Merge branch 'refactor/preconfiguredImages' into version-1

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Patrick Skowronek 2022-03-22 09:54:53 +01:00
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README.md
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# 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.
The second methods is using the systemd management tool you start, stop and update your bridgehead.
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@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;
```

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@ -1,38 +1,21 @@
version: "3.7"
volumes:
connector_db_data:
connector_logs:
patientlist_db_data:
patientlist_logs:
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
c4-connector-db-data:
c4-connector-logs:
patientlist-db-data:
patientlist-logs:
id-manager-logs:
c4-store-db-data:
c4-store-logs:
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:
container_name: bridgehead_c4_connector
image: docker.verbis.dkfz.de/ccp/connector:3
c4-connector:
image: "samply/share-client:c4-feature-environmentPreconfigurationTorben"
environment:
STORE_URL: http://bridgehead_c4_store:8080
LDM_URL: http://bridgehead_c4_store:8080
POSTGRES_HOST: ${CONNECTOR_DB_HOST}
POSTGRES_HOST: "c4-connector-db"
ID_MANAGER_APIKEY: ${MAGICPL_API_KEY_CONNECTOR}
POSTGRES_PASSWORD: ${CONNECTOR_POSTGRES_PASS}
NNGM_PASSWORD: ${NNGM_PASSWORD}
NNGM_MAINZELLISTE_APIKEY: ${NNGM_MAINZELLISTE_APIKEY}
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}/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:
container_name: bridgehead_c4_connector_db
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:
container_name: bridgehead_idmanager
image: docker.verbis.dkfz.de/ccp/idmanager:deploy-c4
id-manager:
image: docker.verbis.dkfz.de/ccp/idmanager:bridgehead-develop
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: ${MAGICPL_OIDC_CLIENT_SECRET}
volumes:
- "idmanager_logs:/usr/local/tomcat/logs"
secrets:
- magicpl.docker.xml
- dktk_bridgehead_info.docker.xml
- proxy.docker.xml
labels:
- "traefik.http.routers.idmanager.rule=PathPrefix(`/id-manager`)"
- "traefik.http.middlewares.idmanager_strip.stripprefix.prefixes=/id-mana\
ger"
- "traefik.http.routers.idmanager.middlewares=idmanager_strip"
- "traefik.http.services.idmanager.loadbalancer.server.port=8080"
TOMCAT_REVERSEPROXY_FQDN: "${HOST}"
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:
###TODO: Move into Image
- internal.env
- ../site-config/dktk.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:
container_name: bridgehead_c4_store
patientlist:
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
TZ: Europe/Berlin
POSTGRES_PASSWORD: ${STORE_POSTGRES_PASS}
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\
aldatamanagement`)"
- "traefik.http.routers.store_c4.rule=PathPrefix(`/c4-localdatamanagement`)"
depends_on:
- store_db
- store-db
restart: always
env_file:
###TODO: Move into Image
- internal.env
store_db:
container_name: bridgehead_c4_store_db
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

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@ -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

View File

@ -1,38 +1,19 @@
version: "3.7"
volumes:
connector_db_data:
connector_logs:
patientlist_db_data:
patientlist_logs:
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
dktk-connector-db-data:
dktk-connector-logs:
patientlist-db-data:
patientlist-logs:
id-manager-logs:
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:
container_name: bridgehead_dktk_connector
image: "samply/share-client:dktk-pr-148"
dktk-connector:
image: "samply/share-client:dktk-feature-environmentPreconfigurationTorben"
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"
PROJECTPSEUDONYMISATION_URL: "http://bridgehead_dktk_idmanager:8080/ID-Manager/html/projectSelection.html"
HTTP_PROXY_USER: ${HTTP_PROXY_USER}
HTTP_PROXY_PASSWORD: ${HTTP_PROXY_PASSWORD}
HTTPS_PROXY_USER: ${HTTPS_PROXY_USER}
HTTPS_PROXY_PASSWORD: ${HTTPS_PROXY_PASSWORD}
env_file:
- ../site-config/dktk.env
# Necessary for the connector to successful check the status of other components on the same host
extra_hosts:
- "host.docker.internal:host-gateway"
- "${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:
container_name: bridgehead_dktk_connector_db
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:
container_name: bridgehead_id-manager
image: docker.verbis.dkfz.de/pseudonymisierung/magicpl:release-0.2.0
id-manager:
image: docker.verbis.dkfz.de/ccp/idmanager:bridgehead-develop
environment:
TOMCAT_REVERSEPROXY_FQDN: ${HOST}/id-manager
MAGICPL_MAINZELLISTE_API_KEY: "123"
MAGICPL_API_KEY: "123"
MAGICPL_API_KEY_CONNECTOR: "123"
MAGICPL_PASSPHRASE: "123"
MAGICPL_MAINZELLISTE_CENTRAL_API_KEY: "123"
MAGICPL_CENTRAL_API_KEY: "123"
MAGICPL_OIDC_CLIENT_ID: "123"
MAGICPL_OIDC_CLIENT_SECRET: "123"
TZ: Europe/Berlin
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_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: ${MAGICPL_OIDC_CLIENT_SECRET}
TOMCAT_REVERSEPROXY_FQDN: "${HOST}"
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
- "id-manager-logs:/usr/local/tomcat/logs"
depends_on:
- patientlist
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
- internal.env
- "traefik.http.routers.id-manager.rule=PathPrefix(`/ID-Manager`)"
- "traefik.http.services.id-manager.loadbalancer.server.port=8080"
patientlist:
container_name: bridgehead_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: ${HOST}/patientlist
TOMCAT_REVERSEPROXY_FQDN: "${HOST}"
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
- "patientlist-logs:/usr/local/tomcat/logs"
labels:
- "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.routers.patientlist.rule=PathPrefix(`/Patientlist`)"
- "traefik.http.services.patientlist.loadbalancer.server.port=8080"
depends_on:
- patientlist_db
- patientlist-db
patientlist_db:
container_name: bridgehead_dktk_patientlist_db
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"

View File

@ -1,14 +1,12 @@
version: '3.4'
volumes:
store-db-data:
name: "store-db-data"
connector-db-data:
name: "connector-db-data"
gbn-connector-logs:
gbn-connector-db-data:
gbn-store-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:
container_name: "bridgehead_gbn_blaze_store"
gbn-connector:
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"

View File

@ -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>

View File

@ -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

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@ -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>

45
lib/init-test-environment.sh Executable file
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@ -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;

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@ -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

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@ -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"

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@ -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
rm landing/index.html
# TODO: Check $1 for proper values
docker-compose -f $1/docker-compose.yml --env-file bridgehead-config/$1.env down