Add Ovis to the CCP modules in the bridgehead by tm16-medma · Pull Request #375 · samply/bridgehead

tm16-medma · 2026-03-19T13:44:57Z

No description provided.

Please ignore the command in mongo :) It will be replaced soon with proper user authentication

…on 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

…fter finishing

- 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

…to patch-1

Update ovis-compose.yml

ccp/modules/ovis-compose.yml

ccp/modules/ovis-setup.sh

lablans · 2026-03-19T13:51:01Z

ccp/modules/ovis-setup.sh

+  mkdir -p "/var/cache/bridgehead/ccp/ovis/mongo/init"
+  mkdir -p "/var/cache/bridgehead/ccp/ovis/shared_data"


Check if they are auto-created by docker runtime

ccp/vars

ccp/modules/ovis-compose.yml

tm16-medma · 2026-03-19T14:03:47Z

Thanks for the comments and your time, we will adjust most of them, others need changes in the application itself for that to work, which takes a bit longer.

ccp/modules/ovis-compose.yml

…tracts Apply the PR #375 review feedback by removing Bridgehead-specific compose/setup overrides that duplicated upstream OVIS behavior and by switching to the upstream-built Mongo image that already contains init logic. - rename CCP OVIS services to consistent upstream-style names (`ovis-*`) and update internal dependencies - switch Mongo service image from direct `mongo:latest` + host-mounted init script to `docker.verbis.dkfz.de/ovis/ovis-backend-mongodb:latest` - remove obsolete Mongo init bind mount (`/docker-entrypoint-initdb.d/init.js`) from compose - drop redundant runtime overrides from compose (`restart`, `command`, `user`, `working_dir`) - remove duplicated app-default/preprocessor env overrides (`OVIS_PREPROC_*`, misc backend defaults) and keep deployment wiring only - fix Mongo connection env usage to `ADDRESS` and point services to `ovis-backend-database-mongodb` - remove temporary root-compat Traefik redirect shim and keep mounted `/ccp-ovis` routing labels - remove setup-time generation of Mongo init.js and related cache directory prep from `ccp/modules/ovis-setup.sh`

Removed unnecessary Traefik router configurations for compatibility.

Updated FHIR credentials to empty strings in ovis-compose.yml

Removed dependency condition on the blaze service.

…tracts Apply the PR #375 review feedback by removing Bridgehead-specific compose/setup overrides that duplicated upstream OVIS behavior and by switching to the upstream-built Mongo image that already contains init logic. - rename CCP OVIS services to consistent upstream-style names (`ovis-*`) and update internal dependencies - switch Mongo service image from direct `mongo:latest` + host-mounted init script to `docker.verbis.dkfz.de/ovis/ovis-backend-mongodb:latest` - remove obsolete Mongo init bind mount (`/docker-entrypoint-initdb.d/init.js`) from compose - drop redundant runtime overrides from compose (`restart`, `command`, `user`, `working_dir`) - remove duplicated app-default/preprocessor env overrides (`OVIS_PREPROC_*`, misc backend defaults) and keep deployment wiring only - fix Mongo connection env usage to `ADDRESS` and point services to `ovis-backend-database-mongodb` - remove temporary root-compat Traefik redirect shim and keep mounted `/ccp-ovis` routing labels - remove setup-time generation of Mongo init.js and related cache directory prep from `ccp/modules/ovis-setup.sh`

ccp/modules/ovis-compose.yml

TKussel · 2026-03-23T11:29:41Z

ccp/modules/ovis-compose.yml

+    environment:
+      # CCP mode: FHIR source configuration (ignored by DEMO image)
+      FHIR_SERVER_URL: http://bridgehead-ccp-blaze:8080/fhir
+      FHIR_USERNAME: ""
+      FHIR_PASSWORD: ""
+      ICD10_FILTER: ""
+      # Required for both CCP and DEMO: preprocessor upload endpoint
+      OVIS_PREPROCESSOR_URL: http://ovis-backend-data-preprocessing:9000/omock
+      # Proxy configuration
+      HTTP_PROXY: ""
+      HTTPS_PROXY: ""
+      NO_PROXY: ""
+      http_proxy: ""
+      https_proxy: ""
+      no_proxy: ""


This remains relevant

Removed proxy configuration from ovis-compose.yml.

Removed unused FHIR configuration variables from ovis-compose.yml.

ccp/modules/ovis-compose.yml

ccp/modules/ovis-setup.sh

Collapse the `/ccp-ovis` slash-redirect and prefix-strip flow into one `ovis-frontend-ccp` router by attaching both middlewares in order (redirect, then strip). This removes redundant router labels while preserving canonical `/ccp-ovis -> /ccp-ovis/` behavior and mounted-path forwarding to the frontend service.

ccp/modules/ovis-compose.yml

Changed the image for the ovis-frontend service to use the new `ovis-frontend-ccp` tag, reflecting the latest version. Removed unnecessary environment variables to streamline the configuration.

Threated and others added 13 commits February 12, 2025 10:45

ovis wip

5ba9efe

Update ovis-compose.yml

3b49faa

Please ignore the command in mongo :) It will be replaced soon with proper user authentication

corrected a syntax error

86a2b78

Updated the fhir-transformer image and init_onco container to sleep a…

1b01bd8

…fter finishing

Merge branch 'patch-1' of https://github.com/tm16-medma/bridgehead in…

c59c425

…to patch-1

adjusted traefik parameters

e8cb85e

Merge pull request #287 from tm16-medma/patch-1

324c2b3

Update ovis-compose.yml

Refactor ovis-compose.yml for latest OVis version

28a93b1

Refactor OVIS setup script for MongoDB initialization

4c8f7cb

Merge branch 'develop' into ovis

d386766

Refactor ovis-compose.yml to add new services

f3009f3

tm16-medma requested a review from a team as a code owner March 19, 2026 13:44

lablans requested changes Mar 19, 2026

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Threated reviewed Mar 19, 2026

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TKussel reviewed Mar 19, 2026

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Threated and others added 11 commits March 23, 2026 11:34

fix treafik routers

d1624c1

Add OVIS_PUBLIC_BASE_PATH environment variable

fb027b7

Add Traefik labels for ovis-frontend-ccp routes

57308d0

Add Traefik labels for ovis-backend services

1a0d12f

Add Traefik labels for ovis-frontend routing

87e8c78

Clean up Traefik router settings in ovis-compose.yml

47b5bb0

Removed unnecessary Traefik router configurations for compatibility.

Add Traefik labels for ovis-frontend routing

3d4f2a4

Update ovis-compose.yml for backend image and import settings

72021fe

Clear FHIR_USERNAME and FHIR_PASSWORD

1981a08

Updated FHIR credentials to empty strings in ovis-compose.yml

Add dependency condition for blaze service

1755298

Remove blaze service dependency from ovis-compose.yml

b7f7878

Removed dependency condition on the blaze service.

tm16-medma and others added 2 commits March 23, 2026 11:34

Update Traefik rules in ovis-compose.yml

921bac1

tm16-medma force-pushed the ovis branch from 6b0493b to 191f5f2 Compare March 23, 2026 10:35

TKussel requested changes Mar 23, 2026

View reviewed changes

tm16-medma added 2 commits March 23, 2026 12:32

Clean up proxy settings in ovis-compose.yml

6ef1fb7

Removed proxy configuration from ovis-compose.yml.

Cleanup FHIR configuration in ovis-compose.yml

014933a

Removed unused FHIR configuration variables from ovis-compose.yml.

Threated requested changes Mar 23, 2026

View reviewed changes

ccp/modules/ovis-compose.yml Outdated Show resolved Hide resolved

ccp/modules/ovis-setup.sh Outdated Show resolved Hide resolved

patrick-skowronek requested changes Mar 23, 2026

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ccp/modules/ovis-compose.yml Outdated Show resolved Hide resolved

Threated approved these changes Mar 23, 2026

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Update OVIS frontend image reference in ovis-compose.yml

d955627

Changed the image for the ovis-frontend service to use the new `ovis-frontend-ccp` tag, reflecting the latest version. Removed unnecessary environment variables to streamline the configuration.

TKussel approved these changes Mar 23, 2026

View reviewed changes

patrick-skowronek approved these changes Mar 23, 2026

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Add Ovis to the CCP modules in the bridgehead#375

Add Ovis to the CCP modules in the bridgehead#375
tm16-medma wants to merge 30 commits intodevelopfrom
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tm16-medma commented Mar 19, 2026

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lablans Mar 19, 2026

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tm16-medma commented Mar 19, 2026

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TKussel Mar 23, 2026

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		mkdir -p "/var/cache/bridgehead/ccp/ovis/mongo/init"
		mkdir -p "/var/cache/bridgehead/ccp/ovis/shared_data"

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tm16-medma commented Mar 19, 2026

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lablans Mar 19, 2026

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tm16-medma commented Mar 19, 2026

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TKussel Mar 23, 2026

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