7 +25,7 @@ services:
       - /var/run/docker.sock:/var/run/docker.sock:ro
 
   landing:
-    container_name: bridgehead_landingpage
+    container_name: landingpage
     image: nginx:stable
     volumes:
       - ../landing/:/usr/share/nginx/html
@@ -51,101 +35,94 @@ services:
       - "traefik.http.services.landing.loadbalancer.server.port=80"
 
   connector:
-    container_name: bridgehead_dktk_connector
+    image: "samply/share-client:dktk-feature-environmentPreconfigurationTorben"
-    image: "samply/share-client:dktk-7"
     environment:
-      TOMCAT_REVERSEPROXY_FQDN: ${HOST}/dktk-connector
+      ID_MANAGER_APIKEY: ${MAGICPL_API_KEY_CONNECTOR}
-      DEPLOYMENT_CONTEXT: dktk-connector
+      POSTGRES_PASSWORD: ${CONNECTOR_POSTGRES_PASS}
-      STORE_URL: ${STORE_URL}
+      HTTP_PROXY_USER: ${HTTP_PROXY_USER}
-      POSTGRES_HOST: ${CONNECTOR_DB_HOST}
+      HTTP_PROXY_PASSWORD: ${HTTP_PROXY_PASSWORD}
-      POSTGRES_PASS: ${CONNECTOR_POSTGRES_PASS}
+      HTTPS_PROXY_USER: ${HTTPS_PROXY_USER}
+      HTTPS_PROXY_PASSWORD: ${HTTPS_PROXY_PASSWORD}
+    env_file:
+      - ../site-config/dktk.env
+    # Necessary for the connector to successful check the status of other components on the same host
+    extra_hosts:
+      - "host.docker.internal:host-gateway"
+      - "${HOST}:${HOSTIP}"
     volumes:
       - "connector_logs:/usr/local/tomcat/logs"
     depends_on:
-      - connector_db
+      - connector-db
     restart: always
     labels:
       - "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
 
-  connector_db:
+  connector-db:
-    container_name: bridgehead_dktk_connector_db
     image: postgres:10.17
     environment:
-      POSTGRES_HOST: ${CONNECTOR_DB_HOST}
+      POSTGRES_DB: "share_v2"
+      POSTGRES_USER: "samplyweb"
       POSTGRES_PASSWORD: ${CONNECTOR_POSTGRES_PASS}
     volumes:
       - "connector_db_data:/var/lib/postgresql/data"
     restart: always
-    env_file:
-    ###TODO: Move into Image
-      - internal.env
 
-  idmanager:
+  id-manager:
-    container_name: bridgehead_id-manager
+    container_name: id-manager
-    image: docker.verbis.dkfz.de/pseudonymisierung/magicpl:release-0.2.0
+    image: docker.verbis.dkfz.de/ccp/idmanager:bridgehead-develop
     environment:
-      TOMCAT_REVERSEPROXY_FQDN: ${HOST}
+      MAGICPL_SITE: ${SITE}
-      DEPLOYMENT_CONTEXT: id-manager
-      MAGICPL_SITE: ${SITEID}
       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: ${MAGICPL_OIDC_CLIENT_SECRET}
-      TZ: Europe/Berlin
+      TOMCAT_REVERSEPROXY_FQDN: "${PROTOCOL}://${HOST}:${PORT}"
+      HTTP_PROXY_USER: ${HTTP_PROXY_USER}
+      HTTP_PROXY_PASSWORD: ${HTTP_PROXY_PASSWORD}
+      HTTPS_PROXY_USER: ${HTTPS_PROXY_USER}
+      HTTPS_PROXY_PASSWORD: ${HTTPS_PROXY_PASSWORD}
+    env_file:
+      - ../site-config/dktk.env
     volumes:
       - "idmanager_logs:/usr/local/tomcat/logs"
-    secrets:
-      - magicpl.docker.xml
-      - dktk_bridgehead_info.docker.xml
-      - proxy.docker.xml
     depends_on:
       - patientlist
     labels:
-      - "traefik.http.routers.idmanager.rule=PathPrefix(`/id-manager`)"
+      - "traefik.http.routers.id-manager.rule=PathPrefix(`/ID-Manager`)"
-      - "traefik.http.services.idmanager.loadbalancer.server.port=8080"
+      - "traefik.http.services.id-manager.loadbalancer.server.port=8080"
-    env_file:
-    ###TODO: Move into Image
-      - internal.env
 
   patientlist:
-    container_name: bridgehead_patientlist
+    container_name: patientlist
-    image: medicalinformatics/mainzelliste:develop
+    image: docker.verbis.dkfz.de/ccp/patientlist:bridgehead-develop
     environment:
+      ML_SITE: ${SITE}
+      ML_API_KEY: ${MAGICPL_MAINZELLISTE_API_KEY}
       ML_DB_PASS: ${ML_DB_PASS}
-      ML_API_KEY: ${ML_API_KEY}
+      TOMCAT_REVERSEPROXY_FQDN: "${PROTOCOL}://${HOST}:${PORT}"
-      ML_SITE: ${SITEID}
-      TOMCAT_REVERSEPROXY_FQDN: ${HOST}
-      DEPLOYMENT_CONTEXT: patientlist
     env_file:
+      - ../site-config/dktk.env
+      # TODO: Implement automatic seed generation in mainzelliste
       - ../site-config/patientlist.env
-      - internal.env
     volumes:
       - "patientlist_logs:/usr/local/tomcat/logs"
-    secrets:
-      - mainzelliste.docker.conf
-      - centralSearchPublicKey
     labels:
-      - "traefik.http.routers.patientlist.rule=PathPrefix(`/patientlist`)"
+      - "traefik.http.routers.patientlist.rule=PathPrefix(`/Patientlist`)"
       - "traefik.http.services.patientlist.loadbalancer.server.port=8080"
     depends_on:
-      - patientlist_db
+      - patientlist-db
 
-  patientlist_db:
+  patientlist-db:
-    container_name: bridgehead_dktk_patientlist_db
+    container_name: patientlist-db
     image: postgres:13.1-alpine
     environment:
+      POSTGRES_DB: mainzelliste
+      POSTGRES_USER: mainzelliste
       POSTGRES_PASSWORD: ${ML_DB_PASS}
+      TZ: "Europe/Berlin"
     volumes:
       - "patientlist_db_data:/var/lib/postgresql/data"
-    env_file:
-    ###TODO: Move into Image
-      - internal.env

dktk/internal.env

@@ -1,56 +0,0 @@
-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_HOST=bridgehead_dktk_patientlist_db
-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
-TZ=Europe/Berlin
-
-MAGICPL_LOG_LEVEL=info
-MAGICPL_MAINZELLISTE_URL=http://patientlist:8080/patientlist
-MAGICPL_MAINZELLISTE_CENTRAL_URL=http://e260-serv-03/central/mainzelliste
-MAGICPL_CENTRAL_URL=http://e260-serv-03/central/api
-MAGICPL_OIDC_PROVIDER=https://auth-test.ccp-it.dktk.dkfz.de

gbn/docker-compose.yml

@@ -8,7 +8,7 @@ volumes:
 
 services:
   traefik:
-    container_name: bridgehead_traefik
+    container_name: traefik
     image: traefik:2.4
     command:
       - --api.insecure=true
@@ -28,7 +28,7 @@ services:
       - /var/run/docker.sock:/var/run/docker.sock:ro
 
   landing:
-    container_name: bridgehead_landingpage
+    container_name: landingpage
     image: nginx:stable
     volumes:
       - ../landing/:/usr/share/nginx/html
@@ -56,8 +56,8 @@ services:
     restart: "always"
 
   connector:
-    container_name: "bridgehead_gbn_connector"
+    container_name: connector
-    image: "samply/share-client:gbn-7"
+    image: "samply/share-client:gbn-feature-environmentPreconfigurationTorben"
     environment:
       POSTGRES_HOST: "bridgehead_gbn_connector_db"
       POSTGRES_PASS: ${CONNECTOR_POSTGRES_PASS}

gbn/internal.env

@@ -1,28 +0,0 @@
-POSTGRES_DB=samply.connector
-POSTGRES_USER=samply
-QUERY_LANGUAGE=CQL
-CONNECTOR_SHARE_URL="http://${HOST}:8080" 
-MDR_URL="https://mdr.germanbiobanknode.de/v3/api/mdr"
-MONITOR_URL=https://ccpit.dktk.dkfz.de/dktk.monitor/rest/info
-no_proxy=bridgehead_gbn_connector,bridgehead_gbn_blaze_store,bridgehead_gbn_connector_db
-TOMCAT_REVERSEPROXY_FQDN=${HOST}/gbn-connector
-DEPLOYMENT_CONTEXT=gbn-connector
-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

init-dev-environment.sh

@@ -0,0 +1,40 @@
+#!/bin/bash
+### This configuration file is intended for fast setup of a developers testenvironment.
+### The settings made here are normally placed in the system units configuration.
+### Refer to the readme on how to do this.
+### On long term we want to move those to a zero knowledge passwort manager like bitwarden.
+
+### Configuration for Network Properties
+# needed by the connector to resolve hosts address for ui-links and service status checks
+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 $1}');
+# needed for the reverse proxy configuration of the services
+export HOST=$(hostname)
+# additional information about the local proxy if necessary
+export HTTP_PROXY_USER=""
+export HTTP_PROXY_PASSWORD=""
+export HTTPS_PROXY_USER=""
+export HTTPS_PROXY_PASSWORD=""
+
+### Configuration for Connector Secrets
+# the password of database connector-db
+export CONNECTOR_POSTGRES_PASS=pleaseChangeThis1
+
+### Configuration for ID-Management Secrets
+# the password of database patientlist-db
+export ML_DB_PASS=pleaseChangeThis2
+
+# the apikey of the localdatamanagement for the patientlist
+export MAGICPL_API_KEY=pleaseChangeThis3
+# the apikey of the id-manager for the patientlist
+export MAGICPL_MAINZELLISTE_API_KEY=pleaseChangeThis4
+# the apikey of the connector for the patientlist
+export MAGICPL_API_KEY_CONNECTOR=pleaseChangeThis5
+
+# the apikey of the id-manager for the central patientlist
+export MAGICPL_MAINZELLISTE_CENTRAL_API_KEY=dktk[CentralS3cr3tKey]KNE;
+# the apikey of the id-manager for the controlnumbergenerator
+export MAGICPL_CENTRAL_API_KEY=dguQJ5IoqUrxCF8fNl6fOl2YvsZAVB1Y;
+# client-id used for autheticating users in central ccp-authentication service
+export MAGICPL_OIDC_CLIENT_ID=bridgehead-developers;
+# client-secret used for autheticating users in central ccp-authentication service
+export MAGICPL_OIDC_CLIENT_SECRET=1de49kn2j36qom15n7vkrve0g7pgh1f5p7v945pkl2hesak74bgek657tgi6or1hu5ji3m9lfrbhfa0g3haq18ebe205al4uoig9ii5;

internal-configuration/bridgehead-common.xml

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
-<bridgehead xmlns="http://schema.samply.de/config/BridgeheadInfo">
-  <!-- NOTE: This file is only used in magicpl -->
-  <name>Brückenkopf</name>
-  <longname>DKTK Brückenkopf Teststandort</longname>
-  <dktkid>MAGICPL_SITE</dktkid>
-  <monitor>NOT_USED</monitor>
-  <interval>string</interval>
-<centralsearch>NOT_USED</centralsearch>
-  <decentralsearch>NOT_USED</decentralsearch>
-  <updateserver>string</updateserver>
-  <queryLanguage>QUERY</queryLanguage>
-</bridgehead>

internal-configuration/magicpl.xml

@@ -1,444 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pathconfig [
-    <!ENTITY localPatientListUrl "MAGICPL_MAINZELLISTE_URL">
-    <!ENTITY localPatientlistApiKey "MAGICPL_MAINZELLISTE_API_KEY">
-    <!ENTITY magicplApiKey "MAGICPL_API_KEY">
-    <!ENTITY magicplApiKeyConnector "MAGICPL_API_KEY_CONNECTOR">
-    <!ENTITY centralPatientListUrl "MAGICPL_MAINZELLISTE_CENTRAL_URL">
-    <!ENTITY centralPatientListApiKey "MAGICPL_MAINZELLISTE_CENTRAL_API_KEY">
-    <!ENTITY centralKNEUrl "MAGICPL_CENTRAL_URL">
-    <!ENTITY centralKNEApiKey "MAGICPL_CENTRAL_API_KEY">
-    <!ENTITY site "MAGICPL_SITE">
-]>
-<pathconfig xmlns="http://www.example.org/Pfade" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-            xsi:schemaLocation="http://www.example.org/Pfade magicpl.xsd ">
-    <paths>
-        <multipath>
-            <name>getId</name>
-            <input>
-                <iorecord ref="IDAT" name="IDAT"/>
-                <iosingle ref="extIDs" name="extIDs"/>
-                <iosingle ref="idTypes" name="idTypes"/>
-                <iosingle ref="consented" name="consented"/>
-                <iosingle ref="auditTrail" name="auditTrail"/>
-                <iosingle ref="sureness" name="sureness"/>
-            </input>
-            <output>
-                <iosingle ref="ids" name="ids"/>
-            </output>
-            <step>
-                <name>getRequestedId</name>
-                <parameters/>
-                <input>
-                    <iorecord ref="IDAT" name="IDAT"/>
-                    <iosingle ref="idTypes" name="idTypes"/>
-                    <iosingle ref="consented" name="consented"/>
-                    <iosingle ref="auditTrail" name="auditTrail"/>
-                    <iosingle ref="sureness" name="sureness"/>
-                </input>
-                <output>
-                    <iosingle ref="ids" name="ids"/>
-                </output>
-                <switch>
-                    <evaluator name="de.pseudonymisierung.magicpl.evaluator.IsConsentedEvaluator">
-                        <parameters>
-                            <parameter name="key">consented</parameter>
-                        </parameters>
-                    </evaluator>
-                    <!-- eventuell muss hier andere unterscheidung genommen werden -->
-                    <case value="true">
-                        <multipath>
-                            <name>getDktkIdWithIdat</name>
-                            <parameters/>
-                            <input>
-                                <iorecord ref="IDAT"/>
-                                <iosingle ref="idTypes" name="idTypes"/>
-                                <iosingle ref="extIDs" name="extIDs"/>
-                                <iosingle ref="consented"/>
-                                <iosingle ref="auditTrail" name="auditTrail"/>
-                                <iosingle ref="sureness" name="sureness"/>
-                            </input>
-                            <output>
-                                <iosingle ref="ids" name="ids"/>
-                            </output>
-                            <step>
-                                <name>getIdToken</name>
-                                <parameters>
-                                    <!-- Hier war lokale Pfade URL angegeben, es soll aber eigentlich zentraler KNE aufgerufen werden -->
-                                    <parameter name="url">&centralKNEUrl;/paths/getIdToken</parameter>
-                                    <parameter name="method">POST</parameter>
-                                    <parameter name="apiKey">&centralKNEApiKey;</parameter>
-                                    <parameter name="excludeIdTypes">BK_&site;_L-ID</parameter>
-                                    <parameter name="excludeIDAT">locallyUniqueId</parameter>
-                                </parameters>
-                                <input>
-                                    <iorecord ref="IDAT" name="IDAT"/>
-                                    <iosingle ref="idTypes" name="idTypes"/>
-                                    <iosingle ref="auditTrail" name="auditTrail"/>
-                                </input>
-                                <output>
-                                    <iosingle ref="tokenId"/>
-                                </output>
-                                <implementation>de.pseudonymisierung.magicpl.processor.PathClient</implementation>
-                            </step>
-                            <step>
-                                <name>getDktkId</name>
-                                <parameters>
-                                    <parameter name="mainzellisteURL">&centralPatientListUrl;</parameter>
-                                    <parameter name="mainzellisteApiKey">&centralPatientListApiKey;</parameter>
-                                    <parameter name="mainzellisteApiVersion">3.2</parameter>
-                                </parameters>
-                                <input>
-                                    <iosingle ref="tokenId"/>
-                                    <iosingle ref="sureness" name="sureness"/>
-                                </input>
-                                <output>
-                                    <iosingle ref="ids" name="ids"/>
-                                </output>
-                                <implementation>de.pseudonymisierung.magicpl.processor.MainzellisteClient</implementation>
-                            </step>
-                            <step>
-                                <name>mapIdStringToExternalId</name>
-                                <parameters>
-                                    <parameter name="map">ids->extIDs</parameter>
-                                </parameters>
-                                <input>
-                                    <iosingle ref="ids" name="ids"/>
-                                </input>
-                                <output>
-                                    <iosingle ref="extIDs" name="extIDs"/>
-                                </output>
-                                <implementation>de.pseudonymisierung.magicpl.processor.InputMapperProcessor</implementation>
-                            </step>
-                            <step>
-                                <name>getLocalTKTExternalId</name>
-                                <parameters>
-                                    <parameter name="mainzellisteURL">&localPatientListUrl;</parameter>
-                                    <parameter name="mainzellisteApiKey">&localPatientlistApiKey;</parameter>
-                                    <parameter name="fieldType">plain</parameter>
-                                </parameters>
-                                <input>
-                                    <iorecord ref="IDAT" name="IDAT"/>
-                                    <iosingle ref="extIDs" name="extIDs"/>
-                                    <iosingle ref="idTypes" name="idTypes"/>
-                                    <iosingle ref="auditTrail" name="auditTrail"/>
-                                </input>
-                                <output>
-                                    <iosingle ref="tokenId"/>
-                                </output>
-                                <!-- TODO: Implementation für Ticket Erzeugung ohne Kontrolnummer -->
-                                <!-- Wird hier eine neue Klasse benötigt oder kann diese hier entsprechend angepasst werden? -->
-                                <implementation>de.pseudonymisierung.magicpl.processor.MainzellisteKNTicketClient</implementation>
-                            </step>
-                            <step>
-                                <name>generateLocalIdExternalId</name>
-                                <parameters>
-                                    <parameter name="mainzellisteURL">&localPatientListUrl;</parameter>
-                                    <parameter name="mainzellisteApiKey">&localPatientlistApiKey;</parameter>
-                                    <parameter name="mainzellisteApiVersion">3.2</parameter>
-                                    <parameter name="idType">BK_&site;_L-ID</parameter>
-                                </parameters>
-                                <input>
-                                    <iosingle ref="tokenId"/>
-                                    <iosingle ref="extIDs" name="extIDs"/>
-                                    <iosingle ref="sureness" name="sureness"/>
-                                </input>
-                                <output>
-                                    <iosingle ref="ids" name="ids"/>
-                                </output>
-                                <implementation>de.pseudonymisierung.magicpl.processor.MainzellisteClient</implementation>
-                            </step>
-                        </multipath>
-                    </case>
-                    <case value="false">
-                        <multipath>
-                            <name>getLocalIdWithIDAT</name>
-                            <input>
-                                <iorecord ref="IDAT" name="IDAT"/>
-                                <iosingle ref="idTypes" name="idTypes"/>
-                                <iosingle ref="auditTrail" name="auditTrail"/>
-                                <iosingle ref="sureness" name="sureness"/>
-                            </input>
-                            <output>
-                                <iosingle ref="ids" name="ids"/>
-                            </output>
-                            <step>
-                                <name>getTKT</name>
-                                <parameters>
-                                    <parameter name="mainzellisteURL">&localPatientListUrl;</parameter>
-                                    <parameter name="mainzellisteApiKey">&localPatientlistApiKey;</parameter>
-                                    <parameter name="fieldType">plain</parameter>
-                                </parameters>
-                                <input>
-                                    <iorecord ref="IDAT" name="IDAT"/>
-                                    <iosingle ref="idTypes" name="idTypes"/>
-                                    <iosingle ref="auditTrail" name="auditTrail"/>
-                                </input>
-                                <output>
-                                    <iosingle ref="tokenId"/>
-                                </output>
-                                <!-- Wird hier eine neue Klasse benötigt oder kann diese hier entsprechend angepasst werden? -->
-                                <implementation>de.pseudonymisierung.magicpl.processor.MainzellisteKNTicketClient</implementation>
-                            </step>
-                            <step>
-                                <name>generateLocalId</name>
-                                <parameters>
-                                    <parameter name="mainzellisteURL">&localPatientListUrl;</parameter>
-                                    <parameter name="mainzellisteApiKey">&localPatientlistApiKey;</parameter>
-                                    <parameter name="mainzellisteApiVersion">3.2</parameter>
-                                    <parameter name="idType">BK_&site;_L-ID</parameter>
-                                </parameters>
-                                <input>
-                                    <iosingle ref="tokenId"/>
-                                    <iosingle ref="sureness" name="sureness"/>
-                                </input>
-                                <output>
-                                    <iosingle ref="ids" name="ids"/>
-                                </output>
-                                <implementation>de.pseudonymisierung.magicpl.processor.MainzellisteClient</implementation>
-                            </step>
-                        </multipath>
-                    </case>
-                </switch>
-            </step>
-        </multipath>
-        <multipath>
-            <name>readPatients</name>
-            <input>
-                <iosingle ref="searchIds" name="searchIds"/>
-                <iosingle ref="resultIds" name="resultIds"/>
-                <iosingle ref="auditTrail" name="auditTrail"/>
-            </input>
-            <output>
-                <iosingle ref="patients" name="patients"/>
-            </output>
-            <step>
-                <name>DecideLocalOrCentralRequest</name>
-                <input>
-                    <iosingle ref="searchIds" name="searchIds"/>
-                    <iosingle ref="resultIds" name="resultIds"/>
-                    <iosingle ref="auditTrail" name="auditTrail"/>
-                </input>
-                <output>
-                    <iosingle ref="patients" name="patients"/>
-                </output>
-                <switch>
-                    <evaluator name="de.pseudonymisierung.magicpl.evaluator.RegexEvaluator">
-                        <parameters>
-                            <parameter name="regex">MDS_\*_G-ID</parameter>
-                            <parameter name="fieldName">resultIds</parameter>
-                        </parameters>
-                    </evaluator>
-                    <case value="true">
-                        <multipath>
-                            <name>readPatientsCentrally</name>
-                            <input>
-                                <iosingle ref="searchIds" name="searchIds"/>
-                                <iosingle ref="resultIds" name="resultIds"/>
-                                <iosingle ref="auditTrail" name="auditTrail"/>
-                            </input>
-                            <output>
-                                <iosingle ref="patients" name="patients"/>
-                            </output>
-                            <step>
-                                <name>createReadTokenCentral</name>
-                                <parameters>
-                                    <parameter name="mainzellisteURL">&centralPatientListUrl;</parameter>
-                                    <parameter name="mainzellisteApiKey">&centralPatientListApiKey;</parameter>
-                                    <parameter name="ignoredIdTypeCheck">true</parameter>
-                                </parameters>
-                                <input>
-                                    <iosingle ref="searchIds" name="searchIds"/>
-                                    <iosingle ref="resultIds" name="resultIds"/>
-                                    <iosingle ref="auditTrail" name="auditTrail"/>
-                                </input>
-                                <output>
-                                    <iosingle ref="tokenId"/>
-                                </output>
-                                <implementation>de.pseudonymisierung.magicpl.processor.MainzellisteReadTokenClient</implementation>
-                            </step>
-                            <step>
-                                <name>resolveReadTokenCentral</name>
-                                <parameters>
-                                    <parameter name="mainzellisteURL">&centralPatientListUrl;</parameter>
-                                    <parameter name="mainzellisteApiKey">&centralPatientListApiKey;</parameter>
-                                </parameters>
-                                <input>
-                                    <iosingle ref="tokenId"/>
-                                </input>
-                                <output>
-                                    <iosingle ref="patients"/>
-                                </output>
-                                <implementation>de.pseudonymisierung.magicpl.processor.MainzellisteReadClient</implementation>
-                            </step>
-                        </multipath>
-                    </case>
-                    <case value="false">
-                        <multipath>
-                            <name>readPatientsLocally</name>
-                            <input>
-                                <iosingle ref="searchIds" name="searchIds"/>
-                                <iosingle ref="resultIds" name="resultIds"/>
-                                <iosingle ref="auditTrail" name="auditTrail"/>
-                            </input>
-                            <output>
-                                <iosingle ref="patients" name="patients"/>
-                            </output>
-                            <step>
-                                <name>createReadToken</name>
-                                <parameters>
-                                    <parameter name="mainzellisteURL">&localPatientListUrl;</parameter>
-                                    <parameter name="mainzellisteApiKey">&localPatientlistApiKey;</parameter>
-                                    <parameter name="ignoredIdTypeCheck">true</parameter>
-                                </parameters>
-                                <input>
-                                    <iosingle ref="searchIds" name="searchIds"/>
-                                    <iosingle ref="resultIds" name="resultIds"/>
-                                    <iosingle ref="auditTrail" name="auditTrail"/>
-                                </input>
-                                <output>
-                                    <iosingle ref="tokenId"/>
-                                </output>
-                                <implementation>de.pseudonymisierung.magicpl.processor.MainzellisteReadTokenClient</implementation>
-                            </step>
-                            <step>
-                                <name>resolveReadToken</name>
-                                <parameters>
-                                    <parameter name="mainzellisteURL">&localPatientListUrl;</parameter>
-                                    <parameter name="mainzellisteApiKey">&localPatientlistApiKey;</parameter>
-                                </parameters>
-                                <input>
-                                    <iosingle ref="tokenId"/>
-                                </input>
-                                <output>
-                                    <iosingle ref="patients"/>
-                                </output>
-                                <implementation>de.pseudonymisierung.magicpl.processor.MainzellisteReadClient</implementation>
-                            </step>
-                        </multipath>
-                    </case>
-                </switch>
-            </step>
-        </multipath>
-    </paths>
-
-    <iodefinitions>
-        <iorecord name="IDAT">
-            <iosingle name="Vorname"/>
-            <iosingle name="Nachname"/>
-            <iosingle name="Fruehere_Namen"/>
-            <iosingle name="Geburtstag"/>
-            <iosingle name="Geburtsmonat"/>
-            <iosingle name="Geburtsjahr"/>
-            <iosingle name="Staatsangehoerigkeit"/>
-            <iosingle name="Geschlecht"/>
-            <!-- external id which will be inputed into paths -->
-            <iosingle name="locallyUniqueId"/>
-        </iorecord>
-        <iosingle name="idTypes" type="ArrayList"/>
-        <iosingle name="ids"/>
-        <!-- iosingle for external Ids which will be transferred between two steps -->
-        <iosingle name="extIDs"/>
-        <iosingle name="consented"/>
-        <iosingle name="tokenId"/>
-        <iosingle name="auditTrail"/>
-        <iosingle name="searchIds"/>
-        <iosingle name="resultIds"/>
-        <iosingle name="patients"/>
-        <iosingle name="sureness"/>
-    </iodefinitions>
-    <authentication>
-      <client>
-        <permissions>getId</permissions>
-        <restrictions>
-          <restriction path="getId">
-            <inputRestriction input="idTypes">
-              <permissibleValues>
-                <value>DKTK000001950_&site;_L-ID</value>
-                <value>DKTK000001950_&site;_G-ID</value>
-              </permissibleValues>
-            </inputRestriction>
-          </restriction>
-        </restrictions>
-        <roles>DKTK000001950_USER</roles>
-      </client>
-      <client>
-        <permissions>getId</permissions>
-        <restrictions>
-          <restriction path="getId">
-            <inputRestriction input="idTypes">
-              <permissibleValues>
-                <value>DKTK000001951_&site;_L-ID</value>
-                <value>DKTK000001951_&site;_G-ID</value>
-              </permissibleValues>
-            </inputRestriction>
-          </restriction>
-        </restrictions>
-        <roles>DKTK000001951_USER</roles>
-      </client>
-      <client>
-        <permissions>getId</permissions>
-        <restrictions>
-          <restriction path="getId">
-            <inputRestriction input="idTypes">
-              <permissibleValues>
-                <value>DKTK000001985_&site;_L-ID</value>
-                <value>DKTK000001985_&site;_G-ID</value>
-              </permissibleValues>
-            </inputRestriction>
-          </restriction>
-        </restrictions>
-        <roles>DKTK000001985_USER</roles>
-      </client>
-      <client>
-        <permissions>getId</permissions>
-        <restrictions>
-          <restriction path="getId">
-            <inputRestriction input="idTypes">
-              <permissibleValues>
-                <value>DKTK000001986_&site;_L-ID</value>
-                <value>DKTK000001986_&site;_G-ID</value>
-              </permissibleValues>
-            </inputRestriction>
-          </restriction>
-        </restrictions>
-        <roles>DKTK000001986_USER</roles>
-      </client>
-      <client>
-        <permissions>getId</permissions>
-        <restrictions>
-          <restriction path="getId">
-            <inputRestriction input="idTypes">
-              <permissibleValues>
-                <value>DKTK999999999_&site;_L-ID</value>
-                <value>DKTK999999999_&site;_G-ID</value>
-              </permissibleValues>
-            </inputRestriction>
-          </restriction>
-        </restrictions>
-        <roles>DKTK999999999_USER</roles>
-      </client>
-      <client>
-        <permissions>getId</permissions>
-        <restrictions>
-          <restriction path="getId">
-            <inputRestriction input="idTypes">
-              <permissibleValues>
-                <value>DKTK000002089_&site;_L-ID</value>
-                <value>DKTK000002089_&site;_G-ID</value>
-              </permissibleValues>
-            </inputRestriction>
-          </restriction>
-        </restrictions>
-        <roles>DKTK000002089_USER</roles>
-      </client>
-      <client>
-        <permissions>getId</permissions>
-        <apiKey>&magicplApiKey;</apiKey>
-      </client>
-      <client>
-        <permissions>readPatients</permissions>
-        <apiKey>&magicplApiKeyConnector;</apiKey>
-      </client>
-    </authentication>
-</pathconfig>

internal-configuration/mainzelliste.conf

@@ -1,227 +0,0 @@
-# For a comprehensive documentation of configuration parameters see the configuration manual
-# ("Konfigurationshandbuch").
-
-# debug mode: If set to true, token handling is disabled (i.e. no tokens are necessary).
-debug = false
-
-# Name of this mainzelliste distribution instance.
-dist = Lokale Patientenliste der CCP-IT am Standort ML_SITE
-
-# Database setup
-db.driver = ML_DB_DRIVER
-db.url = jdbc:ML_DB_TYPE://ML_DB_HOST:ML_DB_PORT/ML_DB_NAME
-db.username = ML_DB_USER
-db.password = ML_DB_PASS
-
-# Logging
-# By default, logs are written to stdout
-gcp.audittrail = true
-
-# Field definitions
-field.Vorname.type = PlainTextField
-field.Nachname.type = PlainTextField
-field.Fruehere_Namen.type = PlainTextField
-field.Geburtstag.type = IntegerField
-field.Geburtsmonat.type = IntegerField
-field.Geburtsjahr.type = IntegerField
-field.Staatsangehoerigkeit.type = PlainTextField
-field.Geschlecht.type = PlainTextField
-field.locallyUniqueId.type = PlainTextField
-
-# Server-side validation
-validator.field.Vorname.required = true
-validator.field.Nachname.required = true
-validator.field.Geburtstag.required = true
-validator.field.Geburtsmonat.required = true
-validator.field.Geburtsjahr.required = true
-
-validator.field.Vorname.format = [A-Za-zäÄöÖüÜß\\.\\-' ]*[A-Za-zäÄöÖüÜß]+[A-Za-zäÄöÖüÜß\\.\\-' ]*
-validator.field.Nachname.format = [A-Za-zäÄöÖüÜß\\.\\-' ]*[A-Za-zäÄöÖüÜß]+[A-Za-zäÄöÖüÜß\\.\\-' ]*
-validator.field.Fruehere_Namen.format = [A-Za-zäÄöÖüÜß\\.\\-' ]*[A-Za-zäÄöÖüÜß]+[A-Za-zäÄöÖüÜß\\.\\-' ]*
-
-# Date validation:
-validator.date.0.fields = Geburtstag, Geburtsmonat, Geburtsjahr
-validator.date.0.format = ddMMyyyy
-
-# Exchange groups
-# An exchange group denotes a set of fields whose values are considered interchangeable.
-# The matcher (currently only EpilinkMatcher) compares the fields in each exchange group to
-# all of its permutations and uses the best matching combination for final decision.
-exchangeGroup.0 = Vorname, Nachname, Fruehere_Namen
-
-# Field transformations
-#
-# Transformations for a field {fieldname} are defined by
-# field.{fieldname}.transformers = {transformerlist}, where
-# transformerlist is a comma-separated list of names of subclasses of FieldTransformer.
-field.Vorname.transformers = StringNormalizer, FirstNameDecomposer
-field.Nachname.transformers = StringNormalizer, GermanLastNameDecomposer
-field.Fruehere_Namen.transformers = StringNormalizer, GermanLastNameDecomposer
-
-# field comparators
-field.Vorname.comparator = NGramComparator
-field.Nachname.comparator = NGramComparator
-field.Fruehere_Namen.comparator = NGramComparator
-
-field.Geburtstag.comparator = BinaryFieldComparator
-field.Geburtsmonat.comparator = BinaryFieldComparator
-field.Geburtsjahr.comparator = BinaryFieldComparator
-
-field.Staatsangehoerigkeit.comparator = BinaryFieldComparator
-field.Geschlecht.comparator = BinaryFieldComparator
-
-# Matcher definition
-# Property matcher defines the class name of the matcher to use, which must be a subclass
-# of Matcher. Currently only EpilinkMatcher and NullMatcher are supported.
-matcher = EpilinkMatcher
-
-# Config for Epilink Matcher
-#
-# matcher.epilink.{fieldname}.frequency: Defines the assumed mean frequency of values
-# for field {fieldname}. This corresponds to the u-probability in the Fellegi-Sunter-Model
-# and can be estimated by the reciprocal of the number of distinct values (i.e. the
-# frequency of "month" is 1 / 12).
-matcher.epilink.Vorname.frequency = 0.000235
-matcher.epilink.Nachname.frequency = 0.0000271
-matcher.epilink.Fruehere_Namen.frequency = 0.0000271
-
-# 1 / 30 (approximate average number of days in a month)
-matcher.epilink.Geburtstag.frequency = 0.0333
-# 1 / 12
-matcher.epilink.Geburtsmonat.frequency = 0.0833
-# example value: birth years for an age range of 35 years (40 - 75).
-matcher.epilink.Geburtsjahr.frequency = 0.0286
-
-# Berechnungsgrundlage: 193 anerkannte + 13 umstrittene Staaten (Quelle: Wikipedia) -> ca. 1 / 200
-matcher.epilink.Staatsangehoerigkeit.frequency = 0.005
-matcher.epilink.Geschlecht.frequency = 0.5
-
-# matcher.epilink.{fieldname}.error_rate defines the assumed error_rate for
-# field {fieldname} (1 - m-probability)
-#
-# The supplied number stem from the evaluation of a German cancer registry
-matcher.epilink.Vorname.errorRate = 0.01
-matcher.epilink.Nachname.errorRate = 0.008
-matcher.epilink.Fruehere_Namen.errorRate = 0.008
-matcher.epilink.Geburtstag.errorRate = 0.005
-matcher.epilink.Geburtsmonat.errorRate = 0.002
-matcher.epilink.Geburtsjahr.errorRate = 0.004
-matcher.epilink.Staatsangehoerigkeit.errorRate = 0.04
-matcher.epilink.Geschlecht.errorRate = 0.04
-
-# matcher.epilink.threshold.match: Defines the minimum weight (in the interval [0,1])
-# for which a pair of records is considered a definite match.
-#
-# matcher.epilink.threshold_non_match: Defines the weight (in the interval [0,1])
-# below which a pair of records is considered a definite non-match. Must be less than or equal
-# to matcher.epilink.threshold_match.
-#
-# Record pairs with a weight w with threshold_non_match <= w < threshold_match are
-# considered possible matches and lead to a tentative PID.
-matcher.epilink.threshold_match = 0.95
-matcher.epilink.threshold_non_match = 0.65
-
-# Blocking
-# The blocking strategy choice depends on the field types after the transformation.
-# If compound fields are passed to the blocker, whether created by a field transformation or as input fields,
-# the type of the subfields is the one that is relevant for the blocking.
-# If exchange groups are used, only one of the fieldnames should be given here. The blocker is applied to
-# the other fields as well.
-
-# Use Soundex for PlainText fields
-blocking.soundex.type = Soundex
-blocking.soundex.fields = Vorname, Nachname, Fruehere_Namen
-
-# Use FieldEquality e.g. for birthday based blocking
-# This can be combined with Soundex blocking.
-blocking.dob.type = FieldEquality
-blocking.dob.fields = Geburtstag, Geburtsmonat, Geburtsjahr
-
-# Servers (apiKey and permission definition)
-servers.0.apiKey = ML_API_KEY
-servers.0.permissions = createSession;showSessionIds;deleteAllPatients;createToken;tt_addPatient;tt_readPatients;tt_editPatient;readConfiguration
-# TODO: Reduce to bridgeheads ip
-servers.0.allowedRemoteAdresses = 0.0.0.0/0
-
-# Allowed format of the callback
-callback.allowedFormat = https://.*
-callback.allowSelfsigned = false
-
-# IdGenerators
-idgenerators = BK_ML_SITE_L-ID, MDS_ML_SITE_L-ID, BK_ML_SITE_G-ID, locallyUniqueId, DKTK000001985_ML_SITE_L-ID, DKTK000001985_ML_SITE_G-ID, DKTK000001986_ML_SITE_L-ID, DKTK000001986_ML_SITE_G-ID, DKTK000001950_ML_SITE_L-ID, DKTK000001950_ML_SITE_G-ID, DKTK000001951_ML_SITE_L-ID, DKTK000001951_ML_SITE_G-ID, DKTK999999999_ML_SITE_L-ID, DKTK999999999_ML_SITE_G-ID, DKTK000002089_ML_SITE_L-ID, DKTK000002089_ML_SITE_G-ID
-
-idgenerators.eagerGeneration = false
-
-# Configuration of the local and global BK Pseudonymes
-idgenerator.BK_ML_SITE_L-ID = PIDGenerator
-idgenerator.BK_ML_SITE_L-ID.k1 = ML_BK_IDGENERATOR_RANDOM_1
-idgenerator.BK_ML_SITE_L-ID.k2 = ML_BK_IDGENERATOR_RANDOM_2
-idgenerator.BK_ML_SITE_L-ID.k3 = ML_BK_IDGENERATOR_RANDOM_3
-
-idgenerator.BK_ML_SITE_G-ID = ExternalIDGenerator
-
-# The unique id from the local datawarehouse
-idgenerator.locallyUniqueId = ExternalIDGenerator
-
-# Configuration for the local mds-id
-idgenerator.MDS_ML_SITE_L-ID = PIDGenerator
-idgenerator.MDS_ML_SITE_L-ID.k1 = ML_MDS_IDGENERATOR_RANDOM_1
-idgenerator.MDS_ML_SITE_L-ID.k2 = ML_MDS_IDGENERATOR_RANDOM_2
-idgenerator.MDS_ML_SITE_L-ID.k3 = ML_MDS_IDGENERATOR_RANDOM_3
-idgenerator.MDS_ML_SITE_L-ID.eager = *
-idgenerator.MDS_ML_SITE_L-ID.exportEncryption = mdsIdEncryption
-# Encryption for export of mds
-crypto.key.mdsIdPublicKey.type = RSA_PUBLIC
-crypto.key.mdsIdPublicKey.uri = file:///run/secrets/centralSearchPublicKey
-crypto.encryption.mdsIdEncryption.key = mdsIdPublicKey
-crypto.encryption.mdsIdEncryption.type = RSA_ENCRYPT
-
-# Configuration of the study specific id-generators
-
-# Configuration for project DKTK000001985
-idgenerator.DKTK000001985_ML_SITE_L-ID = PIDGenerator
-idgenerator.DKTK000001985_ML_SITE_L-ID.k1 = ML_DKTK000001985_IDGENERATOR_RANDOM_1
-idgenerator.DKTK000001985_ML_SITE_L-ID.k2 = ML_DKTK000001985_IDGENERATOR_RANDOM_2
-idgenerator.DKTK000001985_ML_SITE_L-ID.k3 = ML_DKTK000001985_IDGENERATOR_RANDOM_3
-
-idgenerator.DKTK000001985_ML_SITE_G-ID = ExternalIDGenerator
-
-# Configuration for project DKTK000001986
-idgenerator.DKTK000001986_ML_SITE_L-ID = PIDGenerator
-idgenerator.DKTK000001986_ML_SITE_L-ID.k1 = ML_DKTK000001986_IDGENERATOR_RANDOM_1
-idgenerator.DKTK000001986_ML_SITE_L-ID.k2 = ML_DKTK000001986_IDGENERATOR_RANDOM_2
-idgenerator.DKTK000001986_ML_SITE_L-ID.k3 = ML_DKTK000001986_IDGENERATOR_RANDOM_3
-
-idgenerator.DKTK000001986_ML_SITE_G-ID = ExternalIDGenerator
-
-# Configuration for project DKTK000001950
-idgenerator.DKTK000001950_ML_SITE_L-ID = PIDGenerator
-idgenerator.DKTK000001950_ML_SITE_L-ID.k1 = ML_DKTK000001950_IDGENERATOR_RANDOM_1
-idgenerator.DKTK000001950_ML_SITE_L-ID.k2 = ML_DKTK000001950_IDGENERATOR_RANDOM_2
-idgenerator.DKTK000001950_ML_SITE_L-ID.k3 = ML_DKTK000001950_IDGENERATOR_RANDOM_3
-
-idgenerator.DKTK000001950_ML_SITE_G-ID = ExternalIDGenerator
-
-# Configuration for project DKTK000001951
-idgenerator.DKTK000001951_ML_SITE_L-ID = PIDGenerator
-idgenerator.DKTK000001951_ML_SITE_L-ID.k1 = ML_DKTK000001951_IDGENERATOR_RANDOM_1
-idgenerator.DKTK000001951_ML_SITE_L-ID.k2 = ML_DKTK000001951_IDGENERATOR_RANDOM_2
-idgenerator.DKTK000001951_ML_SITE_L-ID.k3 = ML_DKTK000001951_IDGENERATOR_RANDOM_3
-
-idgenerator.DKTK000001951_ML_SITE_G-ID = ExternalIDGenerator
-
-# Configuration for project DKTK999999999
-idgenerator.DKTK999999999_ML_SITE_L-ID = PIDGenerator
-idgenerator.DKTK999999999_ML_SITE_L-ID.k1 = ML_DKTK999999999_IDGENERATOR_RANDOM_1
-idgenerator.DKTK999999999_ML_SITE_L-ID.k2 = ML_DKTK999999999_IDGENERATOR_RANDOM_2
-idgenerator.DKTK999999999_ML_SITE_L-ID.k3 = ML_DKTK999999999_IDGENERATOR_RANDOM_3
-
-idgenerator.DKTK999999999_ML_SITE_G-ID = ExternalIDGenerator
-
-# Configuration for project DKTK000002089
-idgenerator.DKTK000002089_ML_SITE_L-ID = PIDGenerator
-idgenerator.DKTK000002089_ML_SITE_L-ID.k1 = ML_DKTK000002089_IDGENERATOR_RANDOM_1
-idgenerator.DKTK000002089_ML_SITE_L-ID.k2 = ML_DKTK000002089_IDGENERATOR_RANDOM_2
-idgenerator.DKTK000002089_ML_SITE_L-ID.k3 = ML_DKTK000002089_IDGENERATOR_RANDOM_3
-
-idgenerator.DKTK000002089_ML_SITE_G-ID = ExternalIDGenerator

internal-configuration/proxy.xml

@@ -1,21 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<Configuration xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-  xmlns="http://schema.samply.de/common"
-  xsi:schemaLocation="http://schema.samply.de/common http://schema.samply.de/config/Common.Config.xsd ">
-  <Proxy>
-    <HTTP>
-      <Url>HTTP_PROXY_URL</Url>
-      <Username>HTTP_PROXY_USERNAME</Username>
-      <Password>HTTP_PROXY_PASSWORD</Password>
-    </HTTP>
-    <HTTPS>
-      <Url>HTTPS_PROXY_URL</Url>
-      <Username>HTTPS_PROXY_USERNAME</Username>
-      <Password>HTTPS_PROXY_PASSWORD</Password>
-    </HTTPS>
-    <NoProxyHosts>
-      <Host>NO_PROXY_HOSTS</Host>
-    </NoProxyHosts>
-    <Realm/>
-  </Proxy>
-</Configuration>

site.dev.conf

@@ -1,20 +0,0 @@
-#!/bin/bash
-### This is the configuration file for secrets, only your site should know
-
-##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=
-
-###secrets
-## Connector Password
-export CONNECTOR_POSTGRES_PASS=
-
-##ID-Manager
-#This needs to be set if the project is either c4 or dktk
-export