406 Commits

Author	SHA1	Message	Date
juarez	4aa8f0f3ba	Bugfix: Add version in every docker compose file	2024-02-27 12:43:33 +01:00
juarez	ccf0b91f17	#!/bin/bash -e	2024-02-27 12:43:33 +01:00
juarez	720783249d	Bugfix: LDM_AUTH instead of LDM_PASSWORD	2024-02-27 12:43:33 +01:00
juarez	2b3eabe95c	Rename Teiler Backend, Teiler Dashboard and Teiler Orchestrator	2024-02-27 12:43:33 +01:00
juarez	14aece46f7	Add site to exporter and reporter	2024-02-27 12:43:33 +01:00
juarez	ff1f7904ad	Add forward proxy to teiler-core	2024-02-27 12:43:33 +01:00
juarez	8d38adc91e	Bugfix: mtba labels	2024-02-27 12:43:33 +01:00
juarez	cfc3c7c90e	Bugfix: exporter	2024-02-27 12:43:33 +01:00
juarez	963144cc31	Disable datashield	2024-02-27 12:43:33 +01:00
juarez	765613b87f	Bugfix: MTBA path prefix	2024-02-27 12:43:32 +01:00
juarez	2b61775652	Enable datashield	2024-02-27 12:43:32 +01:00
juarez	4b0b17424f	Comment Keycloak volume	2024-02-27 12:43:32 +01:00
juarez	f26a8f7a71	Fix comment in login-compose.yml	2024-02-27 12:43:32 +01:00
juarez	973b5828f6	Remove old comment of exporter-setup.sh	2024-02-27 12:43:32 +01:00
juarez	839e7a4518	Comment on datashield volume	2024-02-27 12:43:32 +01:00
juarez	6cfb42dc9b	Comment on export and report volumes	2024-02-27 12:43:32 +01:00
juarez	5d8bec53c0	Bugfix: JAVA_OPTS for exporter	2024-02-27 12:43:32 +01:00
juarez	c52975f204	Add mtba module documentation	2024-02-27 12:43:32 +01:00
juarez	957fa64ce9	Add teiler-ui module documentation	2024-02-27 12:43:32 +01:00
janskiba	b4805af0a1	Add some docs about beam-connect	2024-02-27 12:43:31 +01:00
juarez	e3b8a7369b	Add login module documentation	2024-02-27 12:43:31 +01:00
juarez	adeaf433dc	Add Exporter module documentation	2024-02-27 12:43:31 +01:00
juarez	846e9c23a7	Add DataSHIELD module documentation	2024-02-27 12:43:31 +01:00
juarez	bb7451d8c3	Add JAVA_OPTS to reporter and exporter	2024-02-27 12:43:31 +01:00
juarez	26165232f0	Enable Login, Teiler and Exporter	2024-02-27 12:43:31 +01:00
juarez	7ed24f667d	Export and QB Curl templates	2024-02-27 12:43:31 +01:00
juarez	d97ac56126	Generate exporter api key automatically	2024-02-27 12:43:31 +01:00
juarez	e7f6c0b1a0	Add default language to ccp	2024-02-27 12:43:31 +01:00
juarez	c4c4f743d2	Remove updater cron of teiler-core	2024-02-27 12:43:31 +01:00
juarez	be9adcbfa2	Remove clean temp files configuration of exporter	2024-02-27 12:43:30 +01:00
juarez	10a362c237	Add explanation why is the volume of exporter-db currently so important for us.	2024-02-27 12:43:30 +01:00
juarez	75c86b79e8	Add Teiler Admin to Keycloak	2024-02-27 12:43:30 +01:00
juarez	a6443a6857	Remove IS_DKTK_SITE	2024-02-27 12:43:30 +01:00
juarez	f3745b973a	User default user rstudio in rstudio	2024-02-27 12:43:30 +01:00
Martin Lablans	50d28d293f	Generate DATASHIELD_CONNECT_SECRET automatically	2024-02-27 12:43:30 +01:00
Martin Lablans	44415369cc	Update ccp/modules/datashield-compose.yml	2024-02-27 12:43:30 +01:00
Martin Lablans	9b8331ed28	Update ccp/modules/datashield-compose.yml	2024-02-27 12:43:30 +01:00
Martin Lablans	73d969e374	Use LDM_PASSWORD for all admin passwords	2024-02-27 12:43:30 +01:00
juarez	840096d1d5	Enable only if true	2024-02-27 12:43:29 +01:00
juarez	43c45f0628	Remove todo in rstudio	2024-02-27 12:43:29 +01:00
juarez	e182e2fbe6	Remove unnecessary version of docker-compose.override files	2024-02-27 12:43:23 +01:00
juarez	c8bafb2461	R-Server rock-base:6.3	2024-02-27 12:42:38 +01:00
juarez	0866cacc5a	User postgres if docker.verbis.dkfz.de	2024-02-27 12:42:38 +01:00
juarez	a1e76a61b8	Remove ports of beam-connect in datashield-compose.yml	2024-02-27 12:42:38 +01:00
juarez	09aa33c912	Generate passwords only if modules are enabled	2024-02-27 12:42:38 +01:00
juarez	36ac8d41c8	Add http scheme to exporter	2024-02-27 12:42:37 +01:00
janskiba	c003999721	Migrate to new app key syntax	2024-02-27 12:42:37 +01:00
juarez	50360d3f41	update new broker	2024-02-27 12:42:37 +01:00
juarez	5148e3382d	Add parameter LOG_FHIR_VALIDATION to exporter	2024-02-27 12:42:37 +01:00
juarez	2d7d1d73b3	Add reporter	2024-02-27 12:42:37 +01:00
janskiba	20c65336e6	Switch to `no-auth` branch of beam-connect	2024-02-27 12:42:37 +01:00
janskiba	276f886546	secrets are readonly by default	2024-02-27 12:42:37 +01:00
janskiba	bc239c0b02	change to dockerhub image	2024-02-27 12:42:37 +01:00
janskiba	6438fc5f4e	Change beam-connect version and load opal cert	2024-02-27 12:42:37 +01:00
janskiba	f2f48869af	Change cert permission and location	2024-02-27 12:42:36 +01:00
juarez	e9e1ce5a65	ccp.conf in teiler-core as secret	2024-02-27 12:42:36 +01:00
juarez	687dbba383	Add opal certificate	2024-02-27 12:42:36 +01:00
juarez	5e376b17ad	Remove unnecessary volumes	2024-02-27 12:42:36 +01:00
juarez	04cf5128b0	Remove mongo db	2024-02-27 12:42:36 +01:00
juarez	43ab59563c	Add Opal Password in Exporter	2024-02-27 12:42:36 +01:00
Martin Lablans	996f53a164	expose beam connect ports	2024-02-27 12:42:36 +01:00
Martin Lablans	b5ce188842	Fix beam connect app id	2024-02-27 12:42:36 +01:00
Martin Lablans	325ae1d574	beam connect and move beam-connect config	2024-02-27 12:42:36 +01:00
juarez	68782d1c32	Experiment	2024-02-27 12:42:35 +01:00
juarez	dfde7c18ff	Experiment	2024-02-27 12:42:35 +01:00
juarez	0b1e0474d7	Add DataSHIELD	2024-02-27 12:42:35 +01:00
juarez	72255e6211	Bugfix: cross origins of exporter	2024-02-27 12:42:35 +01:00
juarez	32de51eefb	Merge id-management-setup with main	2024-02-27 12:42:35 +01:00
juarez	0cfe1d3617	Change salt string for exporter and login	2024-02-27 12:42:35 +01:00
juarez	fe07c63f36	Adapt teiler-ui to traefik	2024-02-27 12:42:35 +01:00
juarez	3a91259a8a	Add keycloak teiler app to teiler-ui	2024-02-27 12:42:35 +01:00
juarez	4bbd2a15fe	Change volume names for teiler components	2024-02-27 12:42:35 +01:00
juarez	0a17bbc81f	Add stripprefix to teiler-ui	2024-02-27 12:42:35 +01:00
juarez	c794508880	Add stripprefix to teiler-core	2024-02-27 12:42:34 +01:00
juarez	3e0bf38018	Add forward strategy to teiler-core	2024-02-27 12:42:34 +01:00
juarez	e2d109558d	Add forward strategy to teiler-core	2024-02-27 12:42:34 +01:00
juarez	9299a201a6	Deactivate traffik for mtba	2024-02-27 12:42:34 +01:00
juarez	c9b1975c9e	Tidy teiler and mtba volumes	2024-02-27 12:42:34 +01:00
juarez	17f52a7907	Add Teiler Core	2024-02-27 12:42:34 +01:00
juarez	4d1a9bb701	Add Endpoint for Teiler	2024-02-27 12:42:34 +01:00
juarez	efc04cea4f	Update Teiler Core config	2024-02-27 12:42:34 +01:00
juarez	8fe03a6cd2	Add original Keycloak config	2024-02-27 12:42:34 +01:00
p.delpy@dkfz-heidelberg.de	c66dac9881	update keykloak config	2024-02-27 12:42:33 +01:00
p.delpy@dkfz-heidelberg.de	38c7f3c24a	beautiful config	2024-02-27 12:42:33 +01:00
juarez	49be101165	Rename teiler to exporter (bugfix)	2024-02-27 12:42:33 +01:00
juarez	6626f860a2	Rename teiler to exporter	2024-02-27 12:42:33 +01:00
juarez	eb17d8c159	Configure login extern URLs	2024-02-27 12:42:33 +01:00
juarez	6340acdbe8	Bugfix: services in teiler-ui-compose.yml	2024-02-27 12:42:32 +01:00
juarez	c916a357dc	Change images of dktk-teiler and dktk-keycloak	2024-02-27 12:42:32 +01:00
juarez	20e2b2a0ed	Add nngm and exliquid modules	2024-02-27 12:42:32 +01:00
juarez	2e6edb6179	Add Teiler UI and Teiler module	2024-02-27 12:42:32 +01:00
Tobias Kussel	c58096aa27	Merge pull request #155 from samply/fix/dnpm-no-proxy ... Add DNPM_NO_PROXY configuration option	2024-02-23 11:37:47 +01:00
Tobias Kussel	3f6e3a2bb4	mount and process trusted certs in dnpm-beam-connect	2024-02-22 15:41:11 +00:00
Tobias Kussel	9937002d06	Add DNPM_NO_PROXY configuration option	2024-02-21 15:04:00 +00:00
Torben Brenner	7d07c0623d	refactor: optimize memory usage of blaze	2024-02-20 15:27:00 +01:00
Tobias Kussel	aac31945a3	Add dnpm echo to dnpm-compose	2024-02-19 08:50:15 +00:00
Martin Lablans	60b2bddf15	Merge pull request #146 from samply/fix/updates ... Fix image updates for image names with vars	2024-02-14 16:37:28 +01:00
janskiba	001b84a774	Revert "Merge pull request #147 from samply/fix/set-focus-version-to-main" ... This reverts commit 6550c0cdab, reversing changes made to 40d991d94e.	2024-02-12 08:55:29 +00:00
Martin Lablans	44ac09b9c1	Bump postgres version to 15.6	2024-02-09 16:58:02 +01:00
Torben Brenner	2d5b6e6932	fix: set focus version to main	2024-02-08 12:30:42 +01:00
Enola Knezevic	ae02526baf	Merge pull request #142 from samply/addTestInstancesForBbmri ... Tested for test GBN and ERIC BHs	2024-01-16 13:03:12 +01:00
Martin Lablans	ea51fc5910	Hotfix Pierre: Use version 1.0.0 for MTBA	2024-01-09 11:32:01 +01:00
Martin Lablans	29fb0e7099	Use focus tag depending on ENVIRONMENT	2024-01-08 15:49:46 +01:00
Tobias Kussel	a80a980cea	Merge pull request #140 from samply/feature/dnpm-node ... Feature/dnpm node	2023-12-18 10:53:39 +01:00
Tobias Kussel	f66f2755d8	Change landing page path override to /landing	2023-12-15 13:32:00 +00:00
Tobias Kussel	c02da838c7	Cleanup dnpm connect module	2023-12-15 09:41:11 +00:00
Tobias Kussel	459fa7f78e	Add DNPM Node feature to minimal	2023-12-15 09:24:06 +00:00
Pierre Delpy	9bf1b42003	set mtba image to latest	2023-11-30 14:58:54 +01:00
juarez	2ba9645ab4	Bugfix: MTBA 1.0.0	2023-11-30 12:29:58 +01:00
Tobias Kussel	2252504d78	add bwhc node module	2023-11-03 07:33:16 +00:00
Tobias Kussel	6bf34b7732	Enable obfuscation for ccp queries	2023-11-02 07:34:56 +00:00
p.delpy@dkfz-heidelberg.de	0555786435	fix bash logic	2023-10-24 07:42:27 +02:00
p.delpy@dkfz-heidelberg.de	262b9bd62e	add adt2fhir-rest service	2023-10-24 07:30:17 +02:00
Torben Brenner	850a8eb973	chore: update postgres from 15.1 to 15.4	2023-09-18 15:06:00 +02:00
Tobias Kussel	169ce2436f	fix dnpm connect env, from bool to string	2023-08-28 17:21:52 +00:00
Tobias Kussel	bba8a03f9f	Use beam-connect:develop for DNPM	2023-08-24 12:22:43 +00:00
Patrick Skowronek	fa973e2cfa	fix: path in mtba setup	2023-08-16 09:37:30 +02:00
Patrick Skowronek	bbda5e917f	Cleanup	2023-08-16 09:35:36 +02:00
Torben Brenner	e69c0ec306	Merge branch 'main' into dktk-migration	2023-08-16 09:14:04 +02:00
Pierre Delpy	829102f23e	Merge branch 'main' into feature/custom-basic-auth	2023-08-15 14:24:19 +02:00
p.delpy@dkfz-heidelberg.de	dc0fc286b1	add generic bash function addBasicAuthUser	2023-08-08 09:28:59 +02:00
Martin Lablans	54d83736c3	Move BBMRI-ERIC, GBN to modules	2023-08-07 15:19:41 +02:00
p.delpy@dkfz-heidelberg.de	788e4ea9f7	add generic bash function addBasicAuthUser	2023-07-27 13:53:20 +02:00
Martin Lablans	6ad91edefb	Don't run Blaze in debug mode	2023-07-27 09:37:19 +02:00
Torben Brenner	0a12720e4c	fix: ensure id-management redirects with ssl	2023-07-25 13:27:21 +02:00
Patrick Skowronek	11db7e2be9	Remove ref to report-hub	2023-06-30 13:36:42 +02:00
Patrick Skowronek	3dec0a7178	Remove EXLIQUID	2023-06-30 13:31:11 +02:00
Patrick Skowronek	9ca3e0059e	Rmoved generated of report-hub secret	2023-06-30 12:33:34 +02:00
Patrick Skowronek	512f335da8	Removed Report-Hub env var	2023-06-30 12:32:25 +02:00
Patrick Skowronek	f510275685	Deleted EXLIQUID setup + compose	2023-06-30 12:30:19 +02:00
Tobias Kussel	6288f809fb	Merge branch 'main' into dktk-migration	2023-06-30 09:02:37 +00:00
Tobias Kussel	dd0c28daf3	Add new dktk root cert	2023-06-30 07:50:18 +00:00
Tobias Kussel	6d94ebd4eb	Add path stripper	2023-06-30 06:02:32 +00:00
Tobias Kussel	a033386464	Absolute path for beam root cert	2023-06-28 15:38:05 +02:00
Tobias Kussel	9f4523cf9e	Absolute path for beam root cert	2023-06-28 14:55:35 +02:00
Tobias Kussel	7b32eed493	Merge branch 'main' into dktk-migration	2023-06-28 13:58:18 +02:00
Tobias Kussel	f0d423fcf7	Adapt to new beam app syntax	2023-06-28 11:48:47 +02:00
Tobias Kussel	3304d2818d	Merge branch 'main' into feature/dnpm-connect	2023-06-28 11:45:45 +02:00
Tobias Kussel	499360712b	Merge pull request #83 from samply/update/blaze-20 ... Change blaze tag to latest	2023-06-28 11:43:57 +02:00
Tobias Kussel	37ed5f5cd9	Merge pull request #88 from samply/new-beam-apikey-naming ... New beam-proxy api key syntax	2023-06-28 11:34:06 +02:00
Martin Lablans	097de41652	focus: Rename SECRET to API_KEY	2023-06-19 15:45:06 +02:00
Martin Lablans	23a500aae9	focus: Rename SECRET to API_KEY	2023-06-19 13:33:26 +02:00
Martin Lablans	b1ee2fa5f4	New beam-proxy api key syntax	2023-06-19 13:25:22 +02:00
Enola	6cbf7915f0	Merge pull request #87 from samply/main ... Merge Focus als Spot replacment from main	2023-06-19 13:21:26 +02:00
Enola Knezevic	5642141f3f	CCP focus develop -> main	2023-06-19 10:32:39 +02:00
Pierre Delpy	149a550940	deactivate exliquid in freiburg	2023-06-19 07:24:39 +02:00
Enola Knezevic	9dadd3efa0	variables	2023-06-16 16:28:22 +02:00
Enola Knezevic	c41ebd226d	DKTK local spot -> focus 🥳	2023-06-16 16:24:48 +02:00
p.delpy@dkfz-heidelberg.de	019304862e	make ID Management skippable for MTBA	2023-06-15 11:02:59 +02:00
Tobias Kussel	71fea9f098	Switch to new dktk broker url with new root cert	2023-06-13 06:16:00 +00:00
Tobias Kussel	ff4fb06ad1	Address review comments	2023-05-19 11:53:03 +00:00
Tobias Kussel	a18b63e190	Use cached beam-connect image for dnpm	2023-05-17 10:04:35 +00:00
Tobias Kussel	f4134bcfca	Remove DNPM-BwHC experiment	2023-05-17 09:26:55 +00:00
Tobias Kussel	4e7f023b8a	Clean up bwhc startup	2023-05-16 10:56:28 +00:00
Patrick Skowronek	2de6504832	Change blaze tag to latest	2023-05-16 11:57:27 +02:00
Tobias Kussel	187945b27e	Merge remote-tracking branch 'origin/main' into feature/dnpm-connect	2023-05-16 09:25:08 +00:00
Tobias Kussel	c9806ad874	Adapt DNPM configuration	2023-05-15 13:43:01 +02:00
Tobias Kussel	498092d36a	Replace deprecated openssl command	2023-05-10 10:59:13 +00:00
Tobias Kussel	3e1659a38d	Modularize DNPM components	2023-05-10 10:54:05 +00:00
p.delpy@dkfz-heidelberg.de	dd0d2c64fd	nngm migration from connector to nngm-rest	2023-05-09 07:55:30 +02:00
Tobias Kussel	503f39820b	Merge branch 'main' into dnpmconnector	2023-04-04 13:02:49 +02:00
Martin Lablans	33b50372c6	Pull docker images from DKFZ mirror	2023-03-09 11:16:34 +01:00
Patrick Skowronek	fdda14c1be	Fixed naming of site in exliquid script	2023-02-23 14:26:59 +01:00
Martin Lablans	90773ea92a	Switch beam images to develop tag	2023-02-21 09:26:53 +01:00
Pierre Delpy	e4ac27061a	Merge pull request #57 from samply/feature/idManagementModule ... Added Module for Id-Management	2023-02-09 10:22:30 +01:00
Torben Brenner	5a7dd1d0ae	fix: Use Mapped Site Id in Patientlist	2023-02-09 10:07:05 +01:00
Torben Brenner	64095ac8dd	feat: Added Upload ApiKey to Patientlist	2023-02-09 09:15:29 +01:00
Torben Brenner	d728ccd886	refactor: Fixated Postgres Version to 15.1 ... All Minor Updates will cause a crashing postgres on start	2023-02-08 15:02:35 +01:00
Torben Brenner	c88919c926	feature: Ensured the mapping to legacy ids works	2023-02-08 14:42:52 +01:00
p.delpy@dkfz-heidelberg.de	e9455a5558	update mtba config	2023-02-07 16:39:43 +01:00
p.delpy@dkfz-heidelberg.de	bce28342f9	update docker and host paths	2023-02-07 16:33:29 +01:00
Torben Brenner	e2d90447f7	refactor: Changed Trigger of the IDM Module	2023-02-07 16:31:58 +01:00
Torben Brenner	a3ba98a2fd	Added Configuration for Local ID-Management	2023-02-07 16:31:58 +01:00
Torben Brenner	2445a59785	refacotr: Restructured passing Patientlist Seeds	2023-02-07 16:26:07 +01:00
Torben Brenner	17d48a3636	refactor: Expect User to select a Backup Directory	2023-02-07 16:23:49 +01:00
Torben Brenner	1befa65f35	refactor: Changed Salt for patientlist db password	2023-02-07 16:23:18 +01:00
Torben Brenner	0d998ab871	refactor: Move persistent data to named volumes	2023-02-07 16:23:18 +01:00
Torben Brenner	1c3fa4fa3f	refactor: Changed Paths for persistent Data	2023-02-07 16:22:28 +01:00
Martin Lablans	6d8e877899	Use beam-proxy "main" tag	2023-02-03 13:28:44 +01:00
Patrick Skowronek	eb37d16b84	Updated Blaze to 0.19	2023-01-31 15:44:30 +01:00
Martin Lablans	4efe356005	Made it even easier for sites	2023-01-19 10:15:12 +00:00
Martin Lablans	af7960e036	Improve documentation	2023-01-19 10:05:03 +00:00
p.delpy@dkfz-heidelberg.de	e7b238de9d	set magicpl instead of patientlist	2023-01-12 08:26:49 +01:00
p.delpy@dkfz-heidelberg.de	e0c9a5ced3	Added MTBA Module	2023-01-12 08:26:49 +01:00
Torben Brenner	4d49351ad2	fix: Included Legacy ID-Mapping (Please Complete)	2023-01-12 08:26:49 +01:00
Torben Brenner	4f0526ddf4	docs: Added Documentation for the IDM Module	2023-01-12 08:26:49 +01:00
Torben Brenner	2a46bd00fd	refactor: Changed Trigger of the IDM Module	2023-01-12 08:26:49 +01:00
Torben Brenner	1ffc9b9cd5	feature: Added automated Backups for PostgreSQL	2023-01-12 08:26:49 +01:00
Torben Brenner	6d24dbce7f	Added Configuration for Local ID-Management	2023-01-12 08:26:49 +01:00
Patrick Skowronek	c9bb317cd2	Fixed vars in exliquid compose	2023-01-04 14:00:08 +01:00
Patrick Skowronek	813dbcc76a	Fixed beam proxy var url	2022-12-12 10:41:18 +01:00
Patrick Skowronek	54fbb58f0d	Added proxy base url	2022-12-12 09:27:50 +01:00
Patrick Skowronek	66999178bf	Added space to Override	2022-12-12 09:22:20 +01:00
patrickskowronekdkfz	d8db3bee6d	Merge pull request #46 from samply/feature/addReportHub ... Feature/add report hub	2022-12-12 08:51:29 +01:00
Martin Lablans	af54f0ca04	Define exliquid sites right inside the common bridgehead scripts	2022-12-06 11:42:18 +01:00
Martin Lablans	ece0dec9c9	Rename exliquid docker containers	2022-12-06 11:33:45 +01:00
Patrick Skowronek	b061bf6350	Fixed compose file for exliquid	2022-12-05 13:18:14 +01:00
Torben Brenner	6297373ed0	refactor: Removed Debug Logging from Beam Proxy	2022-11-25 09:22:17 +01:00
Martin Lablans	f359e06875	Encryption: Add root certs for CCP, BBMRI	2022-11-22 14:24:56 +01:00
Martin Lablans	23aa8f8274	Extra space for nngm compose	2022-11-08 10:54:51 +01:00