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Author SHA1 Message Date
1a714e28ac Added: Teiler documentation 2025-06-11 15:35:12 +02:00
39a02e2b2f Added: Teiler documentation 2025-06-11 13:38:19 +02:00
faa8abd4ee chore: update eric.acc.root.crt.pem (#316) 2025-06-10 16:48:22 +02:00
7693289d4d docs: add Teiler and Exporter to the main README.md (#315)
Co-authored-by: Tobias Kussel <TKussel@users.noreply.github.com>
2025-06-10 11:03:18 +02:00
d482324361 feat: add Teiler and Exporter in BBMRI (#312)
Co-authored-by: Jan <59206115+Threated@users.noreply.github.com>
2025-06-05 16:55:03 +02:00
b7a42f3d3b chore: externalize POSTGRES_TAG and bump postgres to 15.13 (#313) 2025-06-04 14:22:34 +02:00
fd013232f5 Cache public organoid dashboard SQL query (#309) 2025-05-23 15:26:59 +02:00
eb52554892 docs: add faq (#288) 2025-05-22 18:10:40 +02:00
08c695e960 docs: Control import from Directory, improve README (#297) 2025-05-22 18:03:01 +02:00
1513fe1c6c Added section relating to clearing data from Blaze (#303) 2025-05-22 18:01:43 +02:00
af08a9fb08 chore: change some teiler variables (#307) 2025-05-20 16:24:24 +02:00
b95f0efbe7 fix: add own url to teiler dashboard to make it offline compatible (#305) 2025-05-20 09:39:14 +02:00
99567e2b40 fix: Ensure transfair can properly communicate with the fhir server for requests (#304) 2025-05-19 17:01:37 +02:00
Jan
96ff6043a1 feat: allow transfair to talk to services behind the proxy (#296) 2025-05-09 13:52:33 +02:00
Jan
844ce3386e chore(transfair): update transfair config (#298) 2025-05-09 11:30:26 +02:00
9782bf66b6 Code review: Move to /tmp/bridgehead/... 2025-05-08 09:18:02 +02:00
87f0e8ad7f Use temp directory for secret sync cache 2025-05-08 09:18:02 +02:00
Jan
7365be3e7b chore(transfair): add option to disable tls verification (#295) 2025-04-17 12:01:45 +02:00
c5d08c50a4 chore: add BBMRI ERIC acceptance env (#294) 2025-04-16 15:37:55 +02:00
Jan
72ecaadba8 fix: ssh-tunnel-setup.sh (#293) 2025-04-15 11:36:20 +02:00
Jan
2ddd535794 feat: ssh tunnel (#292)
* Added ccp module for a ssh tunnel

Usage details under https://github.com/samply/ssh-tunnel

* chore: update ssh-tunnel image to harbor

* feat: ssh tunnel support diffrent port

* chore: fix indentation

* chore: move to top level modules

* docs: add ssh-tunnel docs

---------

Co-authored-by: Tobias Kussel <tobias.kussel@dkfz-heidelberg.de>
2025-04-14 10:45:15 +02:00
Jan
973547c322 chore(transfair): add new gw option (#291) 2025-04-11 08:37:31 +02:00
Jan
6b649c9233 feat: expose transfair via traefik (#290)
Note: Requires a bridgehead install to generate the basic auth user
2025-04-09 13:19:52 +02:00
3144ee5214 Fix GitLab token syncing for BBMRI 2025-03-31 11:08:59 +02:00
68804dc71b feat: add transfair setup to ccp 2025-03-26 13:11:43 +01:00
e5aebfe382 chore!: update transfair config 2025-03-26 13:11:43 +01:00
6f3aba1eaa feat: support self-signed cert on ttp (#283) 2025-03-12 15:45:55 +01:00
Jan
82ced89b33 chore: unify blaze versioning and upgrade to 0.32 (#277) 2025-03-12 12:52:00 +01:00
5d94bac0e2 Mount queries_to_cache.conf readonly (#282) 2025-03-10 16:03:05 +01:00
83555540f5 chore: update central Secret Sync proxy ID (#280) 2025-03-10 12:08:19 +01:00
e396e00178 Fix/ccp cql cache (#279)
* fix: adapt focus caching to new cql and add focus caching for cce and itcc

---------

Co-authored-by: p.delpy@dkfz-heidelberg.de <p.delpy@dkfz-heidelberg.de>
2025-03-07 12:20:38 +01:00
ecb29830e4 Send the origin of /etc/bridgehead repo to Secret Sync
This is to anticipate an upcoming change in Secret Sync that will allow it to support multiple GitLab servers, e.g. verbis GitLab and BBMRI GitLab.
2025-03-05 11:04:22 +01:00
98121c17e8 Make Codeowners Rule apply to all Files in Repo 2025-02-20 17:28:38 +01:00
e38511e118 Add Codeowners File 2025-02-20 17:20:54 +01:00
8334fac84d fix: use correct obds2fhir-rest image
---------

Co-authored-by: Pierre Delpy <p.delpy@dkfz-heidelberg.de>
2025-02-20 13:48:10 +01:00
8000356b57 docs: explicitly clone main branch (#269) 2025-02-07 11:21:43 +01:00
74d8e68d96 Merge pull request #258 from samply/feat/routine-connector
feat: transFAIR
2025-02-07 10:39:54 +01:00
c568a56651 refactor: set transfair log to info 2025-02-07 10:30:43 +01:00
8384143387 fix: make transfair reach the internal blaze stores 2025-02-07 09:17:17 +01:00
8fe73a8123 fix: support mode without ttp 2025-02-07 09:17:07 +01:00
bca63e82a9 fix: don't use return in transfairSetup
For some reason the return not only exits transfairSetup, but also the
bridgehead script
2025-02-06 15:43:37 +01:00
Jan
721627a78f feat: migrate to new dnpm:dip node (#251)
* feat: migrate to new dnpm:dip node

* hardcode dnpm connector type to broker

* use `SITE_NAME` for dnpm `LOCAL_SITE`

* host central targets in git

* dnpm: add goettingen to central targets

* dnpm: add uksh to central targets

* dnpm: replace named volumes with fs volumes

* chore: change dnpm images

* chore: pin mysql

* dnpm: Secure endpoints for ETL and p2p communications (#254)

* fix authup redirect (#262)

When a OIDC provider is configured, you'll get redirected to authup by Keycloak which redirects you to the DNPM:DIP. 

Currently the url looks like this: https://myserver/authup//someurl
and produces an error. Manually removing the additional / fixes the issue.

* Whitespace formatting

---------

Co-authored-by: Niklas <niklas@ytvwld.de>
Co-authored-by: Niklas Reimer <niklas@backbord.net>
Co-authored-by: Martin Lablans <6804500+lablans@users.noreply.github.com>
2025-02-05 13:24:28 +01:00
Jan
e08ff92401 Merge pull request #268 from samply/main
Main backport
2025-02-05 08:45:35 +01:00
Jan
e3553370b6 feat: unify version handeling (#265) 2025-01-29 13:17:59 +01:00
Jan
1ad73d8f82 fix: properly load oidc secrets (#267) 2025-01-29 10:59:27 +01:00
0b6fa439ba Merge pull request #266 from samply/fix/docker-hub-link
Fixed Docker Hub URL list link
2025-01-29 09:52:26 +01:00
615990b92a Use secret-sync for gitpassword (#257)
---------

Co-authored-by: Tim Schumacher <tim@tschumacher.net>
Co-authored-by: Jan <59206115+Threated@users.noreply.github.com>
Co-authored-by: Tim Schumacher <tim.schumacher@dkfz-heidelberg.de>
2025-01-28 14:53:49 +01:00
db950d6d87 Fixed Docker Hub URL list link 2025-01-28 08:59:57 +00:00
6a71da3dd1 docs: documentation for changing your configuration repository access token (#256) 2025-01-27 10:49:10 +01:00
138a1fa5f1 fix: changed ccp_ppi to use IDMANAGEMENT_FRIENDLY_ID instead of SITE_NAME (#259) 2025-01-27 10:49:10 +01:00
39a87bcf61 Update: Blaze to version 0.31 (#260) 2025-01-27 10:49:10 +01:00
Jan
655d0d24c7 fix: remove restart: always in compose files (#261) 2025-01-27 10:49:10 +01:00
fa0d9fb8b4 restrict additional blaze memory usage 2025-01-24 09:23:08 +00:00
139fcecabe redo transfair setup 2025-01-23 13:27:42 +00:00
2058a7a5c9 update image url 2025-01-23 12:06:43 +00:00
47364f999e wip: routine connector 2025-01-21 13:55:08 +00:00
df1ec21848 Merge pull request #246 from samply/develop
set environment variables needed for the focus blaze-and-sql endpoint to work when fhir2sql is enabled
2024-12-11 10:53:27 +01:00
a4e292dd18 Merge pull request #241 from samply/develop
feat: add focus tags in ccp and bbmri (#240)
2024-10-23 07:24:06 +02:00
75089ab428 Merge pull request #221 from samply/develop
Keep develop in sync with main
2024-10-15 14:30:15 +02:00
52 changed files with 1228 additions and 221 deletions

1
.github/CODEOWNERS vendored Normal file
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@ -0,0 +1 @@
* @samply/bridgehead-developers

134
README.md
View File

@ -22,11 +22,16 @@ This repository is the starting point for any information and tools you will nee
- [TLS terminating proxies](#tls-terminating-proxies) - [TLS terminating proxies](#tls-terminating-proxies)
- [File structure](#file-structure) - [File structure](#file-structure)
- [BBMRI-ERIC Directory entry needed](#bbmri-eric-directory-entry-needed) - [BBMRI-ERIC Directory entry needed](#bbmri-eric-directory-entry-needed)
- [Directory sync tool](#directory-sync-tool)
- [Loading data](#loading-data) - [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) 4. [Things you should know](#things-you-should-know)
- [Auto-Updates](#auto-updates) - [Auto-Updates](#auto-updates)
- [Auto-Backups](#auto-backups) - [Auto-Backups](#auto-backups)
- [Non-Linux OS](#non-linux-os) - [Non-Linux OS](#non-linux-os)
- [FAQ](#faq)
5. [Troubleshooting](#troubleshooting) 5. [Troubleshooting](#troubleshooting)
- [Docker Daemon Proxy Configuration](#docker-daemon-proxy-configuration) - [Docker Daemon Proxy Configuration](#docker-daemon-proxy-configuration)
- [Monitoring](#monitoring) - [Monitoring](#monitoring)
@ -76,7 +81,7 @@ The following URLs need to be accessible (prefix with `https://`):
* git.verbis.dkfz.de * git.verbis.dkfz.de
* To fetch docker images * To fetch docker images
* docker.verbis.dkfz.de * docker.verbis.dkfz.de
* Official Docker, Inc. URLs (subject to change, see [official list](https://docs.docker.com/desktop/all)) * Official Docker, Inc. URLs (subject to change, see [official list](https://docs.docker.com/desktop/setup/allow-list/))
* hub.docker.com * hub.docker.com
* registry-1.docker.io * registry-1.docker.io
* production.cloudflare.docker.com * production.cloudflare.docker.com
@ -154,7 +159,7 @@ Pay special attention to:
Clone the bridgehead repository: Clone the bridgehead repository:
```shell ```shell
sudo mkdir -p /srv/docker/ 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: Then, run the installation script:
@ -301,26 +306,38 @@ Once you have added your biobank to the Directory you got persistent identifier
### Directory sync tool ### Directory sync tool
The Bridgehead's **Directory Sync** is an optional feature that keeps the Directory up to date with your local data, e.g. number of samples. Conversely, it also updates the local FHIR store with the latest contact details etc. from the Directory. You must explicitly set your country specific directory URL, username and password to enable this feature. The Bridgehead's **Directory Sync** is an optional feature that keeps the 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.
You should talk with your local data protection group regarding the information that is published by Directory sync. You should talk with your local data protection group regarding the information that is published by Directory sync.
Full details can be found in [directory_sync_service](https://github.com/samply/directory_sync_service). To enable it, you will need to 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:
To enable it, you will need to set these variables to the ```bbmri.conf``` file of your GitLab repository. Here is an example config:
``` ```
DS_DIRECTORY_USER_NAME=your_directory_username DS_DIRECTORY_USER_NAME=your_directory_username
DS_DIRECTORY_USER_PASS=your_directory_password DS_DIRECTORY_USER_PASS=your_directory_password
``` ```
Please contact your National Node to obtain this information. Please contact your National Node or Directory support (directory-dev@helpdesk.bbmri-eric.eu) to obtain these credentials.
Optionally, you **may** change when you want Directory sync to run by specifying a [cron](https://crontab.guru) expression, e.g. `DS_TIMER_CRON="0 22 * * *"` for 10 pm every evening. 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. 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 ### Loading data
The data accessed by the federated search is held in the Bridgehead in a FHIR store (we use Blaze). The data accessed by the federated search is held in the Bridgehead in a FHIR store (we use Blaze).
@ -340,6 +357,24 @@ The storage space on your hard drive will depend on the number of FHIR resources
For more information on Blaze performance, please refer to [import performance](https://github.com/samply/blaze/blob/master/docs/performance/import.md). 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 #### 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: 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:
@ -347,6 +382,39 @@ Normally, you will need to build your own ETL to feed the Bridgehead. However, t
You can find the profiles for generating FHIR in [Simplifier](https://simplifier.net/bbmri.de/~resources?category=Profile). 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 ## Things you should know
### Auto-Updates ### Auto-Updates
@ -386,6 +454,54 @@ 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. 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 ## Troubleshooting
### Docker Daemon Proxy Configuration ### Docker Daemon Proxy Configuration

View File

@ -4,7 +4,7 @@ version: "3.7"
services: services:
blaze: blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31 image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
container_name: bridgehead-bbmri-blaze container_name: bridgehead-bbmri-blaze
environment: environment:
BASE_URL: "http://bridgehead-bbmri-blaze:8080" BASE_URL: "http://bridgehead-bbmri-blaze:8080"

View File

@ -12,5 +12,7 @@ services:
DS_DIRECTORY_MOCK: ${DS_DIRECTORY_MOCK} DS_DIRECTORY_MOCK: ${DS_DIRECTORY_MOCK}
DS_DIRECTORY_DEFAULT_COLLECTION_ID: ${DS_DIRECTORY_DEFAULT_COLLECTION_ID} DS_DIRECTORY_DEFAULT_COLLECTION_ID: ${DS_DIRECTORY_DEFAULT_COLLECTION_ID}
DS_DIRECTORY_COUNTRY: ${DS_DIRECTORY_COUNTRY} DS_DIRECTORY_COUNTRY: ${DS_DIRECTORY_COUNTRY}
DS_IMPORT_BIOBANKS: ${DS_IMPORT_BIOBANKS:-true}
DS_IMPORT_COLLECTIONS: ${DS_IMPORT_COLLECTIONS:-true}
depends_on: depends_on:
- "blaze" - "blaze"

View File

@ -10,6 +10,10 @@ if [ "${ENABLE_ERIC}" == "true" ]; then
export ERIC_BROKER_ID=broker.bbmri.samply.de export ERIC_BROKER_ID=broker.bbmri.samply.de
export ERIC_ROOT_CERT=eric export ERIC_ROOT_CERT=eric
;; ;;
"acceptance")
export ERIC_BROKER_ID=broker-acc.bbmri-acc.samply.de
export ERIC_ROOT_CERT=eric.acc
;;
"test") "test")
export ERIC_BROKER_ID=broker-test.bbmri-test.samply.de export ERIC_BROKER_ID=broker-test.bbmri-test.samply.de
export ERIC_ROOT_CERT=eric.test export ERIC_ROOT_CERT=eric.test

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

View File

@ -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"

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@ -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

15
bbmri/modules/exporter.md Normal file
View File

@ -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.

View File

@ -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"

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@ -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

19
bbmri/modules/teiler.md Normal file
View File

@ -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.

View File

@ -1,3 +1,9 @@
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 # Makes sense for all European Biobanks
: ${ENABLE_ERIC:=true} : ${ENABLE_ERIC:=true}
@ -5,7 +11,6 @@
: ${ENABLE_GBN:=false} : ${ENABLE_GBN:=false}
FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64} FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64}
PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
for module in $PROJECT/modules/*.sh for module in $PROJECT/modules/*.sh
do do

View File

@ -53,17 +53,47 @@ case "$PROJECT" in
;; ;;
esac esac
# Loads config variables and runs the projects setup script
loadVars() { loadVars() {
# Load variables from /etc/bridgehead and /srv/docker/bridgehead
set -a set -a
# Source the project specific config file
source /etc/bridgehead/$PROJECT.conf || fail_and_report 1 "/etc/bridgehead/$PROJECT.conf not found" source /etc/bridgehead/$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 if [ -e /etc/bridgehead/$PROJECT.local.conf ]; then
log INFO "Applying /etc/bridgehead/$PROJECT.local.conf" log INFO "Applying /etc/bridgehead/$PROJECT.local.conf"
source /etc/bridgehead/$PROJECT.local.conf || fail_and_report 1 "Found /etc/bridgehead/$PROJECT.local.conf but failed to import" source /etc/bridgehead/$PROJECT.local.conf || fail_and_report 1 "Found /etc/bridgehead/$PROJECT.local.conf but failed to import"
fi fi
# Set execution environment on main default to prod else test
if [[ -z "${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" fetchVarsFromVaultByFile /etc/bridgehead/$PROJECT.conf || fail_and_report 1 "Unable to fetchVarsFromVaultByFile"
setHostname setHostname
optimizeBlazeMemoryUsage optimizeBlazeMemoryUsage
# Run project specific setup if it exists
# This will ususally modiy the `OVERRIDE` to include all the compose files that the project depends on
# This is also where projects specify which modules to load
[ -e ./$PROJECT/vars ] && source ./$PROJECT/vars [ -e ./$PROJECT/vars ] && source ./$PROJECT/vars
set +a set +a
@ -79,26 +109,6 @@ loadVars() {
fi fi
detectCompose detectCompose
setupProxy setupProxy
# Set some project-independent default values
: ${ENVIRONMENT:=production}
export ENVIRONMENT
case "$ENVIRONMENT" in
"production")
export FOCUS_TAG=main
export BEAM_TAG=main
;;
"test")
export FOCUS_TAG=develop
export BEAM_TAG=develop
;;
*)
report_error 7 "Environment \"$ENVIRONMENT\" is unknown. Assuming production. FIX THIS!"
export FOCUS_TAG=main
export BEAM_TAG=main
;;
esac
} }
case "$ACTION" in case "$ACTION" in

View File

@ -2,13 +2,14 @@ version: "3.7"
services: services:
blaze: blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31 image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
container_name: bridgehead-cce-blaze container_name: bridgehead-cce-blaze
environment: environment:
BASE_URL: "http://bridgehead-cce-blaze:8080" BASE_URL: "http://bridgehead-cce-blaze:8080"
JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m" JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000} DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP DB_BLOCK_CACHE_SIZE: ${BLAZE_MEMORY_CAP}
CQL_EXPR_CACHE_SIZE: ${BLAZE_CQL_CACHE_CAP:-32}
ENFORCE_REFERENTIAL_INTEGRITY: "false" ENFORCE_REFERENTIAL_INTEGRITY: "false"
volumes: volumes:
- "blaze-data:/app/data" - "blaze-data:/app/data"
@ -31,6 +32,10 @@ services:
BEAM_PROXY_URL: http://beam-proxy:8081 BEAM_PROXY_URL: http://beam-proxy:8081
RETRY_COUNT: ${FOCUS_RETRY_COUNT} RETRY_COUNT: ${FOCUS_RETRY_COUNT}
EPSILON: 0.28 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: depends_on:
- "beam-proxy" - "beam-proxy"
- "blaze" - "blaze"

View File

@ -0,0 +1,2 @@
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

View File

@ -2,7 +2,7 @@ version: "3.7"
services: services:
blaze: blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31 image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
container_name: bridgehead-ccp-blaze container_name: bridgehead-ccp-blaze
environment: environment:
BASE_URL: "http://bridgehead-ccp-blaze:8080" BASE_URL: "http://bridgehead-ccp-blaze:8080"
@ -35,7 +35,7 @@ services:
QUERIES_TO_CACHE: '/queries_to_cache.conf' QUERIES_TO_CACHE: '/queries_to_cache.conf'
ENDPOINT_TYPE: ${FOCUS_ENDPOINT_TYPE:-blaze} ENDPOINT_TYPE: ${FOCUS_ENDPOINT_TYPE:-blaze}
volumes: volumes:
- /srv/docker/bridgehead/ccp/queries_to_cache.conf:/queries_to_cache.conf - /srv/docker/bridgehead/ccp/queries_to_cache.conf:/queries_to_cache.conf:ro
depends_on: depends_on:
- "beam-proxy" - "beam-proxy"
- "blaze" - "blaze"

View File

@ -2,7 +2,7 @@ version: "3.7"
services: services:
blaze-secondary: blaze-secondary:
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31 image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
container_name: bridgehead-ccp-blaze-secondary container_name: bridgehead-ccp-blaze-secondary
environment: environment:
BASE_URL: "http://bridgehead-ccp-blaze-secondary:8080" BASE_URL: "http://bridgehead-ccp-blaze-secondary:8080"

View File

@ -45,7 +45,6 @@ services:
OPAL_PRIVATE_KEY: "/run/secrets/opal-key.pem" OPAL_PRIVATE_KEY: "/run/secrets/opal-key.pem"
OPAL_CERTIFICATE: "/run/secrets/opal-cert.pem" OPAL_CERTIFICATE: "/run/secrets/opal-cert.pem"
OIDC_URL: "${OIDC_URL}" OIDC_URL: "${OIDC_URL}"
OIDC_REALM: "${OIDC_REALM}"
OIDC_CLIENT_ID: "${OIDC_PRIVATE_CLIENT_ID}" OIDC_CLIENT_ID: "${OIDC_PRIVATE_CLIENT_ID}"
OIDC_CLIENT_SECRET: "${OIDC_CLIENT_SECRET}" OIDC_CLIENT_SECRET: "${OIDC_CLIENT_SECRET}"
OIDC_ADMIN_GROUP: "${OIDC_ADMIN_GROUP}" OIDC_ADMIN_GROUP: "${OIDC_ADMIN_GROUP}"
@ -141,7 +140,7 @@ services:
--client-id="${OIDC_PRIVATE_CLIENT_ID}" --client-id="${OIDC_PRIVATE_CLIENT_ID}"
--client-secret="${OIDC_CLIENT_SECRET}" --client-secret="${OIDC_CLIENT_SECRET}"
--redirect-url="https://${HOST}${OAUTH2_CALLBACK}" --redirect-url="https://${HOST}${OAUTH2_CALLBACK}"
--oidc-issuer-url="${OIDC_ISSUER_URL}" --oidc-issuer-url="${OIDC_URL}"
--scope="openid email profile" --scope="openid email profile"
--code-challenge-method="S256" --code-challenge-method="S256"
--skip-provider-button=true --skip-provider-button=true

View File

@ -13,7 +13,7 @@ services:
PROXY_APIKEY: ${DNPM_BEAM_SECRET_SHORT} PROXY_APIKEY: ${DNPM_BEAM_SECRET_SHORT}
APP_ID: dnpm-connect.${PROXY_ID} APP_ID: dnpm-connect.${PROXY_ID}
DISCOVERY_URL: "./conf/central_targets.json" DISCOVERY_URL: "./conf/central_targets.json"
LOCAL_TARGETS_FILE: "./conf/connect_targets.json" LOCAL_TARGETS_FILE: "/conf/connect_targets.json"
HTTP_PROXY: "http://forward_proxy:3128" HTTP_PROXY: "http://forward_proxy:3128"
HTTPS_PROXY: "http://forward_proxy:3128" HTTPS_PROXY: "http://forward_proxy:3128"
NO_PROXY: beam-proxy,dnpm-backend,host.docker.internal${DNPM_ADDITIONAL_NO_PROXY} NO_PROXY: beam-proxy,dnpm-backend,host.docker.internal${DNPM_ADDITIONAL_NO_PROXY}
@ -25,7 +25,7 @@ services:
volumes: volumes:
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
- /etc/bridgehead/dnpm/local_targets.json:/conf/connect_targets.json: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: labels:
- "traefik.enable=true" - "traefik.enable=true"
- "traefik.http.routers.dnpm-connect.rule=PathPrefix(`/dnpm-connect`)" - "traefik.http.routers.dnpm-connect.rule=PathPrefix(`/dnpm-connect`)"

View File

@ -1,34 +1,99 @@
version: "3.7" version: "3.7"
services: services:
dnpm-backend: dnpm-mysql:
image: ghcr.io/kohlbacherlab/bwhc-backend:1.0-snapshot-broker-connector image: mysql:9
container_name: bridgehead-dnpm-backend healthcheck:
test: [ "CMD", "mysqladmin" ,"ping", "-h", "localhost" ]
interval: 3s
timeout: 5s
retries: 5
environment: environment:
- ZPM_SITE=${ZPM_SITE} MYSQL_ROOT_HOST: "%"
- N_RANDOM_FILES=${DNPM_SYNTH_NUM} MYSQL_ROOT_PASSWORD: ${DNPM_MYSQL_ROOT_PASSWORD}
volumes: volumes:
- /etc/bridgehead/dnpm:/bwhc_config:ro - /var/cache/bridgehead/dnpm/mysql:/var/lib/mysql
- ${DNPM_DATA_DIR}:/bwhc_data
labels:
- "traefik.enable=true"
- "traefik.http.routers.bwhc-backend.rule=PathPrefix(`/bwhc`)"
- "traefik.http.services.bwhc-backend.loadbalancer.server.port=9000"
- "traefik.http.routers.bwhc-backend.tls=true"
dnpm-frontend: dnpm-authup:
image: ghcr.io/kohlbacherlab/bwhc-frontend:2209 image: authup/authup:latest
container_name: bridgehead-dnpm-frontend container_name: bridgehead-dnpm-authup
links: volumes:
- dnpm-backend - /var/cache/bridgehead/dnpm/authup:/usr/src/app/writable
depends_on:
dnpm-mysql:
condition: service_healthy
command: server/core start
environment: environment:
- NUXT_HOST=0.0.0.0 - PUBLIC_URL=https://${HOST}/auth/
- NUXT_PORT=8080 - AUTHORIZE_REDIRECT_URL=https://${HOST}
- BACKEND_PROTOCOL=https - ROBOT_ADMIN_ENABLED=true
- BACKEND_HOSTNAME=$HOST - ROBOT_ADMIN_SECRET=${DNPM_AUTHUP_SECRET}
- BACKEND_PORT=443 - ROBOT_ADMIN_SECRET_RESET=true
- DB_TYPE=mysql
- DB_HOST=dnpm-mysql
- DB_USERNAME=root
- DB_PASSWORD=${DNPM_MYSQL_ROOT_PASSWORD}
- DB_DATABASE=auth
labels: labels:
- "traefik.enable=true" - "traefik.enable=true"
- "traefik.http.routers.bwhc-frontend.rule=PathPrefix(`/`)" - "traefik.http.middlewares.authup-strip.stripprefix.prefixes=/auth"
- "traefik.http.services.bwhc-frontend.loadbalancer.server.port=8080" - "traefik.http.routers.dnpm-auth.middlewares=authup-strip"
- "traefik.http.routers.bwhc-frontend.tls=true" - "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`)"

View File

@ -1,28 +1,16 @@
#!/bin/bash #!/bin/bash
if [ -n "${ENABLE_DNPM_NODE}" ]; then if [ -n "${ENABLE_DNPM_NODE}" ]; then
log INFO "DNPM setup detected (BwHC Node) -- will start BwHC node." log INFO "DNPM setup detected -- will start DNPM:DIP node."
OVERRIDE+=" -f ./$PROJECT/modules/dnpm-node-compose.yml" OVERRIDE+=" -f ./$PROJECT/modules/dnpm-node-compose.yml"
# Set variables required for BwHC Node. ZPM_SITE is assumed to be set in /etc/bridgehead/<project>.conf # Set variables required for BwHC Node. ZPM_SITE is assumed to be set in /etc/bridgehead/<project>.conf
DNPM_APPLICATION_SECRET="$(echo \"This is a salt string to generate one consistent password for DNPM. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
if [ -z "${ZPM_SITE+x}" ]; then if [ -z "${ZPM_SITE+x}" ]; then
log ERROR "Mandatory variable ZPM_SITE not defined!" log ERROR "Mandatory variable ZPM_SITE not defined!"
exit 1 exit 1
fi fi
if [ -z "${DNPM_DATA_DIR+x}" ]; then mkdir -p /var/cache/bridgehead/dnpm/ || fail_and_report 1 "Failed to create '/var/cache/bridgehead/dnpm/'. Please run sudo './bridgehead install $PROJECT' again to fix the permissions."
log ERROR "Mandatory variable DNPM_DATA_DIR not defined!" DNPM_SYNTH_NUM=${DNPM_SYNTH_NUM:--1}
exit 1 DNPM_MYSQL_ROOT_PASSWORD="$(generate_simple_password 'dnpm mysql')"
fi DNPM_AUTHUP_SECRET="$(generate_simple_password 'dnpm authup')"
DNPM_SYNTH_NUM=${DNPM_SYNTH_NUM:-0}
if grep -q 'traefik.http.routers.landing.rule=PathPrefix(`/landing`)' /srv/docker/bridgehead/minimal/docker-compose.override.yml 2>/dev/null; then
echo "Override of landing page url already in place"
else
echo "Adding override of landing page url"
if [ -f /srv/docker/bridgehead/minimal/docker-compose.override.yml ]; then
echo -e ' landing:\n labels:\n - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"' >> /srv/docker/bridgehead/minimal/docker-compose.override.yml
else
echo -e 'version: "3.7"\nservices:\n landing:\n labels:\n - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"' >> /srv/docker/bridgehead/minimal/docker-compose.override.yml
fi
fi
fi fi

View File

@ -23,7 +23,6 @@ services:
OIDC_ADMIN_GROUP: "${OIDC_ADMIN_GROUP}" OIDC_ADMIN_GROUP: "${OIDC_ADMIN_GROUP}"
OIDC_CLIENT_ID: "${OIDC_PRIVATE_CLIENT_ID}" OIDC_CLIENT_ID: "${OIDC_PRIVATE_CLIENT_ID}"
OIDC_CLIENT_SECRET: "${OIDC_CLIENT_SECRET}" OIDC_CLIENT_SECRET: "${OIDC_CLIENT_SECRET}"
OIDC_REALM: "${OIDC_REALM}"
OIDC_URL: "${OIDC_URL}" OIDC_URL: "${OIDC_URL}"
labels: labels:

View File

@ -3,7 +3,7 @@ version: "3.7"
services: services:
obds2fhir-rest: obds2fhir-rest:
container_name: bridgehead-obds2fhir-rest container_name: bridgehead-obds2fhir-rest
image: docker.verbis.dkfz.de/ccp/obds2fhir-rest:main image: docker.verbis.dkfz.de/samply/obds2fhir-rest:main
environment: environment:
IDTYPE: BK_${IDMANAGEMENT_FRIENDLY_ID}_L-ID IDTYPE: BK_${IDMANAGEMENT_FRIENDLY_ID}_L-ID
MAINZELLISTE_APIKEY: ${IDMANAGER_LOCAL_PATIENTLIST_APIKEY} MAINZELLISTE_APIKEY: ${IDMANAGER_LOCAL_PATIENTLIST_APIKEY}

View File

@ -31,8 +31,8 @@ services:
environment: environment:
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}" DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend" TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend"
TEILER_DASHBOARD_URL: "https://${HOST}/ccp-teiler-dashboard"
OIDC_URL: "${OIDC_URL}" OIDC_URL: "${OIDC_URL}"
OIDC_REALM: "${OIDC_REALM}"
OIDC_CLIENT_ID: "${OIDC_PUBLIC_CLIENT_ID}" OIDC_CLIENT_ID: "${OIDC_PUBLIC_CLIENT_ID}"
OIDC_TOKEN_GROUP: "${OIDC_GROUP_CLAIM}" OIDC_TOKEN_GROUP: "${OIDC_GROUP_CLAIM}"
TEILER_ADMIN_NAME: "${OPERATOR_FIRST_NAME} ${OPERATOR_LAST_NAME}" TEILER_ADMIN_NAME: "${OPERATOR_FIRST_NAME} ${OPERATOR_LAST_NAME}"
@ -41,7 +41,6 @@ services:
TEILER_PROJECT: "${PROJECT}" TEILER_PROJECT: "${PROJECT}"
EXPORTER_API_KEY: "${EXPORTER_API_KEY}" EXPORTER_API_KEY: "${EXPORTER_API_KEY}"
TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler" TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler"
TEILER_DASHBOARD_HTTP_RELATIVE_PATH: "/ccp-teiler-dashboard"
TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler" TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler"
TEILER_USER: "${OIDC_USER_GROUP}" TEILER_USER: "${OIDC_USER_GROUP}"
TEILER_ADMIN: "${OIDC_ADMIN_GROUP}" TEILER_ADMIN: "${OIDC_ADMIN_GROUP}"
@ -64,18 +63,11 @@ services:
APPLICATION_PORT: "8085" APPLICATION_PORT: "8085"
APPLICATION_ADDRESS: "${HOST}" APPLICATION_ADDRESS: "${HOST}"
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}" DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
CONFIG_ENV_VAR_PATH: "/run/secrets/ccp.conf"
TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler" TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler"
TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler" TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler"
TEILER_DASHBOARD_DE_URL: "https://${HOST}/ccp-teiler-dashboard/de" TEILER_DASHBOARD_DE_URL: "https://${HOST}/ccp-teiler-dashboard/de"
TEILER_DASHBOARD_EN_URL: "https://${HOST}/ccp-teiler-dashboard/en" TEILER_DASHBOARD_EN_URL: "https://${HOST}/ccp-teiler-dashboard/en"
CENTRAX_URL: "${CENTRAXX_URL}"
HTTP_PROXY: "http://forward_proxy:3128" HTTP_PROXY: "http://forward_proxy:3128"
ENABLE_MTBA: "${ENABLE_MTBA}" ENABLE_MTBA: "${ENABLE_MTBA}"
ENABLE_DATASHIELD: "${ENABLE_DATASHIELD}" ENABLE_DATASHIELD: "${ENABLE_DATASHIELD}"
secrets: IDMANAGER_UPLOAD_APIKEY: "${IDMANAGER_UPLOAD_APIKEY}" # Only used to check if the ID Manager is active
- ccp.conf
secrets:
ccp.conf:
file: /etc/bridgehead/ccp.conf

View File

@ -1,19 +1,180 @@
# Teiler # Teiler
This module orchestrates the different microfrontends of the bridgehead as a single page application.
**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 ## 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,...) The **Teiler Orchestrator** is the entry point of the **Single Page Application (SPA)**. It consists of:
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. - 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 ## Teiler Dashboard
It consists on the main dashboard and a set of embedded services.
### Login The **Teiler Dashboard** is the unified interface users interact with after logging in. It provides:
user and password in ccp.local.conf
- 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 ## Teiler Backend
In this component, the microfrontends are configured.
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 apps configuration in the Teiler Backend as described above.
This flexible, modular design enables easy expansion

View File

@ -1,2 +1,3 @@
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
ORGANOID_DASHBOARD_PUBLIC

View File

@ -12,14 +12,9 @@ OIDC_USER_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})"
OIDC_ADMIN_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})_Verwalter" OIDC_ADMIN_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})_Verwalter"
OIDC_PRIVATE_CLIENT_ID=${SITE_ID}-private OIDC_PRIVATE_CLIENT_ID=${SITE_ID}-private
OIDC_PUBLIC_CLIENT_ID=${SITE_ID}-public OIDC_PUBLIC_CLIENT_ID=${SITE_ID}-public
# Use "test-realm-01" for testing OIDC_URL="https://login.verbis.dkfz.de/realms/test-realm-01"
OIDC_REALM="${OIDC_REALM:-master}"
OIDC_URL="https://login.verbis.dkfz.de"
OIDC_ISSUER_URL="${OIDC_URL}/realms/${OIDC_REALM}"
OIDC_GROUP_CLAIM="groups" OIDC_GROUP_CLAIM="groups"
POSTGRES_TAG=15.6-alpine
for module in $PROJECT/modules/*.sh for module in $PROJECT/modules/*.sh
do do
log DEBUG "sourcing $module" log DEBUG "sourcing $module"
@ -30,3 +25,11 @@ idManagementSetup
mtbaSetup mtbaSetup
obds2fhirRestSetup obds2fhirRestSetup
blazeSecondarySetup blazeSecondarySetup
for module in modules/*.sh
do
log DEBUG "sourcing $module"
source $module
done
transfairSetup

View File

@ -2,7 +2,7 @@ version: "3.7"
services: services:
blaze: blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31 image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
container_name: bridgehead-dhki-blaze container_name: bridgehead-dhki-blaze
environment: environment:
BASE_URL: "http://bridgehead-dhki-blaze:8080" BASE_URL: "http://bridgehead-dhki-blaze:8080"
@ -33,7 +33,7 @@ services:
EPSILON: 0.28 EPSILON: 0.28
QUERIES_TO_CACHE: '/queries_to_cache.conf' QUERIES_TO_CACHE: '/queries_to_cache.conf'
volumes: volumes:
- /srv/docker/bridgehead/dhki/queries_to_cache.conf:/queries_to_cache.conf - /srv/docker/bridgehead/dhki/queries_to_cache.conf:/queries_to_cache.conf:ro
depends_on: depends_on:
- "beam-proxy" - "beam-proxy"
- "blaze" - "blaze"

View File

@ -8,8 +8,6 @@ PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
BROKER_URL_FOR_PREREQ=$BROKER_URL BROKER_URL_FOR_PREREQ=$BROKER_URL
POSTGRES_TAG=15.6-alpine
for module in ccp/modules/*.sh for module in ccp/modules/*.sh
do do
log DEBUG "sourcing $module" log DEBUG "sourcing $module"
@ -18,3 +16,11 @@ done
idManagementSetup idManagementSetup
obds2fhirRestSetup obds2fhirRestSetup
for module in modules/*.sh
do
log DEBUG "sourcing $module"
source $module
done
transfairSetup

View File

@ -2,13 +2,14 @@ version: "3.7"
services: services:
blaze: blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31 image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
container_name: bridgehead-itcc-blaze container_name: bridgehead-itcc-blaze
environment: environment:
BASE_URL: "http://bridgehead-itcc-blaze:8080" BASE_URL: "http://bridgehead-itcc-blaze:8080"
JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m" JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000} DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP DB_BLOCK_CACHE_SIZE: ${BLAZE_MEMORY_CAP}
CQL_EXPR_CACHE_SIZE: ${BLAZE_CQL_CACHE_CAP:-32}
ENFORCE_REFERENTIAL_INTEGRITY: "false" ENFORCE_REFERENTIAL_INTEGRITY: "false"
volumes: volumes:
- "blaze-data:/app/data" - "blaze-data:/app/data"
@ -31,6 +32,10 @@ services:
BEAM_PROXY_URL: http://beam-proxy:8081 BEAM_PROXY_URL: http://beam-proxy:8081
RETRY_COUNT: ${FOCUS_RETRY_COUNT} RETRY_COUNT: ${FOCUS_RETRY_COUNT}
EPSILON: 0.28 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: depends_on:
- "beam-proxy" - "beam-proxy"
- "blaze" - "blaze"

View File

@ -0,0 +1,2 @@
bGlicmFyeSBSZXRyaWV2ZQp1c2luZyBGSElSIHZlcnNpb24gJzQuMC4wJwppbmNsdWRlIEZISVJIZWxwZXJzIHZlcnNpb24gJzQuMC4wJwpjb2Rlc3lzdGVtIFNhbXBsZU1hdGVyaWFsVHlwZTogJ2h0dHBzOi8vZmhpci5iYm1yaS5kZS9Db2RlU3lzdGVtL1NhbXBsZU1hdGVyaWFsVHlwZScKCmNvZGVzeXN0ZW0gbG9pbmM6ICdodHRwOi8vbG9pbmMub3JnJwoKY29udGV4dCBQYXRpZW50CkRLVEtfU1RSQVRfR0VOREVSX1NUUkFUSUZJRVIKICBES1RLX1NUUkFUX0RJQUdOT1NJU19TVFJBVElGSUVSCiAgSVRDQ19TVFJBVF9BR0VfQ0xBU1NfU1RSQVRJRklFUgogIERLVEtfU1RSQVRfREVGX0lOX0lOSVRJQUxfUE9QVUxBVElPTgp0cnVl
bGlicmFyeSBSZXRyaWV2ZQp1c2luZyBGSElSIHZlcnNpb24gJzQuMC4wJwppbmNsdWRlIEZISVJIZWxwZXJzIHZlcnNpb24gJzQuMC4wJwpjb2Rlc3lzdGVtIFNhbXBsZU1hdGVyaWFsVHlwZTogJ2h0dHBzOi8vZmhpci5iYm1yaS5kZS9Db2RlU3lzdGVtL1NhbXBsZU1hdGVyaWFsVHlwZScKCmNvZGVzeXN0ZW0gbG9pbmM6ICdodHRwOi8vbG9pbmMub3JnJwpjb2Rlc3lzdGVtIG1vbGVjdWxhck1hcmtlcjogJ2h0dHA6Ly93d3cuZ2VuZW5hbWVzLm9yZycKCmNvbnRleHQgUGF0aWVudApES1RLX1NUUkFUX0dFTkRFUl9TVFJBVElGSUVSCiAgREtUS19TVFJBVF9ESUFHTk9TSVNfU1RSQVRJRklFUgogIElUQ0NfU1RSQVRfQUdFX0NMQVNTX1NUUkFUSUZJRVIKICBES1RLX1NUUkFUX0RFRl9JTl9JTklUSUFMX1BPUFVMQVRJT04KKGV4aXN0cyBmcm9tIFtPYnNlcnZhdGlvbjogQ29kZSAnNjk1NDgtNicgZnJvbSBsb2luY10gTwp3aGVyZSBPLmNvbXBvbmVudC53aGVyZShjb2RlLmNvZGluZyBjb250YWlucyBDb2RlICc0ODAxOC02JyBmcm9tIGxvaW5jKS52YWx1ZS5jb2RpbmcgY29udGFpbnMgQ29kZSAnQlJBRicgZnJvbSBtb2xlY3VsYXJNYXJrZXIp

View File

@ -6,7 +6,7 @@ services:
replicas: 0 #deactivate landing page replicas: 0 #deactivate landing page
blaze: blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31 image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
container_name: bridgehead-kr-blaze container_name: bridgehead-kr-blaze
environment: environment:
BASE_URL: "http://bridgehead-kr-blaze:8080" BASE_URL: "http://bridgehead-kr-blaze:8080"

View File

@ -31,8 +31,8 @@ services:
environment: environment:
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}" DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend" TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend"
TEILER_DASHBOARD_URL: "https://${HOST}/ccp-teiler-dashboard"
OIDC_URL: "${OIDC_URL}" OIDC_URL: "${OIDC_URL}"
OIDC_REALM: "${OIDC_REALM}"
OIDC_CLIENT_ID: "${OIDC_PUBLIC_CLIENT_ID}" OIDC_CLIENT_ID: "${OIDC_PUBLIC_CLIENT_ID}"
OIDC_TOKEN_GROUP: "${OIDC_GROUP_CLAIM}" OIDC_TOKEN_GROUP: "${OIDC_GROUP_CLAIM}"
TEILER_ADMIN_NAME: "${OPERATOR_FIRST_NAME} ${OPERATOR_LAST_NAME}" TEILER_ADMIN_NAME: "${OPERATOR_FIRST_NAME} ${OPERATOR_LAST_NAME}"
@ -41,7 +41,6 @@ services:
TEILER_PROJECT: "${PROJECT}" TEILER_PROJECT: "${PROJECT}"
EXPORTER_API_KEY: "${EXPORTER_API_KEY}" EXPORTER_API_KEY: "${EXPORTER_API_KEY}"
TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler" TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler"
TEILER_DASHBOARD_HTTP_RELATIVE_PATH: "/ccp-teiler-dashboard"
TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler" TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler"
TEILER_USER: "${OIDC_USER_GROUP}" TEILER_USER: "${OIDC_USER_GROUP}"
TEILER_ADMIN: "${OIDC_ADMIN_GROUP}" TEILER_ADMIN: "${OIDC_ADMIN_GROUP}"
@ -69,7 +68,6 @@ services:
TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler" TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler"
TEILER_DASHBOARD_DE_URL: "https://${HOST}/ccp-teiler-dashboard/de" TEILER_DASHBOARD_DE_URL: "https://${HOST}/ccp-teiler-dashboard/de"
TEILER_DASHBOARD_EN_URL: "https://${HOST}/ccp-teiler-dashboard/en" TEILER_DASHBOARD_EN_URL: "https://${HOST}/ccp-teiler-dashboard/en"
CENTRAX_URL: "${CENTRAXX_URL}"
HTTP_PROXY: "http://forward_proxy:3128" HTTP_PROXY: "http://forward_proxy:3128"
ENABLE_MTBA: "${ENABLE_MTBA}" ENABLE_MTBA: "${ENABLE_MTBA}"
ENABLE_DATASHIELD: "${ENABLE_DATASHIELD}" ENABLE_DATASHIELD: "${ENABLE_DATASHIELD}"

View File

@ -313,15 +313,82 @@ function sync_secrets() {
-e ALL_PROXY=$HTTPS_PROXY_FULL_URL \ -e ALL_PROXY=$HTTPS_PROXY_FULL_URL \
-e PROXY_ID=$PROXY_ID \ -e PROXY_ID=$PROXY_ID \
-e BROKER_URL=$BROKER_URL \ -e BROKER_URL=$BROKER_URL \
-e OIDC_PROVIDER=secret-sync-central.oidc-client-enrollment.$BROKER_ID \ -e OIDC_PROVIDER=secret-sync-central.central-secret-sync.$BROKER_ID \
-e SECRET_DEFINITIONS=$secret_sync_args \ -e SECRET_DEFINITIONS=$secret_sync_args \
docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest
set -a # Export variables as environment variables set -a # Export variables as environment variables
source /var/cache/bridgehead/secrets/* source /var/cache/bridgehead/secrets/oidc
set +a # Export variables in the regular way 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() { capitalize_first_letter() {
input="$1" input="$1"
capitalized="$(tr '[:lower:]' '[:upper:]' <<< ${input:0:1})${input:1}" capitalized="$(tr '[:lower:]' '[:upper:]' <<< ${input:0:1})${input:1}"

11
lib/gitlab-token-helper.sh Executable file
View File

@ -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

View File

@ -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

View File

@ -41,6 +41,20 @@ if [ ! -z "$NNGM_CTS_APIKEY" ] && [ -z "$NNGM_AUTH" ]; then
add_basic_auth_user "nngm" $generated_passwd "NNGM_AUTH" $PROJECT add_basic_auth_user "nngm" $generated_passwd "NNGM_AUTH" $PROJECT
fi fi
if [ -z "$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" log "INFO" "Registering system units for bridgehead and bridgehead-update"
cp -v \ cp -v \
lib/systemd/bridgehead\@.service \ lib/systemd/bridgehead\@.service \

View File

@ -19,7 +19,7 @@ fi
hc_send log "Checking for bridgehead updates ..." hc_send log "Checking for bridgehead updates ..."
CONFFILE=/etc/bridgehead/$1.conf CONFFILE=/etc/bridgehead/$PROJECT.conf
if [ ! -e $CONFFILE ]; then if [ ! -e $CONFFILE ]; then
fail_and_report 1 "Configuration file $CONFFILE not found." fail_and_report 1 "Configuration file $CONFFILE not found."
@ -33,7 +33,7 @@ export SITE_ID
checkOwner /srv/docker/bridgehead bridgehead || fail_and_report 1 "Update failed: Wrong permissions in /srv/docker/bridgehead" 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" 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="" CHANGES=""
@ -45,10 +45,6 @@ for DIR in /etc/bridgehead $(pwd); do
if [ -n "$OUT" ]; then if [ -n "$OUT" ]; then
report_error log "The working directory $DIR is modified. Changed files: $OUT" report_error log "The working directory $DIR is modified. Changed files: $OUT"
fi fi
if [ "$(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 $DIR rev-parse --verify HEAD)" old_git_hash="$(git -C $DIR rev-parse --verify HEAD)"
if [ -z "$HTTPS_PROXY_FULL_URL" ]; then if [ -z "$HTTPS_PROXY_FULL_URL" ]; then
log "INFO" "Git is using no proxy!" log "INFO" "Git is using no proxy!"

View File

@ -16,7 +16,7 @@ services:
- --entrypoints.web.http.redirections.entrypoint.scheme=https - --entrypoints.web.http.redirections.entrypoint.scheme=https
labels: labels:
- "traefik.enable=true" - "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.entrypoints=websecure"
- "traefik.http.routers.dashboard.service=api@internal" - "traefik.http.routers.dashboard.service=api@internal"
- "traefik.http.routers.dashboard.tls=true" - "traefik.http.routers.dashboard.tls=true"

View File

@ -0,0 +1,142 @@
{
"sites": [
{
"id": "UKFR",
"name": "Freiburg",
"virtualhost": "ukfr.dnpm.de",
"beamconnect": "dnpm-connect.dnpm-bridge.broker.ccp-it.dktk.dkfz.de"
},
{
"id": "UKHD",
"name": "Heidelberg",
"virtualhost": "ukhd.dnpm.de",
"beamconnect": "dnpm-connect.dnpm-bridge.broker.ccp-it.dktk.dkfz.de"
},
{
"id": "UKT",
"name": "Tübingen",
"virtualhost": "ukt.dnpm.de",
"beamconnect": "dnpm-connect.dnpm-bridge.broker.ccp-it.dktk.dkfz.de"
},
{
"id": "UKU",
"name": "Ulm",
"virtualhost": "uku.dnpm.de",
"beamconnect": "dnpm-connect.dnpm-bridge.broker.ccp-it.dktk.dkfz.de"
},
{
"id": "UM",
"name": "Mainz",
"virtualhost": "um.dnpm.de",
"beamconnect": "dnpm-connect.dnpm-bridge.broker.ccp-it.dktk.dkfz.de"
},
{
"id": "UKMR",
"name": "Marburg",
"virtualhost": "ukmr.dnpm.de",
"beamconnect": "dnpm-connect.dnpm-bridge.broker.ccp-it.dktk.dkfz.de"
},
{
"id": "UKE",
"name": "Hamburg",
"virtualhost": "uke.dnpm.de",
"beamconnect": "dnpm-connect.dnpm-bridge.broker.ccp-it.dktk.dkfz.de"
},
{
"id": "UKA",
"name": "Aachen",
"virtualhost": "uka.dnpm.de",
"beamconnect": "dnpm-connect.dnpm-bridge.broker.ccp-it.dktk.dkfz.de"
},
{
"id": "Charite",
"name": "Berlin",
"virtualhost": "charite.dnpm.de",
"beamconnect": "dnpm-connect.berlin-test.broker.ccp-it.dktk.dkfz.de"
},
{
"id": "MRI",
"name": "Muenchen-tum",
"virtualhost": "mri.dnpm.de",
"beamconnect": "dnpm-connect.muenchen-tum.broker.ccp-it.dktk.dkfz.de"
},
{
"id": "KUM",
"name": "Muenchen-lmu",
"virtualhost": "kum.dnpm.de",
"beamconnect": "dnpm-connect.muenchen-lmu.broker.ccp-it.dktk.dkfz.de"
},
{
"id": "MHH",
"name": "Hannover",
"virtualhost": "mhh.dnpm.de",
"beamconnect": "dnpm-connect.hannover.broker.ccp-it.dktk.dkfz.de"
},
{
"id": "UKDD",
"name": "dresden-dnpm",
"virtualhost": "ukdd.dnpm.de",
"beamconnect": "dnpm-connect.dresden-dnpm.broker.ccp-it.dktk.dkfz.de"
},
{
"id": "UKB",
"name": "Bonn",
"virtualhost": "ukb.dnpm.de",
"beamconnect": "dnpm-connect.bonn-dnpm.broker.ccp-it.dktk.dkfz.de"
},
{
"id": "UKD",
"name": "Duesseldorf",
"virtualhost": "ukd.dnpm.de",
"beamconnect": "dnpm-connect.duesseldorf-dnpm.broker.ccp-it.dktk.dkfz.de"
},
{
"id": "UKK",
"name": "Koeln",
"virtualhost": "ukk.dnpm.de",
"beamconnect": "dnpm-connect.dnpm-bridge.broker.ccp-it.dktk.dkfz.de"
},
{
"id": "UME",
"name": "Essen",
"virtualhost": "ume.dnpm.de",
"beamconnect": "dnpm-connect.essen.broker.ccp-it.dktk.dkfz.de"
},
{
"id": "UKM",
"name": "Muenster",
"virtualhost": "ukm.dnpm.de",
"beamconnect": "dnpm-connect.muenster-dnpm.broker.ccp-it.dktk.dkfz.de"
},
{
"id": "UKF",
"name": "Frankfurt",
"virtualhost": "ukf.dnpm.de",
"beamconnect": "dnpm-connect.frankfurt.broker.ccp-it.dktk.dkfz.de"
},
{
"id": "UMG",
"name": "Goettingen",
"virtualhost": "umg.dnpm.de",
"beamconnect": "dnpm-connect.goettingen.broker.ccp-it.dktk.dkfz.de"
},
{
"id": "UKW",
"name": "Würzburg",
"virtualhost": "ukw.dnpm.de",
"beamconnect": "dnpm-connect.wuerzburg-dnpm.broker.ccp-it.dktk.dkfz.de"
},
{
"id": "UKSH",
"name": "Schleswig-Holstein",
"virtualhost": "uksh.dnpm.de",
"beamconnect": "dnpm-connect.uksh-dnpm.broker.ccp-it.dktk.dkfz.de"
},
{
"id": "TKT",
"name": "Test",
"virtualhost": "tkt.dnpm.de",
"beamconnect": "dnpm-connect.tobias-develop.broker.ccp-it.dktk.dkfz.de"
}
]
}

View File

@ -29,7 +29,7 @@ services:
PROXY_APIKEY: ${DNPM_BEAM_SECRET_SHORT} PROXY_APIKEY: ${DNPM_BEAM_SECRET_SHORT}
APP_ID: dnpm-connect.${DNPM_PROXY_ID} APP_ID: dnpm-connect.${DNPM_PROXY_ID}
DISCOVERY_URL: "./conf/central_targets.json" DISCOVERY_URL: "./conf/central_targets.json"
LOCAL_TARGETS_FILE: "./conf/connect_targets.json" LOCAL_TARGETS_FILE: "/conf/connect_targets.json"
HTTP_PROXY: http://forward_proxy:3128 HTTP_PROXY: http://forward_proxy:3128
HTTPS_PROXY: http://forward_proxy:3128 HTTPS_PROXY: http://forward_proxy:3128
NO_PROXY: dnpm-beam-proxy,dnpm-backend, host.docker.internal${DNPM_ADDITIONAL_NO_PROXY} NO_PROXY: dnpm-beam-proxy,dnpm-backend, host.docker.internal${DNPM_ADDITIONAL_NO_PROXY}
@ -41,7 +41,7 @@ services:
volumes: volumes:
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
- /etc/bridgehead/dnpm/local_targets.json:/conf/connect_targets.json: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: labels:
- "traefik.enable=true" - "traefik.enable=true"
- "traefik.http.routers.dnpm-connect.rule=PathPrefix(`/dnpm-connect`)" - "traefik.http.routers.dnpm-connect.rule=PathPrefix(`/dnpm-connect`)"

View File

@ -1,34 +1,99 @@
version: "3.7" version: "3.7"
services: services:
dnpm-backend: dnpm-mysql:
image: ghcr.io/kohlbacherlab/bwhc-backend:1.0-snapshot-broker-connector image: mysql:9
container_name: bridgehead-dnpm-backend healthcheck:
test: [ "CMD", "mysqladmin" ,"ping", "-h", "localhost" ]
interval: 3s
timeout: 5s
retries: 5
environment: environment:
- ZPM_SITE=${ZPM_SITE} MYSQL_ROOT_HOST: "%"
- N_RANDOM_FILES=${DNPM_SYNTH_NUM} MYSQL_ROOT_PASSWORD: ${DNPM_MYSQL_ROOT_PASSWORD}
volumes: volumes:
- /etc/bridgehead/dnpm:/bwhc_config:ro - /var/cache/bridgehead/dnpm/mysql:/var/lib/mysql
- ${DNPM_DATA_DIR}:/bwhc_data
labels:
- "traefik.enable=true"
- "traefik.http.routers.bwhc-backend.rule=PathPrefix(`/bwhc`)"
- "traefik.http.services.bwhc-backend.loadbalancer.server.port=9000"
- "traefik.http.routers.bwhc-backend.tls=true"
dnpm-frontend: dnpm-authup:
image: ghcr.io/kohlbacherlab/bwhc-frontend:2209 image: authup/authup:latest
container_name: bridgehead-dnpm-frontend container_name: bridgehead-dnpm-authup
links: volumes:
- dnpm-backend - /var/cache/bridgehead/dnpm/authup:/usr/src/app/writable
depends_on:
dnpm-mysql:
condition: service_healthy
command: server/core start
environment: environment:
- NUXT_HOST=0.0.0.0 - PUBLIC_URL=https://${HOST}/auth/
- NUXT_PORT=8080 - AUTHORIZE_REDIRECT_URL=https://${HOST}
- BACKEND_PROTOCOL=https - ROBOT_ADMIN_ENABLED=true
- BACKEND_HOSTNAME=$HOST - ROBOT_ADMIN_SECRET=${DNPM_AUTHUP_SECRET}
- BACKEND_PORT=443 - ROBOT_ADMIN_SECRET_RESET=true
- DB_TYPE=mysql
- DB_HOST=dnpm-mysql
- DB_USERNAME=root
- DB_PASSWORD=${DNPM_MYSQL_ROOT_PASSWORD}
- DB_DATABASE=auth
labels: labels:
- "traefik.enable=true" - "traefik.enable=true"
- "traefik.http.routers.bwhc-frontend.rule=PathPrefix(`/`)" - "traefik.http.middlewares.authup-strip.stripprefix.prefixes=/auth/"
- "traefik.http.services.bwhc-frontend.loadbalancer.server.port=8080" - "traefik.http.routers.dnpm-auth.middlewares=authup-strip"
- "traefik.http.routers.bwhc-frontend.tls=true" - "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`)"

View File

@ -1,28 +1,16 @@
#!/bin/bash #!/bin/bash
if [ -n "${ENABLE_DNPM_NODE}" ]; then if [ -n "${ENABLE_DNPM_NODE}" ]; then
log INFO "DNPM setup detected (BwHC Node) -- will start BwHC node." log INFO "DNPM setup detected -- will start DNPM:DIP node."
OVERRIDE+=" -f ./$PROJECT/modules/dnpm-node-compose.yml" OVERRIDE+=" -f ./$PROJECT/modules/dnpm-node-compose.yml"
# Set variables required for BwHC Node. ZPM_SITE is assumed to be set in /etc/bridgehead/<project>.conf # Set variables required for BwHC Node. ZPM_SITE is assumed to be set in /etc/bridgehead/<project>.conf
DNPM_APPLICATION_SECRET="$(echo \"This is a salt string to generate one consistent password for DNPM. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
if [ -z "${ZPM_SITE+x}" ]; then if [ -z "${ZPM_SITE+x}" ]; then
log ERROR "Mandatory variable ZPM_SITE not defined!" log ERROR "Mandatory variable ZPM_SITE not defined!"
exit 1 exit 1
fi fi
if [ -z "${DNPM_DATA_DIR+x}" ]; then mkdir -p /var/cache/bridgehead/dnpm/ || fail_and_report 1 "Failed to create '/var/cache/bridgehead/dnpm/'. Please run sudo './bridgehead install $PROJECT' again to fix the permissions."
log ERROR "Mandatory variable DNPM_DATA_DIR not defined!" DNPM_SYNTH_NUM=${DNPM_SYNTH_NUM:--1}
exit 1 DNPM_MYSQL_ROOT_PASSWORD="$(generate_simple_password 'dnpm mysql')"
fi DNPM_AUTHUP_SECRET="$(generate_simple_password 'dnpm authup')"
DNPM_SYNTH_NUM=${DNPM_SYNTH_NUM:-0}
if grep -q 'traefik.http.routers.landing.rule=PathPrefix(`/landing`)' /srv/docker/bridgehead/minimal/docker-compose.override.yml 2>/dev/null; then
echo "Override of landing page url already in place"
else
echo "Adding override of landing page url"
if [ -f /srv/docker/bridgehead/minimal/docker-compose.override.yml ]; then
echo -e ' landing:\n labels:\n - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"' >> /srv/docker/bridgehead/minimal/docker-compose.override.yml
else
echo -e 'version: "3.7"\nservices:\n landing:\n labels:\n - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"' >> /srv/docker/bridgehead/minimal/docker-compose.override.yml
fi
fi
fi fi

View File

@ -0,0 +1,17 @@
version: "3.7"
services:
ssh-tunnel:
image: docker.verbis.dkfz.de/cache/samply/ssh-tunnel
container_name: bridgehead-ccp-ssh-tunnel
environment:
SSH_TUNNEL_USERNAME: "${SSH_TUNNEL_USERNAME}"
SSH_TUNNEL_HOST: "${SSH_TUNNEL_HOST}"
SSH_TUNNEL_PORT: "${SSH_TUNNEL_PORT:-22}"
volumes:
- "/etc/bridgehead/ssh-tunnel.conf:/ssh-tunnel.conf:ro"
secrets:
- privkey
secrets:
privkey:
file: /etc/bridgehead/pki/ssh-tunnel.priv.pem

View File

@ -0,0 +1,6 @@
#!/bin/bash
if [ -n "$ENABLE_SSH_TUNNEL" ]; then
log INFO "SSH Tunnel setup detected -- will start SSH Tunnel."
OVERRIDE+=" -f ./modules/ssh-tunnel-compose.yml"
fi

19
modules/ssh-tunnel.md Normal file
View File

@ -0,0 +1,19 @@
# SSH Tunnel Module
This module enables SSH tunneling capabilities for the Bridgehead installation.
The primary use case for this is to connect bridgehead components that are hosted externally due to security concerns.
To connect the new components to the locally running bridgehead infra one is supposed to write a docker-compose.override.yml changing the urls to point to the corresponding forwarded port of the ssh-tunnel container.
## Configuration Variables
- `ENABLE_SSH_TUNNEL`: Required to enable the module
- `SSH_TUNNEL_USERNAME`: Username for SSH connection
- `SSH_TUNNEL_HOST`: Target host for SSH tunnel
- `SSH_TUNNEL_PORT`: SSH port (defaults to 22)
## Configuration Files
The module requires the following files to be present:
- `/etc/bridgehead/ssh-tunnel.conf`: SSH tunnel configuration file. Detailed information can be found [here](https://github.com/samply/ssh-tunnel?tab=readme-ov-file#configuration).
- `/etc/bridgehead/pki/ssh-tunnel.priv.pem`: The SSH private key used to connect to the `SSH_TUNNEL_HOST`. **Passphrases for the key are not supported!**

View File

@ -0,0 +1,86 @@
services:
transfair:
image: docker.verbis.dkfz.de/cache/samply/transfair:latest
container_name: bridgehead-transfair
environment:
# NOTE: Those 3 variables need only to be passed if their set, otherwise transfair will complain about empty url values
- TTP_URL
- TTP_ML_API_KEY
- TTP_GW_SOURCE
- TTP_GW_EPIX_DOMAIN
- TTP_GW_GPAS_DOMAIN
- TTP_TYPE
- TTP_AUTH
- PROJECT_ID_SYSTEM
- FHIR_REQUEST_URL=${FHIR_REQUEST_URL}
- FHIR_INPUT_URL=${FHIR_INPUT_URL}
- FHIR_OUTPUT_URL=${FHIR_OUTPUT_URL:-http://blaze:8080}
- FHIR_REQUEST_CREDENTIALS=${FHIR_REQUEST_CREDENTIALS}
- FHIR_INPUT_CREDENTIALS=${FHIR_INPUT_CREDENTIALS}
- FHIR_OUTPUT_CREDENTIALS=${FHIR_OUTPUT_CREDENTIALS}
- EXCHANGE_ID_SYSTEM=${EXCHANGE_ID_SYSTEM:-SESSION_ID}
- DATABASE_URL=sqlite://transfair/data_requests.sql?mode=rwc
- RUST_LOG=${RUST_LOG:-info}
- TLS_CA_CERTIFICATES_DIR=/conf/trusted-ca-certs
- TLS_DISABLE=${TRANSFAIR_TLS_DISABLE:-false}
- NO_PROXY=${TRANSFAIR_NO_PROXIES}
- ALL_PROXY=http://forward_proxy:3128
volumes:
- /var/cache/bridgehead/${PROJECT}/transfair:/transfair
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
labels:
- "traefik.enable=true"
- "traefik.http.middlewares.transfair-strip.stripprefix.prefixes=/transfair"
- "traefik.http.routers.transfair.middlewares=transfair-strip,transfair-auth"
- "traefik.http.routers.transfair.rule=PathPrefix(`/transfair`)"
- "traefik.http.services.transfair.loadbalancer.server.port=8080"
- "traefik.http.routers.transfair.tls=true"
traefik:
labels:
- "traefik.http.middlewares.transfair-auth.basicauth.users=${TRANSFAIR_AUTH}"
transfair-input-blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
container_name: bridgehead-transfair-input-blaze
environment:
BASE_URL: "http://bridgehead-transfair-input-blaze:8080"
JAVA_TOOL_OPTIONS: "-Xmx1024m"
DB_BLOCK_CACHE_SIZE: 1024
CQL_EXPR_CACHE_SIZE: 8
ENFORCE_REFERENTIAL_INTEGRITY: "false"
volumes:
- "transfair-input-blaze-data:/app/data"
profiles: ["transfair-input-blaze"]
labels:
- "traefik.enable=true"
- "traefik.http.routers.transfair-input-blaze.rule=PathPrefix(`/data-delivery`)"
- "traefik.http.middlewares.transfair-input-strip.stripprefix.prefixes=/data-delivery"
- "traefik.http.services.transfair-input-blaze.loadbalancer.server.port=8080"
- "traefik.http.routers.transfair-input-blaze.middlewares=transfair-input-strip,transfair-auth"
- "traefik.http.routers.transfair-input-blaze.tls=true"
transfair-request-blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
container_name: bridgehead-transfair-request-blaze
environment:
BASE_URL: "http://bridgehead-transfair-request-blaze:8080"
JAVA_TOOL_OPTIONS: "-Xmx1024m"
DB_BLOCK_CACHE_SIZE: 1024
CQL_EXPR_CACHE_SIZE: 8
ENFORCE_REFERENTIAL_INTEGRITY: "false"
volumes:
- "transfair-request-blaze-data:/app/data"
profiles: ["transfair-request-blaze"]
labels:
- "traefik.enable=true"
- "traefik.http.routers.transfair-request-blaze.rule=PathPrefix(`/data-requests`)"
- "traefik.http.middlewares.transfair-request-strip.stripprefix.prefixes=/data-requests"
- "traefik.http.services.transfair-request-blaze.loadbalancer.server.port=8080"
- "traefik.http.routers.transfair-request-blaze.middlewares=transfair-request-strip,transfair-auth"
- "traefik.http.routers.transfair-request-blaze.tls=true"
volumes:
transfair-input-blaze-data:
transfair-request-blaze-data:

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modules/transfair-setup.sh Executable file
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#!/bin/bash -e
function transfairSetup() {
if [[ -n "$TTP_URL" || -n "$EXCHANGE_ID_SYSTEM" ]]; then
echo "Starting transfair."
OVERRIDE+=" -f ./modules/transfair-compose.yml"
if [ -n "$FHIR_INPUT_URL" ]; then
log INFO "TransFAIR input fhir store set to external $FHIR_INPUT_URL"
else
log INFO "TransFAIR input fhir store not set writing to internal blaze"
FHIR_INPUT_URL="http://transfair-input-blaze:8080"
OVERRIDE+=" --profile transfair-input-blaze"
fi
if [ -n "$FHIR_REQUEST_URL" ]; then
log INFO "TransFAIR request fhir store set to external $FHIR_REQUEST_URL"
else
log INFO "TransFAIR request fhir store not set writing to internal blaze"
FHIR_REQUEST_URL="http://transfair-request-blaze:8080"
OVERRIDE+=" --profile transfair-request-blaze"
fi
if [ -n "$TTP_GW_SOURCE" ]; then
log INFO "TransFAIR configured with greifswald as ttp"
TTP_TYPE="greifswald"
elif [ -n "$TTP_ML_API_KEY" ]; then
log INFO "TransFAIR configured with mainzelliste as ttp"
TTP_TYPE="mainzelliste"
else
log INFO "TransFAIR configured without ttp"
fi
TRANSFAIR_NO_PROXIES="transfair-input-blaze,blaze,transfair-requests-blaze"
if [ -n "${TRANSFAIR_NO_PROXY}" ]; then
TRANSFAIR_NO_PROXIES+=",${TRANSFAIR_NO_PROXY}"
fi
fi
}

4
versions/acceptance Normal file
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FOCUS_TAG=develop
BEAM_TAG=develop
BLAZE_TAG=main
POSTGRES_TAG=15.13-alpine

4
versions/prod Normal file
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FOCUS_TAG=main
BEAM_TAG=main
BLAZE_TAG=0.32
POSTGRES_TAG=15.13-alpine

4
versions/test Normal file
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FOCUS_TAG=develop
BEAM_TAG=develop
BLAZE_TAG=main
POSTGRES_TAG=15.13-alpine