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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;
```