Code

Exporter, Teiler, QB, DataSHIELD#164

Code

Merged

patrickskowronekdkfz merged 216 commits intomainsamply/bridgehead:mainfrom feature/datashieldsamply/bridgehead:feature/datashieldCopy head branch name to clipboardMar 19, 2024

+788-27

Commits

Commits on Feb 27, 2024

• Add Teiler UI and Teiler module

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• Add nngm and exliquid modules

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• Change images of dktk-teiler and dktk-keycloak

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• Bugfix: services in teiler-ui-compose.yml

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• Configure login extern URLs

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• Rename teiler to exporter

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• Rename teiler to exporter (bugfix)

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• beautiful config

  

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• update keykloak config

  

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• Add original Keycloak config

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• Update Teiler Core config

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• Add Endpoint for Teiler

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• Add Teiler Core

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• Tidy teiler and mtba volumes

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• Deactivate traffik for mtba

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• Add forward strategy to teiler-core

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• Add forward strategy to teiler-core

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• Add stripprefix to teiler-core

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• Add stripprefix to teiler-ui

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• Change volume names for teiler components

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• Add keycloak teiler app to teiler-ui

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• Adapt teiler-ui to traefik

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• Change salt string for exporter and login

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• Merge id-management-setup with main

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• Bugfix: cross origins of exporter

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• Add DataSHIELD

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• Experiment

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• Add beam connect to docekr-compose

  

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• Experiment

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• beam connect and move beam-connect config

  

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• Fix beam connect app id

  

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• expose beam connect ports

  

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• Add Opal Password in Exporter

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• Remove mongo db

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• Remove unnecessary volumes

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• Add opal certificate

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• ccp.conf in teiler-core as secret

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• Change cert permission and location

  

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• Change beam-connect version and load opal cert

  

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• change to dockerhub image

  

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• secrets are readonly by default

  

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• Switch to no-auth branch of beam-connect

  

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• Add reporter

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• Add parameter LOG_FHIR_VALIDATION to exporter

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• update new broker

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• Migrate to new app key syntax

  

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• Add http scheme to exporter

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• Generate passwords only if modules are enabled

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• Remove ports of beam-connect in datashield-compose.yml

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• User postgres if docker.verbis.dkfz.de

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• R-Server rock-base:6.3

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• Remove unnecessary version of docker-compose.override files

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• Remove todo in rstudio

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• Enable only if true

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• Use LDM_PASSWORD for all admin passwords

  

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• Update ccp/modules/datashield-compose.yml

  

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• Update ccp/modules/datashield-compose.yml

  

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• Generate DATASHIELD_CONNECT_SECRET automatically

  

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• User default user rstudio in rstudio

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• Remove IS_DKTK_SITE

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• Add Teiler Admin to Keycloak

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• Add explanation why is the volume of exporter-db currently so important for us.

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• Remove clean temp files configuration of exporter

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• Remove updater cron of teiler-core

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• Add default language to ccp

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• Generate exporter api key automatically

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• Export and QB Curl templates

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• Enable Login, Teiler and Exporter

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• Add JAVA_OPTS to reporter and exporter

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• Add DataSHIELD module documentation

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• Add Exporter module documentation

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• Add login module documentation

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• Add some docs about beam-connect

  

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• Add teiler-ui module documentation

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• Add mtba module documentation

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• Bugfix: JAVA_OPTS for exporter

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• Comment on export and report volumes

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• Comment on datashield volume

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• Remove old comment of exporter-setup.sh

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• Fix comment in login-compose.yml

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• Comment Keycloak volume

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• Enable datashield

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• Bugfix: MTBA path prefix

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• Disable datashield

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• Bugfix: exporter

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• Bugfix: mtba labels

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• Add forward proxy to teiler-core

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• Add site to exporter and reporter

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• Rename Teiler Backend, Teiler Dashboard and Teiler Orchestrator

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• Bugfix: LDM_AUTH instead of LDM_PASSWORD

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• #!/bin/bash -e

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• Bugfix: Add version in every docker compose file

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• Cache opal in /var/cache/bridgehead

  

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• Autogenerate maps for Opal's beam-connect. To be completed by @Threated with a map-generator in the script.

  

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• Rework commented sections

  

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• Exporter cache

  

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• Move exporter db to /var/cache/bridgehead

  

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• Rewrite comments

  

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• Add ccp to /var/cache/bridgehead/* volumes

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• Auto generate mappings

  

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• Add all sites

  

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• Make sure copy works and the correct owner is set

  

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• Bugfix: Add version of docker-compose

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• Update ccp/modules/mtba.md

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• Postgres 15.4 in datashield, exporter and login

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• Bugfix: Exporter and Reporter /var/cache volumes

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• Prevent anonymous volume creation

  

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• Bugfix: datashield local.json as array

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• Add docu about login in teiler

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• /var/cache for mtba

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• Update export template script: FHIR_QUERY to FHIR_PATH

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• Use newest version of beam-connect

  

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• Make Opal use proxy server

  

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• Use Bridgehead's internal http proxy

  

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• Prevent creation of volumes

  

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• Remove nngmSetup in vars

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• MTBA 1.0.0

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• Externalize postgres version

  

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• Remove unnecessary version of docker-compose.override files

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• Remove unnecessary version of docker-compose.override files

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• Bugfix: Add version in every docker compose file

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• Remove unnecessary version of docker-compose.override files

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• Bugfix: Add version in every docker compose file

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• Add secret sync to the bridgehead

  

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• Update to new secret-sync semantics

  

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• Setup hostname earlier

  

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• Make sure path exists

  

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• Integrate central Keycloak in Teiler

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• Generate addtional redirect url

  

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• Update oidc provider to new url

  

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• Add function generate_redirect_urls

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• Remove port handeling when generating redirect url

  

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• Account for ip address host values

  

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• Bugfix: Export /var/cache/bridgehead/secrets as environment variables

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• Add generate_password function

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• Add R-Studio Admin Password

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• Add keycloak configuration

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• Add Keycloak to MTBA

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• Add proxy to R-Studio for loading R packages

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• Add comment about PASSWORD and DISABLE_AUTH in R-Studio

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• Add oauth2_proxy

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• Better redirect url handeling

  

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• fix: public client generation

  

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• Use develop branch for mtba

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• mtba latest

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• add /oauth2/callback and /mtba to Keycloak private client

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• mtba develop

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• add default template-ids of exporter and reporter

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• move OAUTH2_SECRET

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• fix: Restrict rstudio network access

  

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• feat: Add token-manager to beam

  

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• fix: generate the right beam connect mappings

  

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• fix: Change permissions on new bridgehead dirs

  

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• fix: beam connect site renaming

  

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• fix: chown syntax

  

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• fix: opal ssl cert

  

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• fix: only change permissions on related files

  

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• fix: undo permission changes on startup

  

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• teiler-orchestrator and teiler-dashboard latest

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• Only users of group DataSHIELD can use R-Studio

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• Use last version of mtba

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• Use develop version of mtba

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• Default values for MTBA

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• Added: Enable MTBA and Enable DataSHIELD to Teiler Backend

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• Added: allowed-groups

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• Add central token manager beam id

  

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• Add test sites

  

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• Added: volume for opal metadata db

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• Added: volume for opal metadata db (II)

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• Added: volume for opal metadata db (III)

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• fix: Generate stable passwords

  

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• fix: Use strong pw for opal

  

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• Only sync secrets on startup

  

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• Add dsCCPhos

  

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• refactor: Use jq from docker

  

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• fix: Correctly set file permissions

  

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• fix: Only give writeable dirs the docker role

  

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• Use latest jq

  

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• Added: Proxy to R-Studio oauth2-proxy

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• fix: Use forward proxy for secret sync

  

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• fix: Pull oauth2 proxy from harbor

  

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• fix: secret sync account for minimal override

  

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• refactor: Use beam proxy directly as proxy

  

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• fix: Wait for forward proxy to start

  

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• fix: Start oauth proxy after forward_proxy is ready

  

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• Integrate central Keycloak in Teiler

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• Add Keycloak to MTBA

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• Add oauth2_proxy

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• Removed: / from groups

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• Changed: master realm

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• Changed: replace keycloak with oidc

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• chore: Remame datashield mappings to datashield sites

  

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• chore: Add mannheim to datashield sites

  

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• fix: Update permissions on update

  

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• fix: Fix if syntrax

  

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• Merge pull request #158 from samply/main

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• refactor: Move vars to their setup files

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• Merge pull request #163 from samply/refactor/datashield

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• Merge pull request #145 from samply/feature/datashield-central-keycloak

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• refactor: Move oauth2 proxy related things to datashield setup

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• fix: Dont change ownership of all files under /tmp/bridgehead and /var/cache/bridgehead

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• Remove unnecessary comment

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• Remove todo

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• Rename oauth2_proxy docker service to oauth2-proxy

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• Remove empty line

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• Add warning if ENABLE_EXPORTER is not set or set to true

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• Replace | openssl rsautl -sign with | sha1sum | openssl pkeyutl -sign

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• Changed: TEILER_DEFAULT_LANGUAGE

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• Remove empty file (teiler-ui-compose.yml)

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• Use bridgehead log functions in datashield setup

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• Fix spelling of log WARN

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• Merge branch 'main' into feature/datashield

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