diff --git a/README.md b/README.md index 4286c37..be2aa67 100644 --- a/README.md +++ b/README.md @@ -4,6 +4,8 @@ This repository contains all information and tools to deploy a bridgehead. If yo TODO: Insert comprehensive feature list of the bridgehead? Why would anyone install it? +TODO: TOC + ## Requirements Before starting the installation process, please ensure that following software is available on your system: @@ -24,9 +26,15 @@ 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!". -> 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]() +> 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) -### [Docker Compose](https://docs.docker.com/compose/install/) +You should also check, that the version of docker installed by you is newer than "1.20". To check this, just run + +``` shell +docker --version +``` + +### [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 < /srv/docker/bridgehead/site-config; +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 ; ``` -After this, you need to install the systemd units. This is currently done with the [install-bridgehead.sh script](./install-bridgehead.sh). +You should now be able to access the landing page on your system, e.g "http:///" -You can execute it with +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 ./install-bridgehead.sh +sudo ./stop-bridgehead.sh ; +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]() for this. +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: + +``` 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. ``` conf [Service] @@ -102,25 +163,18 @@ Environment=MAGICPL_OIDC_CLIENT_ID= Environment=MAGICPL_OIDC_CLIENT_SECRET= ``` -For the C4 project, you need to additionally set the "LDM_URL_BASE" setting in the configuration table to null. You need to execute this after starting the bridgehead system unit for c4: - -``` shell -docker exec bridgehead-c4-connector-db-1 bash -c 'psql -U $POSTGRES_USER $POSTGRES_DB -c "UPDATE samply.configuration SET setting=\'\' WHERE name=\'LDM_URL_BASE\'"'; -``` - 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; +sudo systemctl bridgehead@c4.service; ``` - ### GBA/BBMRI-ERIC You can create the site specific configuration with: ``` shell -sudo systemctl edit bridgehead@dktk.service; +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. @@ -140,47 +194,82 @@ To make the configuration effective, you need to tell systemd to reload the conf ``` shell sudo systemctl daemon-reload; -sudo systemctl restart docker; +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](./init-dev-environment.sh). +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| -|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_USER||Your local http proxy user| -|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| + +| 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) -There two methods to start the bridgehead. For Windows, Linux and Mac OS you can use the start-bridgehead.sh to deploy it wit docker-compose. If will also check some other setting of your system. - -The second methods is using the systemd management tool you start, stop and update your bridgehead. - -Just run the install-bridgehead and thats it. +### On a Server +#### Start +This will start a not running bridgehead system unit: +``` shell +sudo systemctl start bridgehead@ +``` +#### Stop +This will stop a running bridgehead system unit: +``` shell +sudo systemctl stop bridgehead@ +``` +#### Update +This will update bridgehead system unit: +``` shell +sudo systemctl start bridgehead-update@ +``` +#### 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 +``` +#### Stop +This shell script stops a specified bridgehead. Choose between "dktk", "c4" and "gbn". +``` shell +./stop-bridgehead +``` +#### 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 @@ -189,8 +278,8 @@ Just run the install-bridgehead and thats it. 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 -git config --global http.proxy http://:; -git config --global https.proxy http://:; +sudo git config --global http.proxy http://:; +sudo git config --global https.proxy http://:; ``` > NOTE: Some proxies may require user and password authentication. You can adjust the settings like this: "http://:@:". > NOTE: It is also possible that a proxy requires https protocol, so you can replace this to. @@ -198,11 +287,9 @@ git config --global https.proxy http://:; You can check that the updated configuration with ``` shell -git config --global --list; +sudo git config --global --list; ``` -Please repeat this configuration for the root user to. Otherwise the update service won't be able to properly update the git repository. - ### 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: diff --git a/dktk/docker-compose.yml b/dktk/docker-compose.yml index 26600d1..e229586 100644 --- a/dktk/docker-compose.yml +++ b/dktk/docker-compose.yml @@ -1,4 +1,3 @@ -# TODO: Is there a reason why the docker-compose files are not at root level? e.g. docker-compose.(dktk|gbn|c4).yml version: "3.7" volumes: dktk-connector-db-data: diff --git a/init-dev-environment.sh b/lib/init-test-environment.sh similarity index 100% rename from init-dev-environment.sh rename to lib/init-test-environment.sh diff --git a/uninstall-bridgehead.sh b/lib/remove-bridgehead-units.sh similarity index 100% rename from uninstall-bridgehead.sh rename to lib/remove-bridgehead-units.sh diff --git a/install-bridgehead.sh b/lib/setup-bridgehead-units.sh similarity index 100% rename from install-bridgehead.sh rename to lib/setup-bridgehead-units.sh diff --git a/start-bridgehead.sh b/start-bridgehead.sh index 0e7272d..418aa39 100755 --- a/start-bridgehead.sh +++ b/start-bridgehead.sh @@ -7,10 +7,10 @@ if ! lib/prerequisites.sh; then log "Prerequisites failed, exiting" exit fi -source site.conf 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" diff --git a/stop-bridgehead.sh b/stop-bridgehead.sh index 6da0228..88f555d 100755 --- a/stop-bridgehead.sh +++ b/stop-bridgehead.sh @@ -1,8 +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