Merge branch 'refactor/preconfiguredImages' into version-1

README.md

@@ -1,44 +1,319 @@
-# bridgehead
+# Bridgehead
+This repository contains all information and tools to deploy a bridgehead. If you have any questions about deploying a bridgehead, please [contact us](mailto:verbis-support@dkfz-heidelberg.de).
 
-This repository contains all tools to deploy a bridgehead with docker. If you have any questions about deploying a bridgehead, please contact us.
+TODO: Insert comprehensive feature list of the bridgehead? Why would anyone install it?
 
-There are some prerequisites, which need to be meet before starting a bridgehead. If you running a Windows or Mac OS machine you should read starting a bridgehead. If you running a Linux machine you can start or install a bridgehead.
+TODO: TOC
 
+## Requirements
+Before starting the installation process, please ensure that following software is available on your system:
 
-## Setup
+### [Git](https://git-scm.com/book/en/v2/Getting-Started-Installing-Git)
+To check that you have a working git installation, please run
+``` shell
+cd ~/;
+git clone https://github.com/octocat/Hello-World.git;
+cat ~/Hello-World/README;
+rm -rf Hello-World;
+```
+If you see the output "Hello World!" your installation should be working.
 
-Clone this repository to /srv/docker/
+### [Docker](https://docs.docker.com/get-docker/)
+To check your docker installation, you can try to execute dockers "Hello World" Image. The command is:
+``` shell
+docker run --rm --name hello-world hello-world;
+```
+Docker will now download the "hello-world" docker image and try to execute it. After the download you should see a message starting with "Hello from Docker!".
 
-The first step is to copy the site.conf. It contains some configuration and secrets for your bridgehead.
+> NOTE: If the download of the image fails (e.g with "connection timed out" message), ensure that you have correctly set the proxy for the docker daemon. Refer to ["Docker Daemon Proxy Configuration" in the "Pitfalls" section](#docker-daemon-proxy-configuration)
 
-With cp site.dev.conf site.conf you can clone the template. You need to set the project accoriding to the which bridgehead you want to start. It's either a GBN/BBMRI-ERIC, DKTK, DKTK-FED or C4 Bridgehead.
+You should also check, that the version of docker installed by you is newer than "1.20". To check this, just run 
 
-Each Project needs a .env file where all the settings are located. Each Project has a template for it in their respective folder. We offer you to setup the file with and also to manage it.
+``` shell
+docker --version
+```
 
-### Git repository
+### [Docker Compose](https://docs.docker.com/compose/cli-command/#installing-compose-v2)
+To check your docker-compose installation, please run the following command. It uses the "hello-world" image from the previous section:
+``` shell
+docker-compose -f - up <<EOF
+version: "3.9"
+services:
+  hello-world:
+    image: hello-world
+EOF
+```
+After executing the command, you should again see the message starting with "Hello from Docker!".
 
-If you already have a git config repository you can clone it with 
+You should also ensure, that the version of docker-compose installed by you is newer than "2.XX". To check this, just run 
 
-git submodule add -f https://"$git_username":"$git_access_token"@code.mitro.dkfz.de/scm/bd/"$site_name_lowercase"-config.git ./site-config
+``` shell
+docker-compose --version
+```
 
-### DKTK
+### [systemd](https://systemd.io/)
+You shouldn't need to install it yourself. If systemd is not available on your system you should get another system.
+To check if systemd is available on your system, please execute
 
-For DKTK set in the site.conf the project to "dkkt". Also, you need to set many settings in the env file. For the API keys you need to contact the Mainzelliste Team. 
+``` shell
+systemctl --version
+```
 
-### DKTK-FED
+## Getting Started
 
-For the DKTK Federate Search put dkkt-fed in the site.conf.
+If your system passed all checks from ["Requirements" section], you are now ready to download the bridgehead.
 
-### GBA/BBMRI-ERIC
+First, clone the repository to the directory "/srv/docker/bridgehead":
 
-Coming soon
+``` shell
+sudo mkdir /srv/docker/;
+sudo git clone https://github.com/samply/bridgehead.git /srv/docker/bridgehead;
+```
+
+Next, you need to configure a set of variables, specific for your site with not so high security concerns. You can visit the configuration template at [GitHub](https://github.com/samply/bridgehead-config). You can download the repositories contents and add them to the "bridgehead-config" directory.
+
+``` shell
+sudo git submodule add -f https://github.com/samply/bridgehead-config.git ./site-config;
+```
+> NOTE: If you are part of the CCP-IT we will provide you another link for the configuration.
+
+You should now be able to run a bridgehead instance. To check if everything works, execute the following:
+``` shell
+sudo ./lib/init-test-environment.sh;
+sudo ./start-bridgehead.sh <dktk/gbn/c4>;
+```
+
+You should now be able to access the landing page on your system, e.g "http://<your-host>/" 
+
+To remove the test-environment, run (make sure you don't have other docker services installed on this system, docker volume prune is destructive!)
+``` shell
+sudo ./stop-bridgehead.sh <dktk/gbn/c4>;
+sudo docker volume prune;
+```
+
+For a server, we highly recommend that you install the system units for managing the bridgehead, provided by us. . You can do this by executing the [setup-bridgehead-units.sh](./lib/setup-bridgehead-units.sh) script:
+``` shell
+sudo ./lib/setup-bridgehead-units.sh
+```
+
+Finally, you need to configure your sites secrets. These are places as configuration for each bridgeheads system unit. Refer to the section for your specific project:
+
+### DKTK/C4
+You can create the site specific configuration with: 
+
+``` shell
+sudo systemctl edit bridgehead@dktk.service;
+```
+
+This will open your default editor allowing you to edit the docker system units configuration. Insert the following lines in the editor and define your machines secrets. You share some of the ID-Management secrets with the central patientlist (Mainz) and controlnumbergenerator (Frankfurt). Refer to the ["Configuration" section](#configuration) for this.
+
+``` conf
+[Service]
+Environment=HOSTIP=
+Environment=HOST=
+Environment=HTTP_PROXY_USER=
+Environment=HTTP_PROXY_PASSWORD=
+Environment=HTTPS_PROXY_USER=
+Environment=HTTPS_PROXY_PASSWORD=
+Environment=CONNECTOR_POSTGRES_PASS=
+Environment=ML_DB_PASS=
+Environment=MAGICPL_API_KEY=
+Environment=MAGICPL_MAINZELLISTE_API_KEY=
+Environment=MAGICPL_API_KEY_CONNECTOR=
+Environment=MAGICPL_MAINZELLISTE_CENTRAL_API_KEY=
+Environment=MAGICPL_CENTRAL_API_KEY=
+Environment=MAGICPL_OIDC_CLIENT_ID=
+Environment=MAGICPL_OIDC_CLIENT_SECRET=
+```
+
+To make the configuration effective, you need to tell systemd to reload the configuration and restart the docker service:
+
+``` shell
+sudo systemctl daemon-reload;
+sudo systemctl bridgehead@dktk.service;
+```
 
 ### C4
+You can create the site specific configuration with: 
 
-Coming soon
+``` shell
+sudo systemctl edit bridgehead@c4.service;
+```
 
+This will open your default editor allowing you to edit the docker system units configuration. Insert the following lines in the editor and define your machines secrets. You share some of the ID-Management secrets with the central patientlist (Mainz) and controlnumbergenerator (Frankfurt). Refer to the ["Configuration" section](#configuration) for this.
 
-## Starting your bridgehead
+``` conf
+[Service]
+Environment=HOSTIP=
+Environment=HOST=
+Environment=HTTP_PROXY_USER=
+Environment=HTTP_PROXY_PASSWORD=
+Environment=HTTPS_PROXY_USER=
+Environment=HTTPS_PROXY_PASSWORD=
+Environment=CONNECTOR_POSTGRES_PASS=
+Environment=STORE_POSTGRES_PASS=
+Environment=ML_DB_PASS=
+Environment=MAGICPL_API_KEY=
+Environment=MAGICPL_MAINZELLISTE_API_KEY=
+Environment=MAGICPL_API_KEY_CONNECTOR=
+Environment=MAGICPL_MAINZELLISTE_CENTRAL_API_KEY=
+Environment=MAGICPL_CENTRAL_API_KEY=
+Environment=MAGICPL_OIDC_CLIENT_ID=
+Environment=MAGICPL_OIDC_CLIENT_SECRET=
+```
 
-There two methods to start the bridgehead. For Windows, Linux and Mac OS you can use the start-bridgehead.sh to start it with docker-compose.
+To make the configuration effective, you need to tell systemd to reload the configuration and restart the docker service:
-The second methods is using the systemd management tool you start, stop and update your bridgehead.
+
+``` shell
+sudo systemctl daemon-reload;
+sudo systemctl bridgehead@c4.service;
+```
+### GBA/BBMRI-ERIC
+
+You can create the site specific configuration with: 
+
+``` shell
+sudo systemctl edit bridgehead@gbn.service;
+```
+
+This will open your default editor allowing you to edit the docker system units configuration. Insert the following lines in the editor and define your machines secrets.
+
+``` conf
+[Service]
+Environment=HOSTIP=
+Environment=HOST=
+Environment=HTTP_PROXY_USER=
+Environment=HTTP_PROXY_PASSWORD=
+Environment=HTTPS_PROXY_USER=
+Environment=HTTPS_PROXY_PASSWORD=
+Environment=CONNECTOR_POSTGRES_PASS=
+```
+
+To make the configuration effective, you need to tell systemd to reload the configuration and restart the docker service:
+
+``` shell
+sudo systemctl daemon-reload;
+sudo systemctl bridgehead@gbn.service;
+```
+
+### Developers
+Because some developers machines doesn't support system units (e.g Windows Subsystem for Linux), we provide a dev environment [configuration script](./lib/init-test-environment.sh).
+It is not recommended to use this script in production!
+
+## Configuration
+
+### Locally Managed Secrets
+This section describes the secrets you need to configure locally through the configuration
+
+| Name                                 | Recommended Value                                                                                 | Description |  
+|--------------------------------------|---------------------------------------------------------------------------------------------------| ----------- |  
+| HTTP_PROXY_USER                      |                                                                                                   | Your local http proxy user |
+| HOSTIP                               | Compute with: `docker run --rm --add-host=host.docker.internal:host-gateway ubuntu cat /etc/hosts | grep 'host.docker.internal' | awk '{print $1}'` | The ip from which docker containers can reach your host system. |
+| HOST                                 | Compute with: `hostname`                                                                          |The hostname from which all components will eventually be available|
+| HTTP_PROXY_PASSWORD                  |                                                                                                   |Your local http proxy user's password|
+| HTTPS_PROXY_USER                     |                                                                                                   |Your local https proxy user|
+| HTTPS_PROXY_PASSWORD                 || Your local https proxy user's password                                                            |
+| CONNECTOR_POSTGRES_PASS              | Random String                                                                                     |The password for your project specific connector.|
+| STORE_POSTGRES_PASS                  | Random String                                                                                     |The password for your local datamanagements database (only relevant in c4)|
+| ML_DB_PASS                           | Random String                                                                                     |The password for your local patientlist database|
+| MAGICPL_API_KEY                      | Random String                                                                                     |The apiKey used by the local datamanagement to create pseudonymes.|
+| MAGICPL_MAINZELLISTE_API_KEY         | Random String                                                                                     |The apiKey used by the local id-manager to communicate with the local patientlist|
+| MAGICPL_API_KEY_CONNECTOR            | Random String                                                                                     |The apiKey used by the connector to communicate with the local patientlist|
+| MAGICPL_MAINZELLISTE_CENTRAL_API_KEY | You need to ask the central patientlists admin for this.                                          |The apiKey for your machine to communicate with the central patientlist|
+| MAGICPL_CENTRAL_API_KEY              | You need to ask the central controlnumbergenerator admin for this.                                |The apiKey for your machine to communicate with the central controlnumbergenerator|
+| MAGICPL_OIDC_CLIENT_ID               || The client id used for your machine, to connect with the central authentication service           |
+| MAGICPL_OIDC_CLIENT_SECRET           || The client secret used for your machine, to connect with the central authentication service       |
+
+### Cooperatively Managed Secrets
+> TODO: Describe secrets from site-config 
+
+## Managing your Bridgehead
+> TODO: Rewrite this section (restart, stop, uninstall, manual updates)
+### On a Server
+#### Start
+This will start a not running bridgehead system unit:
+``` shell
+sudo systemctl start bridgehead@<dktk/c4/gbn>
+```
+#### Stop
+This will stop a running bridgehead system unit:
+``` shell
+sudo systemctl stop bridgehead@<dktk/c4/gbn>
+```
+#### Update
+This will update bridgehead system unit:
+``` shell
+sudo systemctl start bridgehead-update@<dktk/c4/gbn>
+```
+#### Remove the Bridgehead System Units
+If, for some reason you want to remove the installed bridgehead units, we added a [script](./lib/remove-bridgehead-units.sh) you can execute:
+``` shell
+sudo ./lib/remove-bridgehead-units.sh
+```
+
+### On Developers Machine
+For developers, we provide additional scripts for starting and stopping the specif bridgehead:
+#### Start
+This shell script start a specified bridgehead. Choose between "dktk", "c4" and "gbn".
+``` shell
+./start-bridgehead <dktk/c4/gbn>
+```
+#### Stop
+This shell script stops a specified bridgehead. Choose between "dktk", "c4" and "gbn".
+``` shell
+./stop-bridgehead <dktk/c4/gbn>
+```
+#### Update
+This shell script updates the configuration for all bridgeheads installed on your system.
+``` shell
+./update-bridgehead
+```
+> NOTE: If you want to regularly update your developing instance, you can create a CRON job that executes this script.
+## Migration Guide
+> TODO: How to transfer from windows/gbn
+
+## Pitfalls
+### [Git Proxy Configuration](https://gist.github.com/evantoli/f8c23a37eb3558ab8765)
+Unlike most other tools, git doesn't use the default proxy variables "http_proxy" and "https_proxy". To make git use a proxy, you will need to adjust the global git configuration:
+
+``` shell
+sudo git config --global http.proxy http://<your-proxy-host>:<your-proxy-port>;
+sudo git config --global https.proxy http://<your-proxy-host>:<your-proxy-port>;
+```
+> NOTE: Some proxies may require user and password authentication. You can adjust the settings like this: "http://<your-proxy-user>:<your-proxy-user-password>@<your-proxy-host>:<your-proxy-port>".
+> NOTE: It is also possible that a proxy requires https protocol, so you can replace this to.
+
+You can check that the updated configuration with
+
+``` shell
+sudo git config --global --list;
+```
+
+### Docker Daemon Proxy Configuration
+Docker has a background daemon, responsible for downloading images and starting them. To configure the proxy for this daemon, use the systemctl command:
+
+``` shell
+sudo systemctl edit docker
+```
+
+This will open your default editor allowing you to edit the docker system units configuration. Insert the following lines in the editor, replace <your-proxy-host> and <your-proxy-port> with the corresponding values for your machine and save the file:
+``` conf
+[Service]
+Environment=HTTP_PROXY=http://<your-proxy-host>:<your-proxy-port>
+Environment=HTTPS_PROXY=http://<your-proxy-host>:<your-proxy-port>
+Environment=FTP_PROXY=http://<your-proxy-host>:<your-proxy-port>
+```
+> NOTE: Some proxies may require user and password authentication. You can adjust the settings like this: "http://<your-proxy-user>:<your-proxy-user-password>@<your-proxy-host>:<your-proxy-port>".
+> NOTE: It is also possible that a proxy requires https protocol, so you can replace this to.
+
+The file should now be at the location "/etc/systemd/system/docker.service.d/override.conf". You can proof check with
+``` shell
+cat /etc/systemd/system/docker.service.d/override.conf;
+```
+
+To make the configuration effective, you need to tell systemd to reload the configuration and restart the docker service:
+
+``` shell
+sudo systemctl daemon-reload;
+sudo systemctl restart docker;
+```

c4/docker-compose.yml

@@ -1,38 +1,21 @@
 version: "3.7"
 volumes:
-  connector_db_data:
+  c4-connector-db-data:
-  connector_logs:
+  c4-connector-logs:
-  patientlist_db_data:
+  patientlist-db-data:
-  patientlist_logs:
+  patientlist-logs:
-  idmanager_logs:
+  id-manager-logs:
-  store_db_data:
+  c4-store-db-data:
-  store_logs:
+  c4-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
     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 +24,6 @@ services:
       - /var/run/docker.sock:/var/run/docker.sock:ro
 
   landing:
-    container_name: bridgehead_landingpage
     image: nginx:stable
     volumes:
       - ../landing/:/usr/share/nginx/html
@@ -50,106 +32,128 @@ services:
       - "traefik.http.routers.landing.rule=PathPrefix(`/`)"
       - "traefik.http.services.landing.loadbalancer.server.port=80"
 
-  connector:
+  c4-connector:
-    container_name: bridgehead_c4_connector
+    image: "samply/share-client:c4-feature-environmentPreconfigurationTorben"
-    image: docker.verbis.dkfz.de/ccp/connector:3
     environment:
-      STORE_URL: http://bridgehead_c4_store:8080
+      POSTGRES_HOST: "c4-connector-db"
-      LDM_URL: http://bridgehead_c4_store:8080
+      ID_MANAGER_APIKEY: ${MAGICPL_API_KEY_CONNECTOR}
-      POSTGRES_HOST: ${CONNECTOR_DB_HOST}
       POSTGRES_PASSWORD: ${CONNECTOR_POSTGRES_PASS}
-      NNGM_PASSWORD: ${NNGM_PASSWORD}
+      HTTP_PROXY_USER: ${HTTP_PROXY_USER}
-      NNGM_MAINZELLISTE_APIKEY: ${NNGM_MAINZELLISTE_APIKEY}
+      HTTP_PROXY_PASSWORD: ${HTTP_PROXY_PASSWORD}
+      HTTPS_PROXY_USER: ${HTTPS_PROXY_USER}
+      HTTPS_PROXY_PASSWORD: ${HTTPS_PROXY_PASSWORD}
+      LDM_URL: "${PROTOCOL}://${HOST}/c4-localdatamanagement"
+      POSTGRES_PASSWORD: ${CONNECTOR_POSTGRES_PASS}
+    env_file:
+      - ../site-config/c4.env
+    # Necessary for the connector to successful check the status of other components on the same host
+    extra_hosts:
+      - "host.docker.internal:host-gateway"
+      - "${HOST}:${HOSTIP}"
     volumes:
-      - "connector_logs:/usr/local/tomcat/logs"
+      - "c4-connector-logs:/usr/local/tomcat/logs"
+    depends_on:
+      - connector-db
+    restart: always
     labels:
       - "traefik.enable=true"
       - "traefik.http.routers.c4_connector.rule=PathPrefix(`/c4-connector`)"
       - "traefik.http.services.c4_connector.loadbalancer.server.port=8080"
-    depends_on:
-      - connector_db
-    restart: always
-    env_file:
-    ###TODO: Move into Image
-      - internal.env
 
-  connector_db:
+  c4-connector-db:
-    container_name: bridgehead_c4_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"
+      - "c4-connector-db-data:/var/lib/postgresql/data"
     restart: always
-    env_file:
-    ###TODO: Move into Image
-      - internal.env
 
-  idmanager:
+  id-manager:
-    container_name: bridgehead_idmanager
+    image: docker.verbis.dkfz.de/ccp/idmanager:bridgehead-develop
-    image: docker.verbis.dkfz.de/ccp/idmanager:deploy-c4
     environment:
-      TOMCAT_REVERSEPROXY_FQDN: ${HOST}/id-manager
+      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: ${MAGICPL_OIDC_CLIENT_SECRET}
-    volumes:
+      TOMCAT_REVERSEPROXY_FQDN: "${HOST}"
-      - "idmanager_logs:/usr/local/tomcat/logs"
+      HTTP_PROXY_USER: ${HTTP_PROXY_USER}
-    secrets:
+      HTTP_PROXY_PASSWORD: ${HTTP_PROXY_PASSWORD}
-      - magicpl.docker.xml
+      HTTPS_PROXY_USER: ${HTTPS_PROXY_USER}
-      - dktk_bridgehead_info.docker.xml
+      HTTPS_PROXY_PASSWORD: ${HTTPS_PROXY_PASSWORD}
-      - proxy.docker.xml
-    labels:
-      - "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"
     env_file:
-    ###TODO: Move into Image
+      - ../site-config/dktk.env
-      - internal.env
+    volumes:
+      - "id-manager-logs:/usr/local/tomcat/logs"
+    depends_on:
+      - patientlist
+    labels:
+      - "traefik.http.routers.idmanager.rule=PathPrefix(`/ID-Manager`)"
+      - "traefik.http.services.idmanager.loadbalancer.server.port=8080"
 
-  store:
+  patientlist:
-    container_name: bridgehead_c4_store
+    image: docker.verbis.dkfz.de/ccp/patientlist:bridgehead-develop
+    environment:
+      ML_SITE: ${SITE}
+      ML_API_KEY: ${MAGICPL_MAINZELLISTE_API_KEY}
+      ML_DB_PASS: ${ML_DB_PASS}
+      TOMCAT_REVERSEPROXY_FQDN: "${HOST}"
+    env_file:
+      - ../site-config/dktk.env
+      # TODO: Implement automatic seed generation in mainzelliste
+      - ../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:
+    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"
+
+  c4-store:
     image: docker.verbis.dkfz.de/ccp/samply.store:release-5.1.2
     environment:
-      POSTGRES_HOST: bridgehead_c4_store_db
+      MDR_NAMESPACE: "adt,dktk,marker"
+      MDR_VALIDATION: false
+      DEPLOYMENT_CONTEXT: "c4-localdatamanagement"
+      POSTGRES_HOST: c4-store-db
       POSTGRES_PORT: 5432
       POSTGRES_DB: samplystore
       POSTGRES_USER: samplystore
-      POSTGRES_PASSWORD: samplystore
+      POSTGRES_PASSWORD: ${STORE_POSTGRES_PASS}
-      TZ: Europe/Berlin
+      TZ: "Europe/Berlin"
     volumes:
-      - "store_logs:/usr/local/tomcat/logs"
+      - "c4-store-logs:/usr/local/tomcat/logs"
     labels:
       - "traefik.enable=true"
-      - "traefik.http.routers.store_c4.rule=PathPrefix(`/c4-loc\
+      - "traefik.http.routers.store_c4.rule=PathPrefix(`/c4-localdatamanagement`)"
-        aldatamanagement`)"
     depends_on:
-      - store_db
+      - store-db
     restart: always
-    env_file:
-    ###TODO: Move into Image
-      - internal.env
 
-  store_db:
+  c4-store-db:
-    container_name: bridgehead_c4_store_db
     image: postgres:9.5-alpine
     command: postgres -c datestyle='iso, dmy'
     environment:
-      POSTGRES_PORT: 5432
+      TZ: "Europe/Berlin"
       POSTGRES_DB: samplystore
       POSTGRES_USER: samplystore
-      POSTGRES_PASSWORD: samplystore
+      POSTGRES_PASSWORD: ${STORE_POSTGRES_PASS}
     volumes:
-      - "store_db_data:/var/lib/postgresql/data"
+      - "c4-store-db-data:/var/lib/postgresql/data"
     restart: always
-    env_file:
-    ###TODO: Move into Image
-      - internal.env

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

@@ -1,38 +1,19 @@
 version: "3.7"
 volumes:
-  connector_db_data:
+  dktk-connector-db-data:
-  connector_logs:
+  dktk-connector-logs:
-  patientlist_db_data:
+  patientlist-db-data:
-  patientlist_logs:
+  patientlist-logs:
-  idmanager_logs:
+  id-manager-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
     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 +22,6 @@ services:
       - /var/run/docker.sock:/var/run/docker.sock:ro
 
   landing:
-    container_name: bridgehead_landingpage
     image: nginx:stable
     volumes:
       - ../landing/:/usr/share/nginx/html
@@ -50,102 +30,93 @@ services:
       - "traefik.http.routers.landing.rule=PathPrefix(`/`)"
       - "traefik.http.services.landing.loadbalancer.server.port=80"
 
-  connector:
+  dktk-connector:
-    container_name: bridgehead_dktk_connector
+    image: "samply/share-client:dktk-feature-environmentPreconfigurationTorben"
-    image: "samply/share-client:dktk-pr-148"
     environment:
-      STORE_URL: ${STORE_URL}
+      POSTGRES_HOST: "dktk-connector-db"
+      ID_MANAGER_APIKEY: ${MAGICPL_API_KEY_CONNECTOR}
       POSTGRES_PASSWORD: ${CONNECTOR_POSTGRES_PASS}
-      PATIENTLIST_URL: "http://bridgehead_patientlist:8080"
+      HTTP_PROXY_USER: ${HTTP_PROXY_USER}
-      PROJECTPSEUDONYMISATION_URL: "http://bridgehead_dktk_idmanager:8080/ID-Manager/html/projectSelection.html"
+      HTTP_PROXY_PASSWORD: ${HTTP_PROXY_PASSWORD}
+      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"
+      - "dktk-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"
-    ports:
-      - 65395:65395
 
-  connector_db:
+  dktk-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"
+      - "dktk-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
+    image: docker.verbis.dkfz.de/ccp/idmanager:bridgehead-develop
-    image: docker.verbis.dkfz.de/pseudonymisierung/magicpl:release-0.2.0
     environment:
-      TOMCAT_REVERSEPROXY_FQDN: ${HOST}/id-manager
+      MAGICPL_SITE: ${SITE}
-      MAGICPL_MAINZELLISTE_API_KEY: "123"
+      MAGICPL_MAINZELLISTE_API_KEY: ${MAGICPL_MAINZELLISTE_API_KEY}
-      MAGICPL_API_KEY: "123"
+      MAGICPL_API_KEY: ${MAGICPL_API_KEY}
-      MAGICPL_API_KEY_CONNECTOR: "123"
+      MAGICPL_API_KEY_CONNECTOR: ${MAGICPL_API_KEY_CONNECTOR}
-      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: ${MAGICPL_OIDC_CLIENT_SECRET}
-      MAGICPL_OIDC_CLIENT_SECRET: "123"
+      TOMCAT_REVERSEPROXY_FQDN: "${HOST}"
-      TZ: Europe/Berlin
+      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"
+      - "id-manager-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.middlewares.idmanager_strip.stripprefix.prefixes=/id-mana\
+      - "traefik.http.services.id-manager.loadbalancer.server.port=8080"
-        ger"
-      - "traefik.http.routers.idmanager.middlewares=idmanager_strip"
-      - "traefik.http.services.idmanager.loadbalancer.server.port=8080"
-    env_file:
-    ###TODO: Move into Image
-      - internal.env
 
   patientlist:
-    container_name: bridgehead_patientlist
+    image: docker.verbis.dkfz.de/ccp/patientlist:bridgehead-develop
-    image: medicalinformatics/mainzelliste:develop
     environment:
+      ML_SITE: ${SITE}
+      ML_API_KEY: ${MAGICPL_MAINZELLISTE_API_KEY}
       ML_DB_PASS: ${ML_DB_PASS}
-      ML_API_KEY: ${ML_API_KEY}
+      TOMCAT_REVERSEPROXY_FQDN: "${HOST}"
-      TOMCAT_REVERSEPROXY_FQDN: ${HOST}/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"
+      - "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.middlewares.patientlist_strip.stripprefix.prefixes=/patie\
-        ntlist"
-      - "traefik.http.routers.patientlist.middlewares=patientlist_strip"
       - "traefik.http.services.patientlist.loadbalancer.server.port=8080"
     depends_on:
-      - patientlist_db
+      - patientlist-db
 
-  patientlist_db:
+  patientlist-db:
-    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}
+      TZ: "Europe/Berlin"
     volumes:
-      - "patientlist_db_data:/var/lib/postgresql/data"
+      - "patientlist-db-data:/var/lib/postgresql/data"

gbn/docker-compose.yml

@@ -1,14 +1,12 @@
 version: '3.4'
 
 volumes:
-  store-db-data:
+  gbn-connector-logs:
-    name: "store-db-data"
+  gbn-connector-db-data:
-  connector-db-data:
+  gbn-store-db-data:
-    name: "connector-db-data"
 
 services:
   traefik:
-    container_name: bridgehead_traefik
     image: traefik:2.4
     command:
       - --api.insecure=true
@@ -23,7 +21,6 @@ services:
       - /var/run/docker.sock:/var/run/docker.sock:ro
 
   landing:
-    container_name: bridgehead_landingpage
     image: nginx:stable
     volumes:
       - ../landing/:/usr/share/nginx/html
@@ -32,14 +29,53 @@ services:
       - "traefik.http.routers.landing.rule=PathPrefix(`/`)"
       - "traefik.http.services.landing.loadbalancer.server.port=80"
 
-  store:
+  gbn-connector:
-    container_name: "bridgehead_gbn_blaze_store"
+    image: "samply/share-client:gbn-feature-environmentPreconfigurationTorben"
+    environment:
+      POSTGRES_HOST: "gbn-connector-db"
+      POSTGRES_PASSWORD: ${CONNECTOR_POSTGRES_PASS}
+      HTTP_PROXY_USER: ${HTTP_PROXY_USER}
+      HTTP_PROXY_PASSWORD: ${HTTP_PROXY_PASSWORD}
+      HTTPS_PROXY_USER: ${HTTPS_PROXY_USER}
+      HTTPS_PROXY_PASSWORD: ${HTTPS_PROXY_PASSWORD}
+      LDM_URL: "${PROTOCOL}://${HOST}:${PORT}/fhir"
+    env_file:
+      - ../site-config/gbn.env
+    extra_hosts:
+      - "host.docker.internal:host-gateway"
+      - "${HOST}:${HOSTIP}"
+    volumes:
+      - "gbn-connector-logs:/usr/local/tomcat/logs"
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.gbn_connector.rule=PathPrefix(`/gbn-connector`)"
+      - "traefik.http.services.gbn_connector.loadbalancer.server.port=8080"
+    depends_on:
+      - "gbn-connector-db"
+    restart: "always"
+    env_file:
+    ###TODO: Move into Image
+      - internal.env
+
+  gbn-connector-db:
+    image: "postgres:10.17"
+    environment:
+      POSTGRES_DB: "samply.connector"
+      POSTGRES_USER: "samply"
+      POSTGRES_PASSWORD: ${CONNECTOR_POSTGRES_PASS}
+    volumes:
+      - "gbn-connector-db-data:/var/lib/postgresql/data"
+    restart: "always"
+
+  gbn-store:
     image: "samply/blaze:0.15"
     environment:
-      BASE_URL: "http://bridgehead_gbn_blaze_store:8080"
+      BASE_URL: "${PROTOCOL}://${HOST}:${PORT}"
       JAVA_TOOL_OPTIONS: "-Xmx4g"
+    env_file:
+      - ../site-config/gbn.env
     volumes:
-      - "store-db-data:/app/data"
+      - "gbn-store-db-data:/app/data"
     labels:
       - "traefik.enable=true"
       - "traefik.http.middlewares.test-auth.basicauth.users=user:$$apr1$$RjhTX8\
@@ -49,48 +85,3 @@ services:
       - "traefik.http.services.blaze_gbn.loadbalancer.server.port=8080"
       - "traefik.http.routers.blaze_gbn.middlewares=gbn_b_strip,test-auth"
     restart: "always"
-
-  connector:
-    container_name: "bridgehead_gbn_connector"
-    image: "samply/share-client:gbn-7"
-    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"

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/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_1
-idgenerator.DKTK000001985_ML_SITE_L-ID.k3 = ML_DKTK000001985_IDGENERATOR_RANDOM_1
-
-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_1
-idgenerator.DKTK000001986_ML_SITE_L-ID.k3 = ML_DKTK000001986_IDGENERATOR_RANDOM_1
-
-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_1
-idgenerator.DKTK000001950_ML_SITE_L-ID.k3 = ML_DKTK000001950_IDGENERATOR_RANDOM_1
-
-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_1
-idgenerator.DKTK000001951_ML_SITE_L-ID.k3 = ML_DKTK000001951_IDGENERATOR_RANDOM_1
-
-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_1
-idgenerator.DKTK999999999_ML_SITE_L-ID.k3 = ML_DKTK999999999_IDGENERATOR_RANDOM_1
-
-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_1
-idgenerator.DKTK000002089_ML_SITE_L-ID.k3 = ML_DKTK000002089_IDGENERATOR_RANDOM_1
-
-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>

lib/init-test-environment.sh

@@ -0,0 +1,45 @@
+#!/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 Samply Store Secrets
+# the password of database connector-db
+export STORE_POSTGRES_PASS=pleaseChangeThis6
+
+### 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;

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 

start-bridgehead.sh

@@ -7,12 +7,12 @@ if ! lib/prerequisites.sh; then
     log "Prerequisites failed, exiting"
     exit
 fi
-source site.conf
 
 ./lib/generate.sh
 
 log "Starting bridgehead"
 
-docker-compose -f ${project}/docker-compose.yml --env-file site-config/${project}.env up -d
+# TODO: Check $1 for proper values
+docker-compose -f $1/docker-compose.yml --env-file bridgehead-config/$1.env up -d
 
 log "The bridgehead should be in online in a few seconds"

stop-bridgehead.sh

@@ -1,10 +1,8 @@
 #!/bin/bash -e
 
 source lib/functions.sh
-source site.conf
 
 log "Stopping bridgehead"
 
-docker-compose -f ${project}/docker-compose.yml --env-file site-config/${project}.env down
+# TODO: Check $1 for proper values
-
+docker-compose -f $1/docker-compose.yml --env-file bridgehead-config/$1.env down
-rm landing/index.html