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`
- 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
- 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
* sites moved to etc itcc.comf
* mainzelliste test
* volume
* fix image
* db name chaged
* ingest component test
* clean up
* maizelliste env db
* test server ip
* beam sockets
* teswt socket and task
* secure db and ml
* refactor and patient endpoints
* partner id
* new refactor and encription key generation
* db deleted
* keyset to var/
* feat: add Data Quality Agent configuration and setup
* fix: correct environment variable name in Data Quality Agent configuration
* feat: update Data Quality Agent configuration and setup instructions
* feat: update Data Quality Agent setup and documentation
* feat: add volume configuration for agent data in Data Quality Agent compose file
* feat: update volume configuration for Data Quality Agent in compose file
* Update README.md
Co-authored-by: Tobias Kussel <TKussel@users.noreply.github.com>
---------
Co-authored-by: Tobias Kussel <TKussel@users.noreply.github.com>
Right now, Directory sync will only be activated if a username has been
specified. It also needs to run if a login token has been specified,
hence the change in this commit.
The Directory team have requested that we allow token login to the
Directory, where a user uses LSAAI credentials to obtain a token from
the Directory, and then uses this to authenticate Directory sync. This
has been implemented via an environment variable, in an analogous way to
the already existing username/password method.
The default start time for the Directory sync has been shifted to 22:30,
to prevent conflicts with the Bridgehead auto-update.
Relevant changes have been made to the documentation.
Co-authored-by: Torben Brenner <76154651+torbrenner@users.noreply.github.com>
Co-authored-by: Jan <59206115+Threated@users.noreply.github.com>
Co-authored-by: Martin Lablans <6804500+lablans@users.noreply.github.com>
tm16-medma
tm16-medmaandtm16-medma
Skiba Janandtm16-medma
Tim SchumacherandGitHub
Enola KnezevicandGitHub
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afigueroaDkfzandGitHub
Pierre DelpyandGitHub
Martin JurkandGitHub
Radovan TomášikandGitHub
Patrick SkowronekandGitHub
JanandGitHub
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