Tim Schumacher
fd013232f5
Cache public organoid dashboard SQL query ( #309 )
2025-05-23 15:26:59 +02:00
DavidCroftDKFZ
eb52554892
docs: add faq ( #288 )
2025-05-22 18:10:40 +02:00
DavidCroftDKFZ
08c695e960
docs: Control import from Directory, improve README ( #297 )
2025-05-22 18:03:01 +02:00
DavidCroftDKFZ
1513fe1c6c
Added section relating to clearing data from Blaze ( #303 )
2025-05-22 18:01:43 +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
Torben Brenner
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
Martin Lablans
9782bf66b6
Code review: Move to /tmp/bridgehead/...
2025-05-08 09:18:02 +02:00
Tim Schumacher
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
Enola Knezevic
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
Torben Brenner
324c2b336d
Merge pull request #287 from tm16-medma/patch-1
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Update ovis-compose.yml
2025-04-14 08:19:20 +02:00
Jan
973547c322
chore(transfair): add new gw option ( #291 )
2025-04-11 08:37:31 +02:00
tm16-medma
e8cb85eade
adjusted traefik parameters
2025-04-09 14:00:39 +00:00
tm16-medma
c59c425ad4
Merge branch 'patch-1' of https://github.com/tm16-medma/bridgehead into patch-1
2025-04-09 13:45:01 +00:00
tm16-medma
e3f7f5d32b
Refactor Docker Compose
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- 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
Jan
6b649c9233
feat: expose transfair via traefik ( #290 )
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Note: Requires a bridgehead install to generate the basic auth user
2025-04-09 13:19:52 +02:00
tm16-medma
1b01bd81ff
Updated the fhir-transformer image and init_onco container to sleep after finishing
2025-04-03 15:04:01 +02:00
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
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- 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
Tim Schumacher
3144ee5214
Fix GitLab token syncing for BBMRI
2025-03-31 11:08:59 +02:00
janskiba
68804dc71b
feat: add transfair setup to ccp
2025-03-26 13:11:43 +01:00
janskiba
e5aebfe382
chore!: update transfair config
2025-03-26 13:11:43 +01:00
tm16-medma
3b49faaeb4
Update ovis-compose.yml
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Please ignore the command in mongo :) It will be replaced soon with proper user authentication
2025-03-26 11:21:58 +01:00
Torben Brenner
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
Martin Lablans
5d94bac0e2
Mount queries_to_cache.conf readonly ( #282 )
2025-03-10 16:03:05 +01:00
Tim Schumacher
83555540f5
chore: update central Secret Sync proxy ID ( #280 )
2025-03-10 12:08:19 +01:00
Pierre Delpy
e396e00178
Fix/ccp cql cache ( #279 )
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* 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
Tim Schumacher
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
Torben Brenner
98121c17e8
Make Codeowners Rule apply to all Files in Repo
2025-02-20 17:28:38 +01:00
Torben Brenner
e38511e118
Add Codeowners File
2025-02-20 17:20:54 +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
Torben Brenner
8000356b57
docs: explicitly clone main branch ( #269 )
2025-02-07 11:21:43 +01:00
Torben Brenner
74d8e68d96
Merge pull request #258 from samply/feat/routine-connector
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feat: transFAIR
2025-02-07 10:39:54 +01:00
Torben Brenner
c568a56651
refactor: set transfair log to info
2025-02-07 10:30:43 +01:00
Torben Brenner
8384143387
fix: make transfair reach the internal blaze stores
2025-02-07 09:17:17 +01:00
Torben Brenner
8fe73a8123
fix: support mode without ttp
2025-02-07 09:17:07 +01:00
Torben Brenner
bca63e82a9
fix: don't use return in transfairSetup
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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 )
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* 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
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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
Tobias Kussel
0b6fa439ba
Merge pull request #266 from samply/fix/docker-hub-link
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Fixed Docker Hub URL list link
2025-01-29 09:52:26 +01:00
Martin Lablans
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
