commit to trigger the switch

.github/scripts/rename_inactive_branches.py

@@ -1,39 +0,0 @@
-import os
-import requests
-from datetime import datetime, timedelta
-
-# Configuration
-GITHUB_TOKEN = os.getenv('GITHUB_TOKEN')
-REPO = 'samply/bridgehead'
-HEADERS = {'Authorization': f'token {GITHUB_TOKEN}', 'Accept': 'application/vnd.github.v3+json'}
-API_URL = f'https://api.github.com/repos/{REPO}/branches'
-INACTIVE_DAYS = 365
-CUTOFF_DATE = datetime.now() - timedelta(days=INACTIVE_DAYS)
-
-# Fetch all branches
-def get_branches():
-    response = requests.get(API_URL, headers=HEADERS)
-    response.raise_for_status()
-    return response.json() if response.status_code == 200 else []
-
-# Rename inactive branches
-def rename_branch(old_name, new_name):
-    rename_url = f'https://api.github.com/repos/{REPO}/branches/{old_name}/rename'
-    response = requests.post(rename_url, json={'new_name': new_name}, headers=HEADERS)
-    response.raise_for_status()
-    print(f"Renamed branch {old_name} to {new_name}" if response.status_code == 201 else f"Failed to rename {old_name}: {response.status_code}")
-
-# Check if the branch is inactive
-def is_inactive(commit_url):
-    last_commit_date = requests.get(commit_url, headers=HEADERS).json()['commit']['committer']['date']
-    return datetime.strptime(last_commit_date, '%Y-%m-%dT%H:%M:%SZ') < CUTOFF_DATE
-
-# Rename inactive branches
-def main():
-    for branch in get_branches():
-        if is_inactive(branch['commit']['url']):
-            #rename_branch(branch['name'], f"archived/{branch['name']}")
-            print(f"[LOG] Branch '{branch['name']}' is inactive and would be renamed to 'archived/{branch['name']}'")
-
-if __name__ == "__main__":
-    main()

.github/workflows/rename-inactive-branches.yml

@@ -1,27 +0,0 @@
-name: Cleanup - Rename Inactive Branches
-
-on:
-  schedule:
-    - cron: '0 0 * * 0'  # Runs every Sunday at midnight
-
-jobs:
-  archive-stale-branches:
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Checkout Repository
-        uses: actions/checkout@v2
-
-      - name: Set up Python
-        uses: actions/setup-python@v2
-        with:
-          python-version: '3.x'
-
-      - name: Install Libraries
-        run: pip install requests
-
-      - name: Run Script to Rename Inactive Branches
-        run: |
-          python .github/scripts/rename_inactive_branches.py
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.gitignore

@@ -1,7 +1,7 @@
 ##Ignore site configuration
 .gitmodules
 site-config/*
-.idea
+
 ## Ignore site configuration
 */docker-compose.override.yml
 

README.md

@@ -1,5 +1,5 @@
 # Bridgehead
-
+ 
 The Bridgehead is a secure, low-effort solution to connect your research institution to a federated research network. It bundles interoperable, open-source software components into a turnkey package for installation on one of your secure servers. The Bridgehead is pre-configured with sane defaults, centrally monitored and with an absolute minimum of "moving parts" on your side, making it an extremely low-maintenance gateway to data sharing.
 
 This repository is the starting point for any information and tools you will need to deploy a Bridgehead. If you have questions, please [contact us](mailto:verbis-support@dkfz-heidelberg.de).
@@ -21,8 +21,7 @@ This repository is the starting point for any information and tools you will nee
     - [HTTPS Access](#https-access)
     - [TLS terminating proxies](#tls-terminating-proxies)
     - [File structure](#file-structure)
-    - [BBMRI-ERIC Directory entry needed](#bbmri-eric-directory-entry-needed)
+    - [BBMRI-ERIC Directory](#bbmri-eric-directory)
-    - [Loading data](#loading-data)
 4. [Things you should know](#things-you-should-know)
     - [Auto-Updates](#auto-updates)
     - [Auto-Backups](#auto-backups)
@@ -34,10 +33,6 @@ This repository is the starting point for any information and tools you will nee
 
 ## Requirements
 
-The data protection officer at your site will probably want to know exactly what our software does with patient data, and you may need to get their approval before you are allowed to install a Bridgehead. To help you with this, we have provided some data protection concepts:
-
-- [Germany](https://www.bbmri.de/biobanking/it/infrastruktur/datenschutzkonzept/)
-
 ### Hardware
 
 Hardware requirements strongly depend on the specific use-cases of your network as well as on the data it is going to serve. Most use-cases are well-served with the following configuration:
@@ -46,8 +41,6 @@ Hardware requirements strongly depend on the specific use-cases of your network
 - 32 GB RAM
 - 160GB Hard Drive, SSD recommended
 
-We recommend using a dedicated VM for the Bridgehead, with no other applications running on it. While the Bridgehead can, in principle, run on a shared VM, you might run into surprising problems such as resource conflicts (e.g., two apps using tcp port 443).
-
 ### Software
 
 You are strongly recommended to install the Bridgehead under a Linux operating system (but see the section [Non-Linux OS](#non-linux-os)). You will need root (administrator) priveleges on this machine in order to perform the deployment. We recommend the newest Ubuntu LTS server release.
@@ -58,41 +51,22 @@ Ensure the following software (or newer) is installed:
 - docker >= 20.10.1
 - docker-compose >= 2.xx (`docker-compose` and `docker compose` are both supported).
 - systemd
-- curl
 
 We recommend to install Docker(-compose) from its official sources as described on the [Docker website](https://docs.docker.com).
 
-> 📝 Note for Ubuntu: Snap versions of Docker are not supported.
+Note for Ubuntu: Please note that snap versions of Docker are not supported.
 
 ### Network
 
-A Bridgehead communicates to all central components via outgoing HTTPS connections.
+A running Bridgehead requires an outgoing HTTPS proxy to communicate with the central components.
 
-Your site might require an outgoing proxy (i.e. HTTPS forward proxy) to connect to external servers; you should discuss this with your local systems administration. In that case, you will need to note down the URL of the proxy. If the proxy requires authentication, you will also need to make a note of its username and password. This information will be used later on during the installation process. TLS terminating proxies are also supported, see [here](#tls-terminating-proxies). Apart from the Bridgehead itself, you may also need to configure the proxy server in [git](https://gist.github.com/evantoli/f8c23a37eb3558ab8765) and [docker](https://docs.docker.com/network/proxy/).
+Additionally, your site might use its own proxy. You should discuss this with your local systems administration. If a proxy is being used, you will need to note down the URL of the proxy. If it is a secure proxy, then you will also need to make a note of its username and password. This information will be used later on during the installation process.
 
-The following URLs need to be accessible (prefix with `https://`):
+Note that git and Docker may also need to be configured to use this proxy. This is a job for your systems administrators.
-* To fetch code and configuration from git repositories
-  * github.com
-  * git.verbis.dkfz.de
-* To fetch docker images
-  * docker.verbis.dkfz.de
-  * Official Docker, Inc. URLs (subject to change, see [official list](https://docs.docker.com/desktop/all))
-    * hub.docker.com
-    * registry-1.docker.io
-    * production.cloudflare.docker.com
-* To report bridgeheads operational status
-  * healthchecks.verbis.dkfz.de
-* only for DKTK/CCP
-  * broker.ccp-it.dktk.dkfz.de
-* only for BBMRI-ERIC
-  * broker.bbmri.samply.de
-  * gitlab.bbmri-eric.eu
-* only for German Biobank Node
-  * broker.bbmri.de
 
-> 📝 This URL list is subject to change. Instead of the individual names, we highly recommend whitelisting wildcard domains: *.dkfz.de, github.com, *.docker.com, *.docker.io, *.samply.de, *.bbmri.de.
+If there is a site firewall, this needs to be configured so that outgoing calls to the following URLs are allowed: *.dkfz.de, github.com, docker.io, *.docker.io, *.samply.de.
 
-> 📝 Ubuntu's pre-installed uncomplicated firewall (ufw) is known to conflict with Docker, more info [here](https://github.com/chaifeng/ufw-docker).
+Note for Ubuntu: Please note that the uncomplicated firewall (ufw) is known to conflict with Docker [here](https://github.com/chaifeng/ufw-docker).
 
 ## Deployment
 
@@ -125,7 +99,7 @@ Mention:
 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/<project>-bridgehead-configs/dummy.git
+- 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.
 
@@ -202,7 +176,7 @@ sudo systemctl [enable|disable] bridgehead@<PROJECT>.service
 After starting the Bridgehead, you can watch the initialization process with the following command:
 
 ```shell
-/srv/docker/bridgehead/bridgehead logs <project> -f
+journalctl -u bridgehead@bbmri -f
 ```
 
 if this exits with something similar to the following:
@@ -222,9 +196,8 @@ 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
-/srv/docker/bridgehead/bridgehead logs <Project> -f
+journalctl -u bridgehead@bbmri -f
 ```
-This translates to a journalctl command so all the regular journalctl flags can be used.
 
 Once the Bridgehead has passed these checks, take a look at the landing page:
 
@@ -238,7 +211,7 @@ You can either do this in a browser or with curl. If you visit the URL in the br
 curl -k https://localhost
 ```
 
-Should the landing page not show anything, you can inspect the logs of the containers to determine what is going wrong. To do this you can use `./bridgehead docker-logs <Project> -f` to follow the logs of the container. This transaltes to a docker compose logs command meaning all the ususal docker logs flags work.
+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.
 
@@ -262,21 +235,6 @@ Even within your internal network, the Bridgehead enforces HTTPS for all service
 
 All of the Bridgehead's outgoing connections are secured by transport encryption (TLS) and a Bridgehead will refuse to connect if certificate verification fails. If your local forward proxy server performs TLS termination, please place its CA certificate in `/etc/bridgehead/trusted-ca-certs` as a `.pem` file, e.g. `/etc/bridgehead/trusted-ca-certs/mylocalca.pem`. Then, all Bridgehead components will pick up this certificate and trust it for outgoing connections.
 
-To find the certificate file, first run the following:
-
-```
-curl -v https://broker.bbmri.samply.de/v1/health
-```
-
-In the output, look out for the line:
-
-
-```
-successfully set certificate verify locations:
-```
-
-Here a file will be mentioned, perhaps in the directory /etc/ssl/certs. The exact location  will depend on your operating system. This is the file that you need to copy.
-
 ### File structure
 
 - `/srv/docker/bridgehead` contains this git repository with the shell scripts and *project-specific configuration*. In here, all files are identical for all sites. You should not make any changes here.
@@ -289,62 +247,35 @@ Here a file will be mentioned, perhaps in the directory /etc/ssl/certs. The exac
 
 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>`.
 
-### BBMRI-ERIC Directory entry needed
+### BBMRI-ERIC Directory
 
-If you run a biobank, you should be listed together with your collections with in the [Directory](https://directory.bbmri-eric.eu), a BBMRI-ERIC project that catalogs biobanks.
+If you run a biobank, you should register with the [Directory](https://directory.bbmri-eric.eu), a BBMRI-ERIC project that catalogs biobanks.
 
 To do this, contact the BBMRI-ERIC national node for the country where your biobank is based, see [the list of nodes](http://www.bbmri-eric.eu/national-nodes/).
 
-Once you have added your biobank to the Directory you got persistent identifier (PID) for your biobank and unique identifiers (IDs) for your collections. The collection IDs are necessary for the biospecimens assigning to the collections and later in the data flows between BBMRI-ERIC tools. In case you cannot distribute all your biospecimens within collections via assigning the collection IDs, **you should choose one of your sample collections as a default collection for your biobank**. This collection will be automatically used to label any samples that have not been assigned a collection ID in your ETL process. Make a note of this default collection ID, you will need it later on in the installation process.
+Once you have registered, **you should choose one of your sample collections as a default collection for your biobank**. This is the collection that will be automatically used to label any samples that have not been assigned a collection ID in your ETL process. Make a note of this ID, you will need it later on in the installation process.
 
-### Directory sync tool
+The Bridgehead's **Directory Sync** is an optional feature that keeps the Directory up to date with your local data, e.g. number of samples. Conversely, 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.
-
-The Bridgehead's **Directory Sync** is an optional feature that keeps the Directory up to date with your local data, e.g. number of samples. Conversely, 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.
-
-You should talk with your local data protection group regarding the information that is published by Directory sync.
 
 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=your_directory_password
+DS_DIRECTORY_USER_PASS=qwdnqwswdvqHBVGFR9887
+DS_TIMER_CRON="0 22 * * *"
 ```
-Please contact your National Node to obtain this information.
+You must contact the Directory for your national node to find the URL, and to register as a user.
 
-Optionally, you **may** change when you want Directory sync to run by specifying a [cron](https://crontab.guru) expression, e.g. `DS_TIMER_CRON="0 22 * * *"` for 10 pm every evening.
+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.
 
-### Loading data
-
-The data accessed by the federated search is held in the Bridgehead in a FHIR store (we use Blaze).
-
-You can load data into this store by using its FHIR API:
-
-```
-https://<Name of your server>/bbmri-localdatamanagement/fhir
-```
-The name of your server will generally be the full name of the VM that the Bridgehead runs on. You can alternatively supply an IP address.
-
-The FHIR API uses basic auth. You can find the credentials in `/etc/bridgehead/<project>.local.conf`.
-
-Note that if you don't have a DNS certificate for the Bridgehead, you will need to allow an insecure connection. E.g. with curl, use the `-k` flag.
-
-The storage space on your hard drive will depend on the number of FHIR resources that you intend to generate. This will be the sum of the number of patients/subjects, the number of samples, the number of conditions/diseases and the number of observations. As a general rule of thumb, you can assume that each resource will consume about 2 kilobytes of disk space.
-
-For more information on Blaze performance, please refer to [import performance](https://github.com/samply/blaze/blob/master/docs/performance/import.md).
-
-#### ETL for BBMRI and GBA
-
-Normally, you will need to build your own ETL to feed the Bridgehead. However, there is one case where a short cut might be available:
-- If you are using CentraXX as a BIMS and you have a FHIR-Export License, then you can employ standard mapping scripts that access the CentraXX-internal data structures and map the data onto the BBMRI FHIR profile. It may be necessary to adjust a few parameters, but this is nonetheless significantly easier than writing your own ETL.
-
-You can find the profiles for generating FHIR in [Simplifier](https://simplifier.net/bbmri.de/~resources?category=Profile).
-
 ## Things you should know
 
 ### Auto-Updates
@@ -388,28 +319,8 @@ Installation under WSL ought to work, but we have not tested this.
 
 ### 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, you'll need to configure the proxy inside the system unit of docker by creating the file `/etc/systemd/system/docker.service.d/proxy.conf` with the following content:
+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).
 
-``` ini
-[Service]
-Environment="HTTP_PROXY=http://proxy.example.com:3128"
-Environment="HTTPS_PROXY=https://proxy.example.com:3128"
-Environment="NO_PROXY=localhost,127.0.0.1,some-local-docker-registry.example.com,.corp"
-```
-
-After saving the configuration file, you'll need to reload the system daemon for the changes to take effect:
-
-``` shell
-sudo systemctl daemon-reload
-```
-
-and restart the docker daemon:
-
-``` shell
-sudo systemctl restart docker
-```
-
-For more information, please consult the [official documentation](https://docs.docker.com/config/daemon/systemd/#httphttps-proxy).
 
 ### Monitoring
 

bbmri/docker-compose.yml

@@ -4,14 +4,12 @@ version: "3.7"
 
 services:
   blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
+    image: docker.verbis.dkfz.de/cache/samply/blaze:latest
     container_name: bridgehead-bbmri-blaze
     environment:
       BASE_URL: "http://bridgehead-bbmri-blaze:8080"
-      JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
+      JAVA_TOOL_OPTIONS: "-Xmx4g"
-      DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
+      LOG_LEVEL: "debug"
-      DB_BLOCK_CACHE_SIZE: ${BLAZE_MEMORY_CAP}
-      CQL_EXPR_CACHE_SIZE: ${BLAZE_CQL_CACHE_CAP:-32}
       ENFORCE_REFERENTIAL_INTEGRITY: "false"
     volumes:
       - "blaze-data:/app/data"

bbmri/modules/directory-sync-compose.yml

@@ -1,16 +1,8 @@
-version: "3.7"
-
 services:
   directory_sync_service:
     image: "docker.verbis.dkfz.de/cache/samply/directory_sync_service"
     environment:
-      DS_DIRECTORY_URL: ${DS_DIRECTORY_URL:-https://directory.bbmri-eric.eu}
+      DS_DIRECTORY_URL: ${DS_DIRECTORY_URL}
       DS_DIRECTORY_USER_NAME: ${DS_DIRECTORY_USER_NAME}
-      DS_DIRECTORY_USER_PASS: ${DS_DIRECTORY_USER_PASS}
+      DS_DIRECTORY_PASS_CODE: ${DS_DIRECTORY_PASS_CODE}
-      DS_TIMER_CRON: ${DS_TIMER_CRON:-0 22 * * *}
+      DS_TIMER_CRON: ${DS_TIMER_CRON}
-      DS_DIRECTORY_ALLOW_STAR_MODEL: ${DS_DIRECTORY_ALLOW_STAR_MODEL:-true}
-      DS_DIRECTORY_MOCK: ${DS_DIRECTORY_MOCK}
-      DS_DIRECTORY_DEFAULT_COLLECTION_ID: ${DS_DIRECTORY_DEFAULT_COLLECTION_ID}
-      DS_DIRECTORY_COUNTRY: ${DS_DIRECTORY_COUNTRY}
-    depends_on:
-      - "blaze"

bbmri/modules/dnpm-compose.yml

@@ -0,0 +1,50 @@
+version: "3.7"
+
+services:
+  dnpm-beam-proxy:
+    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
+    container_name: bridgehead-dnpm-beam-proxy
+    environment:
+      BROKER_URL: ${DNPM_BROKER_URL}
+      PROXY_ID: ${DNPM_PROXY_ID}
+      APP_dnpm-connect_KEY: ${DNPM_BEAM_SECRET_SHORT}
+      PRIVKEY_FILE: /run/secrets/proxy.pem
+      ALL_PROXY: http://forward_proxy:3128
+      TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
+      ROOTCERT_FILE: /conf/root.crt.pem
+    secrets:
+      - proxy.pem
+    depends_on:
+      - "forward_proxy"
+    volumes:
+      - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
+      - /srv/docker/bridgehead/ccp/root-new.crt.pem:/conf/root.crt.pem:ro
+
+  dnpm-beam-connect:
+    depends_on: [ dnpm-beam-proxy ]
+    image: docker.verbis.dkfz.de/cache/samply/beam-connect:dnpm
+    container_name: bridgehead-dnpm-beam-connect
+    environment:
+      PROXY_URL: http://dnpm-beam-proxy:8081
+      PROXY_APIKEY: ${DNPM_BEAM_SECRET_SHORT}
+      APP_ID: dnpm-connect.${DNPM_PROXY_ID}
+      DISCOVERY_URL: "./conf/central_targets.json"
+      LOCAL_TARGETS_FILE: "./conf/connect_targets.json"
+      HTTP_PROXY: http://forward_proxy:3128
+      HTTPS_PROXY: http://forward_proxy:3128
+      NO_PROXY: dnpm-beam-proxy,dnpm-backend
+      RUST_LOG: ${RUST_LOG:-info}
+    volumes:
+      - /etc/bridgehead/dnpm/local_targets.json:/conf/connect_targets.json:ro
+      - /etc/bridgehead/dnpm/central_targets.json:/conf/central_targets.json:ro
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.dnpm-connect.rule=PathPrefix(`/dnpm-connect`)"
+      - "traefik.http.middlewares.dnpm-connect-strip.stripprefix.prefixes=/dnpm-connect"
+      - "traefik.http.routers.dnpm-connect.middlewares=dnpm-connect-strip"
+      - "traefik.http.services.dnpm-connect.loadbalancer.server.port=8062"
+      - "traefik.http.routers.dnpm-connect.tls=true"
+
+secrets:
+  proxy.pem:
+    file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

bbmri/modules/dnpm-setup.sh

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+if [ -n "${ENABLE_DNPM}" ]; then
+	log INFO "DNPM setup detected (Beam.Connect) -- will start Beam and Beam.Connect for DNPM."
+	OVERRIDE+=" -f ./$PROJECT/modules/dnpm-compose.yml"
+
+	# Set variables required for Beam-Connect
+	DNPM_APPLICATION_SECRET="$(echo \"This is a salt string to generate one consistent password for DNPM. It is not required to be secret.\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
+	DNPM_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
+	DNPM_BROKER_ID="broker.ccp-it.dktk.dkfz.de"
+	DNPM_BROKER_URL="https://${DNPM_BROKER_ID}"
+	DNPM_PROXY_ID="${SITE_ID}.${DNPM_BROKER_ID}"
+fi

bbmri/modules/eric-compose.yml

@@ -2,7 +2,7 @@ version: "3.7"
 
 services:
   focus-eric:
-    image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}-bbmri
+    image: docker.verbis.dkfz.de/cache/samply/focus:main
     container_name: bridgehead-focus-eric
     environment:
       API_KEY: ${ERIC_FOCUS_BEAM_SECRET_SHORT}
@@ -16,7 +16,7 @@ services:
       - "blaze"
 
   beam-proxy-eric:
-    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${BEAM_TAG}
+    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
     container_name: bridgehead-beam-proxy-eric
     environment:
       BROKER_URL: ${ERIC_BROKER_URL}
@@ -32,5 +32,5 @@ services:
       - "forward_proxy"
     volumes:
       - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
-      - /srv/docker/bridgehead/bbmri/modules/${ERIC_ROOT_CERT}.root.crt.pem:/conf/root.crt.pem:ro
+      - /srv/docker/bridgehead/bbmri/modules/eric.root.crt.pem:/conf/root.crt.pem:ro
 

bbmri/modules/eric-setup.sh

@@ -4,23 +4,8 @@ if [ "${ENABLE_ERIC}" == "true" ]; then
 	log INFO "BBMRI-ERIC setup detected -- will start services for BBMRI-ERIC."
 	OVERRIDE+=" -f ./$PROJECT/modules/eric-compose.yml"
 
-	# The environment needs to be defined in /etc/bridgehead
+	# Set required variables
-	case "$ENVIRONMENT" in
+	ERIC_BROKER_ID=broker.bbmri.samply.de
-		"production")
-			export ERIC_BROKER_ID=broker.bbmri.samply.de
-			export ERIC_ROOT_CERT=eric
-			;;
-		"test")
-			export ERIC_BROKER_ID=broker-test.bbmri-test.samply.de
-			export ERIC_ROOT_CERT=eric.test
-			;;
-		*)
-			report_error 6 "Environment \"$ENVIRONMENT\" is unknown. Assuming production. FIX THIS!"
-			export ERIC_BROKER_ID=broker.bbmri.samply.de
-			export ERIC_ROOT_CERT=eric
-			;;
-	esac
-
 	ERIC_BROKER_URL=https://${ERIC_BROKER_ID}
 	ERIC_PROXY_ID=${SITE_ID}.${ERIC_BROKER_ID}
 	ERIC_FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"

bbmri/modules/eric.test.root.crt.pem

@@ -1,20 +0,0 @@
------BEGIN CERTIFICATE-----
-MIIDNTCCAh2gAwIBAgIUJ0g7k2vrdAwNTU38S1/mU8NO26MwDQYJKoZIhvcNAQEL
-BQAwFjEUMBIGA1UEAxMLQnJva2VyLVJvb3QwHhcNMjMwNzEwMTIyMzQxWhcNMzMw
-NzA3MTIyNDExWjAWMRQwEgYDVQQDEwtCcm9rZXItUm9vdDCCASIwDQYJKoZIhvcN
-AQEBBQADggEPADCCAQoCggEBALMvc/fApbsAl+/NXDszNgffNR5llAb9CfxzdnRn
-ryoBqZdPevBYZZfKBARRKjFbXRDdPWbE7erDeo1LiCM6PObXCuT9wmGWJtvfkmqW
-3Z/a75e4r360kceMEGVn4kWpi9dz8s7+oXVZURjW2r13h6pq6xQNZDNlXmpR8wHG
-58TSrQC4n1vzdSwMWdptgOA8Sw8adR7ZJI1yNZpmynB2QolKKNESI7FcSKC/+b+H
-LoPkseAwQG9yJo23qEw1GZS67B47iKIqX2wp9VLQobHw7ncrhKXQLSWq973k/Swp
-7lBdfOsTouf72flLiF1HbdOLcFDmWgIbf5scj2HaQe8b/UcCAwEAAaN7MHkwDgYD
-VR0PAQH/BAQDAgEGMA8GA1UdEwEB/wQFMAMBAf8wHQYDVR0OBBYEFHYxBJiJZieW
-e6G1vwn6Q36/crgNMB8GA1UdIwQYMBaAFHYxBJiJZieWe6G1vwn6Q36/crgNMBYG
-A1UdEQQPMA2CC0Jyb2tlci1Sb290MA0GCSqGSIb3DQEBCwUAA4IBAQCN6WVNYpWJ
-6Z1Ee+otLZYMXhjyR6NUQ5s0aHiug97gB8mTiNlgXiiTgipCbofEmENgh1inYrPC
-WfdXxqOaekSXCQW6nSO1KtBzEYtkN5LrN1cjKqt51P2DbkllinK37wwCS2Kfup1+
-yjhTRxrehSIfsMVK6bTUeSoc8etkgwErZpORhlpqZKWhmOwcMpgsYJJOLhUetqc1
-UNe/254bc0vqHEPT6VI/86c7qAmk1xR0RUfrnKAEqZtUeuoj2fe1L/6yOB16fxt5
-3V3oim7EO6eZCTjDo9fU5DaFiqSMe7WVdr03Na0cWet60XKRH/xaiC6gMWdHWcbh
-vZdXnV1qjlM2
------END CERTIFICATE-----

bbmri/modules/gbn-compose.yml

@@ -2,7 +2,7 @@ version: "3.7"
 
 services:
   focus-gbn:
-    image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}-bbmri
+    image: docker.verbis.dkfz.de/cache/samply/focus:main
     container_name: bridgehead-focus-gbn
     environment:
       API_KEY: ${GBN_FOCUS_BEAM_SECRET_SHORT}
@@ -16,7 +16,7 @@ services:
       - "blaze"
 
   beam-proxy-gbn:
-    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${BEAM_TAG}
+    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
     container_name: bridgehead-beam-proxy-gbn
     environment:
       BROKER_URL: ${GBN_BROKER_URL}
@@ -32,5 +32,5 @@ services:
       - "forward_proxy"
     volumes:
       - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
-      - /srv/docker/bridgehead/bbmri/modules/${GBN_ROOT_CERT}.root.crt.pem:/conf/root.crt.pem:ro
+      - /srv/docker/bridgehead/bbmri/modules/gbn.root.crt.pem:/conf/root.crt.pem:ro
 

bbmri/modules/gbn-setup.sh

@@ -4,25 +4,10 @@ if [ "${ENABLE_GBN}" == "true" ]; then
 	log INFO "GBN setup detected -- will start services for German Biobank Node."
 	OVERRIDE+=" -f ./$PROJECT/modules/gbn-compose.yml"
 
-	# The environment needs to be defined in /etc/bridgehead
+	# Set required variables
-	case "$ENVIRONMENT" in
+	GBN_BROKER_ID='#TODO#'
-		"production")
-			export GBN_BROKER_ID=broker.bbmri.de
-			export GBN_ROOT_CERT=gbn
-			;;
-		"test")
-			export GBN_BROKER_ID=broker.test.bbmri.de
-			export GBN_ROOT_CERT=gbn.test
-			;;
-		*)
-			report_error 6 "Environment \"$ENVIRONMENT\" is unknown. Assuming production. FIX THIS!"
-			export GBN_BROKER_ID=broker.bbmri.de
-			export GBN_ROOT_CERT=gbn
-			;;
-	esac
-	
 	GBN_BROKER_URL=https://${GBN_BROKER_ID}
 	GBN_PROXY_ID=${SITE_ID}.${GBN_BROKER_ID}
 	GBN_FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
-	GBN_SUPPORT_EMAIL=feedback@germanbiobanknode.de
+	GBN_SUPPORT_EMAIL=todo@verbis.dkfz.de
 fi

bbmri/modules/gbn.root.crt.pem

@@ -1,20 +1 @@
------BEGIN CERTIFICATE-----
+#TODO#
-MIIDNTCCAh2gAwIBAgIUckVOQQWZBTC0pWhn1X3lPxAWricwDQYJKoZIhvcNAQEL
-BQAwFjEUMBIGA1UEAxMLQnJva2VyLVJvb3QwHhcNMjMwOTA0MDkwMTQ0WhcNMzMw
-OTAxMDkwMjEzWjAWMRQwEgYDVQQDEwtCcm9rZXItUm9vdDCCASIwDQYJKoZIhvcN
-AQEBBQADggEPADCCAQoCggEBAOOD+CVvteBmu1hKV1QlfbHmiLCnuf6F+9k+1u/b
-6as6k7BURn8KZAxVLWSIwC6x2C7n9CHN9Jieb4DWpS0XmXQVUEpT1/yiLGBdxp2x
-nrbzm7caOunsWsPlGOcXPJKJpzAhcg58RDzXZ+2+shulSmsgPNlWBaLhNL5wj0sQ
-MzbwGVlGIJg18Ye/9WgQkO2ZcnTGb5cRsChKs4H43ZC34ZSSk7wqWg6P3e2xFam1
-YKXBOZzhwHoI4AxUQ+gd6upz5dqcwbaNZm10VP8fMac2dMLw9cOCS0ueDCS4viLd
-A69yds19AndBPMZhoEY1UHafjJ1uITRJQpaaB4vNliX+1rECAwEAAaN7MHkwDgYD
-VR0PAQH/BAQDAgEGMA8GA1UdEwEB/wQFMAMBAf8wHQYDVR0OBBYEFC74YIorSwWD
-/s5ozz3xvqUMDJ3qMB8GA1UdIwQYMBaAFC74YIorSwWD/s5ozz3xvqUMDJ3qMBYG
-A1UdEQQPMA2CC0Jyb2tlci1Sb290MA0GCSqGSIb3DQEBCwUAA4IBAQCzcIccBzYr
-sHCGTGsSyLGBYsuI5yl+hvFOitYTha/mC+XBxq2R6By2WzbfSZtyZkUtC/+FqdCY
-VtMSjbDVXtBgsabfqODBobHmPyOEmNUX4IGcyn06rdM+rHQRah98lF+PhiPPO42F
-9Wj8dkq4/Gf+Yarq31ZbY0sed2sEPZ/bV26Og8Ft9qip5gKwklyakAiCnDIq+QBd
-ltvng3g08AQM0o5KIphP2/WU0UoSk1YPVMjRxuLiFg8xvr2EdCQQ9oA7xbhrmAXe
-242HVW/7KokjmowyWTQlIUGnuGdCOtTl8h74eHTID0YWO68hHkA0J5Ox2j4dZxvw
-HRFTxAR1gGKX
------END CERTIFICATE-----

bbmri/modules/gbn.test.root.crt.pem

@@ -1,20 +0,0 @@
------BEGIN CERTIFICATE-----
-MIIDNTCCAh2gAwIBAgIUQJjusHYR89Xas+kRbg41aHZxfmcwDQYJKoZIhvcNAQEL
-BQAwFjEUMBIGA1UEAxMLQnJva2VyLVJvb3QwHhcNMjMwODIxMDk1MDI1WhcNMzMw
-ODE4MDk1MDU1WjAWMRQwEgYDVQQDEwtCcm9rZXItUm9vdDCCASIwDQYJKoZIhvcN
-AQEBBQADggEPADCCAQoCggEBAMP0jt2tSk23Bu+QeogqlFwjbMnqwRcWGKAOF4ch
-aOK2B5u/BnpqIZDZbhfSIJTv8DPe3+nA2VqRfSiW3HbV0auqxx1ii2ZmHYbvO2P/
-Jj6hyIiYYGqCMRVXk7iB+DfMysQEaSJO/7lJSprlVQCl0u7MAQ4q/szVNwcCm2Xi
-iE00Wlota2xTYjnJHYjeaLZL4kQsjqW2aCWHG4q77Z4NXT+lXN9XXedgoXLhuwWl
-UyHhXPjyCVu1iFzsXwSTodPAETGoInRYMqMA7PrbHZu1b2Jz0BwCQ+bark1td+Mf
-l3uP0QduhZnH6zGO0KyUFRzeiesgabv5bgUeSSsIOVjnLJUCAwEAAaN7MHkwDgYD
-VR0PAQH/BAQDAgEGMA8GA1UdEwEB/wQFMAMBAf8wHQYDVR0OBBYEFME99nPh1Vuo
-7eRaymL2Ps7qGxIdMB8GA1UdIwQYMBaAFME99nPh1Vuo7eRaymL2Ps7qGxIdMBYG
-A1UdEQQPMA2CC0Jyb2tlci1Sb290MA0GCSqGSIb3DQEBCwUAA4IBAQB0WG0xT00R
-5CA0tVHaNo8bQuAXytu566TspKc5vVd3r6mglj/MiSSQG2MVz+GUU6LnnApgln1P
-pvZuyaldB0QdTTLeJVMr/eFtZonlxqcxkj+VW2Y7mRHT7Xx9GQvzKYvSK5m/+xzH
-pAQl8AirgkoZ5b+ltlzM0pDAH204xj3/skmGqM/o0FKzRtpetHYkZPiquHCmO2Cp
-nTMkv7c2qu5t2Dm5q0Tmb7ZRoA1yIYhDn/UfhTAVWQnoMfXK8oB9nkRRb7pAfOXo
-W1K4A+oWqKrJwfIH/Ycnw7hu8hPuGOyIN/PLnLpJp9M2I67vywp5lIvFib4UukyJ
-wJw6/iTienIA
------END CERTIFICATE-----

bbmri/vars

@@ -4,7 +4,7 @@
 # Makes only sense for German Biobanks
 : ${ENABLE_GBN:=false}
 
-FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64}
+FOCUS_RETRY_COUNT=32
 PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
 
 for module in $PROJECT/modules/*.sh
@@ -14,7 +14,7 @@ do
 done
 
 SUPPORT_EMAIL=$ERIC_SUPPORT_EMAIL
-BROKER_URL_FOR_PREREQ="${ERIC_BROKER_URL:-$GBN_BROKER_URL}"
+BROKER_URL_FOR_PREREQ=$ERIC_BROKER_URL
 
 if [ -n "$GBN_SUPPORT_EMAIL" ]; then
     SUPPORT_EMAIL=$GBN_SUPPORT_EMAIL
@@ -34,4 +34,4 @@ function do_enroll {
         echo
         echo "You just received $COUNT certificate signing requests (CSR). Please send $COUNT e-mails, with 1 CSR each, to the respective e-mail address."
     fi
-}
+}

bridgehead

@@ -32,18 +32,6 @@ case "$PROJECT" in
 	bbmri)
 		#nothing extra to do
 		;;
-	cce)
-		#nothing extra to do
-		;;
-	itcc)
-		#nothing extra to do
-		;;
-	kr)
-		#nothing extra to do
-		;;
-	dhki)
-		#nothing extra to do
-		;;
 	minimal)
 		#nothing extra to do
 		;;
@@ -62,8 +50,6 @@ loadVars() {
 		source /etc/bridgehead/$PROJECT.local.conf || fail_and_report 1 "Found /etc/bridgehead/$PROJECT.local.conf but failed to import"
 	fi
 	fetchVarsFromVaultByFile /etc/bridgehead/$PROJECT.conf || fail_and_report 1 "Unable to fetchVarsFromVaultByFile"
-	setHostname
-	optimizeBlazeMemoryUsage
 	[ -e ./$PROJECT/vars ] && source ./$PROJECT/vars
 	set +a
 
@@ -78,27 +64,7 @@ loadVars() {
 		OVERRIDE+=" -f ./$PROJECT/docker-compose.override.yml"
 	fi
 	detectCompose
-	setupProxy
+	setHostname
-
-	# Set some project-independent default values
-	: ${ENVIRONMENT:=production}
-	export ENVIRONMENT
-
-	case "$ENVIRONMENT" in
-		"production")
-			export FOCUS_TAG=main
-			export BEAM_TAG=main
-			;;
-		"test")
-			export FOCUS_TAG=develop
-			export BEAM_TAG=develop
-			;;
-		*)
-			report_error 7 "Environment \"$ENVIRONMENT\" is unknown. Assuming production. FIX THIS!"
-			export FOCUS_TAG=main
-			export BEAM_TAG=main
-			;;
-	esac
 }
 
 case "$ACTION" in
@@ -106,14 +72,11 @@ case "$ACTION" in
 		loadVars
 		hc_send log "Bridgehead $PROJECT startup: Checking requirements ..."
 		checkRequirements
-		sync_secrets
 		hc_send log "Bridgehead $PROJECT startup: Requirements checked out. Now starting bridgehead ..."
 		exec $COMPOSE -p $PROJECT -f ./minimal/docker-compose.yml -f ./$PROJECT/docker-compose.yml $OVERRIDE up --abort-on-container-exit
 		;;
 	stop)
 		loadVars
-		# Kill stale secret-sync instances if present
-		docker kill $(docker ps -q --filter ancestor=docker.verbis.dkfz.de/cache/samply/secret-sync-local) 2>/dev/null || true
 		# HACK: This is temporarily to properly shut down false bridgehead instances (bridgehead-ccp instead ccp)
 		$COMPOSE -p bridgehead-$PROJECT -f ./minimal/docker-compose.yml -f ./$PROJECT/docker-compose.yml $OVERRIDE down
 		exec $COMPOSE -p $PROJECT -f ./minimal/docker-compose.yml -f ./$PROJECT/docker-compose.yml $OVERRIDE down
@@ -122,16 +85,6 @@ case "$ACTION" in
 		bk_is_running
 		exit $?
 		;;
-	logs)
-		loadVars
-		shift 2
-		exec journalctl -u bridgehead@$PROJECT -u bridgehead-update@$PROJECT -a $@
-		;;
-	docker-logs)
-		loadVars
-		shift 2
-		exec $COMPOSE -p $PROJECT -f ./minimal/docker-compose.yml -f ./$PROJECT/docker-compose.yml $OVERRIDE logs -f $@
-		;;
 	update)
 		loadVars
 		exec ./lib/update-bridgehead.sh $PROJECT

cce/docker-compose.yml

@@ -1,63 +0,0 @@
-version: "3.7"
-
-services:
-  blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
-    container_name: bridgehead-cce-blaze
-    environment:
-      BASE_URL: "http://bridgehead-cce-blaze:8080"
-      JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
-      DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
-      DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP
-      ENFORCE_REFERENTIAL_INTEGRITY: "false"
-    volumes:
-      - "blaze-data:/app/data"
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.blaze_cce.rule=PathPrefix(`/cce-localdatamanagement`)"
-      - "traefik.http.middlewares.cce_b_strip.stripprefix.prefixes=/cce-localdatamanagement"
-      - "traefik.http.services.blaze_cce.loadbalancer.server.port=8080"
-      - "traefik.http.routers.blaze_cce.middlewares=cce_b_strip,auth"
-      - "traefik.http.routers.blaze_cce.tls=true"
-
-  focus:
-    image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
-    container_name: bridgehead-focus
-    environment:
-      API_KEY: ${FOCUS_BEAM_SECRET_SHORT}
-      BEAM_APP_ID_LONG: focus.${PROXY_ID}
-      PROXY_ID: ${PROXY_ID}
-      BLAZE_URL: "http://bridgehead-cce-blaze:8080/fhir/"
-      BEAM_PROXY_URL: http://beam-proxy:8081
-      RETRY_COUNT: ${FOCUS_RETRY_COUNT}
-      EPSILON: 0.28
-    depends_on:
-      - "beam-proxy"
-      - "blaze"
-
-  beam-proxy:
-    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${BEAM_TAG}
-    container_name: bridgehead-beam-proxy
-    environment:
-      BROKER_URL: ${BROKER_URL}
-      PROXY_ID: ${PROXY_ID}
-      APP_focus_KEY: ${FOCUS_BEAM_SECRET_SHORT}
-      PRIVKEY_FILE: /run/secrets/proxy.pem
-      ALL_PROXY: http://forward_proxy:3128
-      TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
-      ROOTCERT_FILE: /conf/root.crt.pem
-    secrets:
-      - proxy.pem
-    depends_on:
-      - "forward_proxy"
-    volumes:
-      - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
-      - /srv/docker/bridgehead/cce/root.crt.pem:/conf/root.crt.pem:ro
-
-
-volumes:
-  blaze-data:
-
-secrets:
-  proxy.pem:
-    file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

cce/modules/lens-compose.yml

@@ -1,33 +0,0 @@
-version: "3.7"
-services:
-  landing:
-    container_name: lens_federated-search
-    image: docker.verbis.dkfz.de/ccp/lens:${SITE_ID}
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.landing.rule=PathPrefix(`/`)"
-      - "traefik.http.services.landing.loadbalancer.server.port=80"
-      - "traefik.http.routers.landing.tls=true"
-
-  spot:
-    image: docker.verbis.dkfz.de/ccp-private/central-spot
-    environment:
-      BEAM_SECRET: "${FOCUS_BEAM_SECRET_SHORT}"
-      BEAM_URL: http://beam-proxy:8081
-      BEAM_PROXY_ID: ${SITE_ID}
-      BEAM_BROKER_ID: ${BROKER_ID}
-      BEAM_APP_ID: "focus"
-      PROJECT_METADATA: "cce_supervisors"
-    depends_on:
-      - "beam-proxy"
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.services.spot.loadbalancer.server.port=8080"
-      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowmethods=GET,OPTIONS,POST"
-      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolalloworiginlist=https://${HOST}"
-      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowcredentials=true"
-      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolmaxage=-1"
-      - "traefik.http.routers.spot.rule=Host(`${HOST}`) && PathPrefix(`/backend`)"
-      - "traefik.http.middlewares.stripprefix_spot.stripprefix.prefixes=/backend"
-      - "traefik.http.routers.spot.tls=true"
-      - "traefik.http.routers.spot.middlewares=corsheaders2,stripprefix_spot"

cce/modules/lens-setup.sh

@@ -1,5 +0,0 @@
-#!/bin/bash
-
-if [ -n "$ENABLE_LENS" ];then
-  OVERRIDE+=" -f ./$PROJECT/modules/lens-compose.yml"
-fi

cce/root.crt.pem

@@ -1,20 +0,0 @@
------BEGIN CERTIFICATE-----
-MIIDNTCCAh2gAwIBAgIUW34NEb7bl0+Ywx+I1VKtY5vpAOowDQYJKoZIhvcNAQEL
-BQAwFjEUMBIGA1UEAxMLQnJva2VyLVJvb3QwHhcNMjQwMTIyMTMzNzEzWhcNMzQw
-MTE5MTMzNzQzWjAWMRQwEgYDVQQDEwtCcm9rZXItUm9vdDCCASIwDQYJKoZIhvcN
-AQEBBQADggEPADCCAQoCggEBAL5UegLXTlq3XRRj8LyFs3aF0tpRPVoW9RXp5kFI
-TnBvyO6qjNbMDT/xK+4iDtEX4QQUvsxAKxfXbe9i1jpdwjgH7JHaSGm2IjAiKLqO
-OXQQtguWwfNmmp96Ql13ArLj458YH08xMO/w2NFWGwB/hfARa4z/T0afFuc/tKJf
-XbGCG9xzJ9tmcG45QN8NChGhVvaTweNdVxGWlpHxmi0Mn8OM9CEuB7nPtTTiBuiu
-pRC2zVVmNjVp4ktkAqL7IHOz+/F5nhiz6tOika9oD3376Xj055lPznLcTQn2+4d7
-K7ZrBopCFxIQPjkgmYRLfPejbpdUjK1UVJw7hbWkqWqH7JMCAwEAAaN7MHkwDgYD
-VR0PAQH/BAQDAgEGMA8GA1UdEwEB/wQFMAMBAf8wHQYDVR0OBBYEFGjvRcaIP4HM
-poIguUAK9YL2n7fbMB8GA1UdIwQYMBaAFGjvRcaIP4HMpoIguUAK9YL2n7fbMBYG
-A1UdEQQPMA2CC0Jyb2tlci1Sb290MA0GCSqGSIb3DQEBCwUAA4IBAQCbzycJSaDm
-AXXNJqQ88djrKs5MDXS8RIjS/cu2ayuLaYDe+BzVmUXNA0Vt9nZGdaz63SLLcjpU
-fNSxBfKbwmf7s30AK8Cnfj9q4W/BlBeVizUHQsg1+RQpDIdMrRQrwkXv8mfLw+w5
-3oaXNW6W/8KpBp/H8TBZ6myl6jCbeR3T8EMXBwipMGop/1zkbF01i98Xpqmhx2+l
-n+80ofPsSspOo5XmgCZym8CD/m/oFHmjcvOfpOCvDh4PZ+i37pmbSlCYoMpla3u/
-7MJMP5lugfLBYNDN2p+V4KbHP/cApCDT5UWLOeAWjgiZQtHH5ilDeYqEc1oPjyJt
-Rtup0MTxSJtN
------END CERTIFICATE-----

cce/vars

@@ -1,14 +0,0 @@
-BROKER_ID=test-no-real-data.broker.samply.de
-BROKER_URL=https://${BROKER_ID}
-PROXY_ID=${SITE_ID}.${BROKER_ID}
-FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
-FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64}
-SUPPORT_EMAIL=manoj.waikar@dkfz-heidelberg.de
-PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
-BROKER_URL_FOR_PREREQ=$BROKER_URL
-
-for module in $PROJECT/modules/*.sh
-do
-    log DEBUG "sourcing $module"
-    source $module
-done

ccp/docker-compose.yml

@@ -2,16 +2,12 @@ version: "3.7"
 
 services:
   blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
+    image: docker.verbis.dkfz.de/cache/samply/blaze:latest
     container_name: bridgehead-ccp-blaze
     environment:
       BASE_URL: "http://bridgehead-ccp-blaze:8080"
-      JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
+      JAVA_TOOL_OPTIONS: "-Xmx4g"
-      DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
-      DB_BLOCK_CACHE_SIZE: ${BLAZE_MEMORY_CAP}
-      CQL_EXPR_CACHE_SIZE: ${BLAZE_CQL_CACHE_CAP:-32}
       ENFORCE_REFERENTIAL_INTEGRITY: "false"
-      LOG_LEVEL: ${LOG_LEVEL_BLAZE:-WARN}
     volumes:
       - "blaze-data:/app/data"
     labels:
@@ -23,7 +19,7 @@ services:
       - "traefik.http.routers.blaze_ccp.tls=true"
 
   focus:
-    image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}-dktk
+    image: docker.verbis.dkfz.de/cache/samply/focus:main
     container_name: bridgehead-focus
     environment:
       API_KEY: ${FOCUS_BEAM_SECRET_SHORT}
@@ -32,18 +28,13 @@ services:
       BLAZE_URL: "http://bridgehead-ccp-blaze:8080/fhir/"
       BEAM_PROXY_URL: http://beam-proxy:8081
       RETRY_COUNT: ${FOCUS_RETRY_COUNT}
-      EPSILON: 0.28
+      OBFUSCATE: "no"
-      QUERIES_TO_CACHE: '/queries_to_cache.conf'
-      ENDPOINT_TYPE: ${FOCUS_ENDPOINT_TYPE:-blaze}
-      RUST_LOG: ${LOG_LEVEL_FOCUS:-WARN}
-    volumes:
-      - /srv/docker/bridgehead/ccp/queries_to_cache.conf:/queries_to_cache.conf
     depends_on:
       - "beam-proxy"
       - "blaze"
 
   beam-proxy:
-    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${BEAM_TAG}
+    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
     container_name: bridgehead-beam-proxy
     environment:
       BROKER_URL: ${BROKER_URL}
@@ -53,7 +44,6 @@ services:
       ALL_PROXY: http://forward_proxy:3128
       TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
       ROOTCERT_FILE: /conf/root.crt.pem
-      RUST_LOG: ${LOG_LEVEL_FOCUS:-WARN}
     secrets:
       - proxy.pem
     depends_on:
@@ -62,6 +52,7 @@ services:
       - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
       - /srv/docker/bridgehead/ccp/root.crt.pem:/conf/root.crt.pem:ro
 
+
 volumes:
   blaze-data:
 

ccp/modules/blaze-secondary-compose.yml

@@ -1,33 +0,0 @@
-version: "3.7"
-
-services:
-  blaze-secondary:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
-    container_name: bridgehead-ccp-blaze-secondary
-    environment:
-      BASE_URL: "http://bridgehead-ccp-blaze-secondary:8080"
-      JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
-      DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
-      DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP
-      ENFORCE_REFERENTIAL_INTEGRITY: "false"
-      LOG_LEVEL: ${LOG_LEVEL_BLAZE:-WARN}
-    volumes:
-      - "blaze-secondary-data:/app/data"
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.blaze-secondary_ccp.rule=PathPrefix(`/ccp-localdatamanagement-secondary`)"
-      - "traefik.http.middlewares.ccp_b-secondary_strip.stripprefix.prefixes=/ccp-localdatamanagement-secondary"
-      - "traefik.http.services.blaze-secondary_ccp.loadbalancer.server.port=8080"
-      - "traefik.http.routers.blaze-secondary_ccp.middlewares=ccp_b-secondary_strip,auth"
-      - "traefik.http.routers.blaze-secondary_ccp.tls=true"
-
-  obds2fhir-rest:
-    environment:
-      STORE_PATH: ${STORE_PATH:-http://blaze:8080/fhir}
-
-  exporter:
-    environment:
-      BLAZE_HOST: "blaze-secondary"
-
-volumes:
-  blaze-secondary-data:

ccp/modules/blaze-secondary-setup.sh

@@ -1,11 +0,0 @@
-#!/bin/bash
-
-function blazeSecondarySetup() {
-  if [ -n "$ENABLE_SECONDARY_BLAZE" ]; then
-    log INFO "Secondary Blaze setup detected -- will start second blaze."
-    OVERRIDE+=" -f ./$PROJECT/modules/blaze-secondary-compose.yml"
-    #make oBDS2FHIR ignore ID-Management and replace target Blaze
-    PATIENTLIST_URL=" "
-    STORE_PATH="http://blaze-secondary:8080/fhir"
-  fi
-}

ccp/modules/datashield-compose.yml

@@ -1,176 +0,0 @@
-version: "3.7"
-
-services:
-  rstudio:
-    container_name: bridgehead-rstudio
-    image: docker.verbis.dkfz.de/ccp/dktk-rstudio:latest
-    environment:
-      #DEFAULT_USER: "rstudio" # This line is kept for informational purposes
-      PASSWORD: "${RSTUDIO_ADMIN_PASSWORD}" # It is required, even if the authentication is disabled
-      DISABLE_AUTH: "true" # https://rocker-project.org/images/versioned/rstudio.html#how-to-use
-      HTTP_RELATIVE_PATH: "/rstudio"
-      ALL_PROXY: "http://forward_proxy:3128" # https://rocker-project.org/use/networking.html
-      LOG_LEVEL: ${LOG_LEVEL_RSTUDIO:-WARN}
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.rstudio_ccp.rule=PathPrefix(`/rstudio`)"
-      - "traefik.http.services.rstudio_ccp.loadbalancer.server.port=8787"
-      - "traefik.http.middlewares.rstudio_ccp_strip.stripprefix.prefixes=/rstudio"
-      - "traefik.http.routers.rstudio_ccp.tls=true"
-      - "traefik.http.routers.rstudio_ccp.middlewares=oidcAuth,rstudio_ccp_strip"
-    networks:
-      - rstudio
-
-  opal:
-    container_name: bridgehead-opal
-    image: docker.verbis.dkfz.de/ccp/dktk-opal:latest
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.opal_ccp.rule=PathPrefix(`/opal`)"
-      - "traefik.http.services.opal_ccp.loadbalancer.server.port=8080"
-      - "traefik.http.routers.opal_ccp.tls=true"
-    links:
-      - opal-rserver
-      - opal-db
-    environment:
-      JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC -Dhttps.proxyHost=forward_proxy -Dhttps.proxyPort=3128"
-      # OPAL_ADMINISTRATOR_USER: "administrator" # This line is kept for informational purposes
-      OPAL_ADMINISTRATOR_PASSWORD: "${OPAL_ADMIN_PASSWORD}"
-      POSTGRESDATA_HOST: "opal-db"
-      POSTGRESDATA_DATABASE: "opal"
-      POSTGRESDATA_USER: "opal"
-      POSTGRESDATA_PASSWORD: "${OPAL_DB_PASSWORD}"
-      ROCK_HOSTS: "opal-rserver:8085"
-      APP_URL: "https://${HOST}/opal"
-      APP_CONTEXT_PATH: "/opal"
-      OPAL_PRIVATE_KEY: "/run/secrets/opal-key.pem"
-      OPAL_CERTIFICATE: "/run/secrets/opal-cert.pem"
-      OIDC_URL: "${OIDC_URL}"
-      OIDC_REALM: "${OIDC_REALM}"
-      OIDC_CLIENT_ID: "${OIDC_PRIVATE_CLIENT_ID}"
-      OIDC_CLIENT_SECRET: "${OIDC_CLIENT_SECRET}"
-      OIDC_ADMIN_GROUP: "${OIDC_ADMIN_GROUP}"
-      TOKEN_MANAGER_PASSWORD: "${TOKEN_MANAGER_OPAL_PASSWORD}"
-      EXPORTER_PASSWORD: "${EXPORTER_OPAL_PASSWORD}"
-      BEAM_APP_ID: token-manager.${PROXY_ID}
-      BEAM_SECRET: ${TOKEN_MANAGER_SECRET}
-      BEAM_DATASHIELD_PROXY: request-manager
-      LOG_LEVEL: ${LOG_LEVEL_OPAL:-WARN}
-    volumes:
-      - "/var/cache/bridgehead/ccp/opal-metadata-db:/srv" # Opal metadata
-    secrets:
-      - opal-cert.pem
-      - opal-key.pem
-
-  opal-db:
-    container_name: bridgehead-opal-db
-    image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
-    environment:
-      POSTGRES_PASSWORD: "${OPAL_DB_PASSWORD}" # Set in datashield-setup.sh
-      POSTGRES_USER: "opal"
-      POSTGRES_DB: "opal"
-    volumes:
-      - "/var/cache/bridgehead/ccp/opal-db:/var/lib/postgresql/data" # Opal project data (imported from exporter)
-
-  opal-rserver:
-    container_name: bridgehead-opal-rserver
-    image: docker.verbis.dkfz.de/ccp/dktk-rserver # datashield/rock-base + dsCCPhos
-    tmpfs:
-      - /srv
-    environment:
-      LOG_LEVEL: ${LOG_LEVEL_OPAL:-WARN}
-
-  beam-connect:
-    image: docker.verbis.dkfz.de/cache/samply/beam-connect:develop
-    container_name: bridgehead-datashield-connect
-    environment:
-      PROXY_URL: "http://beam-proxy:8081"
-      TLS_CA_CERTIFICATES_DIR: /run/secrets
-      APP_ID: datashield-connect.${SITE_ID}.${BROKER_ID}
-      PROXY_APIKEY: ${DATASHIELD_CONNECT_SECRET}
-      DISCOVERY_URL: "./map/central.json"
-      LOCAL_TARGETS_FILE: "./map/local.json"
-      NO_AUTH: "true"
-      RUST_LOG: ${LOG_LEVEL_BEAMCONNECT:-WARN}
-    secrets:
-      - opal-cert.pem
-    depends_on:
-      - beam-proxy
-    volumes:
-      - /tmp/bridgehead/opal-map/:/map/:ro
-    networks:
-      - default
-      - rstudio
-
-  traefik:
-    labels:
-      - "traefik.http.middlewares.oidcAuth.forwardAuth.address=http://oauth2-proxy:4180/"
-      - "traefik.http.middlewares.oidcAuth.forwardAuth.trustForwardHeader=true"
-      - "traefik.http.middlewares.oidcAuth.forwardAuth.authResponseHeaders=X-Auth-Request-Access-Token,Authorization"
-    networks:
-      - default
-      - rstudio
-  forward_proxy:
-    networks:
-      - default
-      - rstudio
-
-  beam-proxy:
-    environment:
-      APP_datashield-connect_KEY: ${DATASHIELD_CONNECT_SECRET}
-      APP_token-manager_KEY: ${TOKEN_MANAGER_SECRET}
-
-  # TODO: Allow users of group /DataSHIELD and OIDC_USER_GROUP at the same time:
-  # Maybe a solution would be (https://oauth2-proxy.github.io/oauth2-proxy/configuration/oauth_provider):
-  # --allowed-groups=/DataSHIELD,OIDC_USER_GROUP
-  oauth2-proxy:
-    image: docker.verbis.dkfz.de/cache/oauth2-proxy/oauth2-proxy:latest
-    container_name: bridgehead-oauth2proxy
-    command: >-
-      --allowed-group=DataSHIELD
-      --oidc-groups-claim=${OIDC_GROUP_CLAIM}
-      --auth-logging=true
-      --whitelist-domain=${HOST}
-      --http-address="0.0.0.0:4180"
-      --reverse-proxy=true
-      --upstream="static://202"
-      --email-domain="*"
-      --cookie-name="_BRIDGEHEAD_oauth2"
-      --cookie-secret="${OAUTH2_PROXY_SECRET}"
-      --cookie-expire="12h"
-      --cookie-secure="true"
-      --cookie-httponly="true"
-      #OIDC settings
-      --provider="keycloak-oidc"
-      --provider-display-name="VerbIS Login"
-      --client-id="${OIDC_PRIVATE_CLIENT_ID}"
-      --client-secret="${OIDC_CLIENT_SECRET}"
-      --redirect-url="https://${HOST}${OAUTH2_CALLBACK}"
-      --oidc-issuer-url="${OIDC_ISSUER_URL}"
-      --scope="openid email profile"
-      --code-challenge-method="S256"
-      --skip-provider-button=true
-      #X-Forwarded-Header settings - true/false depending on your needs
-      --pass-basic-auth=true
-      --pass-user-headers=false
-      --pass-access-token=false
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.oauth2_proxy.rule=PathPrefix(`/oauth2`)"
-      - "traefik.http.services.oauth2_proxy.loadbalancer.server.port=4180"
-      - "traefik.http.routers.oauth2_proxy.tls=true"
-    environment:
-      http_proxy: "http://forward_proxy:3128"
-      https_proxy: "http://forward_proxy:3128"
-    depends_on:
-      forward_proxy:
-        condition: service_healthy
-
-secrets:
-  opal-cert.pem:
-    file: /tmp/bridgehead/opal-cert.pem
-  opal-key.pem:
-    file: /tmp/bridgehead/opal-key.pem
-
-networks:
-  rstudio:

ccp/modules/datashield-import-template.xml

@@ -1,157 +0,0 @@
-<template id="opal-ccp" source-id="blaze-store" opal-project="ccp-demo" target-id="opal" >
-
-  <container csv-filename="Patient-${TIMESTAMP}.csv" opal-table="patient" opal-entity-type="Patient">
-    <attribute csv-column="patient-id" opal-value-type="text" primary-key="true" val-fhir-path="Patient.id.value" anonym="Pat" op="EXTRACT_RELATIVE_ID"/>
-    <attribute csv-column="dktk-id-global" opal-value-type="text" val-fhir-path="Patient.identifier.where(type.coding.code = 'Global').value.value"/>
-    <attribute csv-column="dktk-id-lokal" opal-value-type="text" val-fhir-path="Patient.identifier.where(type.coding.code = 'Lokal').value.value" />
-    <attribute csv-column="geburtsdatum" opal-value-type="date" val-fhir-path="Patient.birthDate.value"/>
-    <attribute csv-column="geschlecht" opal-value-type="text" val-fhir-path="Patient.gender.value" />
-    <attribute csv-column="datum_des_letztbekannten_vitalstatus" opal-value-type="date" val-fhir-path="Observation.where(code.coding.code = '75186-7').effective.value" join-fhir-path="/Observation.where(code.coding.code = '75186-7').subject.reference.value"/>
-    <attribute csv-column="vitalstatus" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '75186-7').value.coding.code.value" join-fhir-path="/Observation.where(code.coding.code = '75186-7').subject.reference.value"/>
-    <!--fehlt in ADT2FHIR--><attribute csv-column="tod_tumorbedingt" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '68343-3').value.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.value" join-fhir-path="/Observation.where(code.coding.code = '68343-3').subject.reference.value"/>
-    <!--fehlt in ADT2FHIR--><attribute csv-column="todesursachen" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '68343-3').value.coding.where(system = 'http://dktk.dkfz.de/fhir/onco/core/CodeSystem/JNUCS').code.value" join-fhir-path="/Observation.where(code.coding.code = '68343-3').subject.reference.value"/>
-  </container>
-
-  <container csv-filename="Diagnosis-${TIMESTAMP}.csv" opal-table="diagnosis" opal-entity-type="Diagnosis">
-    <attribute csv-column="diagnosis-id" primary-key="true" opal-value-type="text" val-fhir-path="Condition.id.value" anonym="Dia" op="EXTRACT_RELATIVE_ID"/>
-    <attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="Condition.subject.reference.value" anonym="Pat"/>
-    <attribute csv-column="primaerdiagnose" opal-value-type="text" val-fhir-path="Condition.code.coding.code.value"/>
-    <attribute csv-column="tumor_diagnosedatum" opal-value-type="date" val-fhir-path="Condition.onset.value"/>
-    <attribute csv-column="primaertumor_diagnosetext" opal-value-type="text" val-fhir-path="Condition.code.text.value"/>
-    <attribute csv-column="version_des_icd-10_katalogs" opal-value-type="integer" val-fhir-path="Condition.code.coding.version.value"/>
-    <attribute csv-column="lokalisation" opal-value-type="text" val-fhir-path="Condition.bodySite.coding.where(system = 'urn:oid:2.16.840.1.113883.6.43.1').code.value"/>
-    <attribute csv-column="icd-o_katalog_topographie_version" opal-value-type="text" val-fhir-path="Condition.bodySite.coding.where(system = 'urn:oid:2.16.840.1.113883.6.43.1').version.value"/>
-    <attribute csv-column="seitenlokalisation_nach_adt-gekid" opal-value-type="text" val-fhir-path="Condition.bodySite.coding.where(system = 'http://dktk.dkfz.de/fhir/onco/core/CodeSystem/SeitenlokalisationCS').code.value"/>
-  </container>
-
-  <container csv-filename="Progress-${TIMESTAMP}.csv" opal-table="progress" opal-entity-type="Progress">
-<!--it would be better to generate a an ID, instead of extracting the ClinicalImpression id-->
-    <attribute csv-column="progress-id" primary-key="true" opal-value-type="text" val-fhir-path="ClinicalImpression.id.value" anonym="Pro" op="EXTRACT_RELATIVE_ID"/>
-    <attribute csv-column="diagnosis-id" opal-value-type="text" val-fhir-path="ClinicalImpression.problem.reference.value" anonym="Dia"/>
-    <attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="ClinicalImpression.subject.reference.value" anonym="Pat" />
-    <attribute csv-column="untersuchungs-_befunddatum_im_verlauf" opal-value-type="date" val-fhir-path="ClinicalImpression.effective.value" />
-    <!-- just for evaluation: redundant to Untersuchungs-, Befunddatum im Verlauf-->
-    <attribute csv-column="datum_lokales_oder_regionaeres_rezidiv" opal-value-type="date" val-fhir-path="Observation.where(code.coding.code = 'LA4583-6').effective.value" join-fhir-path="ClinicalImpression.finding.itemReference.reference.value" />
-    <attribute csv-column="gesamtbeurteilung_tumorstatus" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21976-6').value.coding.code.value" join-fhir-path="ClinicalImpression.finding.itemReference.reference.value"/>
-    <attribute csv-column="lokales_oder_regionaeres_rezidiv" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = 'LA4583-6').value.coding.code.value" join-fhir-path="ClinicalImpression.finding.itemReference.reference.value"/>
-    <attribute csv-column="lymphknoten-rezidiv" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = 'LA4370-8').value.coding.code.value" join-fhir-path="ClinicalImpression.finding.itemReference.reference.value" />
-    <attribute csv-column="fernmetastasen" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = 'LA4226-2').value.coding.code.value" join-fhir-path="ClinicalImpression.finding.itemReference.reference.value" />
-  </container>
-
-  <container csv-filename="Histology-${TIMESTAMP}.csv" opal-table="histology" opal-entity-type="Histology" >
-    <attribute csv-column="histology-id" primary-key="true" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '59847-4').id" anonym="His" op="EXTRACT_RELATIVE_ID"/>
-    <attribute csv-column="diagnosis-id" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '59847-4').focus.reference.value" anonym="Dia"/>
-    <attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '59847-4').subject.reference.value" anonym="Pat" />
-    <attribute csv-column="histologie_datum" opal-value-type="date" val-fhir-path="Observation.where(code.coding.code = '59847-4').effective.value"/>
-    <attribute csv-column="icd-o_katalog_morphologie_version" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '59847-4').value.coding.version.value" />
-    <attribute csv-column="morphologie" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '59847-4').value.coding.code.value"/>
-    <attribute csv-column="morphologie-freitext" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '59847-4').value.text.value"/>
-    <attribute csv-column="grading" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '59542-1').value.coding.code.value" join-fhir-path="Observation.where(code.coding.code = '59847-4').hasMember.reference.value"/>
-  </container>
-
-
-  <container csv-filename="Metastasis-${TIMESTAMP}.csv" opal-table="metastasis" opal-entity-type="Metastasis" >
-    <attribute csv-column="metastasis-id" primary-key="true" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21907-1').id" anonym="Met" op="EXTRACT_RELATIVE_ID"/>
-    <attribute csv-column="diagnosis-id" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21907-1').focus.reference.value" anonym="Dia"/>
-    <attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21907-1').subject.reference.value" anonym="Pat" />
-    <attribute csv-column="datum_fernmetastasen" opal-value-type="date" val-fhir-path="Observation.where(code.coding.code = '21907-1').effective.value"/>
-    <attribute csv-column="fernmetastasen_vorhanden" opal-value-type="boolean" val-fhir-path="Observation.where(code.coding.code = '21907-1').value.coding.code.value"/>
-    <attribute csv-column="lokalisation_fernmetastasen" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21907-1').bodySite.coding.code.value"/>
-  </container>
-
-  <container csv-filename="TNM-${TIMESTAMP}.csv" opal-table="tnm" opal-entity-type="TNM">
-    <attribute csv-column="tnm-id" primary-key="true" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').id" anonym="TNM" op="EXTRACT_RELATIVE_ID"/>
-    <attribute csv-column="diagnosis-id" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').focus.reference.value" anonym="Dia"/>
-    <attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').subject.reference.value" anonym="Pat" />
-    <attribute csv-column="datum_der_tnm_dokumentation_datum_befund" opal-value-type="date" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').effective.value"/>
-    <attribute csv-column="uicc_stadium" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').value.coding.code.value"/>
-    <attribute csv-column="tnm-t" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').component.where(code.coding.code = '21905-5' or code.coding.code = '21899-0').value.coding.code.value"/>
-    <attribute csv-column="tnm-n" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').component.where(code.coding.code = '21906-3' or code.coding.code = '21900-6').value.coding.code.value"/>
-    <attribute csv-column="tnm-m" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').component.where(code.coding.code = '21907-1' or code.coding.code = '21901-4').value.coding.code.value"/>
-    <attribute csv-column="c_p_u_preefix_t" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').component.where(code.coding.code = '21905-5' or code.coding.code = '21899-0').extension('http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Extension-TNMcpuPraefix').value.coding.code.value"/>
-    <attribute csv-column="c_p_u_preefix_n" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').component.where(code.coding.code = '21906-3' or code.coding.code = '21900-6').extension('http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Extension-TNMcpuPraefix').value.coding.code.value"/>
-    <attribute csv-column="c_p_u_preefix_m" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').component.where(code.coding.code = '21907-1' or code.coding.code = '21901-4').extension('http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Extension-TNMcpuPraefix').value.coding.code.value"/>
-    <attribute csv-column="tnm-y-symbol" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').component.where(code.coding.code = '59479-6' or code.coding.code = '59479-6').value.coding.code.value"/>
-    <attribute csv-column="tnm-r-symbol" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').component.where(code.coding.code = '21983-2' or code.coding.code = '21983-2').value.coding.code.value"/>
-    <attribute csv-column="tnm-m-symbol" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').component.where(code.coding.code = '42030-7' or code.coding.code = '42030-7').value.coding.code.value"/>
-    <!--nur bei UICC, nicht in ADT2FHIR--><attribute csv-column="tnm-version" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').value.coding.version.value"/>
-  </container>
-
-
-  <container csv-filename="System-Therapy-${TIMESTAMP}.csv" opal-table="system-therapy" opal-entity-type="SystemTherapy">
-    <attribute csv-column="system-therapy-id" primary-key="true" opal-value-type="text" val-fhir-path="MedicationStatement.id" anonym="Sys" op="EXTRACT_RELATIVE_ID"/>
-    <attribute csv-column="diagnosis-id" opal-value-type="text" val-fhir-path="MedicationStatement.reasonReference.reference.value" anonym="Dia"/>
-    <attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="MedicationStatement.subject.reference.value" anonym="Pat" />
-    <attribute csv-column="systemische_therapie_stellung_zu_operativer_therapie" opal-value-type="text" val-fhir-path="MedicationStatement.extension('http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Extension-StellungZurOp').value.coding.code.value"/>
-    <attribute csv-column="intention_chemotherapie" opal-value-type="text" val-fhir-path="MedicationStatement.extension('http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Extension-SYSTIntention').value.coding.code.value"/>
-    <attribute csv-column="therapieart" opal-value-type="text" val-fhir-path="MedicationStatement.category.coding.code.value"/>
-    <attribute csv-column="systemische_therapie_beginn" opal-value-type="date" val-fhir-path="MedicationStatement.effective.start.value"/>
-    <attribute csv-column="systemische_therapie_ende" opal-value-type="date" val-fhir-path="MedicationStatement.effective.end.value"/>
-    <attribute csv-column="systemische_therapie_protokoll" opal-value-type="text" val-fhir-path="MedicationStatement.extension('http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Extension-SystemischeTherapieProtokoll').value.text.value"/>
-    <attribute csv-column="systemische_therapie_substanzen" opal-value-type="text" val-fhir-path="MedicationStatement.medication.text.value"/>
-    <attribute csv-column="chemotherapie" opal-value-type="boolean" val-fhir-path="MedicationStatement.where(category.coding.code = 'CH').exists().value" />
-    <attribute csv-column="hormontherapie" opal-value-type="boolean" val-fhir-path="MedicationStatement.where(category.coding.code = 'HO').exists().value" />
-    <attribute csv-column="immuntherapie" opal-value-type="boolean" val-fhir-path="MedicationStatement.where(category.coding.code = 'IM').exists().value" />
-    <attribute csv-column="knochenmarktransplantation" opal-value-type="boolean" val-fhir-path="MedicationStatement.where(category.coding.code = 'KM').exists().value" />
-    <attribute csv-column="abwartende_strategie" opal-value-type="boolean" val-fhir-path="MedicationStatement.where(category.coding.code = 'WS').exists().value" />
-  </container>
-
-
-  <container csv-filename="Surgery-${TIMESTAMP}.csv" opal-table="surgery" opal-entity-type="Surgery">
-    <attribute csv-column="surgery-id" primary-key="true" opal-value-type="text" val-fhir-path="Procedure.where(category.coding.code = 'OP').id" anonym="Sur" op="EXTRACT_RELATIVE_ID"/>
-    <attribute csv-column="diagnosis-id" opal-value-type="text" val-fhir-path="Procedure.where(category.coding.code = 'OP').reasonReference.reference.value" anonym="Dia"/>
-    <attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="Procedure.where(category.coding.code = 'OP').subject.reference.value" anonym="Pat" />
-    <attribute csv-column="ops-code" opal-value-type="text" val-fhir-path="Procedure.where(category.coding.code = 'OP').code.coding.code.value"/>
-    <attribute csv-column="datum_der_op" opal-value-type="date" val-fhir-path="Procedure.where(category.coding.code = 'OP').performed.value"/>
-    <attribute csv-column="intention_op" opal-value-type="text" val-fhir-path="Procedure.extension('http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Extension-OPIntention').value.coding.code.value"/>
-    <attribute csv-column="lokale_beurteilung_resttumor" opal-value-type="text" val-fhir-path="Procedure.where(category.coding.code = 'OP').outcome.coding.where(system = 'http://dktk.dkfz.de/fhir/onco/core/CodeSystem/LokaleBeurteilungResidualstatusCS').code.value" />
-    <attribute csv-column="gesamtbeurteilung_resttumor" opal-value-type="text" val-fhir-path="Procedure.where(category.coding.code = 'OP').outcome.coding.where(system = 'http://dktk.dkfz.de/fhir/onco/core/CodeSystem/GesamtbeurteilungResidualstatusCS').code.value"  />
-  </container>
-
-
-  <container csv-filename="Radiation-Therapy-${TIMESTAMP}.csv" opal-table="radiation-therapy" opal-entity-type="RadiationTherapy">
-    <attribute csv-column="radiation-therapy-id" primary-key="true" opal-value-type="text" val-fhir-path="Procedure.where(category.coding.code = 'ST').id" anonym="Rad" op="EXTRACT_RELATIVE_ID"/>
-    <attribute csv-column="diagnosis-id" opal-value-type="text" val-fhir-path="Procedure.where(category.coding.code = 'ST').reasonReference.reference.value" anonym="Dia"/>
-    <attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="Procedure.where(category.coding.code = 'ST').subject.reference.value" anonym="Pat" />
-    <attribute csv-column="strahlentherapie_stellung_zu_operativer_therapie" opal-value-type="text" val-fhir-path="Procedure.extension('http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Extension-StellungZurOp').value.coding.code.value"/>
-    <attribute csv-column="intention_strahlentherapie" opal-value-type="text" val-fhir-path="Procedure.extension('http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Extension-SYSTIntention').value.coding.code.value" />
-    <attribute csv-column="strahlentherapie_beginn" opal-value-type="date" val-fhir-path="Procedure.where(category.coding.code = 'ST').performed.start.value"/>
-    <attribute csv-column="strahlentherapie_ende" opal-value-type="date" val-fhir-path="Procedure.where(category.coding.code = 'ST').performed.end.value"/>
-  </container>
-
-
-  <container csv-filename="Molecular-Marker-${TIMESTAMP}.csv" opal-table="molecular-marker" opal-entity-type="MolecularMarker">
-    <attribute csv-column="mol-marker-id" primary-key="true" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '69548-6').id" anonym="Mol" op="EXTRACT_RELATIVE_ID"/>
-    <attribute csv-column="diagnosis-id" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '69548-6').focus.reference.value" anonym="Dia" />
-    <attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '69548-6').subject.reference.value" anonym="Pat" />
-    <attribute csv-column="datum_der_datenerhebung" opal-value-type="date" val-fhir-path="Observation.where(code.coding.code = '69548-6').effective.value"/>
-    <attribute csv-column="marker" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '69548-6').component.value.coding.code.value"/>
-    <attribute csv-column="status_des_molekularen_markers" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '69548-6').value.coding.code.value" />
-    <attribute csv-column="zusaetzliche_alternative_dokumentation" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '69548-6').value.text.value"/>
-  </container>
-
-
-  <container csv-filename="Sample-${TIMESTAMP}.csv" opal-table="sample" opal-entity-type="Sample">
-    <attribute csv-column="sample-id" primary-key="true" opal-value-type="text" val-fhir-path="Specimen.id" anonym="Sam" op="EXTRACT_RELATIVE_ID"/>
-    <attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="Specimen.subject.reference.value" anonym="Pat" />
-    <attribute csv-column="entnahmedatum" opal-value-type="date" val-fhir-path="Specimen.collection.collectedDateTime.value"/>
-    <attribute csv-column="probenart" opal-value-type="text" val-fhir-path="Specimen.type.coding.code.value"/>
-    <attribute csv-column="status" opal-value-type="text" val-fhir-path="Specimen.status.code.value"/>
-    <attribute csv-column="projekt" opal-value-type="text" val-fhir-path="Specimen.identifier.system.value"/>
-   <!-- @TODO: it is still necessary to clarify whether it would not be better to take the quantity of collection.quantity -->
-    <attribute csv-column="menge" opal-value-type="integer" val-fhir-path="Specimen.container.specimenQuantity.value.value"/>
-    <attribute csv-column="einheit" opal-value-type="text" val-fhir-path="Specimen.container.specimenQuantity.unit.value"/>
-    <attribute csv-column="aliquot" opal-value-type="text" val-fhir-path="Specimen.parent.reference.exists().value" />
-  </container>
-
-
-
-
-  <fhir-rev-include>Observation:patient</fhir-rev-include>
-  <fhir-rev-include>Condition:patient</fhir-rev-include>
-  <fhir-rev-include>ClinicalImpression:patient</fhir-rev-include>
-  <fhir-rev-include>MedicationStatement:patient</fhir-rev-include>
-  <fhir-rev-include>Procedure:patient</fhir-rev-include>
-  <fhir-rev-include>Specimen:patient</fhir-rev-include>
-
-</template>

ccp/modules/datashield-setup.sh

@@ -1,44 +0,0 @@
-#!/bin/bash -e
-
-if [ "$ENABLE_DATASHIELD" == true ]; then
-  # HACK: This only works because exporter-setup.sh and teiler-setup.sh are sourced after datashield-setup.sh
-  if [ -z "${ENABLE_EXPORTER}" ] || [ "${ENABLE_EXPORTER}" != "true" ]; then
-    log WARN "The ENABLE_EXPORTER variable is either not set or not set to 'true'."
-  fi
-  OAUTH2_CALLBACK=/oauth2/callback
-  OAUTH2_PROXY_SECRET="$(echo \"This is a salt string to generate one consistent encryption key for the oauth2_proxy. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 32)"
-  add_private_oidc_redirect_url "${OAUTH2_CALLBACK}"
-
-  log INFO "DataSHIELD setup detected -- will start DataSHIELD services."
-  OVERRIDE+=" -f ./$PROJECT/modules/datashield-compose.yml"
-  EXPORTER_OPAL_PASSWORD="$(generate_password \"exporter in Opal\")"
-  TOKEN_MANAGER_OPAL_PASSWORD="$(generate_password \"Token Manager in Opal\")"
-  OPAL_DB_PASSWORD="$(echo \"Opal DB\" | generate_simple_password)"
-  OPAL_ADMIN_PASSWORD="$(generate_password \"admin password for Opal\")"
-  RSTUDIO_ADMIN_PASSWORD="$(generate_password \"admin password for R-Studio\")"
-  DATASHIELD_CONNECT_SECRET="$(echo \"DataShield Connect\" | generate_simple_password)"
-  TOKEN_MANAGER_SECRET="$(echo \"Token Manager\" | generate_simple_password)"
-  if [ ! -e /tmp/bridgehead/opal-cert.pem ]; then
-    mkdir -p /tmp/bridgehead/
-    openssl req -x509 -newkey rsa:4096 -nodes -keyout /tmp/bridgehead/opal-key.pem -out /tmp/bridgehead/opal-cert.pem -days 3650 -subj "/CN=opal/C=DE"
-  fi
-  mkdir -p /tmp/bridgehead/opal-map
-  sites="$(cat ./$PROJECT/modules/datashield-sites.json)"
-  echo "$sites" | docker_jq -n --args '{"sites": input | map({
-    "name": .,
-    "id": .,
-    "virtualhost": "\(.):443",
-    "beamconnect": "datashield-connect.\(.).'"$BROKER_ID"'"
-  })}' $sites >/tmp/bridgehead/opal-map/central.json
-  echo "$sites" | docker_jq -n --args '[{
-    "external": "'"$SITE_ID"':443",
-    "internal": "opal:8443",
-    "allowed": input | map("\(.).'"$BROKER_ID"'")
-  }]' >/tmp/bridgehead/opal-map/local.json
-  if [ "$USER" == "root" ]; then
-    chown -R bridgehead:docker /tmp/bridgehead
-    chmod g+wr /tmp/bridgehead/opal-map/*
-    chmod g+r /tmp/bridgehead/opal-key.pem
-  fi
-  add_private_oidc_redirect_url "/opal/*"
-fi

ccp/modules/datashield-sites.json

@@ -1,15 +0,0 @@
-[
-    "berlin",
-    "muenchen-lmu",
-    "dresden",
-    "freiburg",
-    "muenchen-tum",
-    "tuebingen",
-    "mainz",
-    "frankfurt",
-    "essen",
-    "dktk-datashield-test",
-    "dktk-test",
-    "mannheim",
-    "central-ds-orchestrator"
-]

ccp/modules/datashield.md

@@ -1,28 +0,0 @@
-# DataSHIELD
-This module constitutes the infrastructure to run DataSHIELD within the bridgehead. 
-For more information about DataSHIELD, please visit https://www.datashield.org/
-
-## R-Studio
-To connect to the different bridgeheads of the CCP through DataSHIELD, you can use your own R-Studio environment.
-However, this R-Studio has already installed the DataSHIELD libraries and is integrated within the bridgehead.
-This can save you some time for extra configuration of your R-Studio environment.
-
-## Opal
-This is the core of DataSHIELD. It is made up of Opal, a Postgres database and an R-server.
-For more information about Opal, please visit https://opaldoc.obiba.org
-
-### Opal
-Opal is OBiBa’s core database application for biobanks. 
-
-### Opal-DB
-Opal requires a database to import the data for DataSHIELD. We use a Postgres instance as database. 
-The data is imported within the bridgehead through the exporter.
-
-### Opal-R-Server
-R-Server to execute R scripts in DataSHIELD.
-
-## Beam
-### Beam-Connect
-Beam-Connect is used to route http(s) traffic through beam to enable R-Studio to access data from other bridgeheads that have datashield enabled.
-### Beam-Proxy
-The usual beam proxy used for communication.

ccp/modules/dnpm-compose.yml

@@ -6,7 +6,7 @@ services:
       APP_dnpm-connect_KEY: ${DNPM_BEAM_SECRET_SHORT}
   dnpm-beam-connect:
     depends_on: [ beam-proxy ]
-    image: docker.verbis.dkfz.de/cache/samply/beam-connect:develop
+    image: docker.verbis.dkfz.de/cache/samply/beam-connect:dnpm
     container_name: bridgehead-dnpm-beam-connect
     environment:
       PROXY_URL: http://beam-proxy:8081
@@ -16,14 +16,9 @@ services:
       LOCAL_TARGETS_FILE: "./conf/connect_targets.json"
       HTTP_PROXY: "http://forward_proxy:3128"
       HTTPS_PROXY: "http://forward_proxy:3128"
-      NO_PROXY: beam-proxy,dnpm-backend,host.docker.internal${DNPM_ADDITIONAL_NO_PROXY}
+      NO_PROXY: beam-proxy,dnpm-backend
-      RUST_LOG: ${LOG_LEVEL_BEAMCONNECTDNPM:-WARN}
+      RUST_LOG: ${RUST_LOG:-info}
-      NO_AUTH: "true"
-      TLS_CA_CERTIFICATES_DIR: ./conf/trusted-ca-certs
-    extra_hosts:
-      - "host.docker.internal:host-gateway"
     volumes:
-      - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
       - /etc/bridgehead/dnpm/local_targets.json:/conf/connect_targets.json:ro
       - /etc/bridgehead/dnpm/central_targets.json:/conf/central_targets.json:ro
     labels:
@@ -33,7 +28,3 @@ services:
       - "traefik.http.routers.dnpm-connect.middlewares=dnpm-connect-strip"
       - "traefik.http.services.dnpm-connect.loadbalancer.server.port=8062"
       - "traefik.http.routers.dnpm-connect.tls=true"
-
-  dnpm-echo:
-    image: docker.verbis.dkfz.de/cache/samply/bridgehead-echo:latest
-    container_name: bridgehead-dnpm-echo

ccp/modules/dnpm-node-compose.yml

@@ -1,34 +0,0 @@
-version: "3.7"
-
-services:
-  dnpm-backend:
-    image: ghcr.io/kohlbacherlab/bwhc-backend:1.0-snapshot-broker-connector
-    container_name: bridgehead-dnpm-backend
-    environment:
-      - ZPM_SITE=${ZPM_SITE}
-      - N_RANDOM_FILES=${DNPM_SYNTH_NUM}
-    volumes:
-      - /etc/bridgehead/dnpm:/bwhc_config:ro
-      - ${DNPM_DATA_DIR}:/bwhc_data
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.bwhc-backend.rule=PathPrefix(`/bwhc`)"
-      - "traefik.http.services.bwhc-backend.loadbalancer.server.port=9000"
-      - "traefik.http.routers.bwhc-backend.tls=true"
-
-  dnpm-frontend:
-    image: ghcr.io/kohlbacherlab/bwhc-frontend:2209
-    container_name: bridgehead-dnpm-frontend
-    links:
-      - dnpm-backend
-    environment:
-      - NUXT_HOST=0.0.0.0
-      - NUXT_PORT=8080
-      - BACKEND_PROTOCOL=https
-      - BACKEND_HOSTNAME=$HOST
-      - BACKEND_PORT=443
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.bwhc-frontend.rule=PathPrefix(`/`)"
-      - "traefik.http.services.bwhc-frontend.loadbalancer.server.port=8080"
-      - "traefik.http.routers.bwhc-frontend.tls=true"

ccp/modules/dnpm-node-setup.sh

@@ -1,28 +0,0 @@
-#!/bin/bash
-
-if [ -n "${ENABLE_DNPM_NODE}" ]; then
-	log INFO "DNPM setup detected (BwHC Node) -- will start BwHC node."
-	OVERRIDE+=" -f ./$PROJECT/modules/dnpm-node-compose.yml"
-
-	# Set variables required for BwHC Node. ZPM_SITE is assumed to be set in /etc/bridgehead/<project>.conf
-	DNPM_APPLICATION_SECRET="$(echo \"This is a salt string to generate one consistent password for DNPM. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
-	if [ -z "${ZPM_SITE+x}" ]; then
-		log ERROR "Mandatory variable ZPM_SITE not defined!"
-		exit 1
-	fi
-	if [ -z "${DNPM_DATA_DIR+x}" ]; then
-		log ERROR "Mandatory variable DNPM_DATA_DIR not defined!"
-		exit 1
-	fi
-	DNPM_SYNTH_NUM=${DNPM_SYNTH_NUM:-0}
-	if grep -q 'traefik.http.routers.landing.rule=PathPrefix(`/landing`)' /srv/docker/bridgehead/minimal/docker-compose.override.yml 2>/dev/null; then
-		echo "Override of landing page url already in place"
-	else
-		echo "Adding override of landing page url"
-		if [ -f /srv/docker/bridgehead/minimal/docker-compose.override.yml ]; then
-			echo -e '  landing:\n    labels:\n      - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"' >> /srv/docker/bridgehead/minimal/docker-compose.override.yml
-		else
-			echo -e 'version: "3.7"\nservices:\n  landing:\n    labels:\n      - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"' >> /srv/docker/bridgehead/minimal/docker-compose.override.yml
-		fi
-	fi
-fi

ccp/modules/dnpm-setup.sh

@@ -1,15 +1,10 @@
-#!/bin/bash -e
+#!/bin/bash
 
 if [ -n "${ENABLE_DNPM}" ]; then
 	log INFO "DNPM setup detected (Beam.Connect) -- will start Beam.Connect for DNPM."
 	OVERRIDE+=" -f ./$PROJECT/modules/dnpm-compose.yml"
 
 	# Set variables required for Beam-Connect
+	DNPM_APPLICATION_SECRET="$(echo \"This is a salt string to generate one consistent password for DNPM. It is not required to be secret.\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
 	DNPM_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
-	# If the DNPM_NO_PROXY variable is set, prefix it with a comma (as it gets added to a comma separated list)
-	if [ -n "${DNPM_NO_PROXY}" ]; then
-		DNPM_ADDITIONAL_NO_PROXY=",${DNPM_NO_PROXY}"
-	else
-		DNPM_ADDITIONAL_NO_PROXY=""
-	fi
 fi

ccp/modules/export-and-qb.curl-templates

@@ -1,6 +0,0 @@
-# Full Excel Export
-curl --location --request POST 'https://${HOST}/ccp-exporter/request?query=Patient&query-format=FHIR_PATH&template-id=ccp&output-format=EXCEL' \
---header 'x-api-key: ${EXPORT_API_KEY}'
-
-# QB
-curl --location --request POST 'https://${HOST}/ccp-reporter/generate?template-id=ccp'

ccp/modules/exporter-compose.yml

@@ -1,72 +0,0 @@
-version: "3.7"
-
-services:
-  exporter:
-    image: docker.verbis.dkfz.de/ccp/dktk-exporter:latest
-    container_name: bridgehead-ccp-exporter
-    environment:
-      JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
-      EXPORTER_API_KEY: "${EXPORTER_API_KEY}" # Set in exporter-setup.sh
-      CROSS_ORIGINS: "https://${HOST}"
-      EXPORTER_DB_USER: "exporter"
-      EXPORTER_DB_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
-      EXPORTER_DB_URL: "jdbc:postgresql://exporter-db:5432/exporter"
-      HTTP_RELATIVE_PATH: "/ccp-exporter"
-      SITE: "${SITE_ID}"
-      HTTP_SERVLET_REQUEST_SCHEME: "https"
-      OPAL_PASSWORD: "${EXPORTER_OPAL_PASSWORD}"
-      LOG_LEVEL: ${LOG_LEVEL_EXPORTER:-WARN}
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.exporter_ccp.rule=PathPrefix(`/ccp-exporter`)"
-      - "traefik.http.services.exporter_ccp.loadbalancer.server.port=8092"
-      - "traefik.http.routers.exporter_ccp.tls=true"
-      - "traefik.http.middlewares.exporter_ccp_strip.stripprefix.prefixes=/ccp-exporter"
-      - "traefik.http.routers.exporter_ccp.middlewares=exporter_ccp_strip"
-    volumes:
-      - "/var/cache/bridgehead/ccp/exporter-files:/app/exporter-files/output"
-
-  exporter-db:
-    image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
-    container_name: bridgehead-ccp-exporter-db
-    environment:
-      POSTGRES_USER: "exporter"
-      POSTGRES_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
-      POSTGRES_DB: "exporter"
-    volumes:
-      # Consider removing this volume once we find a solution to save Lens-queries to be executed in the explorer.
-      - "/var/cache/bridgehead/ccp/exporter-db:/var/lib/postgresql/data"
-
-  reporter:
-    image: docker.verbis.dkfz.de/ccp/dktk-reporter:latest
-    container_name: bridgehead-ccp-reporter
-    environment:
-      JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
-      CROSS_ORIGINS: "https://${HOST}"
-      HTTP_RELATIVE_PATH: "/ccp-reporter"
-      SITE: "${SITE_ID}"
-      EXPORTER_API_KEY: "${EXPORTER_API_KEY}" # Set in exporter-setup.sh
-      EXPORTER_URL: "http://exporter:8092"
-      LOG_FHIR_VALIDATION: "false"
-      HTTP_SERVLET_REQUEST_SCHEME: "https"
-      LOG_LEVEL: ${LOG_LEVEL_REPORTER:-WARN}
-
-    # In this initial development state of the bridgehead, we are trying to have so many volumes as possible.
-    # However, in the first executions in the CCP sites, this volume seems to be very important. A report is
-    # a process that can take several hours, because it depends on the exporter.
-    # There is a risk that the bridgehead restarts, losing the already created export.
-
-    volumes:
-      - "/var/cache/bridgehead/ccp/reporter-files:/app/reports"
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.reporter_ccp.rule=PathPrefix(`/ccp-reporter`)"
-      - "traefik.http.services.reporter_ccp.loadbalancer.server.port=8095"
-      - "traefik.http.routers.reporter_ccp.tls=true"
-      - "traefik.http.middlewares.reporter_ccp_strip.stripprefix.prefixes=/ccp-reporter"
-      - "traefik.http.routers.reporter_ccp.middlewares=reporter_ccp_strip"
-
-  focus:
-    environment:
-      EXPORTER_URL: "http://exporter:8092"
-      AUTH_HEADER: "${EXPORTER_API_KEY}"

ccp/modules/exporter-setup.sh

@@ -1,8 +0,0 @@
-#!/bin/bash -e
-
-if [ "$ENABLE_EXPORTER" == true ]; then
-  log INFO "Exporter setup detected -- will start Exporter service."
-  OVERRIDE+=" -f ./$PROJECT/modules/exporter-compose.yml"
-  EXPORTER_DB_PASSWORD="$(echo \"This is a salt string to generate one consistent password for the exporter. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
-  EXPORTER_API_KEY="$(echo \"This is a salt string to generate one consistent API KEY for the exporter. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 64)"
-fi

ccp/modules/exporter.md

@@ -1,15 +0,0 @@
-# Exporter and Reporter
-
-
-## Exporter
-The exporter is a REST API that exports the data of the different databases of the bridgehead in a set of tables.
-It can accept different output formats as CSV, Excel, JSON or XML. It can also export data into Opal.
-
-## Exporter-DB
-It is a database to save queries for its execution in the exporter. 
-The exporter manages also the different executions of the same query in through the database.
-
-## Reporter
-This component is a plugin of the exporter that allows to create more complex Excel reports described in templates.
-It is compatible with different template engines as Groovy, Thymeleaf,...
-It is perfect to generate a document as our traditional CCP quality report.

ccp/modules/fhir2sql-compose.yml

@@ -1,29 +0,0 @@
-version: "3.7"
-
-services:
-  fhir2sql:
-    depends_on:
-      - "dashboard-db"
-      - "blaze"
-    image: docker.verbis.dkfz.de/cache/samply/fhir2sql:latest
-    container_name: bridgehead-ccp-dashboard-fhir2sql
-    environment:
-      BLAZE_BASE_URL: "http://bridgehead-ccp-blaze:8080"
-      PG_HOST: "dashboard-db"
-      PG_USERNAME: "dashboard"
-      PG_PASSWORD: "${DASHBOARD_DB_PASSWORD}" # Set in dashboard-setup.sh
-      PG_DBNAME: "dashboard"
-
-  dashboard-db:
-    image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
-    container_name: bridgehead-ccp-dashboard-db
-    environment:
-      POSTGRES_USER: "dashboard"
-      POSTGRES_PASSWORD: "${DASHBOARD_DB_PASSWORD}" # Set in dashboard-setup.sh
-      POSTGRES_DB: "dashboard"
-    volumes:
-      - "/var/cache/bridgehead/ccp/dashboard-db:/var/lib/postgresql/data"
-
-  focus:
-    environment:
-      POSTGRES_CONNECTION_STRING: "postgresql://dashboard:${DASHBOARD_DB_PASSWORD}@dashboard-db/dashboard"

ccp/modules/fhir2sql-setup.sh

@@ -1,8 +0,0 @@
-#!/bin/bash -e
-
-if [ "$ENABLE_FHIR2SQL" == true ]; then
-  log INFO "Dashboard setup detected -- will start Dashboard backend and FHIR2SQL service."
-  OVERRIDE+=" -f ./$PROJECT/modules/fhir2sql-compose.yml"
-  DASHBOARD_DB_PASSWORD="$(generate_simple_password 'fhir2sql')"
-  FOCUS_ENDPOINT_TYPE="blaze-and-sql"
-fi

ccp/modules/fhir2sql.md

@@ -1,36 +0,0 @@
-# fhir2sql
-fhir2sql connects to Blaze, retrieves data, and syncs it with a PostgreSQL database. The application is designed to run continuously, syncing data at regular intervals.
-The Dashboard module is a optional component of the Bridgehead CCP setup. When enabled, it starts two Docker services: **fhir2sql** and **dashboard-db**. Data held in PostgreSQL is only stored temporarily and Blaze is considered to be the 'leading system' or 'source of truth'.
-
-## Services
-### fhir2sql
-* Image: docker.verbis.dkfz.de/cache/samply/fhir2sql:latest
-* Container name: bridgehead-ccp-dashboard-fhir2sql
-* Depends on: dashboard-db
-* Environment variables:
-  - BLAZE_BASE_URL: The base URL of the Blaze FHIR server (set to http://blaze:8080/fhir/)
-  - PG_HOST: The hostname of the PostgreSQL database (set to dashboard-db)
-  - PG_USERNAME: The username for the PostgreSQL database (set to dashboard)
-  - PG_PASSWORD: The password for the PostgreSQL database (set to the value of DASHBOARD_DB_PASSWORD)
-  - PG_DBNAME: The name of the PostgreSQL database (set to dashboard)
-
-### dashboard-db
-
-* Image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
-* Container name: bridgehead-ccp-dashboard-db
-* Environment variables:
-  - POSTGRES_USER: The username for the PostgreSQL database (set to dashboard)
-  - POSTGRES_PASSWORD: The password for the PostgreSQL database (set to the value of DASHBOARD_DB_PASSWORD)
-  - POSTGRES_DB: The name of the PostgreSQL database (set to dashboard)
-* Volumes:
-  - /var/cache/bridgehead/ccp/dashboard-db:/var/lib/postgresql/data
-
-The volume used by dashboard-db can be removed safely and should be restored to a working order by re-importing data from Blaze.
-
-### Environment Variables
-* DASHBOARD_DB_PASSWORD: A generated password for the PostgreSQL database, created using a salt string and the SHA1 hash function.
-* POSTGRES_TAG: The tag of the PostgreSQL image to use (not set in this module, but required by the dashboard-db service).
-
-
-### Setup
-To enable the Dashboard module, set the ENABLE_FHIR2SQL environment variable to true. The dashboard-setup.sh script will then start the fhir2sql and dashboard-db services, using the environment variables and volumes defined above.

ccp/modules/id-management-compose.yml

@@ -1,5 +1,4 @@
 version: "3.7"
-
 services:
   id-manager:
     image: docker.verbis.dkfz.de/bridgehead/magicpl
@@ -14,39 +13,27 @@ services:
       MAGICPL_CONNECTOR_APIKEY: ${IDMANAGER_READ_APIKEY}
       MAGICPL_CENTRAL_PATIENTLIST_APIKEY: ${IDMANAGER_CENTRAL_PATIENTLIST_APIKEY}
       MAGICPL_CONTROLNUMBERGENERATOR_APIKEY: ${IDMANAGER_CONTROLNUMBERGENERATOR_APIKEY}
-      ML_LOG_LEVEL: ${LOG_LEVEL_IDMANAGER:-WARN}
+      MAGICPL_OIDC_CLIENT_ID: ${IDMANAGER_AUTH_CLIENT_ID}
+      MAGICPL_OIDC_CLIENT_SECRET: ${IDMANAGER_AUTH_CLIENT_SECRET}
     depends_on:
       - patientlist
-      - traefik-forward-auth
     labels:
       - "traefik.enable=true"
-      # Router with Authentication
       - "traefik.http.routers.id-manager.rule=PathPrefix(`/id-manager`)"
+      - "traefik.http.services.id-manager.loadbalancer.server.port=8080"
       - "traefik.http.routers.id-manager.tls=true"
-      - "traefik.http.routers.id-manager.middlewares=traefik-forward-auth-idm"
-      - "traefik.http.routers.id-manager.service=id-manager-service"
-      # Router without Authentication
-      - "traefik.http.routers.id-manager-compatibility.rule=PathPrefix(`/id-manager/paths/translator/getIds`)"
-      - "traefik.http.routers.id-manager-compatibility.tls=true"
-      - "traefik.http.routers.id-manager-compatibility.service=id-manager-service"
-      # Definition of Service
-      - "traefik.http.services.id-manager-service.loadbalancer.server.port=8080"
-      - "traefik.http.services.id-manager-service.loadbalancer.server.scheme=http"
 
   patientlist:
     image: docker.verbis.dkfz.de/bridgehead/mainzelliste
     container_name: bridgehead-patientlist
     environment:
       - TOMCAT_REVERSEPROXY_FQDN=${HOST}
-      - TOMCAT_REVERSEPROXY_SSL=true
       - ML_SITE=${IDMANAGEMENT_FRIENDLY_ID}
       - ML_DB_PASS=${PATIENTLIST_POSTGRES_PASSWORD}
       - ML_API_KEY=${IDMANAGER_LOCAL_PATIENTLIST_APIKEY}
       - ML_UPLOAD_API_KEY=${IDMANAGER_UPLOAD_APIKEY}
       # Add Variables from /etc/patientlist-id-generators.env
       - PATIENTLIST_SEEDS_TRANSFORMED
-      - ML_LOG_LEVEL=${LOG_LEVEL_PATIENTLIST:-WARN}
-      #TODO confirm LOG_LEVEL
     labels:
       - "traefik.enable=true"
       - "traefik.http.routers.patientlist.rule=PathPrefix(`/patientlist`)"
@@ -56,7 +43,7 @@ services:
       - patientlist-db
 
   patientlist-db:
-    image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
+    image: docker.verbis.dkfz.de/cache/postgres:15.1-alpine
     container_name: bridgehead-patientlist-db
     environment:
       POSTGRES_USER: "mainzelliste"
@@ -67,49 +54,5 @@ services:
       # NOTE: Add backups here. This is only imported if /var/lib/bridgehead/data/patientlist/ is empty!!!
       - "/tmp/bridgehead/patientlist/:/docker-entrypoint-initdb.d/"
 
-  traefik-forward-auth:
-    image: docker.verbis.dkfz.de/cache/oauth2-proxy/oauth2-proxy:latest
-    environment:
-      - http_proxy=http://forward_proxy:3128
-      - https_proxy=http://forward_proxy:3128
-      - OAUTH2_PROXY_PROVIDER=oidc
-      - OAUTH2_PROXY_SKIP_PROVIDER_BUTTON=true
-      - OAUTH2_PROXY_OIDC_ISSUER_URL=https://login.verbis.dkfz.de/realms/master
-      - OAUTH2_PROXY_CLIENT_ID=bridgehead-${SITE_ID}
-      - OAUTH2_PROXY_CLIENT_SECRET=${IDMANAGER_AUTH_CLIENT_SECRET}
-      - OAUTH2_PROXY_COOKIE_SECRET=${IDMANAGER_AUTH_COOKIE_SECRET}
-      - OAUTH2_PROXY_COOKIE_NAME=_BRIDGEHEAD_oauth2_idm
-      - OAUTH2_PROXY_COOKIE_DOMAINS=.${HOST}
-      - OAUTH2_PROXY_HTTP_ADDRESS=:4180
-      - OAUTH2_PROXY_REVERSE_PROXY=true
-      - OAUTH2_PROXY_WHITELIST_DOMAINS=.${HOST}
-      - OAUTH2_PROXY_UPSTREAMS=static://202
-      - OAUTH2_PROXY_EMAIL_DOMAINS=*
-      - OAUTH2_PROXY_SCOPE=openid profile email
-      # Pass Authorization Header and some user information to backend services
-      - OAUTH2_PROXY_SET_AUTHORIZATION_HEADER=true
-      - OAUTH2_PROXY_SET_XAUTHREQUEST=true
-      # Keycloak has an expiration time of 60s therefore oauth2-proxy needs to refresh after that
-      - OAUTH2_PROXY_COOKIE_REFRESH=60s
-      - OAUTH2_PROXY_ALLOWED_GROUPS=DKTK-CCP-PPSN
-      - OAUTH2_PROXY_PROXY_PREFIX=/oauth2-idm
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.services.traefik-forward-auth.loadbalancer.server.port=4180"
-      - "traefik.http.routers.traefik-forward-auth.rule=Host(`${HOST}`) && PathPrefix(`/oauth2-idm`)"
-      - "traefik.http.routers.traefik-forward-auth.tls=true"
-      - "traefik.http.middlewares.traefik-forward-auth-idm.forwardauth.address=http://traefik-forward-auth:4180"
-      - "traefik.http.middlewares.traefik-forward-auth-idm.forwardauth.authResponseHeaders=Authorization"
-    depends_on:
-      forward_proxy:
-        condition: service_healthy
-
-  ccp-patient-project-identificator:
-    image: samply/ccp-patient-project-identificator
-    container_name: bridgehead-ccp-patient-project-identificator
-    environment:
-      MAINZELLISTE_APIKEY: ${IDMANAGER_LOCAL_PATIENTLIST_APIKEY}
-      SITE_NAME: ${SITE_NAME}
-
 volumes:
   patientlist-db-data:

ccp/modules/id-management-setup.sh

@@ -1,9 +1,9 @@
-#!/bin/bash -e
+#!/bin/bash
 
 function idManagementSetup() {
 	if [ -n "$IDMANAGER_UPLOAD_APIKEY" ]; then
 		log INFO "id-management setup detected -- will start id-management (mainzelliste & magicpl)."
-		OVERRIDE+=" -f ./ccp/modules/id-management-compose.yml"
+		OVERRIDE+=" -f ./$PROJECT/modules/id-management-compose.yml"
 
 		# Auto Generate local Passwords
 		PATIENTLIST_POSTGRES_PASSWORD="$(echo \"id-management-module-db-password-salt\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
@@ -39,7 +39,6 @@ function applySpecialCases() {
 	result="$1";
 	result="${result/Lmu/LMU}";
 	result="${result/Tum/TUM}";
-	result="${result/Dktk Test/Teststandort}";
 	echo "$result";
 }
 

ccp/modules/mtba-compose.yml

@@ -11,31 +11,22 @@ services:
       ID_MANAGER_API_KEY: ${IDMANAGER_UPLOAD_APIKEY}
       ID_MANAGER_PSEUDONYM_ID_TYPE: BK_${IDMANAGEMENT_FRIENDLY_ID}_L-ID
       ID_MANAGER_URL: http://id-manager:8080/id-manager
-      PATIENT_CSV_FIRST_NAME_HEADER: ${MTBA_PATIENT_CSV_FIRST_NAME_HEADER:-FIRST_NAME}
+      PATIENT_CSV_FIRST_NAME_HEADER: ${MTBA_PATIENT_CSV_FIRST_NAME_HEADER}
-      PATIENT_CSV_LAST_NAME_HEADER: ${MTBA_PATIENT_CSV_LAST_NAME_HEADER:-LAST_NAME}
+      PATIENT_CSV_LAST_NAME_HEADER: ${MTBA_PATIENT_CSV_LAST_NAME_HEADER}
-      PATIENT_CSV_GENDER_HEADER: ${MTBA_PATIENT_CSV_GENDER_HEADER:-GENDER}
+      PATIENT_CSV_GENDER_HEADER: ${MTBA_PATIENT_CSV_GENDER_HEADER}
-      PATIENT_CSV_BIRTHDAY_HEADER: ${MTBA_PATIENT_CSV_BIRTHDAY_HEADER:-BIRTHDAY}
+      PATIENT_CSV_BIRTHDAY_HEADER: ${MTBA_PATIENT_CSV_BIRTHDAY_HEADER}
       CBIOPORTAL_URL:  http://cbioportal:8080
-      FILE_CHARSET: ${MTBA_FILE_CHARSET:-UTF-8}
+      FILE_CHARSET: ${MTBA_FILE_CHARSET}
-      FILE_END_OF_LINE: ${MTBA_FILE_END_OF_LINE:-LF}
+      FILE_END_OF_LINE: ${MTBA_FILE_END_OF_LINE}
-      CSV_DELIMITER: ${MTBA_CSV_DELIMITER:-TAB}
+      CSV_DELIMITER: ${MTBA_CSV_DELIMITER}
-      HTTP_RELATIVE_PATH: "/mtba"
-      OIDC_ADMIN_GROUP: "${OIDC_ADMIN_GROUP}"
-      OIDC_CLIENT_ID: "${OIDC_PRIVATE_CLIENT_ID}"
-      OIDC_CLIENT_SECRET: "${OIDC_CLIENT_SECRET}"
-      OIDC_REALM: "${OIDC_REALM}"
-      OIDC_URL: "${OIDC_URL}"
-      LOG_LEVEL: ${LOG_LEVEL_MTBA:-WARN}
-
     labels:
       - "traefik.enable=true"
-      - "traefik.http.routers.mtba_ccp.rule=PathPrefix(`/mtba`)"
+      - "traefik.http.routers.mtba.rule=PathPrefix(`/`)"
-      - "traefik.http.services.mtba_ccp.loadbalancer.server.port=8480"
+      - "traefik.http.services.mtba.loadbalancer.server.port=80"
-      - "traefik.http.routers.mtba_ccp.tls=true"
+      - "traefik.http.routers.mtba.tls=true"
-
     volumes:
-      - /var/cache/bridgehead/ccp/mtba/input:/app/input
+      - /tmp/bridgehead/mtba/input:/app/input
-      - /var/cache/bridgehead/ccp/mtba/persist:/app/persist
+      - /tmp/bridgehead/mtba/persist:/app/persist
 
   # TODO: Include CBioPortal in Deployment ...
   # NOTE: CBioPortal can't load data while the system is running. So after import of data bridgehead needs to be restarted!

ccp/modules/mtba-setup.sh

@@ -1,12 +1,13 @@
-#!/bin/bash -e
+#!/bin/bash
 
 function mtbaSetup() {
-  if [ -n "$ENABLE_MTBA" ];then
+       # TODO: Check if ID-Management Module is activated!
-    log INFO "MTBA setup detected -- will start MTBA Service and CBioPortal."
+       if [ -n "$ENABLE_MTBA" ];then
-    if [ ! -n "$IDMANAGER_UPLOAD_APIKEY" ]; then
+               log INFO "MTBA setup detected -- will start MTBA Service and CBioPortal."
-      log ERROR "Missing ID-Management Module! Fix this by setting up ID Management:"
+              if [ ! -n "$IDMANAGER_UPLOAD_APIKEY" ]; then
-    fi
+                      log ERROR "Detected MTBA Module configuration but ID-Management Module seems not to be configured!"
-    OVERRIDE+=" -f ./$PROJECT/modules/mtba-compose.yml"
+                      exit 1;
-    add_private_oidc_redirect_url "/mtba/*"
+              fi
-  fi
+               OVERRIDE+=" -f ./$PROJECT/modules/mtba-compose.yml"
-}
+       fi
+}

ccp/modules/mtba.md

@@ -1,6 +0,0 @@
-# Molecular Tumor Board Alliance (MTBA)
-
-In this module, the genetic data to import is stored in a directory (/tmp/bridgehead/mtba/input). A process checks
-regularly if there are files in the directory. The files are pseudonomized when the IDAT is provided. The files are
-combined with clinical data of the blaze and imported in cBioPortal. On the other hand, this files are also imported in
-Blaze.

ccp/modules/nngm-compose.yml

@@ -1,5 +1,4 @@
 version: "3.7"
-
 volumes:
   nngm-rest:
 
@@ -12,7 +11,6 @@ services:
       CTS_API_KEY: ${NNGM_CTS_APIKEY}
       CRYPT_KEY: ${NNGM_CRYPTKEY}
       #CTS_MAGICPL_SITE: ${SITE_ID}TODO
-      LOG_LEVEL: ${LOG_LEVEL_NNGM:-WARN}
     restart: always
     labels:
       - "traefik.enable=true"
@@ -23,6 +21,9 @@ services:
       - "traefik.http.routers.connector.middlewares=connector_strip,auth-nngm"
     volumes:
       - nngm-rest:/var/log
+
   traefik:
     labels:
       - "traefik.http.middlewares.auth-nngm.basicauth.users=${NNGM_AUTH}"
+
+

ccp/modules/nngm-setup.sh

@@ -1,6 +1,8 @@
-#!/bin/bash -e
+#!/bin/bash
 
-if [ -n "$NNGM_CTS_APIKEY" ]; then
+function nngmSetup() {
-  log INFO "nNGM setup detected -- will start nNGM Connector."
+	if [ -n "$NNGM_CTS_APIKEY" ]; then
-  OVERRIDE+=" -f ./$PROJECT/modules/nngm-compose.yml"
+		log INFO "nNGM setup detected -- will start nNGM Connector."
-fi
+		OVERRIDE+=" -f ./$PROJECT/modules/nngm-compose.yml"
+	fi
+	}

ccp/modules/obds2fhir-rest-compose.yml

@@ -1,21 +0,0 @@
-version: "3.7"
-
-services:
-  obds2fhir-rest:
-    container_name: bridgehead-obds2fhir-rest
-    image: docker.verbis.dkfz.de/ccp/obds2fhir-rest:main
-    environment:
-      IDTYPE: BK_${IDMANAGEMENT_FRIENDLY_ID}_L-ID
-      MAINZELLISTE_APIKEY: ${IDMANAGER_LOCAL_PATIENTLIST_APIKEY}
-      SALT: ${LOCAL_SALT}
-      KEEP_INTERNAL_ID: ${KEEP_INTERNAL_ID:-false}
-      MAINZELLISTE_URL: ${PATIENTLIST_URL:-http://patientlist:8080/patientlist}
-      LOG_LEVEL: ${LOG_LEVEL_REPORTER:-WARN}
-    restart: always
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.obds2fhir-rest.rule=PathPrefix(`/obds2fhir-rest`) || PathPrefix(`/adt2fhir-rest`)"
-      - "traefik.http.middlewares.obds2fhir-rest_strip.stripprefix.prefixes=/obds2fhir-rest,/adt2fhir-rest"
-      - "traefik.http.services.obds2fhir-rest.loadbalancer.server.port=8080"
-      - "traefik.http.routers.obds2fhir-rest.tls=true"
-      - "traefik.http.routers.obds2fhir-rest.middlewares=obds2fhir-rest_strip,auth"

ccp/modules/obds2fhir-rest-setup.sh

@@ -1,13 +0,0 @@
-#!/bin/bash
-
-function obds2fhirRestSetup() {
-  if [ -n "$ENABLE_OBDS2FHIR_REST" ]; then
-    log INFO "oBDS2FHIR-REST setup detected -- will start obds2fhir-rest module."
-    if [ ! -n "$IDMANAGER_UPLOAD_APIKEY" ]; then
-      log ERROR "Missing ID-Management Module! Fix this by setting up ID Management:"
-      PATIENTLIST_URL=" "
-    fi
-    OVERRIDE+=" -f ./ccp/modules/obds2fhir-rest-compose.yml"
-    LOCAL_SALT="$(echo \"local-random-salt\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
-  fi
-}

ccp/modules/teiler-compose.yml

@@ -1,83 +0,0 @@
-version: "3.7"
-
-services:
-
-  teiler-orchestrator:
-    image: docker.verbis.dkfz.de/cache/samply/teiler-orchestrator:latest
-    container_name: bridgehead-teiler-orchestrator
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.teiler_orchestrator_ccp.rule=PathPrefix(`/ccp-teiler`)"
-      - "traefik.http.services.teiler_orchestrator_ccp.loadbalancer.server.port=9000"
-      - "traefik.http.routers.teiler_orchestrator_ccp.tls=true"
-      - "traefik.http.middlewares.teiler_orchestrator_ccp_strip.stripprefix.prefixes=/ccp-teiler"
-      - "traefik.http.routers.teiler_orchestrator_ccp.middlewares=teiler_orchestrator_ccp_strip"
-    environment:
-      TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend"
-      TEILER_DASHBOARD_URL: "https://${HOST}/ccp-teiler-dashboard"
-      DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE_LOWER_CASE}"
-      HTTP_RELATIVE_PATH: "/ccp-teiler"
-      LOG_LEVEL: ${LOG_LEVEL_TEILER:-WARN}
-
-  teiler-dashboard:
-    image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:develop
-    container_name: bridgehead-teiler-dashboard
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.teiler_dashboard_ccp.rule=PathPrefix(`/ccp-teiler-dashboard`)"
-      - "traefik.http.services.teiler_dashboard_ccp.loadbalancer.server.port=80"
-      - "traefik.http.routers.teiler_dashboard_ccp.tls=true"
-      - "traefik.http.middlewares.teiler_dashboard_ccp_strip.stripprefix.prefixes=/ccp-teiler-dashboard"
-      - "traefik.http.routers.teiler_dashboard_ccp.middlewares=teiler_dashboard_ccp_strip"
-    environment:
-      DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
-      TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend"
-      OIDC_URL: "${OIDC_URL}"
-      OIDC_REALM: "${OIDC_REALM}"
-      OIDC_CLIENT_ID: "${OIDC_PUBLIC_CLIENT_ID}"
-      OIDC_TOKEN_GROUP: "${OIDC_GROUP_CLAIM}"
-      TEILER_ADMIN_NAME: "${OPERATOR_FIRST_NAME} ${OPERATOR_LAST_NAME}"
-      TEILER_ADMIN_EMAIL: "${OPERATOR_EMAIL}"
-      TEILER_ADMIN_PHONE: "${OPERATOR_PHONE}"
-      TEILER_PROJECT: "${PROJECT}"
-      EXPORTER_API_KEY: "${EXPORTER_API_KEY}"
-      TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler"
-      TEILER_DASHBOARD_HTTP_RELATIVE_PATH: "/ccp-teiler-dashboard"
-      TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler"
-      TEILER_USER: "${OIDC_USER_GROUP}"
-      TEILER_ADMIN: "${OIDC_ADMIN_GROUP}"
-      REPORTER_DEFAULT_TEMPLATE_ID: "ccp-qb"
-      EXPORTER_DEFAULT_TEMPLATE_ID: "ccp"
-      LOG_LEVEL: ${LOG_LEVEL_TEILER:-WARN}
-
-
-  teiler-backend:
-    image: docker.verbis.dkfz.de/ccp/dktk-teiler-backend:latest
-    container_name: bridgehead-teiler-backend
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.teiler_backend_ccp.rule=PathPrefix(`/ccp-teiler-backend`)"
-      - "traefik.http.services.teiler_backend_ccp.loadbalancer.server.port=8085"
-      - "traefik.http.routers.teiler_backend_ccp.tls=true"
-      - "traefik.http.middlewares.teiler_backend_ccp_strip.stripprefix.prefixes=/ccp-teiler-backend"
-      - "traefik.http.routers.teiler_backend_ccp.middlewares=teiler_backend_ccp_strip"
-    environment:
-      APPLICATION_PORT: "8085"
-      APPLICATION_ADDRESS: "${HOST}"
-      DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
-      CONFIG_ENV_VAR_PATH: "/run/secrets/ccp.conf"
-      TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler"
-      TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler"
-      TEILER_DASHBOARD_DE_URL: "https://${HOST}/ccp-teiler-dashboard/de"
-      TEILER_DASHBOARD_EN_URL: "https://${HOST}/ccp-teiler-dashboard/en"
-      CENTRAX_URL: "${CENTRAXX_URL}"
-      HTTP_PROXY: "http://forward_proxy:3128"
-      ENABLE_MTBA: "${ENABLE_MTBA}"
-      ENABLE_DATASHIELD: "${ENABLE_DATASHIELD}"
-      LOG_LEVEL: ${LOG_LEVEL_TEILER:-WARN}
-    secrets:
-      - ccp.conf
-
-secrets:
-  ccp.conf:
-    file: /etc/bridgehead/ccp.conf

ccp/modules/teiler-setup.sh

@@ -1,9 +0,0 @@
-#!/bin/bash -e
-
-if [ "$ENABLE_TEILER" == true ];then
-  log INFO "Teiler setup detected -- will start Teiler services."
-  OVERRIDE+=" -f ./$PROJECT/modules/teiler-compose.yml"
-  TEILER_DEFAULT_LANGUAGE=DE
-  TEILER_DEFAULT_LANGUAGE_LOWER_CASE=${TEILER_DEFAULT_LANGUAGE,,}
-  add_public_oidc_redirect_url "/ccp-teiler/*"
-fi

ccp/modules/teiler.md

@@ -1,19 +0,0 @@
-# Teiler
-This module orchestrates the different microfrontends of the bridgehead as a single page application.  
-
-## Teiler Orchestrator
-Single SPA component that consists on the root HTML site of the single page application and a javascript code that
-gets the information about the microfrontend calling the teiler backend and is responsible for registering them. With the
-resulting mapping, it can initialize, mount and unmount the required microfrontends on the fly. 
-
-The microfrontends run independently in different containers and can be based on different frameworks (Angular, Vue, React,...)
-This microfrontends can run as single alone but need an extension with Single-SPA (https://single-spa.js.org/docs/ecosystem).
-There are also available three templates (Angular, Vue, React) to be directly extended to be used directly in the teiler.
-
-## Teiler Dashboard
-It consists on the main dashboard and a set of embedded services.
-### Login
-user and password in ccp.local.conf
-
-## Teiler Backend
-In this component, the microfrontends are configured.

ccp/queries_to_cache.conf

@@ -1,2 +0,0 @@
-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
-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

ccp/root-new.crt.pem

@@ -0,0 +1,20 @@
+-----BEGIN CERTIFICATE-----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+-----END CERTIFICATE-----

ccp/vars

@@ -2,23 +2,12 @@ BROKER_ID=broker.ccp-it.dktk.dkfz.de
 BROKER_URL=https://${BROKER_ID}
 PROXY_ID=${SITE_ID}.${BROKER_ID}
 FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
-FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64}
+FOCUS_RETRY_COUNT=32
 SUPPORT_EMAIL=support-ccp@dkfz-heidelberg.de
 PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
 
 BROKER_URL_FOR_PREREQ=$BROKER_URL
 
-OIDC_USER_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})"
-OIDC_ADMIN_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})_Verwalter"
-OIDC_PRIVATE_CLIENT_ID=${SITE_ID}-private
-OIDC_PUBLIC_CLIENT_ID=${SITE_ID}-public
-# Use "test-realm-01" for testing
-OIDC_REALM="${OIDC_REALM:-master}"
-OIDC_URL="https://login.verbis.dkfz.de"
-OIDC_ISSUER_URL="${OIDC_URL}/realms/${OIDC_REALM}"
-OIDC_GROUP_CLAIM="groups"
-
-POSTGRES_TAG=15.6-alpine
 
 for module in $PROJECT/modules/*.sh
 do
@@ -27,6 +16,5 @@ do
 done
 
 idManagementSetup
-mtbaSetup
+nngmSetup
-obds2fhirRestSetup
+mtbaSetup
-blazeSecondarySetup

dhki/docker-compose.yml

@@ -1,66 +0,0 @@
-version: "3.7"
-
-services:
-  blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
-    container_name: bridgehead-dhki-blaze
-    environment:
-      BASE_URL: "http://bridgehead-dhki-blaze:8080"
-      JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
-      DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
-      DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP
-      ENFORCE_REFERENTIAL_INTEGRITY: "false"
-    volumes:
-      - "blaze-data:/app/data"
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.blaze_dhki.rule=PathPrefix(`/dhki-localdatamanagement`)"
-      - "traefik.http.middlewares.dhki_b_strip.stripprefix.prefixes=/dhki-localdatamanagement"
-      - "traefik.http.services.blaze_dhki.loadbalancer.server.port=8080"
-      - "traefik.http.routers.blaze_dhki.middlewares=dhki_b_strip,auth"
-      - "traefik.http.routers.blaze_dhki.tls=true"
-
-  focus:
-    image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
-    container_name: bridgehead-focus
-    environment:
-      API_KEY: ${FOCUS_BEAM_SECRET_SHORT}
-      BEAM_APP_ID_LONG: focus.${PROXY_ID}
-      PROXY_ID: ${PROXY_ID}
-      BLAZE_URL: "http://bridgehead-dhki-blaze:8080/fhir/"
-      BEAM_PROXY_URL: http://beam-proxy:8081
-      RETRY_COUNT: ${FOCUS_RETRY_COUNT}
-      EPSILON: 0.28
-      QUERIES_TO_CACHE: '/queries_to_cache.conf'
-    volumes:
-      - /srv/docker/bridgehead/dhki/queries_to_cache.conf:/queries_to_cache.conf
-    depends_on:
-      - "beam-proxy"
-      - "blaze"
-
-  beam-proxy:
-    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_focus_KEY: ${FOCUS_BEAM_SECRET_SHORT}
-      PRIVKEY_FILE: /run/secrets/proxy.pem
-      ALL_PROXY: http://forward_proxy:3128
-      TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
-      ROOTCERT_FILE: /conf/root.crt.pem
-    secrets:
-      - proxy.pem
-    depends_on:
-      - "forward_proxy"
-    volumes:
-      - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
-      - /srv/docker/bridgehead/dhki/root.crt.pem:/conf/root.crt.pem:ro
-
-
-volumes:
-  blaze-data:
-
-secrets:
-  proxy.pem:
-    file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

dhki/queries_to_cache.conf

@@ -1,2 +0,0 @@
-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
-bGlicmFyeSBSZXRyaWV2ZQp1c2luZyBGSElSIHZlcnNpb24gJzQuMC4wJwppbmNsdWRlIEZISVJIZWxwZXJzIHZlcnNpb24gJzQuMC4wJwpjb2Rlc3lzdGVtIFNhbXBsZU1hdGVyaWFsVHlwZTogJ2h0dHBzOi8vZmhpci5iYm1yaS5kZS9Db2RlU3lzdGVtL1NhbXBsZU1hdGVyaWFsVHlwZScKCmNvZGVzeXN0ZW0gbG9pbmM6ICdodHRwOi8vbG9pbmMub3JnJwpjb2Rlc3lzdGVtIGljZDEwOiAnaHR0cDovL2ZoaXIuZGUvQ29kZVN5c3RlbS9iZmFybS9pY2QtMTAtZ20nCmNvZGVzeXN0ZW0gbW9ycGg6ICd1cm46b2lkOjIuMTYuODQwLjEuMTEzODgzLjYuNDMuMScKCmNvbnRleHQgUGF0aWVudAoKREtUS19TVFJBVF9HRU5ERVJfU1RSQVRJRklFUgoKREtUS19TVFJBVF9BR0VfU1RSQVRJRklFUgoKREtUS19TVFJBVF9ERUNFQVNFRF9TVFJBVElGSUVSCgpES1RLX1NUUkFUX0RJQUdOT1NJU19TVFJBVElGSUVSCgpESEtJX1NUUkFUX1NQRUNJTUVOX1NUUkFUSUZJRVIKCkRLVEtfU1RSQVRfUFJPQ0VEVVJFX1NUUkFUSUZJRVIKCkRIS0lfU1RSQVRfTUVESUNBVElPTl9TVFJBVElGSUVSCgpESEtJX1NUUkFUX0VOQ09VTlRFUl9TVFJBVElGSUVSCkRLVEtfU1RSQVRfREVGX0lOX0lOSVRJQUxfUE9QVUxBVElPTgooKChleGlzdHMgW0NvbmRpdGlvbjogQ29kZSAnQzM0LjknIGZyb20gaWNkMTBdKSBvcgooZXhpc3RzIFtDb25kaXRpb246IENvZGUgJ0MzNC44JyBmcm9tIGljZDEwXSkgb3IKKGV4aXN0cyBbQ29uZGl0aW9uOiBDb2RlICdDMzQuMCcgZnJvbSBpY2QxMF0pIG9yCihleGlzdHMgW0NvbmRpdGlvbjogQ29kZSAnQzM0LjInIGZyb20gaWNkMTBdKSBvcgooZXhpc3RzIFtDb25kaXRpb246IENvZGUgJ0MzNC4xJyBmcm9tIGljZDEwXSkgb3IKKGV4aXN0cyBbQ29uZGl0aW9uOiBDb2RlICdDMzQuMycgZnJvbSBpY2QxMF0pKSBhbmQKKChleGlzdHMgZnJvbSBbT2JzZXJ2YXRpb246IENvZGUgJzU5ODQ3LTQnIGZyb20gbG9pbmNdIE8Kd2hlcmUgTy52YWx1ZS5jb2RpbmcuY29kZSBjb250YWlucyAnODE0MC8zJykgb3IKKGV4aXN0cyBmcm9tIFtPYnNlcnZhdGlvbjogQ29kZSAnNTk4NDctNCcgZnJvbSBsb2luY10gTwp3aGVyZSBPLnZhbHVlLmNvZGluZy5jb2RlIGNvbnRhaW5zICc4MTQxLzMnKSBvcgooZXhpc3RzIGZyb20gW09ic2VydmF0aW9uOiBDb2RlICc1OTg0Ny00JyBmcm9tIGxvaW5jXSBPCndoZXJlIE8udmFsdWUuY29kaW5nLmNvZGUgY29udGFpbnMgJzgxNDMvMycpIG9yCihleGlzdHMgZnJvbSBbT2JzZXJ2YXRpb246IENvZGUgJzU5ODQ3LTQnIGZyb20gbG9pbmNdIE8Kd2hlcmUgTy52YWx1ZS5jb2RpbmcuY29kZSBjb250YWlucyAnODE0Ny8zJykgb3IKKGV4aXN0cyBmcm9tIFtPYnNlcnZhdGlvbjogQ29kZSAnNTk4NDctNCcgZnJvbSBsb2luY10gTwp3aGVyZSBPLnZhbHVlLmNvZGluZy5jb2RlIGNvbnRhaW5zICc4MjUwLzMnKSBvcgooZXhpc3RzIGZyb20gW09ic2VydmF0aW9uOiBDb2RlICc1OTg0Ny00JyBmcm9tIGxvaW5jXSBPCndoZXJlIE8udmFsdWUuY29kaW5nLmNvZGUgY29udGFpbnMgJzgyNTEvMycpIG9yCihleGlzdHMgZnJvbSBbT2JzZXJ2YXRpb246IENvZGUgJzU5ODQ3LTQnIGZyb20gbG9pbmNdIE8Kd2hlcmUgTy52YWx1ZS5jb2RpbmcuY29kZSBjb250YWlucyAnODI1Mi8zJykgb3IKKGV4aXN0cyBmcm9tIFtPYnNlcnZhdGlvbjogQ29kZSAnNTk4NDctNCcgZnJvbSBsb2luY10gTwp3aGVyZSBPLnZhbHVlLmNvZGluZy5jb2RlIGNvbnRhaW5zICc4MjUzLzMnKSBvcgooZXhpc3RzIGZyb20gW09ic2VydmF0aW9uOiBDb2RlICc1OTg0Ny00JyBmcm9tIGxvaW5jXSBPCndoZXJlIE8udmFsdWUuY29kaW5nLmNvZGUgY29udGFpbnMgJzgyNTUvMycpIG9yCihleGlzdHMgZnJvbSBbT2JzZXJ2YXRpb246IENvZGUgJzU5ODQ3LTQnIGZyb20gbG9pbmNdIE8Kd2hlcmUgTy52YWx1ZS5jb2RpbmcuY29kZSBjb250YWlucyAnODI2MC8zJykgb3IKKGV4aXN0cyBmcm9tIFtPYnNlcnZhdGlvbjogQ29kZSAnNTk4NDctNCcgZnJvbSBsb2luY10gTwp3aGVyZSBPLnZhbHVlLmNvZGluZy5jb2RlIGNvbnRhaW5zICc4MzEwLzMnKSBvcgooZXhpc3RzIGZyb20gW09ic2VydmF0aW9uOiBDb2RlICc1OTg0Ny00JyBmcm9tIGxvaW5jXSBPCndoZXJlIE8udmFsdWUuY29kaW5nLmNvZGUgY29udGFpbnMgJzgzMzMvMycpIG9yCihleGlzdHMgZnJvbSBbT2JzZXJ2YXRpb246IENvZGUgJzU5ODQ3LTQnIGZyb20gbG9pbmNdIE8Kd2hlcmUgTy52YWx1ZS5jb2RpbmcuY29kZSBjb250YWlucyAnODQ3MC8zJykgb3IKKGV4aXN0cyBmcm9tIFtPYnNlcnZhdGlvbjogQ29kZSAnNTk4NDctNCcgZnJvbSBsb2luY10gTwp3aGVyZSBPLnZhbHVlLmNvZGluZy5jb2RlIGNvbnRhaW5zICc4NDgwLzMnKSBvcgooZXhpc3RzIGZyb20gW09ic2VydmF0aW9uOiBDb2RlICc1OTg0Ny00JyBmcm9tIGxvaW5jXSBPCndoZXJlIE8udmFsdWUuY29kaW5nLmNvZGUgY29udGFpbnMgJzg0OTAvMycpIG9yCihleGlzdHMgZnJvbSBbT2JzZXJ2YXRpb246IENvZGUgJzU5ODQ3LTQnIGZyb20gbG9pbmNdIE8Kd2hlcmUgTy52YWx1ZS5jb2RpbmcuY29kZSBjb250YWlucyAnODU1MC8zJykgb3IKKGV4aXN0cyBmcm9tIFtPYnNlcnZhdGlvbjogQ29kZSAnNTk4NDctNCcgZnJvbSBsb2luY10gTwp3aGVyZSBPLnZhbHVlLmNvZGluZy5jb2RlIGNvbnRhaW5zICc4MDUyLzMnKSkp

dhki/root.crt.pem

@@ -1,20 +0,0 @@
------BEGIN CERTIFICATE-----
-MIIDNTCCAh2gAwIBAgIUSWUPebUMNfJvPKMjdgX+WiH+OXgwDQYJKoZIhvcNAQEL
-BQAwFjEUMBIGA1UEAxMLQnJva2VyLVJvb3QwHhcNMjQwMTA1MDg1NTM4WhcNMzQw
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-eG0eKFUS0REJ
------END CERTIFICATE-----

dhki/vars

@@ -1,20 +0,0 @@
-BROKER_ID=broker.hector.dkfz.de
-BROKER_URL=https://${BROKER_ID}
-PROXY_ID=${SITE_ID}.${BROKER_ID}
-FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
-FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64}
-SUPPORT_EMAIL=support-ccp@dkfz-heidelberg.de
-PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
-
-BROKER_URL_FOR_PREREQ=$BROKER_URL
-
-POSTGRES_TAG=15.6-alpine
-
-for module in ccp/modules/*.sh
-do
-    log DEBUG "sourcing $module"
-    source $module
-done
-
-idManagementSetup
-obds2fhirRestSetup

itcc/docker-compose.yml

@@ -1,63 +0,0 @@
-version: "3.7"
-
-services:
-  blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
-    container_name: bridgehead-itcc-blaze
-    environment:
-      BASE_URL: "http://bridgehead-itcc-blaze:8080"
-      JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
-      DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
-      DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP
-      ENFORCE_REFERENTIAL_INTEGRITY: "false"
-    volumes:
-      - "blaze-data:/app/data"
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.blaze_itcc.rule=PathPrefix(`/itcc-localdatamanagement`)"
-      - "traefik.http.middlewares.itcc_b_strip.stripprefix.prefixes=/itcc-localdatamanagement"
-      - "traefik.http.services.blaze_itcc.loadbalancer.server.port=8080"
-      - "traefik.http.routers.blaze_itcc.middlewares=itcc_b_strip,auth"
-      - "traefik.http.routers.blaze_itcc.tls=true"
-
-  focus:
-    image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
-    container_name: bridgehead-focus
-    environment:
-      API_KEY: ${FOCUS_BEAM_SECRET_SHORT}
-      BEAM_APP_ID_LONG: focus.${PROXY_ID}
-      PROXY_ID: ${PROXY_ID}
-      BLAZE_URL: "http://bridgehead-itcc-blaze:8080/fhir/"
-      BEAM_PROXY_URL: http://beam-proxy:8081
-      RETRY_COUNT: ${FOCUS_RETRY_COUNT}
-      EPSILON: 0.28
-    depends_on:
-      - "beam-proxy"
-      - "blaze"
-
-  beam-proxy:
-    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${BEAM_TAG}
-    container_name: bridgehead-beam-proxy
-    environment:
-      BROKER_URL: ${BROKER_URL}
-      PROXY_ID: ${PROXY_ID}
-      APP_focus_KEY: ${FOCUS_BEAM_SECRET_SHORT}
-      PRIVKEY_FILE: /run/secrets/proxy.pem
-      ALL_PROXY: http://forward_proxy:3128
-      TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
-      ROOTCERT_FILE: /conf/root.crt.pem
-    secrets:
-      - proxy.pem
-    depends_on:
-      - "forward_proxy"
-    volumes:
-      - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
-      - /srv/docker/bridgehead/itcc/root.crt.pem:/conf/root.crt.pem:ro
-
-
-volumes:
-  blaze-data:
-
-secrets:
-  proxy.pem:
-    file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

itcc/modules/lens-compose.yml

@@ -1,33 +0,0 @@
-version: "3.7"
-services:
-  landing:
-    container_name: lens_federated-search
-    image: docker.verbis.dkfz.de/ccp/lens:${SITE_ID}
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.landing.rule=PathPrefix(`/`)"
-      - "traefik.http.services.landing.loadbalancer.server.port=80"
-      - "traefik.http.routers.landing.tls=true"
-
-  spot:
-    image: docker.verbis.dkfz.de/ccp-private/central-spot
-    environment:
-      BEAM_SECRET: "${FOCUS_BEAM_SECRET_SHORT}"
-      BEAM_URL: http://beam-proxy:8081
-      BEAM_PROXY_ID: ${SITE_ID}
-      BEAM_BROKER_ID: ${BROKER_ID}
-      BEAM_APP_ID: "focus"
-      PROJECT_METADATA: "dktk_supervisors"
-    depends_on:
-      - "beam-proxy"
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.services.spot.loadbalancer.server.port=8080"
-      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowmethods=GET,OPTIONS,POST"
-      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolalloworiginlist=https://${HOST}"
-      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowcredentials=true"
-      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolmaxage=-1"
-      - "traefik.http.routers.spot.rule=Host(`${HOST}`) && PathPrefix(`/backend`)"
-      - "traefik.http.middlewares.stripprefix_spot.stripprefix.prefixes=/backend"
-      - "traefik.http.routers.spot.tls=true"
-      - "traefik.http.routers.spot.middlewares=corsheaders2,stripprefix_spot"

itcc/modules/lens-setup.sh

@@ -1,5 +0,0 @@
-#!/bin/bash
-
-if [ -n "$ENABLE_LENS" ];then
-  OVERRIDE+=" -f ./$PROJECT/modules/lens-compose.yml"
-fi

itcc/root.crt.pem

@@ -1,20 +0,0 @@
------BEGIN CERTIFICATE-----
-MIIDNTCCAh2gAwIBAgIUW34NEb7bl0+Ywx+I1VKtY5vpAOowDQYJKoZIhvcNAQEL
-BQAwFjEUMBIGA1UEAxMLQnJva2VyLVJvb3QwHhcNMjQwMTIyMTMzNzEzWhcNMzQw
-MTE5MTMzNzQzWjAWMRQwEgYDVQQDEwtCcm9rZXItUm9vdDCCASIwDQYJKoZIhvcN
-AQEBBQADggEPADCCAQoCggEBAL5UegLXTlq3XRRj8LyFs3aF0tpRPVoW9RXp5kFI
-TnBvyO6qjNbMDT/xK+4iDtEX4QQUvsxAKxfXbe9i1jpdwjgH7JHaSGm2IjAiKLqO
-OXQQtguWwfNmmp96Ql13ArLj458YH08xMO/w2NFWGwB/hfARa4z/T0afFuc/tKJf
-XbGCG9xzJ9tmcG45QN8NChGhVvaTweNdVxGWlpHxmi0Mn8OM9CEuB7nPtTTiBuiu
-pRC2zVVmNjVp4ktkAqL7IHOz+/F5nhiz6tOika9oD3376Xj055lPznLcTQn2+4d7
-K7ZrBopCFxIQPjkgmYRLfPejbpdUjK1UVJw7hbWkqWqH7JMCAwEAAaN7MHkwDgYD
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-poIguUAK9YL2n7fbMB8GA1UdIwQYMBaAFGjvRcaIP4HMpoIguUAK9YL2n7fbMBYG
-A1UdEQQPMA2CC0Jyb2tlci1Sb290MA0GCSqGSIb3DQEBCwUAA4IBAQCbzycJSaDm
-AXXNJqQ88djrKs5MDXS8RIjS/cu2ayuLaYDe+BzVmUXNA0Vt9nZGdaz63SLLcjpU
-fNSxBfKbwmf7s30AK8Cnfj9q4W/BlBeVizUHQsg1+RQpDIdMrRQrwkXv8mfLw+w5
-3oaXNW6W/8KpBp/H8TBZ6myl6jCbeR3T8EMXBwipMGop/1zkbF01i98Xpqmhx2+l
-n+80ofPsSspOo5XmgCZym8CD/m/oFHmjcvOfpOCvDh4PZ+i37pmbSlCYoMpla3u/
-7MJMP5lugfLBYNDN2p+V4KbHP/cApCDT5UWLOeAWjgiZQtHH5ilDeYqEc1oPjyJt
-Rtup0MTxSJtN
------END CERTIFICATE-----

itcc/vars

@@ -1,14 +0,0 @@
-BROKER_ID=test-no-real-data.broker.samply.de
-BROKER_URL=https://${BROKER_ID}
-PROXY_ID=${SITE_ID}.${BROKER_ID}
-FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
-FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64}
-SUPPORT_EMAIL=arturo.macias@dkfz-heidelberg.de
-PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
-BROKER_URL_FOR_PREREQ=$BROKER_URL
-
-for module in $PROJECT/modules/*.sh
-do
-    log DEBUG "sourcing $module"
-    source $module
-done

kr/docker-compose.yml

@@ -1,67 +0,0 @@
-version: "3.7"
-
-services:
-  landing:
-    deploy:
-      replicas: 0 #deactivate landing page
-
-  blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
-    container_name: bridgehead-kr-blaze
-    environment:
-      BASE_URL: "http://bridgehead-kr-blaze:8080"
-      JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
-      DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
-      DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP
-      ENFORCE_REFERENTIAL_INTEGRITY: "false"
-    volumes:
-      - "blaze-data:/app/data"
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.blaze_kr.rule=PathPrefix(`/kr-localdatamanagement`)"
-      - "traefik.http.middlewares.kr_b_strip.stripprefix.prefixes=/kr-localdatamanagement"
-      - "traefik.http.services.blaze_kr.loadbalancer.server.port=8080"
-      - "traefik.http.routers.blaze_kr.middlewares=kr_b_strip,auth"
-      - "traefik.http.routers.blaze_kr.tls=true"
-
-  focus:
-    image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
-    container_name: bridgehead-focus
-    environment:
-      API_KEY: ${FOCUS_BEAM_SECRET_SHORT}
-      BEAM_APP_ID_LONG: focus.${PROXY_ID}
-      PROXY_ID: ${PROXY_ID}
-      BLAZE_URL: "http://bridgehead-kr-blaze:8080/fhir/"
-      BEAM_PROXY_URL: http://beam-proxy:8081
-      RETRY_COUNT: ${FOCUS_RETRY_COUNT}
-      EPSILON: 0.28
-    depends_on:
-      - "beam-proxy"
-      - "blaze"
-
-  beam-proxy:
-    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_focus_KEY: ${FOCUS_BEAM_SECRET_SHORT}
-      PRIVKEY_FILE: /run/secrets/proxy.pem
-      ALL_PROXY: http://forward_proxy:3128
-      TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
-      ROOTCERT_FILE: /conf/root.crt.pem
-    secrets:
-      - proxy.pem
-    depends_on:
-      - "forward_proxy"
-    volumes:
-      - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
-      - /srv/docker/bridgehead/kr/root.crt.pem:/conf/root.crt.pem:ro
-
-
-volumes:
-  blaze-data:
-
-secrets:
-  proxy.pem:
-    file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

kr/modules/export-and-qb.curl-templates

@@ -1,6 +0,0 @@
-# Full Excel Export
-curl --location --request POST 'https://${HOST}/ccp-exporter/request?query=Patient&query-format=FHIR_PATH&template-id=ccp&output-format=EXCEL' \
---header 'x-api-key: ${EXPORT_API_KEY}'
-
-# QB
-curl --location --request POST 'https://${HOST}/ccp-reporter/generate?template-id=ccp'

kr/modules/exporter-compose.yml

@@ -1,67 +0,0 @@
-version: "3.7"
-
-services:
-  exporter:
-    image: docker.verbis.dkfz.de/ccp/dktk-exporter:latest
-    container_name: bridgehead-ccp-exporter
-    environment:
-      JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
-      LOG_LEVEL: "INFO"
-      EXPORTER_API_KEY: "${EXPORTER_API_KEY}" # Set in exporter-setup.sh
-      CROSS_ORIGINS: "https://${HOST}"
-      EXPORTER_DB_USER: "exporter"
-      EXPORTER_DB_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
-      EXPORTER_DB_URL: "jdbc:postgresql://exporter-db:5432/exporter"
-      HTTP_RELATIVE_PATH: "/ccp-exporter"
-      SITE: "${SITE_ID}"
-      HTTP_SERVLET_REQUEST_SCHEME: "https"
-      OPAL_PASSWORD: "${EXPORTER_OPAL_PASSWORD}"
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.exporter_ccp.rule=PathPrefix(`/ccp-exporter`)"
-      - "traefik.http.services.exporter_ccp.loadbalancer.server.port=8092"
-      - "traefik.http.routers.exporter_ccp.tls=true"
-      - "traefik.http.middlewares.exporter_ccp_strip.stripprefix.prefixes=/ccp-exporter"
-      - "traefik.http.routers.exporter_ccp.middlewares=exporter_ccp_strip"
-    volumes:
-      - "/var/cache/bridgehead/ccp/exporter-files:/app/exporter-files/output"
-
-  exporter-db:
-    image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
-    container_name: bridgehead-ccp-exporter-db
-    environment:
-      POSTGRES_USER: "exporter"
-      POSTGRES_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
-      POSTGRES_DB: "exporter"
-    volumes:
-      # Consider removing this volume once we find a solution to save Lens-queries to be executed in the explorer.
-      - "/var/cache/bridgehead/ccp/exporter-db:/var/lib/postgresql/data"
-
-  reporter:
-    image: docker.verbis.dkfz.de/ccp/dktk-reporter:latest
-    container_name: bridgehead-ccp-reporter
-    environment:
-      JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
-      LOG_LEVEL: "INFO"
-      CROSS_ORIGINS: "https://${HOST}"
-      HTTP_RELATIVE_PATH: "/ccp-reporter"
-      SITE: "${SITE_ID}"
-      EXPORTER_API_KEY: "${EXPORTER_API_KEY}" # Set in exporter-setup.sh
-      EXPORTER_URL: "http://exporter:8092"
-      LOG_FHIR_VALIDATION: "false"
-      HTTP_SERVLET_REQUEST_SCHEME: "https"
-
-    # In this initial development state of the bridgehead, we are trying to have so many volumes as possible.
-    # However, in the first executions in the CCP sites, this volume seems to be very important. A report is
-    # a process that can take several hours, because it depends on the exporter.
-    # There is a risk that the bridgehead restarts, losing the already created export.
-
-    volumes:
-      - "/var/cache/bridgehead/ccp/reporter-files:/app/reports"
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.reporter_ccp.rule=PathPrefix(`/ccp-reporter`)"
-      - "traefik.http.services.reporter_ccp.loadbalancer.server.port=8095"
-      - "traefik.http.routers.reporter_ccp.tls=true"
-      - "traefik.http.middlewares.reporter_ccp_strip.stripprefix.prefixes=/ccp-reporter"
-      - "traefik.http.routers.reporter_ccp.middlewares=reporter_ccp_strip"

kr/modules/exporter-setup.sh

@@ -1,8 +0,0 @@
-#!/bin/bash -e
-
-if [ "$ENABLE_EXPORTER" == true ]; then
-  log INFO "Exporter setup detected -- will start Exporter service."
-  OVERRIDE+=" -f ./$PROJECT/modules/exporter-compose.yml"
-  EXPORTER_DB_PASSWORD="$(echo \"This is a salt string to generate one consistent password for the exporter. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
-  EXPORTER_API_KEY="$(echo \"This is a salt string to generate one consistent API KEY for the exporter. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 64)"
-fi

kr/modules/exporter.md

@@ -1,15 +0,0 @@
-# Exporter and Reporter
-
-
-## Exporter
-The exporter is a REST API that exports the data of the different databases of the bridgehead in a set of tables.
-It can accept different output formats as CSV, Excel, JSON or XML. It can also export data into Opal.
-
-## Exporter-DB
-It is a database to save queries for its execution in the exporter. 
-The exporter manages also the different executions of the same query in through the database.
-
-## Reporter
-This component is a plugin of the exporter that allows to create more complex Excel reports described in templates.
-It is compatible with different template engines as Groovy, Thymeleaf,...
-It is perfect to generate a document as our traditional CCP quality report.

kr/modules/lens-compose.yml

@@ -1,35 +0,0 @@
-version: "3.7"
-services:
-  landing:
-    deploy:
-      replicas: 1 #reactivate if lens is in use
-    container_name: lens_federated-search
-    image: docker.verbis.dkfz.de/ccp/lens:${SITE_ID}
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.landing.rule=PathPrefix(`/`)"
-      - "traefik.http.services.landing.loadbalancer.server.port=80"
-      - "traefik.http.routers.landing.tls=true"
-
-  spot:
-    image: docker.verbis.dkfz.de/ccp-private/central-spot
-    environment:
-      BEAM_SECRET: "${FOCUS_BEAM_SECRET_SHORT}"
-      BEAM_URL: http://beam-proxy:8081
-      BEAM_PROXY_ID: ${SITE_ID}
-      BEAM_BROKER_ID: ${BROKER_ID}
-      BEAM_APP_ID: "focus"
-      PROJECT_METADATA: "kr_supervisors"
-    depends_on:
-      - "beam-proxy"
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.services.spot.loadbalancer.server.port=8080"
-      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowmethods=GET,OPTIONS,POST"
-      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolalloworiginlist=https://${HOST}"
-      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowcredentials=true"
-      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolmaxage=-1"
-      - "traefik.http.routers.spot.rule=Host(`${HOST}`) && PathPrefix(`/backend`)"
-      - "traefik.http.middlewares.stripprefix_spot.stripprefix.prefixes=/backend"
-      - "traefik.http.routers.spot.tls=true"
-      - "traefik.http.routers.spot.middlewares=corsheaders2,stripprefix_spot"

kr/modules/lens-setup.sh

@@ -1,5 +0,0 @@
-#!/bin/bash
-
-if [ -n "$ENABLE_LENS" ];then
-  OVERRIDE+=" -f ./$PROJECT/modules/lens-compose.yml"
-fi

kr/modules/obds2fhir-rest-compose.yml

@@ -1,20 +0,0 @@
-version: "3.7"
-
-services:
-  obds2fhir-rest:
-    container_name: bridgehead-obds2fhir-rest
-    image: docker.verbis.dkfz.de/ccp/obds2fhir-rest:main
-    environment:
-      IDTYPE: BK_${IDMANAGEMENT_FRIENDLY_ID}_L-ID
-      MAINZELLISTE_APIKEY: ${IDMANAGER_LOCAL_PATIENTLIST_APIKEY}
-      SALT: ${LOCAL_SALT}
-      KEEP_INTERNAL_ID: ${KEEP_INTERNAL_ID:-false}
-      MAINZELLISTE_URL: ${PATIENTLIST_URL:-http://patientlist:8080/patientlist}
-    restart: always
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.obds2fhir-rest.rule=PathPrefix(`/obds2fhir-rest`) || PathPrefix(`/adt2fhir-rest`)"
-      - "traefik.http.middlewares.obds2fhir-rest_strip.stripprefix.prefixes=/obds2fhir-rest,/adt2fhir-rest"
-      - "traefik.http.services.obds2fhir-rest.loadbalancer.server.port=8080"
-      - "traefik.http.routers.obds2fhir-rest.tls=true"
-      - "traefik.http.routers.obds2fhir-rest.middlewares=obds2fhir-rest_strip,auth"

kr/modules/obds2fhir-rest-setup.sh

@@ -1,13 +0,0 @@
-#!/bin/bash
-
-function obds2fhirRestSetup() {
-  if [ -n "$ENABLE_OBDS2FHIR_REST" ]; then
-    log INFO "oBDS2FHIR-REST setup detected -- will start obds2fhir-rest module."
-    if [ ! -n "$IDMANAGER_UPLOAD_APIKEY" ]; then
-      log ERROR "Missing ID-Management Module! Fix this by setting up ID Management:"
-      PATIENTLIST_URL=" "
-    fi
-    OVERRIDE+=" -f ./$PROJECT/modules/obds2fhir-rest-compose.yml"
-    LOCAL_SALT="$(echo \"local-random-salt\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
-  fi
-}

kr/modules/teiler-compose.yml

@@ -1,81 +0,0 @@
-version: "3.7"
-
-services:
-
-  teiler-orchestrator:
-    image: docker.verbis.dkfz.de/cache/samply/teiler-orchestrator:latest
-    container_name: bridgehead-teiler-orchestrator
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.teiler_orchestrator_ccp.rule=PathPrefix(`/ccp-teiler`)"
-      - "traefik.http.services.teiler_orchestrator_ccp.loadbalancer.server.port=9000"
-      - "traefik.http.routers.teiler_orchestrator_ccp.tls=true"
-      - "traefik.http.middlewares.teiler_orchestrator_ccp_strip.stripprefix.prefixes=/ccp-teiler"
-      - "traefik.http.routers.teiler_orchestrator_ccp.middlewares=teiler_orchestrator_ccp_strip"
-    environment:
-      TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend"
-      TEILER_DASHBOARD_URL: "https://${HOST}/ccp-teiler-dashboard"
-      DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE_LOWER_CASE}"
-      HTTP_RELATIVE_PATH: "/ccp-teiler"
-
-  teiler-dashboard:
-    image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:develop
-    container_name: bridgehead-teiler-dashboard
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.teiler_dashboard_ccp.rule=PathPrefix(`/ccp-teiler-dashboard`)"
-      - "traefik.http.services.teiler_dashboard_ccp.loadbalancer.server.port=80"
-      - "traefik.http.routers.teiler_dashboard_ccp.tls=true"
-      - "traefik.http.middlewares.teiler_dashboard_ccp_strip.stripprefix.prefixes=/ccp-teiler-dashboard"
-      - "traefik.http.routers.teiler_dashboard_ccp.middlewares=teiler_dashboard_ccp_strip"
-    environment:
-      DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
-      TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend"
-      OIDC_URL: "${OIDC_URL}"
-      OIDC_REALM: "${OIDC_REALM}"
-      OIDC_CLIENT_ID: "${OIDC_PUBLIC_CLIENT_ID}"
-      OIDC_TOKEN_GROUP: "${OIDC_GROUP_CLAIM}"
-      TEILER_ADMIN_NAME: "${OPERATOR_FIRST_NAME} ${OPERATOR_LAST_NAME}"
-      TEILER_ADMIN_EMAIL: "${OPERATOR_EMAIL}"
-      TEILER_ADMIN_PHONE: "${OPERATOR_PHONE}"
-      TEILER_PROJECT: "${PROJECT}"
-      EXPORTER_API_KEY: "${EXPORTER_API_KEY}"
-      TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler"
-      TEILER_DASHBOARD_HTTP_RELATIVE_PATH: "/ccp-teiler-dashboard"
-      TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler"
-      TEILER_USER: "${OIDC_USER_GROUP}"
-      TEILER_ADMIN: "${OIDC_ADMIN_GROUP}"
-      REPORTER_DEFAULT_TEMPLATE_ID: "ccp-qb"
-      EXPORTER_DEFAULT_TEMPLATE_ID: "ccp"
-
-
-  teiler-backend:
-    image: docker.verbis.dkfz.de/ccp/dktk-teiler-backend:latest
-    container_name: bridgehead-teiler-backend
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.teiler_backend_ccp.rule=PathPrefix(`/ccp-teiler-backend`)"
-      - "traefik.http.services.teiler_backend_ccp.loadbalancer.server.port=8085"
-      - "traefik.http.routers.teiler_backend_ccp.tls=true"
-      - "traefik.http.middlewares.teiler_backend_ccp_strip.stripprefix.prefixes=/ccp-teiler-backend"
-      - "traefik.http.routers.teiler_backend_ccp.middlewares=teiler_backend_ccp_strip"
-    environment:
-      LOG_LEVEL: "INFO"
-      APPLICATION_PORT: "8085"
-      APPLICATION_ADDRESS: "${HOST}"
-      DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
-      CONFIG_ENV_VAR_PATH: "/run/secrets/ccp.conf"
-      TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler"
-      TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler"
-      TEILER_DASHBOARD_DE_URL: "https://${HOST}/ccp-teiler-dashboard/de"
-      TEILER_DASHBOARD_EN_URL: "https://${HOST}/ccp-teiler-dashboard/en"
-      CENTRAX_URL: "${CENTRAXX_URL}"
-      HTTP_PROXY: "http://forward_proxy:3128"
-      ENABLE_MTBA: "${ENABLE_MTBA}"
-      ENABLE_DATASHIELD: "${ENABLE_DATASHIELD}"
-    secrets:
-      - ccp.conf
-
-secrets:
-  ccp.conf:
-    file: /etc/bridgehead/ccp.conf

kr/modules/teiler-setup.sh

@@ -1,9 +0,0 @@
-#!/bin/bash -e
-
-if [ "$ENABLE_TEILER" == true ];then
-  log INFO "Teiler setup detected -- will start Teiler services."
-  OVERRIDE+=" -f ./$PROJECT/modules/teiler-compose.yml"
-  TEILER_DEFAULT_LANGUAGE=DE
-  TEILER_DEFAULT_LANGUAGE_LOWER_CASE=${TEILER_DEFAULT_LANGUAGE,,}
-  add_public_oidc_redirect_url "/ccp-teiler/*"
-fi

kr/modules/teiler.md

@@ -1,19 +0,0 @@
-# Teiler
-This module orchestrates the different microfrontends of the bridgehead as a single page application.  
-
-## Teiler Orchestrator
-Single SPA component that consists on the root HTML site of the single page application and a javascript code that
-gets the information about the microfrontend calling the teiler backend and is responsible for registering them. With the
-resulting mapping, it can initialize, mount and unmount the required microfrontends on the fly. 
-
-The microfrontends run independently in different containers and can be based on different frameworks (Angular, Vue, React,...)
-This microfrontends can run as single alone but need an extension with Single-SPA (https://single-spa.js.org/docs/ecosystem).
-There are also available three templates (Angular, Vue, React) to be directly extended to be used directly in the teiler.
-
-## Teiler Dashboard
-It consists on the main dashboard and a set of embedded services.
-### Login
-user and password in ccp.local.conf
-
-## Teiler Backend
-In this component, the microfrontends are configured.

kr/root.crt.pem

@@ -1,20 +0,0 @@
------BEGIN CERTIFICATE-----
-MIIDNTCCAh2gAwIBAgIUW34NEb7bl0+Ywx+I1VKtY5vpAOowDQYJKoZIhvcNAQEL
-BQAwFjEUMBIGA1UEAxMLQnJva2VyLVJvb3QwHhcNMjQwMTIyMTMzNzEzWhcNMzQw
-MTE5MTMzNzQzWjAWMRQwEgYDVQQDEwtCcm9rZXItUm9vdDCCASIwDQYJKoZIhvcN
-AQEBBQADggEPADCCAQoCggEBAL5UegLXTlq3XRRj8LyFs3aF0tpRPVoW9RXp5kFI
-TnBvyO6qjNbMDT/xK+4iDtEX4QQUvsxAKxfXbe9i1jpdwjgH7JHaSGm2IjAiKLqO
-OXQQtguWwfNmmp96Ql13ArLj458YH08xMO/w2NFWGwB/hfARa4z/T0afFuc/tKJf
-XbGCG9xzJ9tmcG45QN8NChGhVvaTweNdVxGWlpHxmi0Mn8OM9CEuB7nPtTTiBuiu
-pRC2zVVmNjVp4ktkAqL7IHOz+/F5nhiz6tOika9oD3376Xj055lPznLcTQn2+4d7
-K7ZrBopCFxIQPjkgmYRLfPejbpdUjK1UVJw7hbWkqWqH7JMCAwEAAaN7MHkwDgYD
-VR0PAQH/BAQDAgEGMA8GA1UdEwEB/wQFMAMBAf8wHQYDVR0OBBYEFGjvRcaIP4HM
-poIguUAK9YL2n7fbMB8GA1UdIwQYMBaAFGjvRcaIP4HMpoIguUAK9YL2n7fbMBYG
-A1UdEQQPMA2CC0Jyb2tlci1Sb290MA0GCSqGSIb3DQEBCwUAA4IBAQCbzycJSaDm
-AXXNJqQ88djrKs5MDXS8RIjS/cu2ayuLaYDe+BzVmUXNA0Vt9nZGdaz63SLLcjpU
-fNSxBfKbwmf7s30AK8Cnfj9q4W/BlBeVizUHQsg1+RQpDIdMrRQrwkXv8mfLw+w5
-3oaXNW6W/8KpBp/H8TBZ6myl6jCbeR3T8EMXBwipMGop/1zkbF01i98Xpqmhx2+l
-n+80ofPsSspOo5XmgCZym8CD/m/oFHmjcvOfpOCvDh4PZ+i37pmbSlCYoMpla3u/
-7MJMP5lugfLBYNDN2p+V4KbHP/cApCDT5UWLOeAWjgiZQtHH5ilDeYqEc1oPjyJt
-Rtup0MTxSJtN
------END CERTIFICATE-----

kr/vars

@@ -1,16 +0,0 @@
-BROKER_ID=test-no-real-data.broker.samply.de
-BROKER_URL=https://${BROKER_ID}
-PROXY_ID=${SITE_ID}.${BROKER_ID}
-FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
-FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64}
-SUPPORT_EMAIL=arturo.macias@dkfz-heidelberg.de
-PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
-BROKER_URL_FOR_PREREQ=$BROKER_URL
-
-for module in $PROJECT/modules/*.sh
-do
-    log DEBUG "sourcing $module"
-    source $module
-done
-
-obds2fhirRestSetup

lib/functions.sh

@@ -9,33 +9,6 @@ detectCompose() {
 	fi
 }
 
-setupProxy() {
-	### Note: As the current data protection concepts do not allow communication via HTTP,
-	### we are not setting a proxy for HTTP requests.
-
-	local http="no"
-	local https="no"
-	if [ $HTTPS_PROXY_URL ]; then
-		local proto="$(echo $HTTPS_PROXY_URL | grep :// | sed -e 's,^\(.*://\).*,\1,g')"
-		local fqdn="$(echo ${HTTPS_PROXY_URL/$proto/})"
-		local hostport=$(echo $HTTPS_PROXY_URL | sed -e "s,$proto,,g" | cut -d/ -f1)
-		HTTPS_PROXY_HOST="$(echo $hostport | sed -e 's,:.*,,g')"
-		HTTPS_PROXY_PORT="$(echo $hostport | sed -e 's,^.*:,:,g' -e 's,.*:\([0-9]*\).*,\1,g' -e 's,[^0-9],,g')"
-		if [[ ! -z "$HTTPS_PROXY_USERNAME" && ! -z "$HTTPS_PROXY_PASSWORD" ]]; then
-			local proto="$(echo $HTTPS_PROXY_URL | grep :// | sed -e 's,^\(.*://\).*,\1,g')"
-			local fqdn="$(echo ${HTTPS_PROXY_URL/$proto/})"
-			HTTPS_PROXY_FULL_URL="$(echo $proto$HTTPS_PROXY_USERNAME:$HTTPS_PROXY_PASSWORD@$fqdn)"
-			https="authenticated"
-		else
-			HTTPS_PROXY_FULL_URL=$HTTPS_PROXY_URL
-			https="unauthenticated"
-		fi
-	fi
-
-	log INFO "Configuring proxy servers: $http http proxy (we're not supporting unencrypted comms), $https https proxy"
-	export HTTPS_PROXY_HOST HTTPS_PROXY_PORT HTTPS_PROXY_FULL_URL
-}
-
 exitIfNotRoot() {
   if [ "$EUID" -ne 0 ]; then
     log "ERROR" "Please run as root"
@@ -53,8 +26,8 @@ checkOwner(){
 }
 
 printUsage() {
-	echo "Usage: bridgehead start|stop|logs|docker-logs|is-running|update|install|uninstall|adduser|enroll PROJECTNAME"
+	echo "Usage: bridgehead start|stop|is-running|update|install|uninstall|adduser|enroll PROJECTNAME"
-	echo "PROJECTNAME should be one of ccp|bbmri|cce|itcc|kr|dhki"
+	echo "PROJECTNAME should be one of ccp|bbmri"
 }
 
 checkRequirements() {
@@ -76,7 +49,7 @@ fetchVarsFromVault() {
 
 	set +e
 
-	PASS=$(BW_MASTERPASS="$BW_MASTERPASS" BW_CLIENTID="$BW_CLIENTID" BW_CLIENTSECRET="$BW_CLIENTSECRET" docker run --rm -e BW_MASTERPASS -e BW_CLIENTID -e BW_CLIENTSECRET -e http_proxy docker.verbis.dkfz.de/cache/samply/bridgehead-vaultfetcher:latest $@)
+	PASS=$(BW_MASTERPASS="$BW_MASTERPASS" BW_CLIENTID="$BW_CLIENTID" BW_CLIENTSECRET="$BW_CLIENTSECRET" docker run --rm -e BW_MASTERPASS -e BW_CLIENTID -e BW_CLIENTSECRET -e http_proxy samply/bridgehead-vaultfetcher $@)
 	RET=$?
 
 	if [ $RET -ne 0 ]; then
@@ -155,30 +128,6 @@ setHostname() {
 	fi
 }
 
-# This function optimizes the usage of memory through blaze, according to the official performance tuning guide:
-#   https://github.com/samply/blaze/blob/master/docs/tuning-guide.md
-# Short summary of the adjustments made:
-# - set blaze memory cap to a quarter of the system memory
-# - set db block cache size to a quarter of the system memory
-# - limit resource count allowed in blaze to 1,25M per 4GB available system memory
-optimizeBlazeMemoryUsage() {
-	if [ -z "$BLAZE_MEMORY_CAP" ]; then
-	   system_memory_in_mb=$(LC_ALL=C free -m | grep 'Mem:' | awk '{print $2}');
-	   export BLAZE_MEMORY_CAP=$(($system_memory_in_mb/4));
-	fi
-	if [ -z "$BLAZE_RESOURCE_CACHE_CAP" ]; then
-		available_system_memory_chunks=$((BLAZE_MEMORY_CAP / 1000))
-		if [ $available_system_memory_chunks -eq 0 ]; then
-			log WARN "Only ${BLAZE_MEMORY_CAP} system memory available for Blaze. If your Blaze stores more than 128000 fhir ressources it will run significally slower."
-			export BLAZE_RESOURCE_CACHE_CAP=128000;
-			export BLAZE_CQL_CACHE_CAP=32;
-		else
-			export BLAZE_RESOURCE_CACHE_CAP=$((available_system_memory_chunks * 312500))
-			export BLAZE_CQL_CACHE_CAP=$((($system_memory_in_mb/4)/16));
-		fi
-	fi
-}
-
 # Takes 1) The Backup Directory Path 2) The name of the Service to be backuped
 # Creates 3 Backups: 1) For the past seven days 2) For the current month and 3) for each calendar week
 createEncryptedPostgresBackup(){
@@ -239,7 +188,7 @@ function do_enroll_inner {
 		PARAMS+="--admin-email $SUPPORT_EMAIL"
 	fi
 
-	docker run --rm -v /etc/bridgehead/pki:/etc/bridgehead/pki docker.verbis.dkfz.de/cache/samply/beam-enroll:latest --output-file $PRIVATEKEYFILENAME --proxy-id $MANUAL_PROXY_ID $PARAMS
+	docker run --rm -ti -v /etc/bridgehead/pki:/etc/bridgehead/pki samply/beam-enroll:latest --output-file $PRIVATEKEYFILENAME --proxy-id $MANUAL_PROXY_ID $PARAMS
 	chmod 600 $PRIVATEKEYFILENAME
 }
 
@@ -262,114 +211,4 @@ add_basic_auth_user() {
    fi
  	log DEBUG "Saving clear text credentials in $FILE. If wanted, delete them manually."
    sed -i "/^$NAME/ s|$|\n# User: $USER\n# Password: $PASSWORD|" $FILE
-}
+}
-
-OIDC_PUBLIC_REDIRECT_URLS=${OIDC_PUBLIC_REDIRECT_URLS:-""}
-OIDC_PRIVATE_REDIRECT_URLS=${OIDC_PRIVATE_REDIRECT_URLS:-""}
-
-# Add a redirect url to the public oidc client of the bridgehead
-function add_public_oidc_redirect_url() {
-    if [[ $OIDC_PUBLIC_REDIRECT_URLS == "" ]]; then
-        OIDC_PUBLIC_REDIRECT_URLS+="$(generate_redirect_urls $1)"
-    else 
-        OIDC_PUBLIC_REDIRECT_URLS+=",$(generate_redirect_urls $1)"
-    fi
-}
-
-# Add a redirect url to the private oidc client of the bridgehead
-function add_private_oidc_redirect_url() {
-    if [[ $OIDC_PRIVATE_REDIRECT_URLS == "" ]]; then
-        OIDC_PRIVATE_REDIRECT_URLS+="$(generate_redirect_urls $1)"
-    else 
-        OIDC_PRIVATE_REDIRECT_URLS+=",$(generate_redirect_urls $1)"
-    fi
-}
-
-function sync_secrets() {
-    local delimiter=$'\x1E'
-    local secret_sync_args=""
-    if [[ $OIDC_PRIVATE_REDIRECT_URLS != "" ]]; then
-        secret_sync_args="OIDC:OIDC_CLIENT_SECRET:private;$OIDC_PRIVATE_REDIRECT_URLS"
-    fi
-    if [[ $OIDC_PUBLIC_REDIRECT_URLS != "" ]]; then
-        if [[ $secret_sync_args == "" ]]; then
-            secret_sync_args="OIDC:OIDC_PUBLIC:public;$OIDC_PUBLIC_REDIRECT_URLS"
-        else
-            secret_sync_args+="${delimiter}OIDC:OIDC_PUBLIC:public;$OIDC_PUBLIC_REDIRECT_URLS"
-        fi
-    fi
-    if [[ $secret_sync_args == "" ]]; then
-        return
-    fi
-    mkdir -p /var/cache/bridgehead/secrets/ || fail_and_report 1 "Failed to create '/var/cache/bridgehead/secrets/'. Please run sudo './bridgehead install $PROJECT' again."
-    touch /var/cache/bridgehead/secrets/oidc
-    docker run --rm \
-        -v /var/cache/bridgehead/secrets/oidc:/usr/local/cache \
-        -v $PRIVATEKEYFILENAME:/run/secrets/privkey.pem:ro \
-        -v /srv/docker/bridgehead/$PROJECT/root.crt.pem:/run/secrets/root.crt.pem:ro \
-        -v /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro \
-        -e TLS_CA_CERTIFICATES_DIR=/conf/trusted-ca-certs \
-        -e NO_PROXY=localhost,127.0.0.1 \
-        -e ALL_PROXY=$HTTPS_PROXY_FULL_URL \
-        -e PROXY_ID=$PROXY_ID \
-        -e BROKER_URL=$BROKER_URL \
-        -e OIDC_PROVIDER=secret-sync-central.oidc-client-enrollment.$BROKER_ID \
-        -e SECRET_DEFINITIONS=$secret_sync_args \
-        docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest
-
-    set -a # Export variables as environment variables
-    source /var/cache/bridgehead/secrets/*
-    set +a # Export variables in the regular way
-}
-
-capitalize_first_letter() {
-    input="$1"
-    capitalized="$(tr '[:lower:]' '[:upper:]' <<< ${input:0:1})${input:1}"
-    echo "$capitalized"
-}
-
-# Generate a string of ',' separated string of redirect urls relative to $HOST.
-# $1 will be appended to the url
-# If the host looks like dev-jan.inet.dkfz-heidelberg.de it will generate urls with dev-jan and the original $HOST as url Authorities
-function generate_redirect_urls(){
-    local redirect_urls="https://${HOST}$1"
-    local host_without_proxy="$(echo "$HOST" | cut -d '.' -f1)"
-    # Only append second url if its different and the host is not an ip address
-    if [[ "$HOST" != "$host_without_proxy" && ! "$HOST" =~ ^[0-9]+\.[0-9]+\.[0-9]+\.[0-9]+$ ]]; then
-        redirect_urls+=",https://$host_without_proxy$1"
-    fi
-    echo "$redirect_urls"
-}
-
-# This password contains at least one special char, a random number and a random upper and lower case letter
-generate_password(){
-  local seed_text="$1"
-  local seed_num=$(awk 'BEGIN{FS=""} NR==1{print $10}' /etc/bridgehead/pki/${SITE_ID}.priv.pem | od -An -tuC)
-  local nums="1234567890"
-  local n=$(echo "$seed_num" | awk '{print $1 % 10}')
-  local random_digit=${nums:$n:1}
-  local n=$(echo "$seed_num" | awk '{print $1 % 26}')
-  local upper="ABCDEFGHIJKLMNOPQRSTUVWXYZ"
-  local lower="abcdefghijklmnopqrstuvwxyz"
-  local random_upper=${upper:$n:1}
-  local random_lower=${lower:$n:1}
-  local n=$(echo "$seed_num" | awk '{print $1 % 8}')
-  local special='@#$%^&+='
-  local random_special=${special:$n:1}
-
-  local combined_text="This is a salt string to generate one consistent password for ${seed_text}. It is not required to be secret."
-  local main_password=$(echo "${combined_text}" | sha1sum | openssl pkeyutl -sign -inkey "/etc/bridgehead/pki/${SITE_ID}.priv.pem" 2> /dev/null | base64 | head -c 26 | sed 's/\//A/g')
-
-  echo "${main_password}${random_digit}${random_upper}${random_lower}${random_special}"
-}
-
-# This password only contains alphanumeric characters
-generate_simple_password(){
-  local seed_text="$1"
-  local combined_text="This is a salt string to generate one consistent password for ${seed_text}. It is not required to be secret."
-  echo "${combined_text}" | sha1sum | openssl pkeyutl -sign -inkey "/etc/bridgehead/pki/${SITE_ID}.priv.pem" 2> /dev/null | base64 | head -c 26 | sed 's/[+\/]/A/g'
-}
-
-docker_jq() {
-    docker run --rm -i docker.verbis.dkfz.de/cache/jqlang/jq:latest "$@"
-}

lib/monitoring.sh

@@ -47,8 +47,8 @@ function hc_send(){
 
     if [ -n "$2" ]; then
         MSG="$2\n\nDocker stats:\n$UPTIME"
-        echo -e "$MSG" | https_proxy=$HTTPS_PROXY_FULL_URL curl --max-time 5 -A "$USER_AGENT" -s -o /dev/null -X POST --data-binary @- "$HCURL"/"$1" || log WARN "Monitoring failed: Unable to send data to $HCURL/$1"
+        echo -e "$MSG" | https_proxy=$HTTPS_PROXY_URL curl --max-time 5 -A "$USER_AGENT" -s -o /dev/null -X POST --data-binary @- "$HCURL"/"$1" || log WARN "Monitoring failed: Unable to send data to $HCURL/$1"
     else
-        https_proxy=$HTTPS_PROXY_FULL_URL curl --max-time 5 -A "$USER_AGENT" -s -o /dev/null "$HCURL"/"$1" || log WARN "Monitoring failed: Unable to send data to $HCURL/$1"
+        https_proxy=$HTTPS_PROXY_URL curl --max-time 5 -A "$USER_AGENT" -s -o /dev/null "$HCURL"/"$1" || log WARN "Monitoring failed: Unable to send data to $HCURL/$1"
     fi
 }

lib/prepare-system.sh

@@ -52,21 +52,6 @@ case "$PROJECT" in
 	bbmri)
 		site_configuration_repository_middle="git.verbis.dkfz.de/bbmri-bridgehead-configs/"
 		;;
-	cce)
-		site_configuration_repository_middle="git.verbis.dkfz.de/cce-sites/"
-		;;
-	itcc)
-		site_configuration_repository_middle="git.verbis.dkfz.de/itcc-sites/"
-        ;;
-    dhki)
-        site_configuration_repository_middle="git.verbis.dkfz.de/dhki/"
-		;;
-	kr)
-		site_configuration_repository_middle="git.verbis.dkfz.de/krebsregister-sites/"
-		;;
-	dhki)
-		site_configuration_repository_middle="git.verbis.dkfz.de/dhki/"
-		;;
 	minimal)
 		site_configuration_repository_middle="git.verbis.dkfz.de/minimal-bridgehead-configs/"
 		;;
@@ -104,9 +89,6 @@ elif [[ "$DEV_MODE" == "DEV" ]]; then
 fi
 
 chown -R bridgehead /etc/bridgehead /srv/docker/bridgehead
-mkdir -p /tmp/bridgehead /var/cache/bridgehead
-chown -R bridgehead:docker /tmp/bridgehead /var/cache/bridgehead
-chmod -R g+wr /var/cache/bridgehead /tmp/bridgehead
 
 log INFO "System preparation is completed and configuration is present."
 

lib/prerequisites.sh

@@ -3,20 +3,18 @@
 source lib/functions.sh
 
 detectCompose
-CONFIG_DIR="/etc/bridgehead/"
-COMPONENT_DIR="/srv/docker/bridgehead/"
 
 if ! id "bridgehead" &>/dev/null; then
   log ERROR "User bridgehead does not exist. Please run bridgehead install $PROJECT"
   exit 1
 fi
 
-checkOwner "${CONFIG_DIR}" bridgehead || exit 1
+checkOwner /srv/docker/bridgehead bridgehead || exit 1
-checkOwner "${COMPONENT_DIR}" bridgehead || exit 1
+checkOwner /etc/bridgehead bridgehead || exit 1
 
 ## Check if user is a su
 log INFO "Checking if all prerequisites are met ..."
-prerequisites="git docker curl"
+prerequisites="git docker"
 for prerequisite in $prerequisites; do
   $prerequisite --version 2>&1
   is_available=$?
@@ -34,31 +32,31 @@ fi
 log INFO "Checking configuration ..."
 
 ## Download submodule
-if [ ! -d "${CONFIG_DIR}" ]; then
+if [ ! -d "/etc/bridgehead/" ]; then
-  fail_and_report 1 "Please set up the config folder at ${CONFIG_DIR}. Instruction are in the readme."
+  fail_and_report 1 "Please set up the config folder at /etc/bridgehead. Instruction are in the readme."
 fi
 
 # TODO: Check all required variables here in a generic loop
 
 #check if project env is present
-if [ -d "${CONFIG_DIR}${PROJECT}.conf" ]; then
+if [ -d "/etc/bridgehead/${PROJECT}.conf" ]; then
-   fail_and_report 1 "Project config not found. Please copy the template from ${PROJECT} and put it under ${CONFIG_DIR}${PROJECT}.conf."
+   fail_and_report 1 "Project config not found. Please copy the template from ${PROJECT} and put it under /etc/bridgehead-config/${PROJECT}.conf."
 fi
 
 # TODO: Make sure you're in the right directory, or, even better, be independent from the working directory.
 
 log INFO "Checking ssl cert for accessing bridgehead via https"
 
-if [ ! -d "${CONFIG_DIR}traefik-tls" ]; then
+if [ ! -d "/etc/bridgehead/traefik-tls" ]; then
   log WARN "TLS certs for accessing bridgehead via https missing, we'll now create a self-signed one. Please consider getting an officially signed one (e.g. via Let's Encrypt ...) and put into /etc/bridgehead/traefik-tls"
   mkdir -p /etc/bridgehead/traefik-tls
 fi
 
-if [ ! -e "${CONFIG_DIR}traefik-tls/fullchain.pem" ]; then
+if [ ! -e "/etc/bridgehead/traefik-tls/fullchain.pem" ]; then
   openssl req -x509 -newkey rsa:4096 -nodes -keyout /etc/bridgehead/traefik-tls/privkey.pem -out /etc/bridgehead/traefik-tls/fullchain.pem -days 3650 -subj "/CN=$HOST"
 fi
 
-if [ -e "${CONFIG_DIR}"vault.conf ]; then
+if [ -e /etc/bridgehead/vault.conf ]; then
   if [ "$(stat -c "%a %U" /etc/bridgehead/vault.conf)" != "600 bridgehead" ]; then
     fail_and_report 1 "/etc/bridgehead/vault.conf has wrong owner/permissions. To correct this issue, run chmod 600 /etc/bridgehead/vault.conf && chown bridgehead /etc/bridgehead/vault.conf."
   fi
@@ -66,54 +64,48 @@ fi
 
 log INFO "Checking network access ($BROKER_URL_FOR_PREREQ) ..."
 
-source "${CONFIG_DIR}${PROJECT}".conf
+source /etc/bridgehead/${PROJECT}.conf
 source ${PROJECT}/vars
 
-if [ "${PROJECT}" != "minimal" ]; then
+set +e
-  set +e
+SERVERTIME="$(https_proxy=$HTTPS_PROXY_URL curl -m 5 -s -I $BROKER_URL_FOR_PREREQ 2>&1 | grep -i -e '^Date: ' | sed -e 's/^Date: //i')"
-  SERVERTIME="$(https_proxy=$HTTPS_PROXY_FULL_URL curl -m 5 -s -I $BROKER_URL_FOR_PREREQ 2>&1 | grep -i -e '^Date: ' | sed -e 's/^Date: //i')"
+RET=$?
-  RET=$?
+set -e
-  set -e
+if [ $RET -ne 0 ]; then
-  if [ $RET -ne 0 ]; then
+	log WARN "Unable to connect to Samply.Beam broker at $BROKER_URL_FOR_PREREQ. Please check your proxy settings.\nThe currently configured proxy was \"$HTTPS_PROXY_URL\". This error is normal when using proxy authentication."
-	  log WARN "Unable to connect to Samply.Beam broker at $BROKER_URL_FOR_PREREQ. Please check your proxy settings.\nThe currently configured proxy was \"$HTTPS_PROXY_URL\". This error is normal when using proxy authentication."
+	log WARN "Unable to check clock skew due to previous error."
-  	log WARN "Unable to check clock skew due to previous error."
+else
-  else
+	log INFO "Checking clock skew ..."
-	  log INFO "Checking clock skew ..."
 
-    SERVERTIME_AS_TIMESTAMP=$(date --date="$SERVERTIME" +%s)
+	SERVERTIME_AS_TIMESTAMP=$(date --date="$SERVERTIME" +%s)
-	  MYTIME=$(date +%s)
+	MYTIME=$(date +%s)
-	  SKEW=$(($SERVERTIME_AS_TIMESTAMP - $MYTIME))
+	SKEW=$(($SERVERTIME_AS_TIMESTAMP - $MYTIME))
-	  SKEW=$(echo $SKEW | awk -F- '{print $NF}')
+	SKEW=$(echo $SKEW | awk -F- '{print $NF}')
-	  SYNCTEXT="For example, consider entering a correct NTP server (e.g. your institution's Active Directory Domain Controller in /etc/systemd/timesyncd.conf (option NTP=) and restart systemd-timesyncd."
+	SYNCTEXT="For example, consider entering a correct NTP server (e.g. your institution's Active Directory Domain Controller in /etc/systemd/timesyncd.conf (option NTP=) and restart systemd-timesyncd."
-	  if [ $SKEW -ge 300 ]; then
+	if [ $SKEW -ge 300 ]; then
-		  report_error 5 "Your clock is not synchronized (${SKEW}s off). This will cause Samply.Beam's certificate will fail. Please setup time synchronization. $SYNCTEXT"
+		report_error 5 "Your clock is not synchronized (${SKEW}s off). This will cause Samply.Beam's certificate will fail. Please setup time synchronization. $SYNCTEXT"
-		  exit 1
+		exit 1
-	  elif [ $SKEW -ge 60 ]; then
+	elif [ $SKEW -ge 60 ]; then
-		  log WARN "Your clock is more than a minute off (${SKEW}s). Consider syncing to a time server. $SYNCTEXT"
+		log WARN "Your clock is more than a minute off (${SKEW}s). Consider syncing to a time server. $SYNCTEXT"
-	  fi
+	fi
-  fi
 fi
+
 checkPrivKey() {
-  if [ -e "${CONFIG_DIR}pki/${SITE_ID}.priv.pem" ]; then
+  if [ -e /etc/bridgehead/pki/${SITE_ID}.priv.pem ]; then
     log INFO "Success - private key found."
   else
-    log ERROR "Unable to find private key at ${CONFIG_DIR}pki/${SITE_ID}.priv.pem. To fix, please run\n  bridgehead enroll ${PROJECT}\nand follow the instructions."
+    log ERROR "Unable to find private key at /etc/bridgehead/pki/${SITE_ID}.priv.pem. To fix, please run\n  bridgehead enroll ${PROJECT}\nand follow the instructions."
     return 1
   fi
   return 0
 }
 
-if [[ "$@" =~ "noprivkey" ||  "${PROJECT}" != "minimal" ]]; then
+if [[ "$@" =~ "noprivkey" ]]; then
   log INFO "Skipping check for private key for now."
 else
   checkPrivKey || exit 1
 fi
 
-for dir in  "${CONFIG_DIR}" "${COMPONENT_DIR}"; do
-  log INFO "Checking branch: $(cd $dir && echo "$dir $(git branch --show-current)")"
-  hc_send log "Checking branch: $(cd $dir && echo "$dir $(git branch --show-current)")"
-done
-
 log INFO "Success - all prerequisites are met!"
 hc_send log "Success - all prerequisites are met!"
 

lib/systemd/bridgehead-update@.timer

@@ -1,9 +1,8 @@
 [Unit]
-Description=Daily Updates at 6am of Bridgehead (%i)
+Description=Hourly Updates of Bridgehead (%i)
 
 [Timer]
-OnCalendar=*-*-* 06:00:00
+OnCalendar=*-*-* *:00:00
-Persistent=true
 
 [Install]
 WantedBy=basic.target

lib/update-bridgehead.sh

@@ -30,7 +30,7 @@ source $CONFFILE
 assertVarsNotEmpty SITE_ID || fail_and_report 1 "Update failed: SITE_ID empty"
 export SITE_ID
 
-checkOwner /srv/docker/bridgehead bridgehead || fail_and_report 1 "Update failed: Wrong permissions in /srv/docker/bridgehead"
+checkOwner . bridgehead || fail_and_report 1 "Update failed: Wrong permissions in $(pwd)"
 checkOwner /etc/bridgehead bridgehead || fail_and_report 1 "Update failed: Wrong permissions in /etc/bridgehead"
 
 CREDHELPER="/srv/docker/bridgehead/lib/gitpassword.sh"
@@ -50,12 +50,12 @@ for DIR in /etc/bridgehead $(pwd); do
     git -C $DIR config credential.helper "$CREDHELPER"
   fi
   old_git_hash="$(git -C $DIR rev-parse --verify HEAD)"
-  if [ -z "$HTTPS_PROXY_FULL_URL" ]; then
+  if [ -z "$HTTP_PROXY_URL" ]; then
     log "INFO" "Git is using no proxy!"
     OUT=$(retry 5 git -C $DIR fetch 2>&1 && retry 5 git -C $DIR pull 2>&1)
   else
-    log "INFO" "Git is using proxy ${HTTPS_PROXY_URL} from ${CONFFILE}"
+    log "INFO" "Git is using proxy ${HTTP_PROXY_URL} from ${CONFFILE}"
-    OUT=$(retry 5 git -c http.proxy=$HTTPS_PROXY_FULL_URL -c https.proxy=$HTTPS_PROXY_FULL_URL -C $DIR fetch 2>&1 && retry 5 git -c http.proxy=$HTTPS_PROXY_FULL_URL -c https.proxy=$HTTPS_PROXY_FULL_URL -C $DIR pull 2>&1)
+    OUT=$(retry 5 git -c http.proxy=$HTTP_PROXY_URL -c https.proxy=$HTTPS_PROXY_URL -C $DIR fetch 2>&1 && retry 5 git -c http.proxy=$HTTP_PROXY_URL -c https.proxy=$HTTPS_PROXY_URL -C $DIR pull 2>&1)
   fi
   if [ $? -ne 0 ]; then
     report_error log "Unable to update git $DIR: $OUT"
@@ -80,13 +80,19 @@ 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=$new_git_hash"
     fi
     git_updated="true"
+    if [ "$DIR" == "/srv/docker/bridgehead" ]; then
+      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
   fi
 done
 
 # Check docker updates
 log "INFO" "Checking for updates to running docker images ..."
 docker_updated="false"
-for IMAGE in $($COMPOSE -p $PROJECT -f ./minimal/docker-compose.yml -f ./$PROJECT/docker-compose.yml $OVERRIDE config | grep "image:" | sed -e 's_^.*image: \(.*\).*$_\1_g; s_\"__g'); do
+for IMAGE in $(cat $PROJECT/docker-compose.yml ${OVERRIDE//-f/} minimal/docker-compose.yml | grep -v "^#" | grep "image:" | sed -e 's_^.*image: \(.*\).*$_\1_g; s_\"__g'); do
   log "INFO" "Checking for Updates of Image: $IMAGE"
   if docker pull $IMAGE | grep "Downloaded newer image"; then
     CHANGE="Image $IMAGE updated."
@@ -116,7 +122,7 @@ if [ -n "${BACKUP_DIRECTORY}" ]; then
     mkdir -p "$BACKUP_DIRECTORY"
     chown -R "$BACKUP_DIRECTORY" bridgehead;
   fi
-  checkOwner "$BACKUP_DIRECTORY" bridgehead || fail_and_report 1 "Automatic maintenance failed: Wrong permissions for backup directory $BACKUP_DIRECTORY"
+  checkOwner "$BACKUP_DIRECTORY" bridgehead || fail_and_report 1 "Automatic maintenance failed: Wrong permissions for backup directory $(pwd)"
   # Collect all container names that contain '-db'
   BACKUP_SERVICES="$(docker ps --filter name=-db --format "{{.Names}}" | tr "\n" "\ ")"
   log INFO "Performing automatic maintenance: Creating Backups for $BACKUP_SERVICES";

minimal/docker-compose.yml

@@ -10,13 +10,13 @@ services:
       - --providers.docker=true
       - --providers.docker.exposedbydefault=false
       - --providers.file.directory=/configuration/
-      - --api.dashboard=false
+      - --api.dashboard=true
       - --accesslog=true
       - --entrypoints.web.http.redirections.entrypoint.to=websecure
       - --entrypoints.web.http.redirections.entrypoint.scheme=https
     labels:
       - "traefik.enable=true"
-      - "traefik.http.routers.dashboard.rule=PathPrefix(`/api`) || PathPrefix(`/dashboard/`)"
+      - "traefik.http.routers.dashboard.rule=PathPrefix(`/api`) || PathPrefix(`/dashboard`)"
       - "traefik.http.routers.dashboard.entrypoints=websecure"
       - "traefik.http.routers.dashboard.service=api@internal"
       - "traefik.http.routers.dashboard.tls=true"
@@ -35,20 +35,17 @@ services:
     image: docker.verbis.dkfz.de/cache/samply/bridgehead-forward-proxy:latest
     environment:
       HTTPS_PROXY: ${HTTPS_PROXY_URL}
-      HTTPS_PROXY_USERNAME: ${HTTPS_PROXY_USERNAME}
+      USERNAME: ${HTTPS_PROXY_USERNAME}
-      HTTPS_PROXY_PASSWORD: ${HTTPS_PROXY_PASSWORD}
+      PASSWORD: ${HTTPS_PROXY_PASSWORD}
     tmpfs:
       - /var/log/squid
       - /var/spool/squid
     volumes:
       - /etc/bridgehead/trusted-ca-certs:/docker/custom-certs/:ro
-    healthcheck:
-      # Wait 1s before marking this service healthy. Required for the oauth2-proxy to talk to the OIDC provider on startup which will fail if the forward proxy is not started yet.
-      test: ["CMD", "sleep", "1"]
 
   landing:
     container_name: bridgehead-landingpage
-    image: docker.verbis.dkfz.de/cache/samply/bridgehead-landingpage:main
+    image: docker.verbis.dkfz.de/cache/samply/bridgehead-landingpage:master
     labels:
       - "traefik.enable=true"
       - "traefik.http.routers.landing.rule=PathPrefix(`/`)"
@@ -58,4 +55,5 @@ services:
       HOST: ${HOST}
       PROJECT: ${PROJECT}
       SITE_NAME: ${SITE_NAME}
-      ENVIRONMENT: ${ENVIRONMENT}
+
+

minimal/modules/dnpm-compose.yml

@@ -2,7 +2,7 @@ version: "3.7"
 
 services:
   dnpm-beam-proxy:
-    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${BEAM_TAG}
+    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
     container_name: bridgehead-dnpm-beam-proxy
     environment:
       BROKER_URL: ${DNPM_BROKER_URL}
@@ -18,11 +18,11 @@ services:
       - "forward_proxy"
     volumes:
       - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
-      - /srv/docker/bridgehead/ccp/root.crt.pem:/conf/root.crt.pem:ro
+      - /srv/docker/bridgehead/ccp/root-new.crt.pem:/conf/root.crt.pem:ro
 
   dnpm-beam-connect:
     depends_on: [ dnpm-beam-proxy ]
-    image: docker.verbis.dkfz.de/cache/samply/beam-connect:develop
+    image: docker.verbis.dkfz.de/cache/samply/beam-connect:dnpm
     container_name: bridgehead-dnpm-beam-connect
     environment:
       PROXY_URL: http://dnpm-beam-proxy:8081
@@ -32,14 +32,9 @@ services:
       LOCAL_TARGETS_FILE: "./conf/connect_targets.json"
       HTTP_PROXY: http://forward_proxy:3128
       HTTPS_PROXY: http://forward_proxy:3128
-      NO_PROXY: dnpm-beam-proxy,dnpm-backend, host.docker.internal${DNPM_ADDITIONAL_NO_PROXY}
+      NO_PROXY: dnpm-beam-proxy,dnpm-backend
       RUST_LOG: ${RUST_LOG:-info}
-      NO_AUTH: "true"
-      TLS_CA_CERTIFICATES_DIR: ./conf/trusted-ca-certs
-    extra_hosts:
-      - "host.docker.internal:host-gateway"
     volumes:
-      - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
       - /etc/bridgehead/dnpm/local_targets.json:/conf/connect_targets.json:ro
       - /etc/bridgehead/dnpm/central_targets.json:/conf/central_targets.json:ro
     labels:
@@ -50,10 +45,6 @@ services:
       - "traefik.http.services.dnpm-connect.loadbalancer.server.port=8062"
       - "traefik.http.routers.dnpm-connect.tls=true"
 
-  dnpm-echo:
-    image: docker.verbis.dkfz.de/cache/samply/bridgehead-echo:latest
-    container_name: bridgehead-dnpm-echo
-
 secrets:
   proxy.pem:
     file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

minimal/modules/dnpm-node-compose.yml

@@ -1,34 +0,0 @@
-version: "3.7"
-
-services:
-  dnpm-backend:
-    image: ghcr.io/kohlbacherlab/bwhc-backend:1.0-snapshot-broker-connector
-    container_name: bridgehead-dnpm-backend
-    environment:
-      - ZPM_SITE=${ZPM_SITE}
-      - N_RANDOM_FILES=${DNPM_SYNTH_NUM}
-    volumes:
-      - /etc/bridgehead/dnpm:/bwhc_config:ro
-      - ${DNPM_DATA_DIR}:/bwhc_data
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.bwhc-backend.rule=PathPrefix(`/bwhc`)"
-      - "traefik.http.services.bwhc-backend.loadbalancer.server.port=9000"
-      - "traefik.http.routers.bwhc-backend.tls=true"
-
-  dnpm-frontend:
-    image: ghcr.io/kohlbacherlab/bwhc-frontend:2209
-    container_name: bridgehead-dnpm-frontend
-    links:
-      - dnpm-backend
-    environment:
-      - NUXT_HOST=0.0.0.0
-      - NUXT_PORT=8080
-      - BACKEND_PROTOCOL=https
-      - BACKEND_HOSTNAME=$HOST
-      - BACKEND_PORT=443
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.bwhc-frontend.rule=PathPrefix(`/`)"
-      - "traefik.http.services.bwhc-frontend.loadbalancer.server.port=8080"
-      - "traefik.http.routers.bwhc-frontend.tls=true"

minimal/modules/dnpm-node-setup.sh

@@ -1,28 +0,0 @@
-#!/bin/bash
-
-if [ -n "${ENABLE_DNPM_NODE}" ]; then
-	log INFO "DNPM setup detected (BwHC Node) -- will start BwHC node."
-	OVERRIDE+=" -f ./$PROJECT/modules/dnpm-node-compose.yml"
-
-	# Set variables required for BwHC Node. ZPM_SITE is assumed to be set in /etc/bridgehead/<project>.conf
-	DNPM_APPLICATION_SECRET="$(echo \"This is a salt string to generate one consistent password for DNPM. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
-	if [ -z "${ZPM_SITE+x}" ]; then
-		log ERROR "Mandatory variable ZPM_SITE not defined!"
-		exit 1
-	fi
-	if [ -z "${DNPM_DATA_DIR+x}" ]; then
-		log ERROR "Mandatory variable DNPM_DATA_DIR not defined!"
-		exit 1
-	fi
-	DNPM_SYNTH_NUM=${DNPM_SYNTH_NUM:-0}
-	if grep -q 'traefik.http.routers.landing.rule=PathPrefix(`/landing`)' /srv/docker/bridgehead/minimal/docker-compose.override.yml 2>/dev/null; then
-		echo "Override of landing page url already in place"
-	else
-		echo "Adding override of landing page url"
-		if [ -f /srv/docker/bridgehead/minimal/docker-compose.override.yml ]; then
-			echo -e '  landing:\n    labels:\n      - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"' >> /srv/docker/bridgehead/minimal/docker-compose.override.yml
-		else
-			echo -e 'version: "3.7"\nservices:\n  landing:\n    labels:\n      - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"' >> /srv/docker/bridgehead/minimal/docker-compose.override.yml
-		fi
-	fi
-fi

minimal/modules/dnpm-setup.sh

@@ -5,18 +5,9 @@ if [ -n "${ENABLE_DNPM}" ]; then
 	OVERRIDE+=" -f ./$PROJECT/modules/dnpm-compose.yml"
 
 	# Set variables required for Beam-Connect
+	DNPM_APPLICATION_SECRET="$(echo \"This is a salt string to generate one consistent password for DNPM. It is not required to be secret.\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
 	DNPM_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
 	DNPM_BROKER_ID="broker.ccp-it.dktk.dkfz.de"
 	DNPM_BROKER_URL="https://${DNPM_BROKER_ID}"
-	if [ -z ${BROKER_URL_FOR_PREREQ+x} ]; then
-		BROKER_URL_FOR_PREREQ=$DNPM_BROKER_URL
-		log DEBUG "No Broker for clock check set; using $DNPM_BROKER_URL"
-	fi
 	DNPM_PROXY_ID="${SITE_ID}.${DNPM_BROKER_ID}"
-	# If the DNPM_NO_PROXY variable is set, prefix it with a comma (as it gets added to a comma separated list)
-	if [ -n "${DNPM_NO_PROXY}" ]; then
-		DNPM_ADDITIONAL_NO_PROXY=",${DNPM_NO_PROXY}"
-	else
-		DNPM_ADDITIONAL_NO_PROXY=""
-	fi
 fi

minimal/modules/nngm-compose.yml

@@ -1,29 +0,0 @@
-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: ${SITE_ID}TODO
-    restart: always
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.connector.rule=PathPrefix(`/nngm-connector`)"
-      - "traefik.http.middlewares.connector_strip.stripprefix.prefixes=/nngm-connector"
-      - "traefik.http.services.connector.loadbalancer.server.port=8080"
-      - "traefik.http.routers.connector.tls=true"
-      - "traefik.http.routers.connector.middlewares=connector_strip,auth-nngm"
-    volumes:
-      - nngm-rest:/var/log
-
-  traefik:
-    labels:
-      - "traefik.http.middlewares.auth-nngm.basicauth.users=${NNGM_AUTH}"
-
-

minimal/modules/nngm-setup.sh

@@ -1,6 +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