Added: Teiler documentation

Co-authored-by: Tobias Kussel <TKussel@users.noreply.github.com>

.github/CODEOWNERS

@@ -0,0 +1 @@
+*  @samply/bridgehead-developers

.github/scripts/rename_inactive_branches.py

@@ -0,0 +1,39 @@
+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

@@ -0,0 +1,27 @@
+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).
@@ -21,11 +21,17 @@ 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](#bbmri-eric-directory)
+    - [BBMRI-ERIC Directory entry needed](#bbmri-eric-directory-entry-needed)
+    - [Directory sync tool](#directory-sync-tool)
+    - [Loading data](#loading-data)
+    - [Teiler (Frontend)](#teiler-frontend)
+    - [Data Exporter Service](#data-exporter-service)
+      - [Data Quality Report](#data-quality-report)
 4. [Things you should know](#things-you-should-know)
     - [Auto-Updates](#auto-updates)
     - [Auto-Backups](#auto-backups)
     - [Non-Linux OS](#non-linux-os)
+    - [FAQ](#faq)
 5. [Troubleshooting](#troubleshooting)
     - [Docker Daemon Proxy Configuration](#docker-daemon-proxy-configuration)
     - [Monitoring](#monitoring)
@@ -33,6 +39,10 @@ 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:
@@ -41,6 +51,8 @@ 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.
@@ -51,22 +63,41 @@ 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: Please note that snap versions of Docker are not supported.
+> 📝 Note for Ubuntu: Snap versions of Docker are not supported.
 
 ### Network
 
-A running Bridgehead requires an outgoing HTTPS proxy to communicate with the central components.
+A Bridgehead communicates to all central components via outgoing HTTPS connections.
 
-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.
+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/).
 
-Note that git and Docker may also need to be configured to use this proxy. This is a job for your systems administrators.
+The following URLs need to be accessible (prefix with `https://`):
+* 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/setup/allow-list/))
+    * 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
 
-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.
+> 📝 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.
 
-Note for Ubuntu: Please note that the uncomplicated firewall (ufw) is known to conflict with Docker [here](https://github.com/chaifeng/ufw-docker).
+> 📝 Ubuntu's pre-installed uncomplicated firewall (ufw) is known to conflict with Docker, more info [here](https://github.com/chaifeng/ufw-docker).
 
 ## Deployment
 
@@ -99,7 +130,7 @@ 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/bbmri-bridgehead-configs/dummy.git
+- Repository URL containing the acces token eg. https://BH_Dummy:dummy_token@git.verbis.dkfz.de/<project>-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.
 
@@ -128,7 +159,7 @@ Pay special attention to:
 Clone the bridgehead repository:
 ```shell
 sudo mkdir -p /srv/docker/
-sudo git clone https://github.com/samply/bridgehead.git /srv/docker/bridgehead
+sudo git clone -b main https://github.com/samply/bridgehead.git /srv/docker/bridgehead
 ```
 
 Then, run the installation script:
@@ -176,7 +207,7 @@ sudo systemctl [enable|disable] bridgehead@<PROJECT>.service
 After starting the Bridgehead, you can watch the initialization process with the following command:
 
 ```shell
-journalctl -u bridgehead@bbmri -f
+/srv/docker/bridgehead/bridgehead logs <project> -f
 ```
 
 if this exits with something similar to the following:
@@ -196,8 +227,9 @@ docker ps
 There should be 6 - 10 Docker proceses. If there are fewer, then you know that something has gone wrong. To see what is going on, run:
 
 ```shell
-journalctl -u bridgehead@bbmri -f
+/srv/docker/bridgehead/bridgehead logs <Project> -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:
 
@@ -211,7 +243,7 @@ You can either do this in a browser or with curl. If you visit the URL in the br
 curl -k https://localhost
 ```
 
-If you get errors when you do this, you need to use ```docker logs``` to examine your landing page container in order to determine what is going wrong.
+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 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.
 
@@ -227,6 +259,8 @@ sh bridgehead uninstall
 
 ## Site-specific configuration
 
+[How to Change Config Access Token](docs/update-access-token.md)
+
 ### HTTPS Access
 
 Even within your internal network, the Bridgehead enforces HTTPS for all services. During the installation, a self-signed, long-lived certificate was created for you. To increase security, you can simply replace the files under `/etc/bridgehead/traefik-tls` with ones from established certification authorities such as [Let's Encrypt](https://letsencrypt.org) or [DFN-AAI](https://www.aai.dfn.de).
@@ -235,6 +269,21 @@ 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.
@@ -247,35 +296,125 @@ All of the Bridgehead's outgoing connections are secured by transport encryption
 
 Your Bridgehead's actual data is not stored in the above directories, but in named docker volumes, see `docker volume ls` and `docker volume inspect <volume_name>`.
 
-### BBMRI-ERIC Directory
+### BBMRI-ERIC Directory entry needed
 
-If you run a biobank, you should register with the [Directory](https://directory.bbmri-eric.eu), a BBMRI-ERIC project that catalogs biobanks.
+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.
 
 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 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.
+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.
 
-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.
+### Directory sync tool
 
-Full details can be found in [directory_sync_service](https://github.com/samply/directory_sync_service).
+The Bridgehead's **Directory Sync** is an optional feature that keeps the BBMRI-ERIC Directory up to date with your local data, e.g. number of samples. Conversely, it can also update the local FHIR store with the latest contact details etc. from the  BBMRI-ERIC Directory.
 
-To enable it, you will need to set these variables to the ```bbmri.conf``` file of your GitLab repository. Here is an example config:
+You should talk with your local data protection group regarding the information that is published by Directory sync.
+
+To enable it, you will need to explicitly set the username and password variables for BBMRI-ERIC Directory login in the configuration file of your GitLab repository (e.g. ```bbmri.conf```). Here is an example minimal config:
 
 ```
-### Directory sync service
-DS_DIRECTORY_URL=https://directory.bbmri-eric.eu
 DS_DIRECTORY_USER_NAME=your_directory_username
-DS_DIRECTORY_USER_PASS=qwdnqwswdvqHBVGFR9887
+DS_DIRECTORY_USER_PASS=your_directory_password
-DS_TIMER_CRON="0 22 * * *"
 ```
-You must contact the Directory for your national node to find the URL, and to register as a user.
+Please contact your National Node or Directory support (directory-dev@helpdesk.bbmri-eric.eu) to obtain these credentials.
 
-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.
+The following environment variables can be used from within your config file to control the behavior of Directory sync:
 
-Once you edited the gitlab config, the bridgehead will autoupdate the config with the values and will sync the data.
+| Variable                           | Purpose                                                                                                                                                              | Default if not specified               |
+|:-----------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------|
+| DS_DIRECTORY_URL                   | Base URL of the Directory                                                                                                                                            | https://directory-backend.molgenis.net |
+| DS_DIRECTORY_USER_NAME             | User name for logging in to Directory **Mandatory**                                                                                                                  |                                        |
+| DS_DIRECTORY_USER_PASS             | Password for logging in to Directory **Mandatory**                                                                                                                   |                                        |
+| DS_DIRECTORY_DEFAULT_COLLECTION_ID | ID of collection to be used if not in samples                                                                                                                        |                                        |
+| DS_DIRECTORY_ALLOW_STAR_MODEL      | Set to 'True' to send star model info to Directory                                                                                                                   | True                                  |
+| DS_FHIR_STORE_URL                  | URL for FHIR store                                                                                                                                                   | http://bridgehead-bbmri-blaze:8080     |
+| DS_TIMER_CRON                      | Execution interval for Directory sync, [cron](https://crontab.guru) format                                                                                           | 0 22 * * *                             |
+| DS_IMPORT_BIOBANKS                 | Set to 'True' to import biobank metadata from Directory                                                                                                              | True                                  |
+| DS_IMPORT_COLLECTIONS              | Set to 'True' to import collection metadata from Directory                                                                                                           | True                                  |
+
+Once you have finished editing the config, the Bridgehead will autoupdate the config with the values and will sync data at regular intervals, using the time specified in DS_TIMER_CRON.
 
 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.
 
+More details of Directory sync can be found in [directory_sync_service](https://github.com/samply/directory_sync_service).
+
+### 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).
+
+### Clearing data
+
+The Bridgehead's FHIR store, Blaze, saves its data in a Docker volume. This means that the data will persist even if you stop the Bridgehead. You can clear existing data from the FHIR store by deleting the relevant Docker volume.
+
+First, stop the Bridgehead:
+```shell
+sudo systemctl stop bridgehead@<PROJECT>.service
+```
+Now remove the volume:
+```shell
+docker volume rm <PROJECT>_blaze-data
+```
+Finally, restart the Bridgehead:
+```shell
+sudo systemctl start bridgehead@<PROJECT>.service
+```
+You will need to do this for example if you are using a VM as a test environment and you subsequently want to use the same VM for production.
+
+#### 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).
+
+### Teiler (Frontend)
+
+Teiler is the web-based frontend of the Bridgehead, providing access to its various internal, and external services and components.   
+To learn how to integrate your custom module into Teiler, please refer to https://github.com/samply/teiler-dashboard.
+- To activate Teiler, set the following environment variable in your `<PROJECT>.conf` file:  
+
+```bash
+ENABLE_TEILER=true
+```
+[For further information](ccp/modules/teiler.md)  
+
+### Data Exporter Service
+
+The Exporter is a dedicated service for extracting and exporting Bridgehead data in (tabular) formats such as Excel, CSV, Opal, JSON, XML, ...  
+- To enable the Exporter service, set the following environment variable in your `<PROJECT>.conf` file:  
+
+```bash
+ENABLE_EXPORTER=true
+```
+
+#### Data Quality Report
+To assess the quality and plausibility of your imported data, the Reporter component is pre-configured to generate Excel reports with data quality metrics and statistical analyses. Reporter is part of the Exporter and can be enabled by setting the same environment variable in your `<PROJECT>.conf` file:
+```bash
+ENABLE_EXPORTER=true
+```
+
+For convenience, it's recommended to enable the Teiler web frontend alongside the Exporter to access export and quality control features via a web interface: set the following environment varibles in your `<PROJECT>.conf` file:
+```bash
+ENABLE_TEILER=true
+ENABLE_EXPORTER=true
+```
+[For further information](ccp/modules/exporter.md)  
+
 ## Things you should know
 
 ### Auto-Updates
@@ -315,12 +454,80 @@ We have tested the installation procedure with an Ubuntu 22.04 guest system runn
 
 Installation under WSL ought to work, but we have not tested this.
 
+### FAQ
+
+**Q: How is the security of GitHub pulls, volumes/containers, and image signing ensured?**
+
+A: Changes to Git branches that could be delivered to sites (main and develop) must be accepted via a pull request with at least two positive reviews.
+Containers/images are not built manually, but rather automatically through a CI/CD pipeline, so that an image can be rolled back to a defined code version at any time without changes.
+**Note:** If firewall access for (outgoing) connections to GitHub and/or Docker Hub is problematic at the site, mirrors for both services are available, operated by the DKFZ.
+
+**Q: How is authentication between users and components regulated?**
+
+A: When setting up a Bridgehead, a private key and a so-called Certificate Sign Request (CSR) are generated locally. This CSR is manually signed by the broker operator, which allows the Bridgehead access to the network infrastructure.
+All communication runs via Samply.Beam and is therefore end-to-end encrypted, but also signed. This allows the integrity and authenticity of the sender to be technically verified (which happens automatically both in the broker and at the recipients).
+The connection to the broker is additionally secured using traditional TLS (transport encryption over https).
+
+**Q: Are there any statistics on incoming traffic from the Bridgehead (what goes in and what goes out)?**
+
+A: Incoming and outgoing traffic can only enter/leave the Bridgehead via a forward or reverse proxy, respectively. These components log all connections.
+Statistical analysis is not currently being conducted, but is on the roadmap for some projects. We are also working on a dashboard for all tasks/responses delivered via Samply.Beam.
+
+**Q: How is container access controlled, and what permission level is used?**
+
+A: Currently, it is not possible to run the Bridgehead "out-of-the-box" as a rootless Docker Compose stack. The main reason is the operation of the reverse proxy (Traefik), which binds to the privileged ports 80 (HTTP) and 443 (HTTPS).
+Otherwise, there are no known technical obstacles, although we don't have concrete experience implementing this.
+At the file system level, a "bridgehead" user is created during installation, which manages the configuration and Bridgehead folders.
+
+**Q: Is a cloud installation (not a company-owned one, but an external service provider) possible?**
+
+A: Technically, yes. This is primarily a data protection issue between the participant and their cloud provider.
+The Bridgehead contains a data storage system that, during use, contains sensitive patient and sample data.
+There are cloud providers with whom appropriately worded contracts can be concluded to make this possible.
+Of course, the details must be discussed with the responsible data protection officer.
+
+**Q: What needs to be considered regarding the Docker distribution/registry, and how is it used here?**
+
+A: The Bridgehead images are located both in Docker Hub and mirrored in a registry operated by the DKFZ.
+The latter is used by default, avoiding potential issues with Docker Hub URL activation or rate limits.
+When using automatic updates (highly recommended), an daily check is performed for:
+- site configuration updates
+- Bridgehead software updates
+- container image updates
+
+If updates are found, they are downloaded and applied.
+See the first question for the control mechanism.
+
+**Q: Is data only transferred one-way (Bridgehead/FHIR Store → Central/Locator), or is two-way access necessary?**
+
+A: By using Samply.Beam, only one outgoing connection to the broker is required at the network level (i.e., Bridgehead → Broker).
+
 ## Troubleshooting
 
 ### Docker Daemon Proxy Configuration
 
-Docker has a background daemon, responsible for downloading images and starting them. Sometimes, proxy configuration from your system won't carry over and it will fail to download images. In that case, configure the proxy for this daemon as described in the [official documentation](https://docs.docker.com).
+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:
 
+``` 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

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

bbmri/modules/directory-sync-compose.yml

@@ -1,8 +1,18 @@
+version: "3.7"
+
 services:
   directory_sync_service:
     image: "docker.verbis.dkfz.de/cache/samply/directory_sync_service"
     environment:
-      DS_DIRECTORY_URL: ${DS_DIRECTORY_URL}
+      DS_DIRECTORY_URL: ${DS_DIRECTORY_URL:-https://directory.bbmri-eric.eu}
       DS_DIRECTORY_USER_NAME: ${DS_DIRECTORY_USER_NAME}
-      DS_DIRECTORY_PASS_CODE: ${DS_DIRECTORY_PASS_CODE}
+      DS_DIRECTORY_USER_PASS: ${DS_DIRECTORY_USER_PASS}
-      DS_TIMER_CRON: ${DS_TIMER_CRON}
+      DS_TIMER_CRON: ${DS_TIMER_CRON:-0 22 * * *}
+      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}
+      DS_IMPORT_BIOBANKS: ${DS_IMPORT_BIOBANKS:-true}
+      DS_IMPORT_COLLECTIONS: ${DS_IMPORT_COLLECTIONS:-true}
+    depends_on:
+      - "blaze"

bbmri/modules/dnpm-compose.yml

@@ -1,50 +0,0 @@
-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

@@ -1,13 +0,0 @@
-#!/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:main
+    image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}-bbmri
     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:develop
+    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${BEAM_TAG}
     container_name: bridgehead-beam-proxy-eric
     environment:
       BROKER_URL: ${ERIC_BROKER_URL}
@@ -32,5 +32,5 @@ services:
       - "forward_proxy"
     volumes:
       - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
-      - /srv/docker/bridgehead/bbmri/modules/eric.root.crt.pem:/conf/root.crt.pem:ro
+      - /srv/docker/bridgehead/bbmri/modules/${ERIC_ROOT_CERT}.root.crt.pem:/conf/root.crt.pem:ro
 

bbmri/modules/eric-setup.sh

@@ -4,8 +4,27 @@ if [ "${ENABLE_ERIC}" == "true" ]; then
 	log INFO "BBMRI-ERIC setup detected -- will start services for BBMRI-ERIC."
 	OVERRIDE+=" -f ./$PROJECT/modules/eric-compose.yml"
 
-	# Set required variables
+	# The environment needs to be defined in /etc/bridgehead
-	ERIC_BROKER_ID=broker.bbmri.samply.de
+	case "$ENVIRONMENT" in
+		"production")
+			export ERIC_BROKER_ID=broker.bbmri.samply.de
+			export ERIC_ROOT_CERT=eric
+			;;
+		"acceptance")
+			export ERIC_BROKER_ID=broker-acc.bbmri-acc.samply.de
+			export ERIC_ROOT_CERT=eric.acc
+			;;
+		"test")
+			export ERIC_BROKER_ID=broker-test.bbmri-test.samply.de
+			export ERIC_ROOT_CERT=eric.test
+			;;
+		*)
+			report_error 6 "Environment \"$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.acc.root.crt.pem

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

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

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

bbmri/modules/exporter-compose.yml

@@ -0,0 +1,86 @@
+version: "3.7"
+
+services:
+  exporter:
+    image: docker.verbis.dkfz.de/ccp/dktk-exporter:latest
+    container_name: bridgehead-bbmri-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: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
+      EXPORTER_DB_URL: "jdbc:postgresql://exporter-db:5432/exporter"
+      HTTP_RELATIVE_PATH: "/bbmri-exporter"
+      SITE: "${SITE_ID}"
+      HTTP_SERVLET_REQUEST_SCHEME: "https"
+      OPAL_PASSWORD: "${EXPORTER_OPAL_PASSWORD}"
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.exporter_bbmri.rule=PathPrefix(`/bbmri-exporter`)"
+      - "traefik.http.services.exporter_bbmri.loadbalancer.server.port=8092"
+      - "traefik.http.routers.exporter_bbmri.tls=true"
+      - "traefik.http.middlewares.exporter_bbmri_strip.stripprefix.prefixes=/bbmri-exporter"
+      - "traefik.http.routers.exporter_bbmri.middlewares=exporter_bbmri_strip"
+      # Main router
+      - "traefik.http.routers.exporter_bbmri.priority=20"
+
+      # API router
+      - "traefik.http.routers.exporter_bbmri_api.middlewares=exporter_bbmri_strip,exporter_auth"
+      - "traefik.http.routers.exporter_bbmri_api.rule=PathRegexp(`/bbmri-exporter/.+`)"
+      - "traefik.http.routers.exporter_bbmri_api.tls=true"
+      - "traefik.http.routers.exporter_bbmri_api.priority=25"
+
+      # Shared middlewares
+      - "traefik.http.middlewares.exporter_auth.basicauth.users=${EXPORTER_USER}"
+
+    volumes:
+      - "/var/cache/bridgehead/bbmri/exporter-files:/app/exporter-files/output"
+
+  exporter-db:
+    image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
+    container_name: bridgehead-bbmri-exporter-db
+    environment:
+      POSTGRES_USER: "exporter"
+      POSTGRES_PASSWORD: "${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/bbmri/exporter-db:/var/lib/postgresql/data"
+
+  reporter:
+    image: docker.verbis.dkfz.de/ccp/dktk-reporter:latest
+    container_name: bridgehead-bbmri-reporter
+    environment:
+      JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
+      LOG_LEVEL: "INFO"
+      CROSS_ORIGINS: "https://${HOST}"
+      HTTP_RELATIVE_PATH: "/bbmri-reporter"
+      SITE: "${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 bbmri 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/bbmri/reporter-files:/app/reports"
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.reporter_bbmri.rule=PathPrefix(`/bbmri-reporter`)"
+      - "traefik.http.services.reporter_bbmri.loadbalancer.server.port=8095"
+      - "traefik.http.routers.reporter_bbmri.tls=true"
+      - "traefik.http.middlewares.reporter_bbmri_strip.stripprefix.prefixes=/bbmri-reporter"
+      - "traefik.http.routers.reporter_bbmri.middlewares=reporter_bbmri_strip"
+      - "traefik.http.routers.reporter_bbmri.priority=20"
+
+      - "traefik.http.routers.reporter_bbmri_api.middlewares=reporter_bbmri_strip,exporter_auth"
+      - "traefik.http.routers.reporter_bbmri_api.rule=PathRegexp(`/bbmri-reporter/.+`)"
+      - "traefik.http.routers.reporter_bbmri_api.tls=true"
+      - "traefik.http.routers.reporter_bbmri_api.priority=25"
+

bbmri/modules/exporter-setup.sh

@@ -0,0 +1,8 @@
+#!/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

bbmri/modules/exporter.md

@@ -0,0 +1,15 @@
+# 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.

bbmri/modules/gbn-compose.yml

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

bbmri/modules/gbn-setup.sh

@@ -4,10 +4,25 @@ if [ "${ENABLE_GBN}" == "true" ]; then
 	log INFO "GBN setup detected -- will start services for German Biobank Node."
 	OVERRIDE+=" -f ./$PROJECT/modules/gbn-compose.yml"
 
-	# Set required variables
+	# The environment needs to be defined in /etc/bridgehead
-	GBN_BROKER_ID='#TODO#'
+	case "$ENVIRONMENT" in
+		"production")
+			export GBN_BROKER_ID=broker.bbmri.de
+			export GBN_ROOT_CERT=gbn
+			;;
+		"test")
+			export GBN_BROKER_ID=broker.test.bbmri.de
+			export GBN_ROOT_CERT=gbn.test
+			;;
+		*)
+			report_error 6 "Environment \"$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=todo@verbis.dkfz.de
+	GBN_SUPPORT_EMAIL=feedback@germanbiobanknode.de
 fi

bbmri/modules/gbn.root.crt.pem

@@ -1 +1,20 @@
-#TODO#
+-----BEGIN CERTIFICATE-----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+-----END CERTIFICATE-----

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

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

bbmri/modules/teiler-compose.yml

@@ -0,0 +1,70 @@
+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_bbmri.rule=PathPrefix(`/bbmri-teiler`)"
+      - "traefik.http.services.teiler_orchestrator_bbmri.loadbalancer.server.port=9000"
+      - "traefik.http.routers.teiler_orchestrator_bbmri.tls=true"
+      - "traefik.http.middlewares.teiler_orchestrator_bbmri_strip.stripprefix.prefixes=/bbmri-teiler"
+      - "traefik.http.routers.teiler_orchestrator_bbmri.middlewares=teiler_orchestrator_bbmri_strip"
+    environment:
+      TEILER_BACKEND_URL: "https://${HOST}/bbmri-teiler-backend"
+      TEILER_DASHBOARD_URL: "https://${HOST}/bbmri-teiler-dashboard"
+      DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE_LOWER_CASE}"
+      HTTP_RELATIVE_PATH: "/bbmri-teiler"
+
+  teiler-dashboard:
+    image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:develop
+    container_name: bridgehead-teiler-dashboard
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.teiler_dashboard_bbmri.rule=PathPrefix(`/bbmri-teiler-dashboard`)"
+      - "traefik.http.services.teiler_dashboard_bbmri.loadbalancer.server.port=80"
+      - "traefik.http.routers.teiler_dashboard_bbmri.tls=true"
+      - "traefik.http.middlewares.teiler_dashboard_bbmri_strip.stripprefix.prefixes=/bbmri-teiler-dashboard"
+      - "traefik.http.routers.teiler_dashboard_bbmri.middlewares=teiler_dashboard_bbmri_strip"
+    environment:
+      DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
+      TEILER_BACKEND_URL: "https://${HOST}/bbmri-teiler-backend"
+      TEILER_DASHBOARD_URL: "https://${HOST}/bbmri-teiler-dashboard"
+      OIDC_URL: "${OIDC_URL}"
+      OIDC_CLIENT_ID: "${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}/bbmri-teiler"
+      TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/bbmri-teiler"
+      TEILER_USER: "${OIDC_USER_GROUP}"
+      TEILER_ADMIN: "${OIDC_ADMIN_GROUP}"
+      REPORTER_DEFAULT_TEMPLATE_ID: "bbmri-qb"
+      EXPORTER_DEFAULT_TEMPLATE_ID: "bbmri"
+
+
+  teiler-backend:
+    image: docker.verbis.dkfz.de/ccp/bbmri-teiler-backend:latest
+    container_name: bridgehead-teiler-backend
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.teiler_backend_bbmri.rule=PathPrefix(`/bbmri-teiler-backend`)"
+      - "traefik.http.services.teiler_backend_bbmri.loadbalancer.server.port=8085"
+      - "traefik.http.routers.teiler_backend_bbmri.tls=true"
+      - "traefik.http.middlewares.teiler_backend_bbmri_strip.stripprefix.prefixes=/bbmri-teiler-backend"
+      - "traefik.http.routers.teiler_backend_bbmri.middlewares=teiler_backend_bbmri_strip"
+    environment:
+      LOG_LEVEL: "INFO"
+      APPLICATION_PORT: "8085"
+      APPLICATION_ADDRESS: "${HOST}"
+      DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
+      TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/bbmri-teiler"
+      TEILER_ORCHESTRATOR_URL: "https://${HOST}/bbmri-teiler"
+      TEILER_DASHBOARD_DE_URL: "https://${HOST}/bbmri-teiler-dashboard/de"
+      TEILER_DASHBOARD_EN_URL: "https://${HOST}/bbmri-teiler-dashboard/en"
+      HTTP_PROXY: "http://forward_proxy:3128"

bbmri/modules/teiler-setup.sh

@@ -0,0 +1,8 @@
+#!/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=EN
+  TEILER_DEFAULT_LANGUAGE_LOWER_CASE=${TEILER_DEFAULT_LANGUAGE,,}
+fi

bbmri/modules/teiler.md

@@ -0,0 +1,19 @@
+# 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.

bbmri/vars

@@ -1,11 +1,16 @@
+BROKER_ID=broker-test.bbmri-test.samply.de
+BROKER_URL=https://${BROKER_ID}
+PROXY_ID=${SITE_ID}.${BROKER_ID}
+PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
+BROKER_URL_FOR_PREREQ=$BROKER_URL
+
 # Makes sense for all European Biobanks
 : ${ENABLE_ERIC:=true}
 
 # Makes only sense for German Biobanks
 : ${ENABLE_GBN:=false}
 
-FOCUS_RETRY_COUNT=32
+FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64}
-PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
 
 for module in $PROJECT/modules/*.sh
 do
@@ -14,7 +19,7 @@ do
 done
 
 SUPPORT_EMAIL=$ERIC_SUPPORT_EMAIL
-BROKER_URL_FOR_PREREQ=$ERIC_BROKER_URL
+BROKER_URL_FOR_PREREQ="${ERIC_BROKER_URL:-$GBN_BROKER_URL}"
 
 if [ -n "$GBN_SUPPORT_EMAIL" ]; then
     SUPPORT_EMAIL=$GBN_SUPPORT_EMAIL
@@ -34,4 +39,4 @@ 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

@@ -32,6 +32,18 @@ case "$PROJECT" in
 	bbmri)
 		#nothing extra to do
 		;;
+	cce)
+		#nothing extra to do
+		;;
+	itcc)
+		#nothing extra to do
+		;;
+	kr)
+		#nothing extra to do
+		;;
+	dhki)
+		#nothing extra to do
+		;;
 	minimal)
 		#nothing extra to do
 		;;
@@ -41,15 +53,47 @@ case "$PROJECT" in
 		;;
 esac
 
+# Loads config variables and runs the projects setup script
 loadVars() {
-	# Load variables from /etc/bridgehead and /srv/docker/bridgehead
 	set -a
+	# Source the project specific config file
 	source /etc/bridgehead/$PROJECT.conf || fail_and_report 1 "/etc/bridgehead/$PROJECT.conf not found"
+	# Source the project specific local config file if present
+	# This file is ignored by git as oposed to the regular config file as it contains private site information like etl auth data
 	if [ -e /etc/bridgehead/$PROJECT.local.conf ]; then
 		log INFO "Applying /etc/bridgehead/$PROJECT.local.conf"
 		source /etc/bridgehead/$PROJECT.local.conf || fail_and_report 1 "Found /etc/bridgehead/$PROJECT.local.conf but failed to import"
 	fi
+	# Set execution environment on main default to prod else test
+	if [[ -z "${ENVIRONMENT+x}" ]]; then
+		if [ "$(git rev-parse --abbrev-ref HEAD)" == "main" ]; then
+			ENVIRONMENT="production"
+		else
+			ENVIRONMENT="test" # we have acceptance environment in BBMRI ERIC and it would be more appropriate to default to that one in case the data they have in BH is real, but I'm gonna leave it as is for backward compatibility
+		fi
+	fi
+	# Source the versions of the images components 
+	case "$ENVIRONMENT" in
+		"production")
+			source ./versions/prod
+			;;
+		"test")
+			source ./versions/test
+			;;
+		"acceptance")
+			source ./versions/acceptance
+			;;
+		*)
+			report_error 7 "Environment \"$ENVIRONMENT\" is unknown. Assuming production. FIX THIS!"
+			source ./versions/prod
+			;;
+	esac
 	fetchVarsFromVaultByFile /etc/bridgehead/$PROJECT.conf || fail_and_report 1 "Unable to fetchVarsFromVaultByFile"
+	setHostname
+	optimizeBlazeMemoryUsage
+	# Run project specific setup if it exists
+	# This will ususally modiy the `OVERRIDE` to include all the compose files that the project depends on
+	# This is also where projects specify which modules to load
 	[ -e ./$PROJECT/vars ] && source ./$PROJECT/vars
 	set +a
 
@@ -64,7 +108,7 @@ loadVars() {
 		OVERRIDE+=" -f ./$PROJECT/docker-compose.override.yml"
 	fi
 	detectCompose
-	setHostname
+	setupProxy
 }
 
 case "$ACTION" in
@@ -72,11 +116,14 @@ case "$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 $OVERRIDE down
@@ -85,6 +132,16 @@ case "$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

@@ -0,0 +1,68 @@
+version: "3.7"
+
+services:
+  blaze:
+    image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
+    container_name: bridgehead-cce-blaze
+    environment:
+      BASE_URL: "http://bridgehead-cce-blaze:8080"
+      JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
+      DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
+      DB_BLOCK_CACHE_SIZE: ${BLAZE_MEMORY_CAP}
+      CQL_EXPR_CACHE_SIZE: ${BLAZE_CQL_CACHE_CAP:-32}
+      ENFORCE_REFERENTIAL_INTEGRITY: "false"
+    volumes:
+      - "blaze-data:/app/data"
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.blaze_cce.rule=PathPrefix(`/cce-localdatamanagement`)"
+      - "traefik.http.middlewares.cce_b_strip.stripprefix.prefixes=/cce-localdatamanagement"
+      - "traefik.http.services.blaze_cce.loadbalancer.server.port=8080"
+      - "traefik.http.routers.blaze_cce.middlewares=cce_b_strip,auth"
+      - "traefik.http.routers.blaze_cce.tls=true"
+
+  focus:
+    image: docker.verbis.dkfz.de/cache/samply/focus:${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
+      QUERIES_TO_CACHE: '/queries_to_cache.conf'
+      ENDPOINT_TYPE: ${FOCUS_ENDPOINT_TYPE:-blaze}
+    volumes:
+      - /srv/docker/bridgehead/cce/queries_to_cache.conf:/queries_to_cache.conf:ro
+    depends_on:
+      - "beam-proxy"
+      - "blaze"
+
+  beam-proxy:
+    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${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

@@ -0,0 +1,33 @@
+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

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

cce/queries_to_cache.conf

@@ -0,0 +1,2 @@
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
+bGlicmFyeSBSZXRyaWV2ZQp1c2luZyBGSElSIHZlcnNpb24gJzQuMC4wJwppbmNsdWRlIEZISVJIZWxwZXJzIHZlcnNpb24gJzQuMC4wJwpjb2Rlc3lzdGVtIFNhbXBsZU1hdGVyaWFsVHlwZTogJ2h0dHBzOi8vZmhpci5iYm1yaS5kZS9Db2RlU3lzdGVtL1NhbXBsZU1hdGVyaWFsVHlwZScKCmNvZGVzeXN0ZW0gbG9pbmM6ICdodHRwOi8vbG9pbmMub3JnJwpjb2Rlc3lzdGVtIGljZDEwOiAnaHR0cDovL2ZoaXIuZGUvQ29kZVN5c3RlbS9iZmFybS9pY2QtMTAtZ20nCmNvZGVzeXN0ZW0gbW9ycGg6ICd1cm46b2lkOjIuMTYuODQwLjEuMTEzODgzLjYuNDMuMScKCmNvbnRleHQgUGF0aWVudAoKREtUS19TVFJBVF9HRU5ERVJfU1RSQVRJRklFUgoKREtUS19TVFJBVF9BR0VfU1RSQVRJRklFUgoKREtUS19TVFJBVF9ERUNFQVNFRF9TVFJBVElGSUVSCgpES1RLX1NUUkFUX0RJQUdOT1NJU19TVFJBVElGSUVSCgpES1RLX1NUUkFUX1NQRUNJTUVOX1NUUkFUSUZJRVIKCkRLVEtfU1RSQVRfUFJPQ0VEVVJFX1NUUkFUSUZJRVIKCkRLVEtfU1RSQVRfTUVESUNBVElPTl9TVFJBVElGSUVSCkRLVEtfU1RSQVRfREVGX0lOX0lOSVRJQUxfUE9QVUxBVElPTgooKGV4aXN0cyBbQ29uZGl0aW9uOiBDb2RlICdDNjEnIGZyb20gaWNkMTBdKSBhbmQKKChleGlzdHMgZnJvbSBbT2JzZXJ2YXRpb246IENvZGUgJzU5ODQ3LTQnIGZyb20gbG9pbmNdIE8Kd2hlcmUgTy52YWx1ZS5jb2RpbmcuY29kZSBjb250YWlucyAnODE0MC8zJykgb3IKKGV4aXN0cyBmcm9tIFtPYnNlcnZhdGlvbjogQ29kZSAnNTk4NDctNCcgZnJvbSBsb2luY10gTwp3aGVyZSBPLnZhbHVlLmNvZGluZy5jb2RlIGNvbnRhaW5zICc4MTQ3LzMnKSBvcgooZXhpc3RzIGZyb20gW09ic2VydmF0aW9uOiBDb2RlICc1OTg0Ny00JyBmcm9tIGxvaW5jXSBPCndoZXJlIE8udmFsdWUuY29kaW5nLmNvZGUgY29udGFpbnMgJzg0ODAvMycpIG9yCihleGlzdHMgZnJvbSBbT2JzZXJ2YXRpb246IENvZGUgJzU5ODQ3LTQnIGZyb20gbG9pbmNdIE8Kd2hlcmUgTy52YWx1ZS5jb2RpbmcuY29kZSBjb250YWlucyAnODUwMC8zJykpKQ==

cce/root.crt.pem

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

cce/vars

@@ -0,0 +1,14 @@
+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

@@ -2,11 +2,14 @@ version: "3.7"
 
 services:
   blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:latest
+    image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
     container_name: bridgehead-ccp-blaze
     environment:
       BASE_URL: "http://bridgehead-ccp-blaze:8080"
-      JAVA_TOOL_OPTIONS: "-Xmx4g"
+      JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
+      DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
+      DB_BLOCK_CACHE_SIZE: ${BLAZE_MEMORY_CAP}
+      CQL_EXPR_CACHE_SIZE: ${BLAZE_CQL_CACHE_CAP:-32}
       ENFORCE_REFERENTIAL_INTEGRITY: "false"
     volumes:
       - "blaze-data:/app/data"
@@ -19,7 +22,7 @@ services:
       - "traefik.http.routers.blaze_ccp.tls=true"
 
   focus:
-    image: docker.verbis.dkfz.de/cache/samply/focus:main
+    image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}-dktk
     container_name: bridgehead-focus
     environment:
       API_KEY: ${FOCUS_BEAM_SECRET_SHORT}
@@ -28,13 +31,17 @@ services:
       BLAZE_URL: "http://bridgehead-ccp-blaze:8080/fhir/"
       BEAM_PROXY_URL: http://beam-proxy:8081
       RETRY_COUNT: ${FOCUS_RETRY_COUNT}
-      OBFUSCATE: "no"
+      EPSILON: 0.28
+      QUERIES_TO_CACHE: '/queries_to_cache.conf'
+      ENDPOINT_TYPE: ${FOCUS_ENDPOINT_TYPE:-blaze}
+    volumes:
+      - /srv/docker/bridgehead/ccp/queries_to_cache.conf:/queries_to_cache.conf:ro
     depends_on:
       - "beam-proxy"
       - "blaze"
 
   beam-proxy:
-    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
+    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${BEAM_TAG}
     container_name: bridgehead-beam-proxy
     environment:
       BROKER_URL: ${BROKER_URL}
@@ -52,7 +59,6 @@ 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

@@ -0,0 +1,32 @@
+version: "3.7"
+
+services:
+  blaze-secondary:
+    image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
+    container_name: bridgehead-ccp-blaze-secondary
+    environment:
+      BASE_URL: "http://bridgehead-ccp-blaze-secondary:8080"
+      JAVA_TOOL_OPTIONS: "-Xmx${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"
+    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

@@ -0,0 +1,11 @@
+#!/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

@@ -0,0 +1,170 @@
+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: "${RSTUDIO_ADMIN_PASSWORD}" # It is required, even if the authentication is disabled
+      DISABLE_AUTH: "true" # https://rocker-project.org/images/versioned/rstudio.html#how-to-use
+      HTTP_RELATIVE_PATH: "/rstudio"
+      ALL_PROXY: "http://forward_proxy:3128" # https://rocker-project.org/use/networking.html
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.rstudio_ccp.rule=PathPrefix(`/rstudio`)"
+      - "traefik.http.services.rstudio_ccp.loadbalancer.server.port=8787"
+      - "traefik.http.middlewares.rstudio_ccp_strip.stripprefix.prefixes=/rstudio"
+      - "traefik.http.routers.rstudio_ccp.tls=true"
+      - "traefik.http.routers.rstudio_ccp.middlewares=oidcAuth,rstudio_ccp_strip"
+    networks:
+      - rstudio
+
+  opal:
+    container_name: bridgehead-opal
+    image: docker.verbis.dkfz.de/ccp/dktk-opal:latest
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.opal_ccp.rule=PathPrefix(`/opal`)"
+      - "traefik.http.services.opal_ccp.loadbalancer.server.port=8080"
+      - "traefik.http.routers.opal_ccp.tls=true"
+    links:
+      - opal-rserver
+      - opal-db
+    environment:
+      JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC -Dhttps.proxyHost=forward_proxy -Dhttps.proxyPort=3128"
+      # OPAL_ADMINISTRATOR_USER: "administrator" # This line is kept for informational purposes
+      OPAL_ADMINISTRATOR_PASSWORD: "${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: "${OIDC_URL}"
+      OIDC_CLIENT_ID: "${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: ${TOKEN_MANAGER_SECRET}
+      BEAM_DATASHIELD_PROXY: request-manager
+    volumes:
+      - "/var/cache/bridgehead/ccp/opal-metadata-db:/srv" # Opal metadata
+    secrets:
+      - opal-cert.pem
+      - opal-key.pem
+
+  opal-db:
+    container_name: bridgehead-opal-db
+    image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
+    environment:
+      POSTGRES_PASSWORD: "${OPAL_DB_PASSWORD}" # Set in datashield-setup.sh
+      POSTGRES_USER: "opal"
+      POSTGRES_DB: "opal"
+    volumes:
+      - "/var/cache/bridgehead/ccp/opal-db:/var/lib/postgresql/data" # Opal project data (imported from exporter)
+
+  opal-rserver:
+    container_name: bridgehead-opal-rserver
+    image: docker.verbis.dkfz.de/ccp/dktk-rserver # datashield/rock-base + dsCCPhos
+    tmpfs:
+      - /srv
+
+  beam-connect:
+    image: docker.verbis.dkfz.de/cache/samply/beam-connect:develop
+    container_name: bridgehead-datashield-connect
+    environment:
+      PROXY_URL: "http://beam-proxy:8081"
+      TLS_CA_CERTIFICATES_DIR: /run/secrets
+      APP_ID: datashield-connect.${SITE_ID}.${BROKER_ID}
+      PROXY_APIKEY: ${DATASHIELD_CONNECT_SECRET}
+      DISCOVERY_URL: "./map/central.json"
+      LOCAL_TARGETS_FILE: "./map/local.json"
+      NO_AUTH: "true"
+    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_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

@@ -0,0 +1,157 @@
+<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

@@ -0,0 +1,44 @@
+#!/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

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

ccp/modules/datashield.md

@@ -0,0 +1,28 @@
+# 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

@@ -6,21 +6,26 @@ 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:dnpm
+    image: docker.verbis.dkfz.de/cache/samply/beam-connect:develop
     container_name: bridgehead-dnpm-beam-connect
     environment:
       PROXY_URL: http://beam-proxy:8081
       PROXY_APIKEY: ${DNPM_BEAM_SECRET_SHORT}
       APP_ID: dnpm-connect.${PROXY_ID}
       DISCOVERY_URL: "./conf/central_targets.json"
-      LOCAL_TARGETS_FILE: "./conf/connect_targets.json"
+      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
+      NO_PROXY: beam-proxy,dnpm-backend,host.docker.internal${DNPM_ADDITIONAL_NO_PROXY}
       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
+      - /srv/docker/bridgehead/minimal/modules/dnpm-central-targets.json:/conf/central_targets.json:ro
     labels:
       - "traefik.enable=true"
       - "traefik.http.routers.dnpm-connect.rule=PathPrefix(`/dnpm-connect`)"
@@ -28,3 +33,7 @@ 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

@@ -0,0 +1,99 @@
+version: "3.7"
+
+services:
+  dnpm-mysql:
+    image: mysql:9
+    healthcheck:
+      test: [ "CMD", "mysqladmin" ,"ping", "-h", "localhost" ]
+      interval: 3s
+      timeout: 5s
+      retries: 5
+    environment:
+      MYSQL_ROOT_HOST: "%"
+      MYSQL_ROOT_PASSWORD: ${DNPM_MYSQL_ROOT_PASSWORD}
+    volumes:
+      - /var/cache/bridgehead/dnpm/mysql:/var/lib/mysql
+
+  dnpm-authup:
+    image: authup/authup:latest
+    container_name: bridgehead-dnpm-authup
+    volumes:
+      - /var/cache/bridgehead/dnpm/authup:/usr/src/app/writable
+    depends_on:
+      dnpm-mysql:
+        condition: service_healthy
+    command: server/core start
+    environment:
+      - PUBLIC_URL=https://${HOST}/auth/
+      - AUTHORIZE_REDIRECT_URL=https://${HOST}
+      - ROBOT_ADMIN_ENABLED=true
+      - ROBOT_ADMIN_SECRET=${DNPM_AUTHUP_SECRET}
+      - ROBOT_ADMIN_SECRET_RESET=true
+      - DB_TYPE=mysql
+      - DB_HOST=dnpm-mysql
+      - DB_USERNAME=root
+      - DB_PASSWORD=${DNPM_MYSQL_ROOT_PASSWORD}
+      - DB_DATABASE=auth
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.middlewares.authup-strip.stripprefix.prefixes=/auth"
+      - "traefik.http.routers.dnpm-auth.middlewares=authup-strip"
+      - "traefik.http.routers.dnpm-auth.rule=PathPrefix(`/auth`)"
+      - "traefik.http.services.dnpm-auth.loadbalancer.server.port=3000"
+      - "traefik.http.routers.dnpm-auth.tls=true"
+
+  dnpm-portal:
+    image: ghcr.io/dnpm-dip/portal:latest
+    container_name: bridgehead-dnpm-portal
+    environment:
+      - NUXT_API_URL=http://dnpm-backend:9000/
+      - NUXT_PUBLIC_API_URL=https://${HOST}/api/
+      - NUXT_AUTHUP_URL=http://dnpm-authup:3000/
+      - NUXT_PUBLIC_AUTHUP_URL=https://${HOST}/auth/
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.dnpm-frontend.rule=PathPrefix(`/`)"
+      - "traefik.http.services.dnpm-frontend.loadbalancer.server.port=3000"
+      - "traefik.http.routers.dnpm-frontend.tls=true"
+
+  dnpm-backend:
+    container_name: bridgehead-dnpm-backend
+    image: ghcr.io/dnpm-dip/backend:latest
+    environment:
+      - LOCAL_SITE=${ZPM_SITE}:${SITE_NAME}   # Format: {Site-ID}:{Site-name}, e.g. UKT:Tübingen
+      - RD_RANDOM_DATA=${DNPM_SYNTH_NUM:--1}
+      - MTB_RANDOM_DATA=${DNPM_SYNTH_NUM:--1}
+      - HATEOAS_HOST=https://${HOST}
+      - CONNECTOR_TYPE=broker
+      - AUTHUP_URL=robot://system:${DNPM_AUTHUP_SECRET}@http://dnpm-authup:3000
+    volumes:
+      - /etc/bridgehead/dnpm/config:/dnpm_config
+      - /var/cache/bridgehead/dnpm/backend-data:/dnpm_data
+    depends_on:
+      dnpm-authup:
+        condition: service_healthy
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.services.dnpm-backend.loadbalancer.server.port=9000"
+      # expose everything
+      - "traefik.http.routers.dnpm-backend.rule=PathPrefix(`/api`)"
+      - "traefik.http.routers.dnpm-backend.tls=true"
+      - "traefik.http.routers.dnpm-backend.service=dnpm-backend"
+      # except ETL
+      - "traefik.http.routers.dnpm-backend-etl.rule=PathRegexp(`^/api(/.*)?etl(/.*)?$`)"
+      - "traefik.http.routers.dnpm-backend-etl.tls=true"
+      - "traefik.http.routers.dnpm-backend-etl.service=dnpm-backend"
+      # this needs an ETL processor with support for basic auth
+      - "traefik.http.routers.dnpm-backend-etl.middlewares=auth"
+      # except peer-to-peer
+      - "traefik.http.routers.dnpm-backend-peer.rule=PathRegexp(`^/api(/.*)?/peer2peer(/.*)?$`)"
+      - "traefik.http.routers.dnpm-backend-peer.tls=true"
+      - "traefik.http.routers.dnpm-backend-peer.service=dnpm-backend"
+      - "traefik.http.routers.dnpm-backend-peer.middlewares=dnpm-backend-peer"
+      # this effectively denies all requests
+      # this is okay, because requests from peers don't go through Traefik
+      - "traefik.http.middlewares.dnpm-backend-peer.ipWhiteList.sourceRange=0.0.0.0/32"
+
+  landing:
+    labels:
+      - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"

ccp/modules/dnpm-node-setup.sh

@@ -0,0 +1,16 @@
+#!/bin/bash
+
+if [ -n "${ENABLE_DNPM_NODE}" ]; then
+	log INFO "DNPM setup detected -- will start DNPM:DIP node."
+	OVERRIDE+=" -f ./$PROJECT/modules/dnpm-node-compose.yml"
+
+	# Set variables required for BwHC Node. ZPM_SITE is assumed to be set in /etc/bridgehead/<project>.conf
+	if [ -z "${ZPM_SITE+x}" ]; then
+		log ERROR "Mandatory variable ZPM_SITE not defined!"
+		exit 1
+	fi
+    mkdir -p /var/cache/bridgehead/dnpm/ || fail_and_report 1 "Failed to create '/var/cache/bridgehead/dnpm/'. Please run sudo './bridgehead install $PROJECT' again to fix the permissions."
+    DNPM_SYNTH_NUM=${DNPM_SYNTH_NUM:--1}
+    DNPM_MYSQL_ROOT_PASSWORD="$(generate_simple_password 'dnpm mysql')"
+    DNPM_AUTHUP_SECRET="$(generate_simple_password 'dnpm authup')"
+fi

ccp/modules/dnpm-setup.sh

@@ -1,10 +1,15 @@
-#!/bin/bash
+#!/bin/bash -e
 
 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

@@ -0,0 +1,6 @@
+# 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

@@ -0,0 +1,72 @@
+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"
+
+  focus:
+    environment:
+      EXPORTER_URL: "http://exporter:8092"
+      EXPORTER_API_KEY: "${EXPORTER_API_KEY}"

ccp/modules/exporter-setup.sh

@@ -0,0 +1,8 @@
+#!/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

@@ -0,0 +1,15 @@
+# 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

@@ -0,0 +1,29 @@
+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

@@ -0,0 +1,8 @@
+#!/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

@@ -0,0 +1,36 @@
+# 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

@@ -1,4 +1,5 @@
 version: "3.7"
+
 services:
   id-manager:
     image: docker.verbis.dkfz.de/bridgehead/magicpl
@@ -13,21 +14,30 @@ services:
       MAGICPL_CONNECTOR_APIKEY: ${IDMANAGER_READ_APIKEY}
       MAGICPL_CENTRAL_PATIENTLIST_APIKEY: ${IDMANAGER_CENTRAL_PATIENTLIST_APIKEY}
       MAGICPL_CONTROLNUMBERGENERATOR_APIKEY: ${IDMANAGER_CONTROLNUMBERGENERATOR_APIKEY}
-      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}
@@ -43,7 +53,7 @@ services:
       - patientlist-db
 
   patientlist-db:
-    image: docker.verbis.dkfz.de/cache/postgres:15.1-alpine
+    image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
     container_name: bridgehead-patientlist-db
     environment:
       POSTGRES_USER: "mainzelliste"
@@ -54,5 +64,49 @@ 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: docker.verbis.dkfz.de/cache/samply/ccp-patient-project-identificator
+    container_name: bridgehead-ccp-patient-project-identificator
+    environment:
+      MAINZELLISTE_APIKEY: ${IDMANAGER_LOCAL_PATIENTLIST_APIKEY}
+      SITE_NAME: ${IDMANAGEMENT_FRIENDLY_ID}
+
 volumes:
   patientlist-db-data:

ccp/modules/id-management-setup.sh

@@ -1,9 +1,9 @@
-#!/bin/bash
+#!/bin/bash -e
 
 function idManagementSetup() {
 	if [ -n "$IDMANAGER_UPLOAD_APIKEY" ]; then
 		log INFO "id-management setup detected -- will start id-management (mainzelliste & magicpl)."
-		OVERRIDE+=" -f ./$PROJECT/modules/id-management-compose.yml"
+		OVERRIDE+=" -f ./ccp/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)"
@@ -39,6 +39,7 @@ function applySpecialCases() {
 	result="$1";
 	result="${result/Lmu/LMU}";
 	result="${result/Tum/TUM}";
+	result="${result/Dktk Test/Teststandort}";
 	echo "$result";
 }
 

ccp/modules/mtba-compose.yml

@@ -11,22 +11,29 @@ 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}
+      PATIENT_CSV_FIRST_NAME_HEADER: ${MTBA_PATIENT_CSV_FIRST_NAME_HEADER:-FIRST_NAME}
-      PATIENT_CSV_LAST_NAME_HEADER: ${MTBA_PATIENT_CSV_LAST_NAME_HEADER}
+      PATIENT_CSV_LAST_NAME_HEADER: ${MTBA_PATIENT_CSV_LAST_NAME_HEADER:-LAST_NAME}
-      PATIENT_CSV_GENDER_HEADER: ${MTBA_PATIENT_CSV_GENDER_HEADER}
+      PATIENT_CSV_GENDER_HEADER: ${MTBA_PATIENT_CSV_GENDER_HEADER:-GENDER}
-      PATIENT_CSV_BIRTHDAY_HEADER: ${MTBA_PATIENT_CSV_BIRTHDAY_HEADER}
+      PATIENT_CSV_BIRTHDAY_HEADER: ${MTBA_PATIENT_CSV_BIRTHDAY_HEADER:-BIRTHDAY}
       CBIOPORTAL_URL:  http://cbioportal:8080
-      FILE_CHARSET: ${MTBA_FILE_CHARSET}
+      FILE_CHARSET: ${MTBA_FILE_CHARSET:-UTF-8}
-      FILE_END_OF_LINE: ${MTBA_FILE_END_OF_LINE}
+      FILE_END_OF_LINE: ${MTBA_FILE_END_OF_LINE:-LF}
-      CSV_DELIMITER: ${MTBA_CSV_DELIMITER}
+      CSV_DELIMITER: ${MTBA_CSV_DELIMITER:-TAB}
+      HTTP_RELATIVE_PATH: "/mtba"
+      OIDC_ADMIN_GROUP: "${OIDC_ADMIN_GROUP}"
+      OIDC_CLIENT_ID: "${OIDC_PRIVATE_CLIENT_ID}"
+      OIDC_CLIENT_SECRET: "${OIDC_CLIENT_SECRET}"
+      OIDC_URL: "${OIDC_URL}"
+
     labels:
       - "traefik.enable=true"
-      - "traefik.http.routers.mtba.rule=PathPrefix(`/`)"
+      - "traefik.http.routers.mtba_ccp.rule=PathPrefix(`/mtba`)"
-      - "traefik.http.services.mtba.loadbalancer.server.port=80"
+      - "traefik.http.services.mtba_ccp.loadbalancer.server.port=8480"
-      - "traefik.http.routers.mtba.tls=true"
+      - "traefik.http.routers.mtba_ccp.tls=true"
+
     volumes:
-      - /tmp/bridgehead/mtba/input:/app/input
+      - /var/cache/bridgehead/ccp/mtba/input:/app/input
-      - /tmp/bridgehead/mtba/persist:/app/persist
+      - /var/cache/bridgehead/ccp/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

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

ccp/modules/mtba.md

@@ -0,0 +1,6 @@
+# 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

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

ccp/modules/nngm-setup.sh

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

ccp/modules/obds2fhir-rest-compose.yml

@@ -0,0 +1,19 @@
+version: "3.7"
+
+services:
+  obds2fhir-rest:
+    container_name: bridgehead-obds2fhir-rest
+    image: docker.verbis.dkfz.de/samply/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}
+    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

@@ -0,0 +1,13 @@
+#!/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

@@ -0,0 +1,73 @@
+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://${HOST}/ccp-teiler-backend"
+      TEILER_DASHBOARD_URL: "https://${HOST}/ccp-teiler-dashboard"
+      OIDC_URL: "${OIDC_URL}"
+      OIDC_CLIENT_ID: "${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_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}"
+      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://${HOST}/ccp-teiler-dashboard/en"
+      HTTP_PROXY: "http://forward_proxy:3128"
+      ENABLE_MTBA: "${ENABLE_MTBA}"
+      ENABLE_DATASHIELD: "${ENABLE_DATASHIELD}"
+      IDMANAGER_UPLOAD_APIKEY: "${IDMANAGER_UPLOAD_APIKEY}" # Only used to check if the ID Manager is active

ccp/modules/teiler-setup.sh

@@ -0,0 +1,9 @@
+#!/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

@@ -0,0 +1,180 @@
+# Teiler
+
+**Teiler** is the central frontend of the **bridgehead system**. It brings together multiple independent tools—each built as a **microfrontend**—into a single, unified web application.
+
+Users interact with Teiler as one coherent interface, but behind the scenes, it dynamically integrates and displays self-contained modules developed with different technologies (**Angular**, **Vue**, **React**, etc.). This modular approach makes Teiler highly flexible, allowing teams to develop, deploy, and maintain features independently.
+
+Teiler ensures:
+
+* **A consistent look and feel** across tools.
+* **Smooth navigation** between components.
+* **Seamless user authentication** across the entire interface.
+
+Each independent tool integrated into Teiler is called a **bridgehead app**. A bridgehead app can be:
+
+- A fully standalone microfrontend with its own frontend and backend services.
+- An embedded service inside the Teiler Dashboard.
+- An external link to another service, possibly hosted on a central server or elsewhere in the federated research network.
+
+The modularity of Teiler enables it to adapt easily to the evolving needs of the research federated network by simply adding, updating, or removing bridgehead apps.
+
+Below is a breakdown of Teiler's internal components that make this orchestration possible.
+
+- [Teiler Orchestrator](#teiler-orchestrator)  
+- [Teiler Dashboard](#teiler-dashboard)  
+- [Teiler Backend](#teiler-backend)
+
+---
+
+## Teiler Orchestrator
+
+The **Teiler Orchestrator** is the entry point of the **Single Page Application (SPA)**. It consists of:
+
+- An **HTML root page**.
+- A **JavaScript layer** that:
+  - **Retrieves microfrontend configurations** from the backend.
+  - **Registers and manages** the microfrontends using [**Single-SPA**](https://single-spa.js.org/), the framework Teiler uses to create and coordinate its microfrontend environment.
+
+Using this information, the orchestrator dynamically **loads the correct microfrontend** for a given route and manages its **lifecycle** (*init*, *mount*, *unmount*) in real time.
+
+**Microfrontends** run in their own containers and can be implemented with any major frontend framework. To be compatible with Teiler, they must integrate with **Single-SPA**.
+
+To encourage developers to create their own microfrontends and integrate them into Teiler, we provide **starter templates** for **Angular**, **Vue**, and **React**. Developing a new microfrontend is straightforward:
+
+1. Use one of the templates.
+2. Extend it with your own functionality.
+3. Add its configuration in the **Teiler Backend**.
+
+This modular approach accelerates development and fosters collaboration.
+
+**GitHub repository:** [https://github.com/samply/teiler-orchestrator](https://github.com/samply/teiler-orchestrator)
+
+---
+
+## Teiler Dashboard
+
+The **Teiler Dashboard** is the unified interface users interact with after logging in. It provides:
+
+- A **single point of access** where various bridgehead apps are embedded as microfrontends.
+- **Central navigation** and **session management** for a smooth user experience.
+
+### Authentication and Authorization
+
+Teiler uses **OpenID Connect (OIDC)** for user authentication, accessible via the **top navigation bar**.
+
+We consider three possible **application roles**:
+
+| Role   | Description                                               |
+|--------|-----------------------------------------------------------|
+| Public | Accessible by any user without the need to log in         |
+| User   | Normal users working with various bridgehead applications |
+| Admin  | Bridgehead system administrators                           |
+
+It is possible to **deactivate OIDC authentication** entirely. In such cases, **all apps must have at least the public role** to allow access. While this may be suitable for development or testing, we **strongly encourage** at least some external authentication mechanism or network-level access control to secure the bridgehead environment.
+
+Alternatively, basic authentication can be enforced through the existing **Traefik infrastructure** integrated with the bridgehead.
+
+**GitHub repository:** [https://github.com/samply/teiler-dashboard](https://github.com/samply/teiler-dashboard)
+
+---
+
+## Teiler Backend
+
+The **Teiler Backend** serves as the central configuration hub for all microfrontends and bridgehead apps. It defines:
+
+- Which bridgehead apps are available.
+- Their loading URLs and routes.
+- Optional metadata such as display names, icons, roles, and activation status.
+
+It enables the orchestrator to remain **generic and flexible**, adapting dynamically to whatever apps are defined in the backend configuration.
+
+### Assets Directory
+
+There is an **assets** directory where you can save images and other static files to be accessible to your microfrontends. This helps configure and customize apps more easily and quickly.
+
+Assets can be referenced via:
+
+```
+<Teiler Backend URL>/assets/<filename>
+```
+
+### App Configuration via Environment Variables
+
+Apps are configured using environment variables with the following structure:
+
+```
+TEILER_APP<Number>_<suffix>
+Optional: TEILER_APP<Number>_<LanguageCode>_<suffix>
+```
+
+- The **number** is just for grouping variables for a single app and has no intrinsic meaning.
+- The **app** is the unit within Teiler, shown as a box in the dashboard.
+- Apps can be:
+  - Embedded apps inside the Teiler Dashboard (there is a helper Python script for generating embedded apps: [create-embedded-app.py](https://github.com/samply/teiler-dashboard/blob/main/create-embedded-app.py))
+  - External links (e.g., central services outside the local bridgehead instance)
+- An app's frontend (microfrontend or embedded app) can either contain the entire functionality or serve as a frontend communicating with other backend microservices in the bridgehead.
+
+Currently supported languages in the main projects DKTK and BBMRI are **English (EN)** and **German (DE)**, but the system can be extended to other languages.
+
+The Teiler Dashboard requests variables from the backend for each app and passes the desired language code. If a language-specific variable is unavailable, the default language value is returned.
+
+### App Availability Monitoring
+
+The Teiler Backend regularly **pings apps** to check availability and displays status messages such as:
+
+- "Frontend not available"
+- "Backend not available"
+- "Frontend and Backend not available"
+
+### Accepted TEILER_APP Variable Suffixes
+
+| Suffix           | Description                                                                                                   |
+|------------------|---------------------------------------------------------------------------------------------------------------|
+| NAME             | Identifier of the app (no spaces). For embedded apps, must match the identifier defined in Teiler Dashboard.  |
+| TITLE            | Display title shown to users.                                                                                  |
+| DESCRIPTION      | Brief description of the app.                                                                                   |
+| BACKENDURL       | URL of the backend microservice (if applicable).                                                              |
+| BACKENDCHECKURL  | URL that the backend pings to verify backend availability. Defaults to BACKENDURL if not specified.             |
+| SOURCEURL        | URL of the microfrontend or external link (not used for embedded apps).                                        |
+| SOURCECHECKURL   | URL to ping to check microfrontend or external link availability. Defaults to SOURCEURL if not specified.       |
+| ROLES            | Comma-separated roles allowed: `TEILER_PUBLIC`, `TEILER_USER`, `TEILER_ADMIN`.                                 |
+| ISACTIVATED      | `true` or `false`. Used to temporarily deactivate an app without deleting its config.                           |
+| ICONCLASS        | Bootstrap icon class to display in app box (e.g., `"bi bi-search"`).                                           |
+| ICONSOURCEURL    | URL to an image icon. Prefer using local assets instead of external URLs.                                       |
+| ORDER            | Relative display order of the app in the dashboard.                                                            |
+| ISEXTERNALLINK   | `true` or `false`. Indicates if the app is an external link outside the local bridgehead.                       |
+| ISLOCAL          | `true` or `false`. Indicates if the app runs locally within the bridgehead site or on a central server.         |
+
+*Note:* Embedded apps often have many of these variables preconfigured and may not require manual specification. See the [Teiler Dashboard documentation](https://github.com/samply/teiler-dashboard) for details.
+
+### Additional Teiler Backend Variables for Dashboard Configuration
+
+| Variable Prefix                    | Description                                                                                                  |
+|------------------------------------|--------------------------------------------------------------------------------------------------------------|
+| TEILER_DASHBOARD_                  | General configuration of the dashboard.                                                                     |
+| TEILER_DASHBOARD_&lt;LangCode&gt;_ | Language-specific configuration overrides.                                                                   |
+
+Important suffixes include:
+
+| Suffix           | Description                                                      |
+|------------------|------------------------------------------------------------------|
+| WELCOME_TITLE    | Title shown on the initial screen before login.                  |
+| WELCOME_TEXT     | Welcome message or instructions before login.                    |
+| FURTHER_INFO     | Additional informational text or links.                          |
+| BACKGROUND_IMAGE_URL | URL to a background image (SVG recommended for scalability).  |
+| LOGO_URL         | URL to the project or bridgehead logo.                           |
+| LOGO_HEIGHT      | Height of the displayed logo.                                    |
+| LOGO_TEXT        | Title text of the bridgehead (e.g., "DKTK Bridgehead").          |
+| COLOR_PALETTE    | JSON link to color palettes for text, lines, icons, and background (especially for SVGs).                   |
+| COLOR_PROFILE    | Selected color profile from the palette.                         |
+| FONT             | Font family for the dashboard text.                             |
+
+---
+
+**GitHub repository:** [https://github.com/samply/teiler-backend](https://github.com/samply/teiler-backend)
+
+---
+
+If you want to create your own bridgehead app and integrate it into Teiler, start by selecting a template or building a microfrontend compatible with **Single-SPA**. Then add your app’s configuration in the Teiler Backend as described above.
+
+This flexible, modular design enables easy expansion

ccp/queries_to_cache.conf

@@ -0,0 +1,3 @@
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+ORGANOID_DASHBOARD_PUBLIC

ccp/root-new.crt.pem

@@ -1,20 +0,0 @@
------BEGIN CERTIFICATE-----
-MIIDNTCCAh2gAwIBAgIUN7yzueIZzwpe8PaPEIMY8zoH+eMwDQYJKoZIhvcNAQEL
-BQAwFjEUMBIGA1UEAxMLQnJva2VyLVJvb3QwHhcNMjMwNTIzMTAxNzIzWhcNMzMw
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-4PLRF6gqiEY1mcGknJrXj1ff/X0nRY/m6cnHNXz0Cvh8oPOtbdfGgfZjID2/fJNP
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-VR0PAQH/BAQDAgEGMA8GA1UdEwEB/wQFMAMBAf8wHQYDVR0OBBYEFEa70kcseqU5
-bHx2zSt4bG21HokhMB8GA1UdIwQYMBaAFEa70kcseqU5bHx2zSt4bG21HokhMBYG
-A1UdEQQPMA2CC0Jyb2tlci1Sb290MA0GCSqGSIb3DQEBCwUAA4IBAQCGmE7NXW4T
-6J4mV3b132cGEMD7grx5JeiXK5EHMlswUS+Odz0NcBNzhUHdG4WVMbrilHbI5Ua+
-6jdKx5WwnqzjQvElP0MCw6sH/35gbokWgk1provOP99WOFRsQs+9Sm8M2XtMf9HZ
-m3wABwU/O+dhZZ1OT1PjSZD0OKWKqH/KvlsoF5R6P888KpeYFiIWiUNS5z21Jm8A
-ZcllJjiRJ60EmDwSUOQVJJSMOvtr6xTZDZLtAKSN8zN08lsNGzyrFwqjDwU0WTqp
-scMXEGBsWQjlvxqDnXyljepR0oqRIjOvgrWaIgbxcnu98tK/OdBGwlAPKNUW7Crr
-vO+eHxl9iqd4
------END CERTIFICATE-----

ccp/vars

@@ -2,12 +2,18 @@ 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=32
+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
 
+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
+OIDC_URL="https://login.verbis.dkfz.de/realms/test-realm-01"
+OIDC_GROUP_CLAIM="groups"
 
 for module in $PROJECT/modules/*.sh
 do
@@ -16,5 +22,14 @@ do
 done
 
 idManagementSetup
-nngmSetup
+mtbaSetup
-mtbaSetup
+obds2fhirRestSetup
+blazeSecondarySetup
+
+for module in modules/*.sh
+do
+    log DEBUG "sourcing $module"
+    source $module
+done
+
+transfairSetup

dhki/docker-compose.yml

@@ -0,0 +1,66 @@
+version: "3.7"
+
+services:
+  blaze:
+    image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
+    container_name: bridgehead-dhki-blaze
+    environment:
+      BASE_URL: "http://bridgehead-dhki-blaze:8080"
+      JAVA_TOOL_OPTIONS: "-Xmx${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:ro
+    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

@@ -0,0 +1,2 @@
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dhki/root.crt.pem

@@ -0,0 +1,20 @@
+-----BEGIN CERTIFICATE-----
+MIIDNTCCAh2gAwIBAgIUSWUPebUMNfJvPKMjdgX+WiH+OXgwDQYJKoZIhvcNAQEL
+BQAwFjEUMBIGA1UEAxMLQnJva2VyLVJvb3QwHhcNMjQwMTA1MDg1NTM4WhcNMzQw
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+kf5W9CVXllSFaJe5r994ovgyHvK2ucWwe8l8iMJbQhH79oKi/9uJMCD6aUXnpg1K
+nPHW1lsVx6foqYWijdBdtFU2i7LSH2OYo0nb1PgRnY/SABV63JHfJnqW9dZy4f7G
+rpsvvrmFrKmEnCZH0n6qveY3Z5bMD94Yx0ebkCTYEqAw3pV65gwxrzBTpEg6dgF0
+eG0eKFUS0REJ
+-----END CERTIFICATE-----

dhki/vars

@@ -0,0 +1,26 @@
+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
+
+for module in ccp/modules/*.sh
+do
+    log DEBUG "sourcing $module"
+    source $module
+done
+
+idManagementSetup
+obds2fhirRestSetup
+
+for module in modules/*.sh
+do
+    log DEBUG "sourcing $module"
+    source $module
+done
+
+transfairSetup

docs/update-access-token.md

@@ -0,0 +1,42 @@
+## How to Change Config Access Token
+
+### 1. Generate a New Access Token
+
+1. Go to your Git configuration repository provider, it might be either [git.verbis.dkfz.de](https://git.verbis.dkfz.de) or [gitlab.bbmri-eric.eu](https://gitlab.bbmri-eric.eu).  
+2. Navigate to the configuration repository for your site.  
+3. Go to **Settings → Access Tokens** to check if your Access Token is valid or expired.  
+   - **If expired**, create a new Access Token.  
+4. Configure the new Access Token with the following settings:  
+   - **Expiration date**: One year from today, minus one day.  
+   - **Role**: Developer.  
+   - **Scope**: Only `read_repository`.  
+5. Save the newly generated Access Token in a secure location.  
+
+---
+
+### 2. Replace the Old Access Token
+
+1. Navigate to `/etc/bridgehead` in your system.  
+2. Run the following command to retrieve the current Git remote URL:  
+   ```bash
+   git remote get-url origin
+   ```
+   Example output:  
+   ```
+   https://name40dkfz-heidelberg.de:<old_access_token>@git.verbis.dkfz.de/bbmri-bridgehead-configs/test.git
+   ```
+3. Replace `<old_access_token>` with your new Access Token in the URL.  
+4. Set the updated URL using the following command:  
+   ```bash
+   git remote set-url origin https://name40dkfz-heidelberg.de:<new_access_token>@git.verbis.dkfz.de/bbmri-bridgehead-configs/test.git
+   
+   ```
+
+5. Start the Bridgehead update service by running:  
+   ```bash
+   systemctl start bridgehead-update@<project>
+   ```
+6. View the output to ensure the update process is successful:  
+   ```bash
+   journalctl -u bridgehead-update@<project> -f
+   ```

itcc/docker-compose.yml

@@ -0,0 +1,68 @@
+version: "3.7"
+
+services:
+  blaze:
+    image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
+    container_name: bridgehead-itcc-blaze
+    environment:
+      BASE_URL: "http://bridgehead-itcc-blaze:8080"
+      JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
+      DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
+      DB_BLOCK_CACHE_SIZE: ${BLAZE_MEMORY_CAP}
+      CQL_EXPR_CACHE_SIZE: ${BLAZE_CQL_CACHE_CAP:-32}
+      ENFORCE_REFERENTIAL_INTEGRITY: "false"
+    volumes:
+      - "blaze-data:/app/data"
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.blaze_itcc.rule=PathPrefix(`/itcc-localdatamanagement`)"
+      - "traefik.http.middlewares.itcc_b_strip.stripprefix.prefixes=/itcc-localdatamanagement"
+      - "traefik.http.services.blaze_itcc.loadbalancer.server.port=8080"
+      - "traefik.http.routers.blaze_itcc.middlewares=itcc_b_strip,auth"
+      - "traefik.http.routers.blaze_itcc.tls=true"
+
+  focus:
+    image: docker.verbis.dkfz.de/cache/samply/focus:${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
+      QUERIES_TO_CACHE: '/queries_to_cache.conf'
+      ENDPOINT_TYPE: ${FOCUS_ENDPOINT_TYPE:-blaze}
+    volumes:
+      - /srv/docker/bridgehead/itcc/queries_to_cache.conf:/queries_to_cache.conf:ro
+    depends_on:
+      - "beam-proxy"
+      - "blaze"
+
+  beam-proxy:
+    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${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

@@ -0,0 +1,33 @@
+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

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

itcc/queries_to_cache.conf

@@ -0,0 +1,2 @@
+bGlicmFyeSBSZXRyaWV2ZQp1c2luZyBGSElSIHZlcnNpb24gJzQuMC4wJwppbmNsdWRlIEZISVJIZWxwZXJzIHZlcnNpb24gJzQuMC4wJwpjb2Rlc3lzdGVtIFNhbXBsZU1hdGVyaWFsVHlwZTogJ2h0dHBzOi8vZmhpci5iYm1yaS5kZS9Db2RlU3lzdGVtL1NhbXBsZU1hdGVyaWFsVHlwZScKCmNvZGVzeXN0ZW0gbG9pbmM6ICdodHRwOi8vbG9pbmMub3JnJwoKY29udGV4dCBQYXRpZW50CkRLVEtfU1RSQVRfR0VOREVSX1NUUkFUSUZJRVIKICBES1RLX1NUUkFUX0RJQUdOT1NJU19TVFJBVElGSUVSCiAgSVRDQ19TVFJBVF9BR0VfQ0xBU1NfU1RSQVRJRklFUgogIERLVEtfU1RSQVRfREVGX0lOX0lOSVRJQUxfUE9QVUxBVElPTgp0cnVl
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

itcc/root.crt.pem

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

itcc/vars

@@ -0,0 +1,14 @@
+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

@@ -0,0 +1,67 @@
+version: "3.7"
+
+services:
+  landing:
+    deploy:
+      replicas: 0 #deactivate landing page
+
+  blaze:
+    image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
+    container_name: bridgehead-kr-blaze
+    environment:
+      BASE_URL: "http://bridgehead-kr-blaze:8080"
+      JAVA_TOOL_OPTIONS: "-Xmx${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

@@ -0,0 +1,6 @@
+# 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

@@ -0,0 +1,67 @@
+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

@@ -0,0 +1,8 @@
+#!/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

@@ -0,0 +1,15 @@
+# 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

@@ -0,0 +1,35 @@
+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

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

kr/modules/obds2fhir-rest-compose.yml

@@ -0,0 +1,19 @@
+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}
+    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

@@ -0,0 +1,13 @@
+#!/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

@@ -0,0 +1,79 @@
+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://${HOST}/ccp-teiler-backend"
+      TEILER_DASHBOARD_URL: "https://${HOST}/ccp-teiler-dashboard"
+      OIDC_URL: "${OIDC_URL}"
+      OIDC_CLIENT_ID: "${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_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://${HOST}/ccp-teiler-dashboard/en"
+      HTTP_PROXY: "http://forward_proxy:3128"
+      ENABLE_MTBA: "${ENABLE_MTBA}"
+      ENABLE_DATASHIELD: "${ENABLE_DATASHIELD}"
+    secrets:
+      - ccp.conf
+
+secrets:
+  ccp.conf:
+    file: /etc/bridgehead/ccp.conf

kr/modules/teiler-setup.sh

@@ -0,0 +1,9 @@
+#!/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

@@ -0,0 +1,19 @@
+# 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

@@ -0,0 +1,20 @@
+-----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

@@ -0,0 +1,16 @@
+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

@@ -9,6 +9,33 @@ 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"
@@ -26,8 +53,8 @@ checkOwner(){
 }
 
 printUsage() {
-	echo "Usage: bridgehead start|stop|is-running|update|install|uninstall|adduser|enroll PROJECTNAME"
+	echo "Usage: bridgehead start|stop|logs|docker-logs|is-running|update|install|uninstall|adduser|enroll PROJECTNAME"
-	echo "PROJECTNAME should be one of ccp|bbmri"
+	echo "PROJECTNAME should be one of ccp|bbmri|cce|itcc|kr|dhki"
 }
 
 checkRequirements() {
@@ -49,7 +76,7 @@ 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 samply/bridgehead-vaultfetcher $@)
+	PASS=$(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 $@)
 	RET=$?
 
 	if [ $RET -ne 0 ]; then
@@ -89,7 +116,7 @@ assertVarsNotEmpty() {
 	MISSING_VARS=""
 
 	for VAR in $@; do
-	if [ -z "${!VAR}" ]; then
+		if [ -z "${!VAR}" ]; then
 			MISSING_VARS+="$VAR "
 		fi
 	done
@@ -128,6 +155,30 @@ 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(){
@@ -188,7 +239,7 @@ function do_enroll_inner {
 		PARAMS+="--admin-email $SUPPORT_EMAIL"
 	fi
 
-	docker run --rm -ti -v /etc/bridgehead/pki:/etc/bridgehead/pki samply/beam-enroll:latest --output-file $PRIVATEKEYFILENAME --proxy-id $MANUAL_PROXY_ID $PARAMS
+	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
 	chmod 600 $PRIVATEKEYFILENAME
 }
 
@@ -211,4 +262,181 @@ 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=$BROKER_URL \
+        -e OIDC_PROVIDER=secret-sync-central.central-secret-sync.$BROKER_ID \
+        -e SECRET_DEFINITIONS=$secret_sync_args \
+        docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest
+
+    set -a # Export variables as environment variables
+    source /var/cache/bridgehead/secrets/oidc
+    set +a # Export variables in the regular way
+}
+
+function secret_sync_gitlab_token() {
+    # Map the origin of the git repository /etc/bridgehead to the prefix recognized by Secret Sync
+    local gitlab
+    case "$(git -C /etc/bridgehead remote get-url origin)" in
+        *git.verbis.dkfz.de*) gitlab=verbis;;
+        *gitlab.bbmri-eric.eu*) gitlab=bbmri;;
+        *)
+            log "WARN" "Not running Secret Sync because the git repository /etc/bridgehead has unknown origin"
+            return
+            ;;
+    esac
+
+    if [ "$PROJECT" == "bbmri" ]; then
+        # If the project is BBMRI, use the BBMRI-ERIC broker and not the GBN broker
+        proxy_id=$ERIC_PROXY_ID
+        broker_url=$ERIC_BROKER_URL
+        broker_id=$ERIC_BROKER_ID
+        root_crt_file="/srv/docker/bridgehead/bbmri/modules/${ERIC_ROOT_CERT}.root.crt.pem"
+    else
+        proxy_id=$PROXY_ID
+        broker_url=$BROKER_URL
+        broker_id=$BROKER_ID
+        root_crt_file="/srv/docker/bridgehead/$PROJECT/root.crt.pem"
+    fi
+
+    # Create a temporary directory for Secret Sync that is valid per boot
+    secret_sync_tempdir="/tmp/bridgehead/secret-sync.boot-$(cat /proc/sys/kernel/random/boot_id)"
+    mkdir -p $secret_sync_tempdir
+
+    # Use Secret Sync to validate the GitLab token in $secret_sync_tempdir/cache.
+    # If it is missing or expired, Secret Sync will create a new token and write it to the file.
+    # The git credential helper reads the token from the file during git pull.
+    log "INFO" "Running Secret Sync for the GitLab token (gitlab=$gitlab)"
+    docker pull docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest # make sure we have the latest image
+    docker run --rm \
+        -v $PRIVATEKEYFILENAME:/run/secrets/privkey.pem:ro \
+        -v $root_crt_file:/run/secrets/root.crt.pem:ro \
+        -v /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro \
+        -v $secret_sync_tempdir:/secret-sync/ \
+        -e CACHE_PATH=/secret-sync/gitlab-token \
+        -e TLS_CA_CERTIFICATES_DIR=/conf/trusted-ca-certs \
+        -e NO_PROXY=localhost,127.0.0.1 \
+        -e ALL_PROXY=$HTTPS_PROXY_FULL_URL \
+        -e PROXY_ID=$proxy_id \
+        -e BROKER_URL=$broker_url \
+        -e GITLAB_PROJECT_ACCESS_TOKEN_PROVIDER=secret-sync-central.central-secret-sync.$broker_id \
+        -e SECRET_DEFINITIONS=GitLabProjectAccessToken:BRIDGEHEAD_CONFIG_REPO_TOKEN:$gitlab \
+        docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest
+    if [ $? -eq 0 ]; then
+        log "INFO" "Secret Sync was successful"
+        # In the past we used to hardcode tokens into the repository URL. We have to remove those now for the git credential helper to become effective.
+        CLEAN_REPO="$(git -C /etc/bridgehead remote get-url origin | sed -E 's|https://[^@]+@|https://|')"
+        git -C /etc/bridgehead remote set-url origin "$CLEAN_REPO"
+        # Set the git credential helper
+        git -C /etc/bridgehead config credential.helper /srv/docker/bridgehead/lib/gitlab-token-helper.sh
+    else
+        log "WARN" "Secret Sync failed"
+        # Remove the git credential helper
+        git -C /etc/bridgehead config --unset credential.helper
+    fi
+
+    # In the past the git credential helper was also set for /srv/docker/bridgehead but never used.
+    # Let's remove it to avoid confusion. This line can be removed at some point the future when we
+    # believe that it was removed on all/most production servers.
+    git -C /srv/docker/bridgehead config --unset credential.helper
+}
+
+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/gitlab-token-helper.sh

@@ -0,0 +1,11 @@
+#!/bin/bash
+
+[ "$1" = "get" ] || exit
+
+source "/tmp/bridgehead/secret-sync.boot-$(cat /proc/sys/kernel/random/boot_id)/gitlab-token"
+
+# Any non-empty username works, only the token matters
+cat << EOF
+username=bk
+password=$BRIDGEHEAD_CONFIG_REPO_TOKEN
+EOF

lib/gitpassword.sh

@@ -1,41 +0,0 @@
-#!/bin/bash
-
-if [ "$1" != "get" ]; then
-	echo "Usage: $0 get"
-	exit 1
-fi
-
-baseDir() {
-	# see https://stackoverflow.com/questions/59895
-	SOURCE=${BASH_SOURCE[0]}
-	while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
-		DIR=$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )
-		SOURCE=$(readlink "$SOURCE")
-		[[ $SOURCE != /* ]] && SOURCE=$DIR/$SOURCE # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
-        done
-        DIR=$( cd -P "$( dirname "$SOURCE" )/.." >/dev/null 2>&1 && pwd )
-        echo $DIR
-}
-
-BASE=$(baseDir)
-cd $BASE
-
-source lib/functions.sh
-
-assertVarsNotEmpty SITE_ID || fail_and_report 1 "gitpassword.sh failed: SITE_ID is empty."
-
-PARAMS="$(cat)"
-GITHOST=$(echo "$PARAMS" | grep "^host=" | sed 's/host=\(.*\)/\1/g')
-
-fetchVarsFromVault GIT_PASSWORD
-
-if [ -z "${GIT_PASSWORD}" ]; then
-	fail_and_report 1 "gitpassword.sh failed: Git password not found."
-fi
-
-cat <<EOF
-protocol=https
-host=$GITHOST
-username=bk-${SITE_ID}
-password=${GIT_PASSWORD}
-EOF

lib/install-bridgehead.sh

@@ -41,6 +41,20 @@ if [ ! -z "$NNGM_CTS_APIKEY" ] && [ -z "$NNGM_AUTH" ]; then
   add_basic_auth_user "nngm" $generated_passwd "NNGM_AUTH" $PROJECT
 fi
 
+if [ -z "$TRANSFAIR_AUTH" ]; then
+  if [[ -n "$TTP_URL" || -n "$EXCHANGE_ID_SYSTEM" ]]; then
+    log "INFO" "Now generating basic auth user for transfair API (see adduser in bridgehead for more information). "
+    generated_passwd="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 32)"
+    add_basic_auth_user "transfair" $generated_passwd "TRANSFAIR_AUTH" $PROJECT
+  fi
+fi
+
+if [ -z "$EXPORTER_USER" ]; then
+  log "INFO" "Now generating basic auth for the exporter and reporter (see adduser in bridgehead for more information). "
+  generated_passwd="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 32)"
+  add_basic_auth_user $PROJECT $generated_passwd "EXPORTER_USER" $PROJECT
+fi
+
 log "INFO" "Registering system units for bridgehead and bridgehead-update"
 cp -v \
     lib/systemd/bridgehead\@.service \

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_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=$HTTPS_PROXY_FULL_URL curl --max-time 5 -A "$USER_AGENT" -s -o /dev/null -X POST --data-binary @- "$HCURL"/"$1" || log WARN "Monitoring failed: Unable to send data to $HCURL/$1"
     else
-        https_proxy=$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/$1"
+        https_proxy=$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"
     fi
 }

lib/prepare-system.sh

@@ -52,6 +52,21 @@ case "$PROJECT" in
 	bbmri)
 		site_configuration_repository_middle="git.verbis.dkfz.de/bbmri-bridgehead-configs/"
 		;;
+	cce)
+		site_configuration_repository_middle="git.verbis.dkfz.de/cce-sites/"
+		;;
+	itcc)
+		site_configuration_repository_middle="git.verbis.dkfz.de/itcc-sites/"
+        ;;
+    dhki)
+        site_configuration_repository_middle="git.verbis.dkfz.de/dhki/"
+		;;
+	kr)
+		site_configuration_repository_middle="git.verbis.dkfz.de/krebsregister-sites/"
+		;;
+	dhki)
+		site_configuration_repository_middle="git.verbis.dkfz.de/dhki/"
+		;;
 	minimal)
 		site_configuration_repository_middle="git.verbis.dkfz.de/minimal-bridgehead-configs/"
 		;;
@@ -89,6 +104,9 @@ elif [[ "$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

@@ -3,18 +3,20 @@
 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 /srv/docker/bridgehead bridgehead || exit 1
+checkOwner "${CONFIG_DIR}" bridgehead || exit 1
-checkOwner /etc/bridgehead bridgehead || exit 1
+checkOwner "${COMPONENT_DIR}" bridgehead || exit 1
 
 ## Check if user is a su
 log INFO "Checking if all prerequisites are met ..."
-prerequisites="git docker"
+prerequisites="git docker curl"
 for prerequisite in $prerequisites; do
   $prerequisite --version 2>&1
   is_available=$?
@@ -32,31 +34,31 @@ fi
 log INFO "Checking configuration ..."
 
 ## Download submodule
-if [ ! -d "/etc/bridgehead/" ]; then
+if [ ! -d "${CONFIG_DIR}" ]; then
-  fail_and_report 1 "Please set up the config folder at /etc/bridgehead. Instruction are in the readme."
+  fail_and_report 1 "Please set up the config folder at ${CONFIG_DIR}. Instruction are in the readme."
 fi
 
 # TODO: Check all required variables here in a generic loop
 
 #check if project env is present
-if [ -d "/etc/bridgehead/${PROJECT}.conf" ]; then
+if [ -d "${CONFIG_DIR}${PROJECT}.conf" ]; then
-   fail_and_report 1 "Project config not found. Please copy the template from ${PROJECT} and put it under /etc/bridgehead-config/${PROJECT}.conf."
+   fail_and_report 1 "Project config not found. Please copy the template from ${PROJECT} and put it under ${CONFIG_DIR}${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 "/etc/bridgehead/traefik-tls" ]; then
+if [ ! -d "${CONFIG_DIR}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 "/etc/bridgehead/traefik-tls/fullchain.pem" ]; then
+if [ ! -e "${CONFIG_DIR}traefik-tls/fullchain.pem" ]; then
   openssl req -x509 -newkey rsa:4096 -nodes -keyout /etc/bridgehead/traefik-tls/privkey.pem -out /etc/bridgehead/traefik-tls/fullchain.pem -days 3650 -subj "/CN=$HOST"
 fi
 
-if [ -e /etc/bridgehead/vault.conf ]; then
+if [ -e "${CONFIG_DIR}"vault.conf ]; then
   if [ "$(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
@@ -64,48 +66,54 @@ fi
 
 log INFO "Checking network access ($BROKER_URL_FOR_PREREQ) ..."
 
-source /etc/bridgehead/${PROJECT}.conf
+source "${CONFIG_DIR}${PROJECT}".conf
 source ${PROJECT}/vars
 
-set +e
+if [ "${PROJECT}" != "minimal" ]; then
-SERVERTIME="$(https_proxy=$HTTPS_PROXY_URL curl -m 5 -s -I $BROKER_URL_FOR_PREREQ 2>&1 | grep -i -e '^Date: ' | sed -e 's/^Date: //i')"
+  set +e
-RET=$?
+  SERVERTIME="$(https_proxy=$HTTPS_PROXY_FULL_URL curl -m 5 -s -I $BROKER_URL_FOR_PREREQ 2>&1 | grep -i -e '^Date: ' | sed -e 's/^Date: //i')"
-set -e
+  RET=$?
-if [ $RET -ne 0 ]; then
+  set -e
-	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."
+  if [ $RET -ne 0 ]; then
-	log WARN "Unable to check clock skew due to previous error."
+	  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."
-else
+  	log WARN "Unable to check clock skew due to previous error."
-	log INFO "Checking clock skew ..."
+  else
+	  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. $SYNCTEXT"
-	fi
+	  fi
+  fi
 fi
-
 checkPrivKey() {
-  if [ -e /etc/bridgehead/pki/${SITE_ID}.priv.pem ]; then
+  if [ -e "${CONFIG_DIR}pki/${SITE_ID}.priv.pem" ]; then
     log INFO "Success - private key found."
   else
-    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."
+    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."
     return 1
   fi
   return 0
 }
 
-if [[ "$@" =~ "noprivkey" ]]; then
+if [[ "$@" =~ "noprivkey" ||  "${PROJECT}" != "minimal" ]]; 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

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

lib/update-bridgehead.sh

@@ -19,7 +19,7 @@ fi
 
 hc_send log "Checking for bridgehead updates ..."
 
-CONFFILE=/etc/bridgehead/$1.conf
+CONFFILE=/etc/bridgehead/$PROJECT.conf
 
 if [ ! -e $CONFFILE ]; then
   fail_and_report 1 "Configuration file $CONFFILE not found."
@@ -30,10 +30,10 @@ source $CONFFILE
 assertVarsNotEmpty SITE_ID || fail_and_report 1 "Update failed: SITE_ID empty"
 export SITE_ID
 
-checkOwner . bridgehead || fail_and_report 1 "Update failed: Wrong permissions in $(pwd)"
+checkOwner /srv/docker/bridgehead bridgehead || fail_and_report 1 "Update failed: Wrong permissions in /srv/docker/bridgehead"
 checkOwner /etc/bridgehead bridgehead || fail_and_report 1 "Update failed: Wrong permissions in /etc/bridgehead"
 
-CREDHELPER="/srv/docker/bridgehead/lib/gitpassword.sh"
+secret_sync_gitlab_token
 
 CHANGES=""
 
@@ -45,20 +45,17 @@ for DIR in /etc/bridgehead $(pwd); do
   if [ -n "$OUT" ]; then
     report_error log "The working directory $DIR is modified. Changed files: $OUT"
   fi
-  if [ "$(git -C $DIR config --get credential.helper)" != "$CREDHELPER" ]; then
-    log "INFO" "Configuring repo to use bridgehead git credential helper."
-    git -C $DIR config credential.helper "$CREDHELPER"
-  fi
   old_git_hash="$(git -C $DIR rev-parse --verify HEAD)"
-  if [ -z "$HTTP_PROXY_URL" ]; then
+  if [ -z "$HTTPS_PROXY_FULL_URL" ]; then
     log "INFO" "Git is using no proxy!"
     OUT=$(retry 5 git -C $DIR fetch 2>&1 && retry 5 git -C $DIR pull 2>&1)
   else
-    log "INFO" "Git is using proxy ${HTTP_PROXY_URL} from ${CONFFILE}"
+    log "INFO" "Git is using proxy ${HTTPS_PROXY_URL} from ${CONFFILE}"
-    OUT=$(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 $DIR pull 2>&1)
+    OUT=$(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)
   fi
   if [ $? -ne 0 ]; then
-    report_error log "Unable to update git $DIR: $OUT"
+    OUT_SAN=$(echo $OUT | sed -E 's|://[^:]+:[^@]+@|://credentials@|g')
+    report_error log "Unable to update git $DIR: $OUT_SAN"
   fi
 
   new_git_hash="$(git -C $DIR rev-parse --verify HEAD)"
@@ -80,19 +77,13 @@ 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 $(cat $PROJECT/docker-compose.yml ${OVERRIDE//-f/} minimal/docker-compose.yml | grep -v "^#" | grep "image:" | sed -e 's_^.*image: \(.*\).*$_\1_g; s_\"__g'); do
+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
   log "INFO" "Checking for Updates of Image: $IMAGE"
   if docker pull $IMAGE | grep "Downloaded newer image"; then
     CHANGE="Image $IMAGE updated."
@@ -122,7 +113,7 @@ if [ -n "${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 $(pwd)"
+  checkOwner "$BACKUP_DIRECTORY" bridgehead || fail_and_report 1 "Automatic maintenance failed: Wrong permissions for backup directory $BACKUP_DIRECTORY"
   # Collect all container names that contain '-db'
   BACKUP_SERVICES="$(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=true
+      - --api.dashboard=false
       - --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(`/dashboard/`)"
       - "traefik.http.routers.dashboard.entrypoints=websecure"
       - "traefik.http.routers.dashboard.service=api@internal"
       - "traefik.http.routers.dashboard.tls=true"
@@ -35,17 +35,20 @@ services:
     image: docker.verbis.dkfz.de/cache/samply/bridgehead-forward-proxy:latest
     environment:
       HTTPS_PROXY: ${HTTPS_PROXY_URL}
-      USERNAME: ${HTTPS_PROXY_USERNAME}
+      HTTPS_PROXY_USERNAME: ${HTTPS_PROXY_USERNAME}
-      PASSWORD: ${HTTPS_PROXY_PASSWORD}
+      HTTPS_PROXY_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:master
+    image: docker.verbis.dkfz.de/cache/samply/bridgehead-landingpage:main
     labels:
       - "traefik.enable=true"
       - "traefik.http.routers.landing.rule=PathPrefix(`/`)"
@@ -55,5 +58,4 @@ services:
       HOST: ${HOST}
       PROJECT: ${PROJECT}
       SITE_NAME: ${SITE_NAME}
-
+      ENVIRONMENT: ${ENVIRONMENT}
-