fix: switch sites that are still on this branch to main

Removed non-functioning links from Table of Contents

.gitignore

@@ -1,6 +1,6 @@
 ##Ignore site configuration
 .gitmodules
 site-config/*
-.idea
+
 ## Ignore site configuration
 */docker-compose.override.yml

README.md

@@ -6,24 +6,29 @@ This repository is the starting point for any information and tools you will nee
 
 1. [Requirements](#requirements)
     - [Hardware](#hardware)
-    - [System](#system)
-      - [Git](#git)
-      - [Docker](#docker)
+    - [Software](#software)
+    - [Network](#network)
 2. [Deployment](#deployment)
-    - [Installation](#installation)
+    - [Site name](#site-name)
+    - [Projects](#projects)
+    - [GitLab repository](#gitlab-repository)
+    - [Base Installation](#base-installation)
     - [Register with Samply.Beam](#register-with-samplybeam)
     - [Starting and stopping your Bridgehead](#starting-and-stopping-your-bridgehead)
-    - [Auto-starting your Bridgehead when the server starts](#auto-starting-your-bridgehead-when-the-server-starts)
-3. [Additional Services](#additional-Services)
-    - [Monitoring](#monitoring)
-    - [Register with a Directory](#register-with-a-Directory)
-4. [Site-specific configuration](#site-specific-configuration)
+    - [Testing your new Bridgehead](#testing-your-new-bridgehead)
+    - [De-installing a Bridgehead](#de-installing-a-bridgehead)
+3. [Site-specific configuration](#site-specific-configuration)
     - [HTTPS Access](#https-access)
-    - [Locally Managed Secrets](#locally-managed-secrets)
-    - [Git Proxy Configuration](#git-proxy-configuration)
-    - [Docker Daemon Proxy Configuration](#docker-daemon-proxy-configuration)
+    - [TLS terminating proxies](#tls-terminating-proxies)
+    - [File structure](#file-structure)
+4. [Things you should know](#things-you-should-know)
+    - [Auto-Updates](#auto-updates)
+    - [Auto-Backups](#auto-backups)
     - [Non-Linux OS](#non-linux-os)
-5. [License](#license)
+5. [Troubleshooting](#troubleshooting)
+    - [Docker Daemon Proxy Configuration](#docker-daemon-proxy-configuration)
+    - [Monitoring](#monitoring)
+6. [License](#license)
 
 ## Requirements
 
@@ -58,10 +63,62 @@ Note for Ubuntu: Please note that the uncomplicated firewall (ufw) is known to c
 
 ## Deployment
 
+### Site name
+
+You will need to choose a short name for your site. This is not a URL, just a simple identifying string. For the examples below, we will use "your-site-name", but you should obviously choose something that is meaningful to you and which is unique.
+
+Site names should adhere to the following conventions:
+
+- They should be lower-case.
+- They should generally be named after the city where your site is based, e.g. ```karlsruhe```.
+- If you have a multi-part name, please use a hypen ("-") as separator, e.g. ```le-havre```.
+- If your site is for testing purposes, rather than production, please append "-test", e.g. ```zaragoza-test```.
+- If you are a developer and you are making changes to the Bridgehead, please use your name and prepend "dev-", e.g. ```dev-joe-doe```.
+
+### GitLab repository
+
+In order to be able to install, you will need to have your own repository in GitLab for your site's configuration settings. This allows automated updates of the Bridgehead software.
+
+To request a new repository, please contact your research network administration or send an email to one of the project specific addresses:
+
+- For the bbmri project: bridgehead@helpdesk.bbmri-eric.eu.
+- For the ccp project: support-ccp@dkfz-heidelberg.de
+
+Mention:
+- which project you belong to, i.e. "bbmri" or "ccp"
+- site name (According to conventions listed above)
+- operator name and email
+
+We will set the repository up for you. We will then send you:
+
+- A Repository Short Name (RSN). Beware: this is distinct from your site name.
+- Repository URL containing the acces token eg. https://BH_Dummy:dummy_token@git.verbis.dkfz.de/bbmri-bridgehead-configs/dummy.git
+
+During the installation, your Bridgehead will download your site's configuration from GitLab and you can review the details provided to us by email.
+
+
 ### Base Installation
 
-First, clone the repository to the directory `/srv/docker/bridgehead`:
+First, download your site specific configuration repository:
+```shell
+sudo mkdir -p /etc/bridgehead/
+sudo git clone <REPO_URL_FROM_EMAIL> /etc/bridgehead/
+```
 
+Review the site configuration:
+```shell
+sudo cat /etc/bridgehead/bbmri.conf
+```
+
+Pay special attention to:
+
+- SITE_NAME
+- SITE_ID
+- OPERATOR_FIRST_NAME
+- OPERATOR_LAST_NAME
+- OPERATOR_EMAIL
+
+Clone the bridgehead repository:
 ```shell
 sudo mkdir -p /srv/docker/
 sudo git clone https://github.com/samply/bridgehead.git /srv/docker/bridgehead
@@ -74,8 +131,6 @@ cd /srv/docker/bridgehead
 sudo ./bridgehead install <PROJECT>
 ```
 
-... and follow the instructions on the screen. You should then be prompted to do the next step:
-
 ### Register with Samply.Beam
 
 Many Bridgehead services rely on the secure, performant and flexible messaging middleware called [Samply.Beam](https://github.com/samply/beam). You will need to register ("enroll") with Samply.Beam by creating a cryptographic key pair for your bridgehead:
@@ -109,6 +164,60 @@ To enable/disable autostart, run
 sudo systemctl [enable|disable] bridgehead@<PROJECT>.service
 ```
 
+### Testing your new Bridgehead
+
+After starting the Bridgehead, you can watch the initialization process with the following command:
+
+```shell
+journalctl -u bridgehead@bbmri -f
+```
+
+if this exits with something similar to the following:
+
+```
+bridgehead@bbmri.service: Main process exited, code=exited, status=1/FAILURE
+```
+
+Then you know that there was a problem with starting the Bridgehead. Scroll up the printout to find the cause of the error.
+
+Once the Bridgehead is running, you can also view the individual Docker processes with:
+
+```shell
+docker ps
+```
+
+There should be 6 - 10 Docker proceses. If there are fewer, then you know that something has gone wrong. To see what is going on, run:
+
+```shell
+journalctl -u bridgehead@bbmri -f
+```
+
+Once the Bridgehead has passed these checks, take a look at the landing page:
+
+```
+https://localhost
+```
+
+You can either do this in a browser or with curl. If you visit the URL in the browser, you will neet to click through several warnings, because you will initially be using a self-signed certificate. With curl, you can bypass these checks:
+
+```shell
+curl -k https://localhost
+```
+
+If you get errors when you do this, you need to use ```docker logs``` to examine your landing page container in order to determine what is going wrong.
+
+If you have chosen to take part in our monitoring program (by setting the ```MONITOR_APIKEY``` variable in the configuration), you will be informed by email when problems are detected in your Bridgehead.
+
+### De-installing a Bridgehead
+
+You may decide that you want to remove a Bridgehead installation from your machine, e.g. if you want to migrate it to a new location or if you want to start a fresh installation because the initial attempts did not work.
+
+To do this, run:
+
+```shell
+sh bridgehead uninstall
+```
+
 ## Site-specific configuration
 
 ### HTTPS Access
@@ -131,6 +240,29 @@ All of the Bridgehead's outgoing connections are secured by transport encryption
 
 Your Bridgehead's actual data is not stored in the above directories, but in named docker volumes, see `docker volume ls` and `docker volume inspect <volume_name>`.
 
+### Directory sync
+
+This is an optional feature for bbmri projects. It keeps the [BBMRI Directory](https://directory.bbmri-eric.eu/) up to date with your local data eg. number of samples. It also updates the local FHIR store with the latest contact details etc. from the Directory.  You must explicitly set your country specific directory url, username and password to enable this feature.
+
+Full details can be found in [directory_sync_service](https://github.com/samply/directory_sync_service).
+
+To enable it, you will need to set these variables to the ```bbmri.conf``` file of your GitLab repository. Here is an example config:
+
+```
+### Directory sync service
+DS_DIRECTORY_URL=https://directory.bbmri-eric.eu
+DS_DIRECTORY_USER_NAME=your_directory_username
+DS_DIRECTORY_USER_PASS=qwdnqwswdvqHBVGFR9887
+DS_TIMER_CRON="0 22 * * *"
+```
+You must contact the Directory for your national node to find the URL, and to register as a user.
+
+Additionally, you should choose when you want Directory sync to run. In the example above, this is set to happen at 10 pm every evening. You can modify this to suit your requirements. The timer specification should follow the [cron](https://crontab.guru) convention.
+
+Once you edited the gitlab config. The bridgehead will autoupdate the config with the values and will sync the data.
+
+There will be a delay before the effects of Directory sync become visible. First, you will need to wait until the time you have specified in ```TIMER_CRON```. Second, the information will then be synchronized from your national node with the central European Directory. This can take up to 24 hours.
+
 ## Things you should know
 
 ### Auto-Updates
@@ -140,6 +272,7 @@ Your Bridgehead will automatically and regularly check for updates. Whenever som
 If you would like to understand what happens exactly and when, please check the systemd units deployed during the [installation](#base-installation) via `systemctl cat bridgehead-update@<PROJECT>.service` and `systemctl cat bridgehead-update@<PROJECT.timer`.
 
 ### Auto-Backups
+
 Some of the components in the bridgehead will store persistent data. For those components, we integrated an automated backup solution in the bridgehead updates. It will automatically save the backup in multiple files
 
 1) Last-XX, were XX represents a weekday to allow re-import of at least one version of the database for each of the past seven days.
@@ -148,20 +281,9 @@ Some of the components in the bridgehead will store persistent data. For those c
 
 To enable the Auto-Backup feature, please set the Variable `BACKUP_DIRECTORY` in your sites configuration.
 
-### Monitoring
+### Development Installation
 
-To keep all Bridgeheads up and working and detect any errors before a user does, a central monitoring 
-
-- Your Bridgehead itself will report relevant system events, such as successful/failed updates, restarts, performance metrics or version numbers.
-- Your Bridgehead is also monitored from the outside by your network's central components. For example, the federated search will regularly perform a black-box test by sending an empty query to your Bridgehead and checking if the results make sense.
-
-In all monitoring cases, obviously no sensitive information is transmitted, in particular not any patient-related data. Aggregated data, e.g. total amount of datasets, may be transmitted for diagnostic purposes.
-
-## Troubleshooting
-
-### Docker Daemon Proxy Configuration
-
-Docker has a background daemon, responsible for downloading images and starting them. Sometimes, proxy configuration from your system won't carry over and it will fail to download images. In that case, configure the proxy for this daemon as described in the [official documentation](https://docs.docker.com).
+By using `./bridgehead dev-install <projectname>` instead of `install`, you can install a developer bridgehead. The difference is, that you can provide an arbitrary configuration repository during the installation, meaning that it does not have to adhere to the usual naming scheme. This allows for better decoupling between development and production configurations.
 
 ### Non-Linux OS
 
@@ -180,6 +302,22 @@ We have tested the installation procedure with an Ubuntu 22.04 guest system runn
 
 Installation under WSL ought to work, but we have not tested this.
 
+## Troubleshooting
+
+### Docker Daemon Proxy Configuration
+
+Docker has a background daemon, responsible for downloading images and starting them. Sometimes, proxy configuration from your system won't carry over and it will fail to download images. In that case, configure the proxy for this daemon as described in the [official documentation](https://docs.docker.com).
+
+
+### Monitoring
+
+To keep all Bridgeheads up and working and detect any errors before a user does, a central monitoring 
+
+- Your Bridgehead itself will report relevant system events, such as successful/failed updates, restarts, performance metrics or version numbers.
+- Your Bridgehead is also monitored from the outside by your network's central components. For example, the federated search will regularly perform a black-box test by sending an empty query to your Bridgehead and checking if the results make sense.
+
+In all monitoring cases, obviously no sensitive information is transmitted, in particular not any patient-related data. Aggregated data, e.g. total amount of datasets, may be transmitted for diagnostic purposes.
+
 ## License
 
 Copyright 2019 - 2022 The Samply Community

bbmri/directory-sync-compose.yml

@@ -0,0 +1,8 @@
+services:
+  directory_sync_service:
+    image: "docker.verbis.dkfz.de/cache/samply/directory_sync_service"
+    environment:
+      DS_DIRECTORY_URL: ${DS_DIRECTORY_URL}
+      DS_DIRECTORY_USER_NAME: ${DS_DIRECTORY_USER_NAME}
+      DS_DIRECTORY_PASS_CODE: ${DS_DIRECTORY_PASS_CODE}
+      DS_TIMER_CRON: ${DS_TIMER_CRON}

bbmri/directory-sync.sh

@@ -0,0 +1,8 @@
+#!/bin/bash
+
+function dirSetup() {
+	if [ -n "$DS_DIRECTORY_USER_NAME" ]; then
+		log INFO "Directory sync setup detected -- will start directory sync service."
+		OVERRIDE+=" -f ./$PROJECT/directory-sync-compose.yml"
+	fi
+}

bbmri/docker-compose.yml

@@ -3,7 +3,7 @@ version: "3.7"
 services:
   traefik:
     container_name: bridgehead-traefik
-    image: traefik:latest
+    image: docker.verbis.dkfz.de/cache/traefik:latest
     command:
       - --entrypoints.web.address=:80
       - --entrypoints.websecure.address=:443
@@ -32,7 +32,7 @@ services:
 
   forward_proxy:
     container_name: bridgehead-forward-proxy
-    image: samply/bridgehead-forward-proxy:latest
+    image: docker.verbis.dkfz.de/cache/samply/bridgehead-forward-proxy:latest
     environment:
       HTTPS_PROXY: ${HTTPS_PROXY_URL}
       USERNAME: ${HTTPS_PROXY_USERNAME}
@@ -42,7 +42,7 @@ services:
 
   landing:
     container_name: bridgehead-landingpage
-    image: samply/bridgehead-landingpage:master
+    image: docker.verbis.dkfz.de/cache/samply/bridgehead-landingpage:master
     labels:
       - "traefik.enable=true"
       - "traefik.http.routers.landing.rule=PathPrefix(`/`)"
@@ -54,7 +54,7 @@ services:
       SITE_NAME: ${SITE_NAME}
 
   blaze:
-    image: "samply/blaze:0.19"
+    image: docker.verbis.dkfz.de/cache/samply/blaze:0.19
     container_name: bridgehead-bbmri-blaze
     environment:
       BASE_URL: "http://bridgehead-bbmri-blaze:8080"
@@ -71,27 +71,28 @@ services:
       - "traefik.http.routers.blaze_ccp.middlewares=ccp_b_strip,auth"
       - "traefik.http.routers.blaze_ccp.tls=true"
 
-  spot:
-    image: samply/spot:latest
-    container_name: bridgehead-spot
+  focus:
+    image: docker.verbis.dkfz.de/cache/samply/focus:develop
+    container_name: bridgehead-focus
     environment:
-      SECRET: ${SPOT_BEAM_SECRET_LONG}
-      APPID: spot
+      API_KEY: ${FOCUS_BEAM_SECRET_SHORT}
+      BEAM_APP_ID_LONG: focus.${PROXY_ID}
       PROXY_ID: ${PROXY_ID}
-      LDM_URL: http://bridgehead-bbmri-blaze:8080/fhir
-      BEAM_PROXY: http://beam-proxy:8081
+      BLAZE_URL: "http://bridgehead-bbmri-blaze:8080/fhir/"
+      BEAM_PROXY_URL: http://beam-proxy:8081
+      RETRY_COUNT: ${FOCUS_RETRY_COUNT}
     depends_on:
       - "beam-proxy"
       - "blaze"
 
   beam-proxy:
-    image: samply/beam-proxy:main
+    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
     container_name: bridgehead-beam-proxy
     environment:
       BROKER_URL: ${BROKER_URL}
       PROXY_ID: ${PROXY_ID}
-      APP_0_ID: spot
-      APP_0_KEY: ${SPOT_BEAM_SECRET_SHORT}
+      APP_0_ID: focus
+      APP_0_KEY: ${FOCUS_BEAM_SECRET_SHORT}
       PRIVKEY_FILE: /run/secrets/proxy.pem
       ALL_PROXY: http://forward_proxy:3128
       TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs

bbmri/vars

@@ -1,7 +1,11 @@
 BROKER_ID=broker.bbmri.samply.de
 BROKER_URL=https://${BROKER_ID}
 PROXY_ID=${SITE_ID}.${BROKER_ID}
-SPOT_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
-SPOT_BEAM_SECRET_LONG="ApiKey spot.${PROXY_ID} ${SPOT_BEAM_SECRET_SHORT}"
+FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
+FOCUS_RETRY_COUNT=32
 SUPPORT_EMAIL=bridgehead@helpdesk.bbmri-eric.eu
 PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
+
+# This will load directory-sync setup.
+source $PROJECT/directory-sync.sh
+dirSetup

bridgehead

@@ -70,14 +70,25 @@ case "$ACTION" in
 		;;
 	stop)
 		loadVars
+		# HACK: This is tempoarily to properly shut down false bridgehead instances (bridgehead-ccp instead ccp)
+		$COMPOSE -p bridgehead-$PROJECT -f ./$PROJECT/docker-compose.yml $OVERRIDE down
 		exec $COMPOSE -f ./$PROJECT/docker-compose.yml $OVERRIDE down
 		;;
+	is-running)
+		bk_is_running
+		exit $?
+		;;
 	update)
 		loadVars
 		exec ./lib/update-bridgehead.sh $PROJECT
 		;;
 	install)
-		source ./lib/prepare-system.sh
+		source ./lib/prepare-system.sh NODEV
+		loadVars
+		exec ./lib/install-bridgehead.sh $PROJECT
+		;;
+	dev-install)
+		exec ./lib/prepare-system.sh DEV
 		loadVars
 		exec ./lib/install-bridgehead.sh $PROJECT
 		;;

ccp/docker-compose.yml

@@ -3,7 +3,7 @@ version: "3.7"
 services:
   traefik:
     container_name: bridgehead-traefik
-    image: traefik:latest
+    image: docker.verbis.dkfz.de/cache/traefik:latest
     command:
       - --entrypoints.web.address=:80
       - --entrypoints.websecure.address=:443
@@ -32,7 +32,7 @@ services:
 
   forward_proxy:
     container_name: bridgehead-forward-proxy
-    image: samply/bridgehead-forward-proxy:latest
+    image: docker.verbis.dkfz.de/cache/samply/bridgehead-forward-proxy:latest
     environment:
       HTTPS_PROXY: ${HTTPS_PROXY_URL}
       USERNAME: ${HTTPS_PROXY_USERNAME}
@@ -42,7 +42,7 @@ services:
 
   landing:
     container_name: bridgehead-landingpage
-    image: samply/bridgehead-landingpage:master
+    image: docker.verbis.dkfz.de/cache/samply/bridgehead-landingpage:master
     labels:
       - "traefik.enable=true"
       - "traefik.http.routers.landing.rule=PathPrefix(`/`)"
@@ -54,7 +54,7 @@ services:
       SITE_NAME: ${SITE_NAME}
 
   blaze:
-    image: "samply/blaze:0.19"
+    image: docker.verbis.dkfz.de/cache/samply/blaze:0.19
     container_name: bridgehead-ccp-blaze
     environment:
       BASE_URL: "http://bridgehead-ccp-blaze:8080"
@@ -72,7 +72,7 @@ services:
       - "traefik.http.routers.blaze_ccp.tls=true"
 
   spot:
-    image: samply/spot:latest
+    image: docker.verbis.dkfz.de/cache/samply/spot:latest
     container_name: bridgehead-spot
     environment:
       SECRET: ${SPOT_BEAM_SECRET_LONG}
@@ -85,7 +85,7 @@ services:
       - "blaze"
 
   beam-proxy:
-    image: samply/beam-proxy:main
+    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
     container_name: bridgehead-beam-proxy
     environment:
       BROKER_URL: ${BROKER_URL}

ccp/exliquid-compose.yml

@@ -2,7 +2,7 @@ version: "3.7"
 
 services:
   exliquid-task-store:
-    image: "samply/blaze:0.19"
+    image: docker.verbis.dkfz.de/cache/samply/blaze:0.19
     container_name: bridgehead-exliquid-task-store
     environment:
       BASE_URL: "http://bridgehead-exliquid-task-store:8080"
@@ -13,7 +13,7 @@ services:
       - "traefik.enable=false"
 
   exliquid-report-hub:
-    image: "samply/report-hub:latest"
+    image: docker.verbis.dkfz.de/cache/samply/report-hub:latest
     container_name: bridgehead-exliquid-report-hub
     environment:
       SPRING_WEBFLUX_BASE_PATH: "/exliquid"

ccp/exliquid-setup.sh

@@ -0,0 +1,19 @@
+#!/bin/bash
+
+function exliquidSetup() {
+	case ${SITE_ID} in
+		berlin|dresden|essen|frankfurt|freiburg|luebeck|mainz|muenchen-lmu|muenchen-tum|mannheim|tuebingen)
+			EXLIQUID=1
+			;;
+		dktk-test)
+			EXLIQUID=1
+			;;
+		*)
+			EXLIQUID=0
+			;;
+	esac
+	if [[ $EXLIQUID -eq 1 ]]; then
+		log INFO "EXLIQUID setup detected -- will start Report-Hub."
+		OVERRIDE+=" -f ./$PROJECT/exliquid-compose.yml"
+	fi
+}

ccp/modules/exliquid-setup.sh

@@ -1,17 +0,0 @@
-#!/bin/bash
-
-case ${SITE_ID} in
-  berlin|dresden|essen|frankfurt|freiburg|luebeck|mainz|muenchen-lmu|muenchen-tu|mannheim|tuebingen)
-    EXLIQUID=1
-    ;;
-  dktk-test)
-    EXLIQUID=1
-    ;;
-  *)
-    EXLIQUID=0
-    ;;
-esac
-if [[ $EXLIQUID -eq 1 ]]; then
-  log INFO "EXLIQUID setup detected -- will start Report-Hub."
-  OVERRIDE+=" -f ./$PROJECT/modules/exliquid-compose.yml"
-fi

ccp/modules/exporter-compose.yml

@@ -1,42 +0,0 @@
-version: "3.7"
-
-services:
-  exporter:
-    image: docker.verbis.dkfz.de/ccp/dktk-exporter:latest
-    container_name: bridgehead-ccp-exporter
-    environment:
-      LOG_LEVEL: "INFO"
-      EXPORTER_API_KEY: "${EXPORTER_API_KEY}"
-      CROSS_ORIGINS: "https://${HOST}/ccp-teiler-root-config"
-      EXPORTER_DB_USER: "exporter"
-      EXPORTER_DB_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
-      EXPORTER_DB_URL: "jdbc:postgresql://exporter-db:5432/exporter"
-      CLEAN_TEMP_FILES_CRON_EXPRESSION: "0 0 1 * * *"
-      TEMP_FILES_LIFETIME_IN_DAYS: "1"
-      CLEAN_WRITE_FILES_CRON_EXPRESSION: "0 0 2 * * *"
-      WRITE_FILES_LIFETIME_IN_DAYS: "30"
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.exporter_ccp.rule=PathPrefix(`/ccp-exporter`)"
-      - "traefik.http.services.exporter_ccp.loadbalancer.server.port=8092"
-      - "traefik.http.routers.exporter_ccp.tls=true"
-      - "traefik.http.routers.exporter_ccp.middlewares=auth"
-    volumes:
-      - "exporter:/app/exporter-files"
-
-  exporter-db:
-    image: postgres:15.1-alpine
-    container_name: bridgehead-ccp-exporter-db
-    environment:
-      POSTGRES_USER: "exporter"
-      POSTGRES_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
-      POSTGRES_DB: "exporter"
-    volumes:
-      - "exporter-db:/var/lib/postgresql/data"
-
-
-volumes:
-  exporter-db:
-    name: "exporter-db"
-  exporter:
-    name: "exporter"

ccp/modules/exporter-setup.sh

@@ -1,8 +0,0 @@
-#!/bin/bash
-
-if [ -n "$ENABLE_EXPORTER" ];then
-  log INFO "Exporter setup detected -- will start Exporter service."
-  OVERRIDE+=" -f ./$PROJECT/modules/exporter-compose.yml"
-fi
-# TODO: Generate password in another way so that not all passwords are the same?
-EXPORTER_DB_PASSWORD="$(echo \"This is a salt string to generate one consistent password. It is not required to be secret.\" | openssl rsautl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"

ccp/modules/id-management-compose.yml

@@ -42,7 +42,7 @@ services:
       - patientlist-db
 
   patientlist-db:
-    image: postgres:15.1-alpine
+    image: docker.verbis.dkfz.de/cache/postgres:15.1-alpine
     container_name: bridgehead-patientlist-db
     environment:
       POSTGRES_USER: "mainzelliste"

ccp/modules/id-management-setup.sh

@@ -1,5 +1,21 @@
 #!/bin/bash
 
+function idManagementSetup() {
+	if [ -n "$IDMANAGER_UPLOAD_APIKEY" ]; then
+		log INFO "id-management setup detected -- will start id-management (mainzelliste & magicpl)."
+		OVERRIDE+=" -f ./$PROJECT/modules/id-management-compose.yml"
+
+		# Auto Generate local Passwords
+		PATIENTLIST_POSTGRES_PASSWORD="$(echo \"id-management-module-db-password-salt\" | openssl rsautl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
+		IDMANAGER_LOCAL_PATIENTLIST_APIKEY="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
+
+		# Transform Seeds Configuration to pass it to the Mainzelliste Container
+		PATIENTLIST_SEEDS_TRANSFORMED="$(declare -p PATIENTLIST_SEEDS | tr -d '\"' | sed 's/\[/\[\"/g' | sed 's/\]/\"\]/g')"
+
+		# Ensure old ids are working !!!
+		export IDMANAGEMENT_FRIENDLY_ID=$(legacyIdMapping "$SITE_ID")
+	fi
+}
 
 # Transform into single string array, e.g. 'dktk-test' to 'dktk test'
 # Usage: transformToSingleStringArray 'dktk-test' -> 'dktk test'
@@ -34,18 +50,3 @@ function legacyIdMapping() {
 	normalized_string=$(applySpecialCases "$uppercase_string");
 	echo "$normalized_string" | tr -d ' '
 }
-
-if [ -n "$IDMANAGER_UPLOAD_APIKEY" ]; then
-  log INFO "id-management setup detected -- will start id-management (mainzelliste & magicpl)."
-  OVERRIDE+=" -f ./$PROJECT/modules/id-management-compose.yml"
-
-  # Auto Generate local Passwords
-  PATIENTLIST_POSTGRES_PASSWORD="$(echo \"id-management-module-db-password-salt\" | openssl rsautl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
-  IDMANAGER_LOCAL_PATIENTLIST_APIKEY="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
-
-  # Transform Seeds Configuration to pass it to the Mainzelliste Container
-  PATIENTLIST_SEEDS_TRANSFORMED="$(declare -p PATIENTLIST_SEEDS | tr -d '\"' | sed 's/\[/\[\"/g' | sed 's/\]/\"\]/g')"
-
-  # Ensure old ids are working !!!
-  export IDMANAGEMENT_FRIENDLY_ID=$(legacyIdMapping "$SITE_ID")
-fi

ccp/modules/mtba-setup.sh

@@ -1,10 +0,0 @@
-#!/bin/bash
-
-if [ -n "$ENABLE_MTBA" ];then
-  log INFO "MTBA setup detected -- will start MTBA Service and CBioPortal."
-  if [ ! -n "$IDMANAGER_UPLOAD_APIKEY" ]; then
-    log ERROR "Detected MTBA Module configuration but ID-Management Module seems not to be configured!"
-    exit 1;
-  fi
-  OVERRIDE+=" -f ./$PROJECT/modules/mtba-compose.yml"
-fi

ccp/modules/nngm-compose.yml

@@ -1,32 +0,0 @@
-version: "3.7"
-
-services:
-  connector:
-    container_name: bridgehead-nngm-connector
-    image: docker.verbis.dkfz.de/ccp/connector:bk2
-    environment:
-      POSTGRES_PASSWORD: ${CONNECTOR_POSTGRES_PASSWORD}
-      NNGM_MAGICPL_APIKEY: ${NNGM_MAGICPL_APIKEY}
-      NNGM_MAINZELLISTE_APIKEY: ${NNGM_MAINZELLISTE_APIKEY}
-      NNGM_CTS_APIKEY: ${NNGM_CTS_APIKEY}
-      NNGM_CRYPTKEY: ${NNGM_CRYPTKEY}
-    restart: always
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.connector.rule=PathPrefix(`/ccp-connector`)"
-      - "traefik.http.services.connector.loadbalancer.server.port=8080"
-      - "traefik.http.routers.connector.tls=true"
-
-  connector_db:
-    image: postgres:9.5-alpine
-    container_name: bridgehead-nngm-connector-db
-    volumes:
-      - "connector_db_data:/var/lib/postgresql/data"
-    environment:
-      POSTGRES_DB: "samplyconnector"
-      POSTGRES_USER: "samplyconnector"
-      POSTGRES_PASSWORD: ${CONNECTOR_POSTGRES_PASSWORD}
-    restart: always
-
-volumes:
-  connector_db_data:

ccp/modules/nngm-setup.sh

@@ -1,7 +0,0 @@
-#!/bin/bash
-
-if [ -n "$NNGM_CTS_APIKEY" ]; then
-  log INFO "nNGM setup detected -- will start nNGM Connector."
-  OVERRIDE+=" -f ./$PROJECT/modules/nngm-compose.yml"
-fi
-CONNECTOR_POSTGRES_PASSWORD="$(echo \"This is a salt string to generate one consistent password. It is not required to be secret.\" | openssl rsautl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"

ccp/modules/opal-compose.yml

@@ -1,79 +0,0 @@
-version: "3.7"
-
-services:
-
-  ############################################ DataSHIELD Client (Rocker R-Studio)
-  rstudio:
-    image: docker.verbis.dkfz.de/dktk/bridgehead-rstudio:latest
-    container_name: bridgehead-rstudio
-    #TODO: Connect with Keycloak: https://rocker-project.org/images/versioned/rstudio.html
-    environment:
-      USER: "ruser"
-      PASSWORD: "${RSTUDIO_PASSWORD}"
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.login.rule=PathPrefix(`/rstudio`)"
-      - "traefik.http.services.login.loadbalancer.server.port=8787"
-      - "traefik.http.routers.login.tls=true"
-    volumes:
-      - "rstudio-config:/home/rstudio/.config/rstudio"
-      - "rstudio-workspace:/home/rstudio/workspace"
-      - "rstudio-user-files:/home/user-files"
-
-  ############################################ DataSHIELD Server (Opal)
-  opal:
-    image: obiba/opal:4.5
-    container_name: bridgehead-opal
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.login.rule=PathPrefix(`/opal`)"
-      - "traefik.http.services.login.loadbalancer.server.port=8080" #TODO: HTTPS -> 8443
-      - "traefik.http.routers.login.tls=true"
-    links:
-      - opal-rserver
-      - opal-mongo
-      - opal-db
-    environment:
-      JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
-      # OPAL_ADMINISTRATOR_USER: "administrator"
-      OPAL_ADMINISTRATOR_PASSWORD: "${OPAL_ADMINISTRATOR_PASSWORD}"
-      MONGO_HOST: "opal-mongo"
-      MONGO_PORT: "27017"
-      POSTGRESDATA_HOST: "opal-db"
-      POSTGRESDATA_DATABASE: "opal"
-      POSTGRESDATA_USER: "opal"
-      POSTGRESDATA_PASSWORD: "${OPAL_DB_PASSWORD}"
-
-      ROCK_HOSTS: "opal-rserver:8085"
-    volumes:
-      - "opal:/srv"
-
-  opal-mongo: # IDs
-    image: mongo:4.2 # TODO: Update mongo:6.0.4
-    container_name: bridgehead-opal-mongo
-
-  opal-db: # Data
-    image: postgres:15.1
-    container_name: bridgehead-opal-db
-    environment:
-      POSTGRES_PASSWORD: "${OPAL_DB_PASSWORD}"
-      POSTGRES_USER: "opal"
-      POSTGRES_DB: "opal"
-    volumes:
-      - "opal-db:/var/lib/postgresql/data"
-
-  opal-rserver:
-    image: datashield/rock-base:6.2-R4.2  # https://datashield.discourse.group/t/ds-aggregate-method-error/416/4
-    container_name: bridgehead-opal-rserver
-
-volumes:
-  rstudio-config:
-    name: "rstudio-config"
-  rstudio-workspace:
-    name: "rstudio-workspace"
-  rstudio-user-files:
-    name: "rstudio-user-files"
-  opal-db:
-    name: "opal-db"
-  opal:
-    name: "opal"

ccp/modules/opal-setup.sh

@@ -1,7 +0,0 @@
-#!/bin/bash
-
-if [ "$ENABLE_OPAL" == true ];then
-  log INFO "Opal setup detected -- will start Opal services."
-  OVERRIDE+=" -f ./$PROJECT/modules/opal-compose.yml"
-fi
-OPAL_DB_PASSWORD="$(echo \"This is a salt string to generate one consistent password. It is not required to be secret.\" | openssl rsautl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"

ccp/modules/teiler-ui-compose.yml

@@ -1,267 +0,0 @@
-version: "3.7"
-
-services:
-  ############################################ Keycloak
-  login-db:
-    image: "postgres:15.1"
-    container_name: bridgehead-login-db
-    environment:
-      POSTGRES_USER: "keycloak"
-      POSTGRES_PASSWORD: "${KEYCLOAK_DB_PASSWORD}" # Set in teiler-setup.sh
-      POSTGRES_DB: "keycloak"
-    volumes:
-      - "login-db:/var/lib/postgresql/data"
-
-  login:
-    #image: "jboss/keycloak:16.1.1"
-    image: docker.verbis.dkfz.de/ccp/dktk-keycloak:latest
-    container_name: bridgehead-login
-    environment:
-      KEYCLOAK_ADMIN: "admin"
-      KEYCLOAK_ADMIN_PASSWORD: "${KEYCLOAK_ADMIN_PASSWORD}"
-      KC_DB_PASSWORD: "${KEYCLOAK_DB_PASSWORD}" # Set in teiler-setup.sh
-      KC_HOSTNAME_URL: "https://${HOST}/login"
-      KC_HOSTNAME_STRICT: "false"
-      KC_PROXY_ADDRESS_FORWARDING: "true"
-      TEILER_ROOT_CONFIG_EXTERN_URL: "https://${HOST}/ccp-teiler"
-    command:
-      - start-dev --import-realm --proxy edge --http-relative-path=/login
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.login.rule=PathPrefix(`/login`)"
-      - "traefik.http.services.login.loadbalancer.server.port=8080"
-      - "traefik.http.routers.login.tls=true"
-    depends_on:
-      - login-db
-
-  ############################################ Teiler-UI
-  teiler-root-config:
-    image: samply/teiler-root-config:developer
-    container_name: bridgehead-teiler-root-config
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.teiler_root_config_ccp.rule=PathPrefix(`/ccp-teiler`)"
-      - "traefik.http.services.teiler_root_config_ccp.loadbalancer.server.port=9000"
-      - "traefik.http.routers.teiler_root_config_ccp.tls=true"
-    environment:
-      TEILER_CORE_URL: "https://${HOST}/ccp-teiler-core"
-      TEILER_UI_URL: "https://${HOST}/ccp-teiler-ui"
-      DEFAULT_LANGUAGE: "de"
-
-  teiler-ui:
-    image: samply/teiler-ui:developer
-    container_name: bridgehead-teiler-ui
-    #  ports:
-    #    - 4200:80
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.teiler_ui_ccp.rule=PathPrefix(`/ccp-teiler-ui`)"
-      - "traefik.http.services.teiler_ui_ccp.loadbalancer.server.port=80"
-      - "traefik.http.routers.teiler_ui_ccp.tls=true"
-    environment:
-      DEFAULT_LANGUAGE: "DE"
-      TEILER_CORE_URL: "https://${HOST}/ccp-teiler-core"
-      KEYCLOAK_URL: "https://${HOST}/login"
-      KEYCLOAK_REALM: "teiler-ui"
-      KEYCLOAK_CLIENT_ID: "teiler-ui"
-      TEILER_ADMIN_NAME: "${OPERATOR_FIRST_NAME} ${OPERATOR_LAST_NAME}"
-      TEILER_ADMIN_EMAIL: "${OPERATOR_EMAIL}"
-      TEILER_ADMIN_PHONE: "${OPERATOR_PHONE}"
-      TEILER_PROJECT: "${PROJECT}"
-
-  teiler-core:
-    image: samply/teiler-core:developer
-    container_name: bridgehead-teiler-core
-    volumes:
-      - "/etc/bridgehead/ccp.conf:/app/ccp.conf"
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.teiler_core_ccp.rule=PathPrefix(`/ccp-teiler-core`)"
-      - "traefik.http.services.teiler_core_ccp.loadbalancer.server.port=8085"
-      - "traefik.http.routers.teiler_core_ccp.tls=true"
-    environment:
-      LOG_LEVEL: "INFO"
-      APPLICATION_PORT: "8085"
-      DEFAULT_LANGUAGE: "DE"
-      CONFIG_ENV_VAR_PATH: "/app/ccp.conf"
-      TEILER_CONFIG_UPDATER_CRON: "0 1 * * * *"
-      TEILER_ROOT_CONFIG_URL: "https://${HOST}/ccp-teiler"
-      TEILER_UI_DE_URL: "https://${HOST}/ccp-teiler-ui/de"
-      TEILER_UI_EN_URL: "https://${HOST}/ccp-teiler-ui/en"
-      TEILER_APP1_NAME: "config"
-      #    TEILER_APP2_NAME: "quality-report"
-      TEILER_APP3_NAME: "keycloak"
-      TEILER_APP3_TITLE: "Keycloak"
-      TEILER_APP4_DESCRIPTION_EN: "Authentication site"
-      TEILER_APP4_DESCRIPTION_DE: "Authentifizierungsseite"
-      TEILER_APP4_SOURCEURL: "https://${HOST}/login/auth/"
-      TEILER_APP4_ROLES: "TEILER_ADMIN"
-      TEILER_APP4_ISACTIVATED: "true"
-      TEILER_APP4_ICONSOURCEURL: "https://upload.wikimedia.org/wikipedia/commons/2/29/Keycloak_Logo.png"
-      TEILER_APP4_ORDER: "5"
-      TEILER_APP4_ISEXTERNALLINK: "true"
-      TEILER_APP4_ISLOCAL: "true"
-      #    TEILER_APP5_NAME: "pgadmin"
-      #    TEILER_APP5_TITLE: "PgAdmin"
-      #    TEILER_APP5_DESCRIPTION: "Database Management"
-      #    TEILER_APP5_SOURCEURL: "http://localhost:5000"
-      #    TEILER_APP5_ROLES: "TEILER_ADMIN"
-      #    TEILER_APP5_ISACTIVATED: "true"
-      #    TEILER_APP5_ICONSOURCEURL: "https://user-images.githubusercontent.com/24623425/36042969-f87531d4-0d8a-11e8-9dee-e87ab8c6a9e3.png"
-      #    TEILER_APP5_ORDER: "6"
-      #    TEILER_APP5_ISEXTERNALLINK: "true"
-      #    TEILER_APP5_ISLOCAL: "true"
-      TEILER_APP6_NAME: "ldm"
-      TEILER_APP6_TITLE_EN: "Local data management"
-      TEILER_APP6_TITLE_DE: "Lokales Datenmanagement"
-      TEILER_APP6_DESCRIPTION_EN: "Local Data Management"
-      TEILER_APP6_DESCRIPTION_DE: "Lokales Datenmanagement"
-      TEILER_APP6_SOURCEURL: "${CENTRAXX_URL}"
-      TEILER_APP6_ROLES: "TEILER_PUBLIC"
-      TEILER_APP6_ISACTIVATED: "${IS_DKTK_SITE}"
-      TEILER_APP6_ICONCLASS: "bi bi-server"
-      TEILER_APP6_ORDER: "7"
-      TEILER_APP6_ISEXTERNALLINK: "true"
-      TEILER_APP6_ISLOCAL: "true"
-      TEILER_APP7_NAME: "id-manager"
-      TEILER_APP7_TITLE: "ID-Manager"
-      TEILER_APP7_DESCRIPTION: "ID Manager"
-      TEILER_APP7_SOURCEURL: "https://${HOST}/id-manager/index.html"
-      TEILER_APP7_ROLES: "TEILER_PUBLIC"
-      TEILER_APP7_ISACTIVATED: "true"
-      TEILER_APP7_ICONCLASS: "bi bi-person-bounding-box"
-      TEILER_APP7_ORDER: "8"
-      TEILER_APP7_ISEXTERNALLINK: "true"
-      TEILER_APP7_ISLOCAL: "true"
-      TEILER_APP8_NAME: "patient-list"
-      TEILER_APP8_TITLE_EN: "Patient List"
-      TEILER_APP8_TITLE_DE: "Patientenliste"
-      TEILER_APP8_DESCRIPTION_EN: "Patient List"
-      TEILER_APP8_DESCRIPTION_DE: "Patientenliste"
-      TEILER_APP8_SOURCEURL: "https://${HOST}/patientlist"
-      TEILER_APP8_ROLES: "TEILER_PUBLIC"
-      TEILER_APP8_ISACTIVATED: "true"
-      TEILER_APP8_ICONCLASS: "bi bi-person-rolodex"
-      TEILER_APP8_ORDER: "9"
-      TEILER_APP8_ISEXTERNALLINK: "true"
-      TEILER_APP8_ISLOCAL: "true"
-      TEILER_APP9_NAME: "project-pseudonymisation"
-      TEILER_APP9_TITLE_EN: "Project Pseudonymisation"
-      TEILER_APP9_TITLE_DE: "Projectpseudonymisierung"
-      TEILER_APP9_DESCRIPTION_EN: "Project Pseudonymisation"
-      TEILER_APP9_DESCRIPTION_DE: "Projectpseudonymisierung"
-      TEILER_APP9_SOURCEURL: "https://${HOST}/id-manager/html/projectSelection.html"
-      TEILER_APP9_ROLES: "TEILER_PUBLIC"
-      TEILER_APP9_ISACTIVATED: "true"
-      TEILER_APP9_ICONCLASS: "bi bi-person-lines-fill"
-      TEILER_APP9_ORDER: "10"
-      TEILER_APP9_ISEXTERNALLINK: "true"
-      TEILER_APP9_ISLOCAL: "true"
-      TEILER_APP10_NAME: "federated-search"
-      TEILER_APP10_TITLE: "Lens"
-      TEILER_APP10_DESCRIPTION_EN: "Federated Search"
-      TEILER_APP10_DESCRIPTION_DE: "Föderierte Suche"
-      TEILER_APP10_SOURCEURL: "https://demo.lens.samply.de/"
-      TEILER_APP10_ROLES: "TEILER_PUBLIC"
-      TEILER_APP10_ISACTIVATED: "true"
-      TEILER_APP10_ICONCLASS: "bi bi-search"
-      TEILER_APP10_ORDER: "13"
-      TEILER_APP10_ISEXTERNALLINK: "true"
-      TEILER_APP10_ISLOCAL: "false"
-      TEILER_APP11_NAME: "central-patient-list"
-      TEILER_APP11_TITLE_EN: "Central Patient List"
-      TEILER_APP11_TITLE_DE: "Zentrale Patientenliste"
-      TEILER_APP11_DESCRIPTION_EN: "Central Patient List"
-      TEILER_APP11_DESCRIPTION_DE: "Zentrale Patientenliste"
-      TEILER_APP11_SOURCEURL: "https://patientlist.ccp-it.dktk.dkfz.de/"
-      TEILER_APP11_ROLES: "TEILER_PUBLIC"
-      TEILER_APP11_ISACTIVATED: "true"
-      TEILER_APP11_ICONCLASS: "bi bi-person-rolodex"
-      TEILER_APP11_ORDER: "14"
-      TEILER_APP11_ISEXTERNALLINK: "true"
-      TEILER_APP11_ISLOCAL: "false"
-      TEILER_APP12_NAME: "central id-manager"
-      TEILER_APP12_TITLE_EN: "Central ID-Manager"
-      TEILER_APP12_TITLE_DE: "Zentraler ID-Manager"
-      TEILER_APP12_DESCRIPTION_EN: "Central ID Manager"
-      TEILER_APP12_DESCRIPTION_DE: "Zentraler ID-Manager"
-      TEILER_APP12_SOURCEURL: "https://dktk-kne.kgu.de/"
-      TEILER_APP12_ROLES: "TEILER_PUBLIC"
-      TEILER_APP12_ISACTIVATED: "true"
-      TEILER_APP12_ICONCLASS: "bi bi-person-bounding-box"
-      TEILER_APP12_ORDER: "15"
-      TEILER_APP12_ISEXTERNALLINK: "true"
-      TEILER_APP12_ISLOCAL: "false"
-      # TODO: Icinga to be replaced by Zabbix
-      TEILER_APP13_NAME: "monitoring"
-      TEILER_APP13_TITLE: "Icinga"
-      TEILER_APP13_DESCRIPTION: "Icinga Monitoring"
-      TEILER_APP13_SOURCEURL: "https://monitor.vmitro.de/icingaweb2/dashboard"
-      TEILER_APP13_ROLES: "TEILER_ADMIN"
-      TEILER_APP13_ISACTIVATED: "true"
-      TEILER_APP13_ICONSOURCEURL: "https://images.ctfassets.net/o7xu9whrs0u9/QmL67mCGdRQ8PBcuKHGnF/858c0aee95762f59d67b25073f9483c2/icinga-logo.png"
-      TEILER_APP13_ORDER: "16"
-      TEILER_APP13_ISEXTERNALLINK: "true"
-      TEILER_APP13_ISLOCAL: "false"
-      #    TEILER_APP14_NAME: "function-tests"
-      #    TEILER_APP15_NAME: "event-log"
-      TEILER_APP16_NAME: "active-inquiries"
-      TEILER_APP16_BACKENDURL: "https://${HOST}/ccp-exporter"
-      TEILER_APP17_NAME: "archived-inquiries"
-      TEILER_APP17_BACKENDURL: "https://${HOST}/ccp-exporter"
-      TEILER_APP18_NAME: "failed-inquiries"
-      TEILER_APP18_BACKENDURL: "https://${HOST}/ccp-exporter"
-      TEILER_APP19_NAME: "inquiry"
-      TEILER_APP19_INMENU: "false"
-      #    TEILER_APP20_NAME: "cbioportal"
-      #    TEILER_APP20_TITLE: "cBioportal"
-      #    TEILER_APP20_DESCRIPTION: "Interactive exploration of multidimensional cancer genomics data sets"
-      #    TEILER_APP20_SOURCEURL: "http://localhost:8082"
-      #    TEILER_APP20_ROLES: "TEILER_USER"
-      #    TEILER_APP20_ISACTIVATED: "true"
-      #    TEILER_APP20_ICONSOURCEURL: "https://docs.cbioportal.org/images/cbio-logo.png"
-      #    TEILER_APP20_ORDER: "17"
-      #    TEILER_APP20_ISEXTERNALLINK: "true"
-      #    TEILER_APP20_ISLOCAL: "true"
-      #    TEILER_APP21_NAME: "mtba-bp"
-      #    TEILER_APP21_TITLE: "MTBA-BP"
-      #    TEILER_APP21_DESCRIPTION: "MTBA Camunda Business Process"
-      #    TEILER_APP21_SOURCEURL: "http://localhost:8480"
-      #    TEILER_APP21_ROLES: "TEILER_ADMIN"
-      #    TEILER_APP21_ISACTIVATED: "true"
-      #    TEILER_APP21_ICONSOURCEURL: "https://camunda.com/wp-content/uploads/2020/05/logo-camunda-black.svg"
-      #    TEILER_APP21_ORDER: "18"
-      #    TEILER_APP21_ISEXTERNALLINK: "true"
-      #    TEILER_APP21_ISLOCAL: "true"
-      TEILER_APP22_NAME: "dialog-quali"
-      TEILER_APP22_INMENU: "false"
-      TEILER_APP23_NAME: "dialog-uploads"
-      TEILER_APP23_INMENU: "false"
-      TEILER_APP24_NAME: "inquiry-dialog"
-      TEILER_APP24_INMENU: "false"
-      TEILER_APP25_NAME: "dialog-tests"
-      TEILER_APP25_INMENU: "false"
-      TEILER_APP26_NAME: "opal"
-      TEILER_APP26_TITLE: "Opal"
-      TEILER_APP26_DESCRIPTION: "Opal is OBiBa’s core database application for biobanks."
-      TEILER_APP26_SOURCEURL: "https://${HOST}/opal"
-      TEILER_APP26_ROLES: "TEILER_USER"
-      TEILER_APP26_ISACTIVATED: "true"
-      TEILER_APP26_ICONSOURCEURL: "https://www.obiba.org/assets/themes/bootstrap/img/obiba-logo-small.png"
-      TEILER_APP26_ORDER: "19"
-      TEILER_APP26_ISEXTERNALLINK: "true"
-      TEILER_APP26_ISLOCAL: "true"
-      TEILER_APP27_NAME: "rstudio"
-      TEILER_APP27_TITLE: "R Studio"
-      TEILER_APP27_DESCRIPTION: "RStudio is an integrated development environment (IDE) for R and Python."
-      TEILER_APP27_SOURCEURL: "https://${HOST}/rstudio"
-      TEILER_APP27_ROLES: "TEILER_USER"
-      TEILER_APP27_ISACTIVATED: "true"
-      TEILER_APP27_ICONSOURCEURL: "https://rstudio.com/wp-content/uploads/2018/10/RStudio-Logo-Flat.png"
-      TEILER_APP27_ORDER: "20"
-      TEILER_APP27_ISEXTERNALLINK: "true"
-      TEILER_APP27_ISLOCAL: "true"
-
-volumes:
-  login-db:
-    name: "login-db"

ccp/modules/teiler-ui-setup.sh

@@ -1,7 +0,0 @@
-#!/bin/bash
-
-if [ "$ENABLE_TEILER" == true ];then
-  log INFO "Teiler-UI setup detected -- will start Teiler-UI services."
-  OVERRIDE+=" -f ./$PROJECT/modules/teiler-ui-compose.yml"
-fi
-KEYCLOAK_DB_PASSWORD="$(echo \"This is a salt string to generate one consistent password. It is not required to be secret.\" | openssl rsautl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"

ccp/mtba-compose.yml

@@ -2,7 +2,7 @@ version: "3.7"
 
 services:
   mtba:
-    image: samply/mtba:develop
+    image: docker.verbis.dkfz.de/cache/samply/mtba:develop
     container_name: bridgehead-mtba
     environment:
       BLAZE_STORE_URL: http://blaze:8080

ccp/nngm-compose.yml

@@ -0,0 +1,24 @@
+version: "3.7"
+volumes:
+  nngm-rest:
+
+services:
+  connector:
+    container_name: bridgehead-connector
+    image: docker.verbis.dkfz.de/ccp/nngm-rest:main
+    environment:
+      CTS_MAGICPL_API_KEY: ${NNGM_MAGICPL_APIKEY}
+      CTS_API_KEY: ${NNGM_CTS_APIKEY}
+      CRYPT_KEY: ${NNGM_CRYPTKEY}
+      #CTS_MAGICPL_SITE: ${SITE_ID}TODO
+    restart: always
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.connector.rule=PathPrefix(`/nngm-connector`)"
+      - "traefik.http.middlewares.connector_strip.stripprefix.prefixes=/nngm-connector"
+      - "traefik.http.services.connector.loadbalancer.server.port=8080"
+      - "traefik.http.routers.connector.tls=true"
+      - "traefik.http.routers.connector.middlewares=connector_strip,auth"
+    volumes:
+      - nngm-rest:/var/log
+

ccp/nngm-setup.sh

@@ -0,0 +1,24 @@
+#!/bin/bash
+##nNGM vars:
+#NNGM_MAGICPL_APIKEY
+#NNGM_CTS_APIKEY
+#NNGM_CRYPTKEY
+
+function nngmSetup() {
+	if [ -n "$NNGM_CTS_APIKEY" ]; then
+		log INFO "nNGM setup detected -- will start nNGM Connector."
+		OVERRIDE+=" -f ./$PROJECT/nngm-compose.yml"
+	fi
+	}
+
+function mtbaSetup() {
+	# TODO: Check if ID-Management Module is activated!
+	if [ -n "$ENABLE_MTBA" ];then
+		log INFO "MTBA setup detected -- will start MTBA Service and CBioPortal."
+		if [ ! -n "$IDMANAGER_UPLOAD_APIKEY" ]; then
+			log ERROR "Detected MTBA Module configuration but ID-Management Module seems not to be configured!"
+			exit 1;
+		fi
+		OVERRIDE+=" -f ./$PROJECT/mtba-compose.yml"
+	fi
+}

ccp/vars

@@ -8,8 +8,12 @@ REPORTHUB_BEAM_SECRET_LONG="ApiKey report-hub.${PROXY_ID} ${REPORTHUB_BEAM_SECRE
 SUPPORT_EMAIL=support-ccp@dkfz-heidelberg.de
 PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
 
-for module in $PROJECT/modules/*.sh
-do
-    log INFO "sourcing $module"
-    source $module
-done
+# This will load id-management setup. Effective only if id-management configuration is defined.
+source $PROJECT/modules/id-management-setup.sh
+idManagementSetup
+# This will load nngm setup. Effective only if nngm configuration is defined.
+source $PROJECT/nngm-setup.sh
+nngmSetup
+source $PROJECT/exliquid-setup.sh
+exliquidSetup
+mtbaSetup

lib/functions.sh

@@ -11,7 +11,7 @@ detectCompose() {
 
 getLdmPassword() {
 	if [ -n "$LDM_PASSWORD" ]; then
-		docker run --rm httpd:alpine htpasswd -nb $PROJECT $LDM_PASSWORD | tr -d '\n' | tr -d '\r'
+		docker run --rm docker.verbis.dkfz.de/cache/httpd:alpine htpasswd -nb $PROJECT $LDM_PASSWORD | tr -d '\n' | tr -d '\r'
 	else
 		echo -n ""
 	fi
@@ -34,7 +34,7 @@ checkOwner(){
 }
 
 printUsage() {
-	echo "Usage: bridgehead start|stop|update|install|uninstall|enroll PROJECTNAME"
+	echo "Usage: bridgehead start|stop|is-running|update|install|uninstall|enroll PROJECTNAME"
 	echo "PROJECTNAME should be one of ccp|bbmri"
 }
 
@@ -169,6 +169,17 @@ function retry {
   return 0
 }
 
+function bk_is_running {
+	detectCompose
+	RUNNING="$($COMPOSE -p $PROJECT -f ./$PROJECT/docker-compose.yml $OVERRIDE ps -q)"
+	NUMBEROFRUNNING=$(echo "$RUNNING" | wc -l)
+	if [ $NUMBEROFRUNNING -ge 2 ]; then
+		return 0
+	else
+		return 1
+	fi
+}
+
 ##Setting Network properties
 # currently not needed
 #export HOSTIP=$(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}');

lib/prepare-system.sh

@@ -1,10 +1,21 @@
 #!/bin/bash -e
 
+DEV_MODE="${1:-NODEV}"
+
 source lib/log.sh
 source lib/functions.sh
 
 log "INFO" "Preparing your system for bridgehead installation ..."
 
+# Check, if running in WSL
+if [[ $(grep -i Microsoft /proc/version) ]]; then
+    # Check, if systemd is available
+    if [ "$(systemctl is-system-running)" = "offline" ]; then
+        log "ERROR" "It seems you have no active systemd environment in your WSL environment. Please follow the guide in https://devblogs.microsoft.com/commandline/systemd-support-is-now-available-in-wsl/"
+        exit 1
+    fi
+fi
+
 # Create the bridgehead user
 if id bridgehead &>/dev/null; then
     log "INFO" "Existing user with id $(id -u bridgehead) will be used by the bridgehead system units."
@@ -14,7 +25,12 @@ else
 fi
 
 # Clone the OpenSource repository of bridgehead
-bridgehead_repository_url="https://github.com/samply/bridgehead.git"
+set +e
+bridgehead_repository_url=$(git remote get-url origin)
+if [ $? -ne 0 ]; then
+    bridgehead_repository_url="https://github.com/samply/bridgehead.git"
+fi
+set -e
 if [ -d "/srv/docker/bridgehead" ]; then
     current_owner=$(stat -c '%U' /srv/docker/bridgehead)
     if [ "$(su -c 'git -C /srv/docker/bridgehead remote get-url origin' $current_owner)" == "$bridgehead_repository_url" ]; then
@@ -26,7 +42,7 @@ if [ -d "/srv/docker/bridgehead" ]; then
 else
     log "INFO" "Cloning $bridgehead_repository_url to /srv/docker/bridgehead"
     mkdir -p /srv/docker/
-    git clone bridgehead_repository_url /srv/docker/bridgehead
+    git clone $bridgehead_repository_url /srv/docker/bridgehead
 fi
 
 case "$PROJECT" in
@@ -50,7 +66,7 @@ if [ -d /etc/bridgehead ]; then
     else
         log "WARN" "Your site configuration repository in /etc/bridgehead seems to have another origin than git.verbis.dkfz.de. Please check if the repository is correctly cloned!"
     fi
-else
+elif [[ "$DEV_MODE" == "NODEV" ]]; then
     log "INFO" "Now cloning your site configuration repository for you."
     read -p "Please enter your site: " site
     read -s -p "Please enter the bridgehead's access token for your site configuration repository (will not be echoed): " access_token
@@ -59,9 +75,13 @@ else
     if [ $? -gt 0 ]; then
         log "ERROR" "Unable to clone your configuration repository. Please obtain correct access data and try again."
     fi
+elif [[ "$DEV_MODE" == "DEV" ]]; then
+    log "INFO" "Now cloning your developer configuration repository for you."
+    read -p "Please enter your config repository URL: " url
+    git clone "$url" /etc/bridgehead
 fi
 
 chown -R bridgehead /etc/bridgehead /srv/docker/bridgehead
 
-log INFO "System preparation is completed and private key is present."
+log INFO "System preparation is completed and configuration is present."
 

lib/update-bridgehead.sh

@@ -4,10 +4,15 @@ source lib/functions.sh
 AUTO_HOUSEKEEPING=${AUTO_HOUSEKEEPING:-true}
 
 if [ "$AUTO_HOUSEKEEPING" == "true" ]; then
-	A="Performing automatic maintenance: Cleaning docker images."
+	A="Performing automatic maintenance: "
+	if bk_is_running; then
+		A="$A Cleaning docker images."
+		docker system prune -a -f
+	else
+		A="$A Not cleaning docker images since BK is not running."
+	fi
 	hc_send log "$A"
 	log INFO "$A"
-	docker system prune -a -f
 else
 	log WARN "Automatic housekeeping disabled (variable AUTO_HOUSEKEEPING != \"true\")"
 fi
@@ -75,6 +80,10 @@ for DIR in /etc/bridgehead $(pwd); do
       log "INFO" "You can review all changes on the repository with $git_repository_url/compare?from=$old_git_hash&to=$new_git_hash"
     fi
     git_updated="true"
+    git -C "$DIR" checkout main
+    REPORT_BRANCH_NAME=$(git -C "$DIR" branch --show-current)
+    REPORT_STATUS_CHECK=$(git -C "$DIR" status --porcelain)
+    report_error 7 "MAINTENANCE: Switched Branch to main, you are now on branch $REPORT_BRANCH_NAME \n see status \n $REPORT_STATUS_CHECK"
   fi
 done