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d1624c1068ad5d0bd0aed94102d5dd13630b4a0a
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290 Commits

Author SHA1 Message Date
Skiba Jan
d1624c1068 fix treafik routers 2026-03-23 11:34:55 +01:00
tm16-medma
f3009f347e Refactor ovis-compose.yml to add new services 2026-03-17 15:59:15 +01:00
Skiba, Jan
d386766e13 Merge branch 'develop' into ovis 2026-03-17 15:38:01 +01:00
tm16-medma
4c8f7cb119 Refactor OVIS setup script for MongoDB initialization 2026-03-02 09:14:39 +01:00
tm16-medma
28a93b191c Refactor ovis-compose.yml for latest OVis version 2026-03-02 09:14:05 +01:00
Niklas Reimer
ab6e05826f feat(dnpm): set timezone to Europe/Berlin (#359) 2025-11-12 10:25:20 +01:00
djuarezgf
66a1bd1122 docs: add initial documentation for Samply.Exporter and Samply.Teiler (#350) 2025-10-20 11:16:41 +02:00
Jan
e0754853d8 feat(dnpm): change to new api-gateway image (#337) 2025-08-19 16:35:52 +02:00
djuarezgf
ada3226044 Replace hardcoded image: ...:develop references with version variables (#335) 
* added: Teiler Dashboard Version

* added: MTBA Version

* added: beam proxy tag version
 2025-07-30 11:21:10 +02:00
Jan
9c8d0ee8f5 fix(dnpm): fix env subsitution (#333) 2025-07-25 10:58:07 +02:00
djuarezgf
fcad7104f0 mtba: fallback to keycloak test server pending migration 2025-07-23 09:53:14 +02:00
djuarezgf
7e13e251f8 feat: migrate PSP to Authentik (#329) 2025-07-22 11:34:49 +02:00
Jan
2cfdc3ac3e feat(dnpm): allow setting custom dnpm image tag (#326) 2025-07-07 15:36:14 +02:00
djuarezgf
43b24c2a62 Fixed: Authentik URL for Opal (#328) 
* Fixed: Authentik URL for Opal

* Removed: Unnecessary OIDC config in CCE and BBMRI

* KR with basic auth instead of OIDC
 2025-07-07 15:35:54 +02:00
Jan
4c6f9e0f13 feat: remove local rstudio (#322) 2025-06-27 10:55:53 +02:00
djuarezgf
141f1f22d0 Use relative paths in teiler (#320) 2025-06-18 17:04:09 +02:00
djuarezgf
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
djuarezgf
af08a9fb08 chore: change some teiler variables (#307) 2025-05-20 16:24:24 +02:00
djuarezgf
b95f0efbe7 fix: add own url to teiler dashboard to make it offline compatible (#305) 2025-05-20 09:39:14 +02:00
tm16-medma
e8cb85eade adjusted traefik parameters 2025-04-09 14:00:39 +00:00
tm16-medma
e3f7f5d32b Refactor Docker Compose 
- Replaced GUI_HOST with HOST
- Removed NODE_ENV
- Combine init_onco and backend service
- removed node_modules and .svelte-kit volumes
- removed mongodb volumes
- adjusted http_proxy and https_proxy
- adjusted path prefix from oaut2 to oauth2-ovis
- removed network-mode "host" in fhir-transformer service
 2025-04-09 13:43:53 +00:00
tm16-medma
86a2b78d8f corrected a syntax error 2025-04-01 10:57:02 +00:00
tm16-medma
cf1ba43d39 refactor: restructure ovis-compose.yml and added MongoDB initialization to sh 
- Removed the traefik service and renamed traefik-forward-auth to ovis- with ovis-traefik-forward-auth the labels, however would need help there as i got no knowledge of how OAuth2 works (Torben initialized that container)
- Updated MongoDB service configuration to include a direct initialization script for user and operation collections in the sh instead of in the compose directly
- Adjusted volume paths to only use the /var/cache/bridgehead/ccp directory
- Adjusted frontend and backend service labels for Traefik routing to not use ports
- Cleaned up unnecessary network definitions and volumes.
- Renamed FHIR Server URL to bridgehead-ccp-blaze:8080/fhir
- Removed redundant entrypoint (python main.py) of fhir transformer
 2025-04-01 10:46:48 +00:00
tm16-medma
3b49faaeb4 Update ovis-compose.yml 
Please ignore the command in mongo :) It will be replaced soon with proper user authentication
 2025-03-26 11:21:58 +01:00
Jan
82ced89b33 chore: unify blaze versioning and upgrade to 0.32 (#277) 2025-03-12 12:52:00 +01:00
Pierre Delpy
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
janskiba
5ba9efe8d3 ovis wip 2025-02-12 10:45:48 +00:00
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
patrickskowronekdkfz
1003cd73cf fix: changed ccp_ppi to use IDMANAGEMENT_FRIENDLY_ID instead of SITE_NAME (#259) 2025-01-21 09:30:20 +01:00
patrickskowronekdkfz
3d1105b97c Update: Blaze to version 0.31 (#260) 2025-01-21 09:28:47 +01:00
Jan
5c28e704d2 fix: remove restart: always in compose files (#261) 2025-01-21 09:27:27 +01:00
Enola Knezevic
45aefd24e5 renamed exporter API key to EXPORTER_API_KEY (#252) 2024-12-06 11:27:38 +01:00
patrickskowronekdkfz
122ff16bb1 fix: use verbis cache image instead of docker-hub (#250) 2024-11-12 09:58:17 +01:00
djuarezgf
967e45624e Add exporter configuration to focus (#249) 2024-11-05 15:46:00 +01:00
Tobias Kussel
8cd5b93b95 Merge pull request #237 from samply/feat/ccp-ppi 
Feat/ccp ppi
 2024-11-05 13:59:01 +01:00
Jan
52c24ee6fa fix(fhir2sql): add the postgres connection string to focus (#245) 2024-11-05 13:34:36 +01:00
davidmscholz
26712d3567 feat: add and set FOCUS_ENDPOINT_TYPE to support fhir2sql (#244) 
* add and set FOCUS_ENDPOINT_TYPE

Co-authored-by: Jan <59206115+Threated@users.noreply.github.com>

---------

Co-authored-by: davidmscholz <david.scholz@dkfz-heidelberg.de>
Co-authored-by: Jan <59206115+Threated@users.noreply.github.com>
 2024-10-30 15:21:15 +01:00
Patrick Skowronek
23981062bb Move ppi to id-management 2024-10-10 13:27:24 +02:00
Torben Brenner
eb2955872f fix: allow usage of centraxx interface without login 
Before this change CentraXX was redirected to the
central login servers then interacting with the id-management
 2024-10-01 13:30:23 +02:00
p.delpy@dkfz-heidelberg.de
f0bdb5c146 fix: re-add modules 2024-09-12 09:25:38 +02:00
davidmscholz
ed8dacaa59 Fix fhir2sql db pw generation (#219) 
fix postgresql password generation so that the password does not contain problematic characters that mess with the connection string
 2024-08-29 09:15:22 +02:00
Jan
3fe781255b feat: Configure beam-connect to trust ds-orchestrator beam proxy (#220) 2024-08-29 09:07:50 +02:00
Torben Brenner
6228cb3762 fix: specify host for id-management login 
Otherwise traefik will match the route with the one specified in datashield-compose.yml
 2024-08-19 17:09:10 +02:00
Torben Brenner
33843fe961 fix: switch id-management to keycloak 2024-08-19 14:43:21 +02:00
Tobias Kussel
9c941853bd Merge pull request #196 from samply/new-dashboard-backend 
Add new/additional dashboard backend
 2024-08-01 10:05:32 +02:00
Tobias Kussel
2e5aeabca8 Rename fhir2sql module files 2024-07-30 07:44:47 +00:00
Tobias Kussel
af44b6b446 Fix depends_on syntax 2024-07-30 07:40:49 +00:00
davidmscholz
5ed07423f3 fix dashboard-compose 2024-07-30 09:24:07 +02:00
davidmscholz
df08d67839 add optional dashboard module 2024-07-29 10:45:00 +02:00
djuarezgf
293810f254 Added: exporter with blaze-secondary 2024-07-18 14:06:47 +02:00