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bridgehead
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46 Commits

Author SHA1 Message Date
Gerhard Salvini 105495d6cd Made compatible with ehds2 branch 2024-07-10 14:51:16 +02:00
DavidCroftDKFZ 93e73838c6 Made comments compatible with ehds2 branch 2024-07-10 14:39:46 +02:00
Gerhard Salvini e309dc495a Improved docker-compose for transFAIR 
In particular, corrected the code for detecting CSV files in the data directory.
The old code could not handle more than one CSV file.
 2024-06-18 15:28:37 +02:00
Gerhard Salvini 53cdd49fd7 Improved docs, turned off obfuscation 
ECDC does not want obfuscated results.
 2024-03-28 11:04:08 +01:00
Gerhard Salvini 36a97ecc20 Removed ECDC URLs and certificates from dev branch 2024-03-27 16:04:25 +01:00
Gerhard Salvini 1b82207934 Migrated TransFAIR start logic from launch file to docker-compose 
The start-up logic for TransFAIR is specific to the ECDC/EHDS2 Bridgehead,
and did not belong in the TransFAIR repo. This commit fixes that.

It also honours the change of the TransFAIR branch name for this
project, "ehds2".
 2024-03-26 17:00:42 +01:00
Gerhard Salvini 4880c5cc9b Remove dependancy on local blazectl image 2024-03-20 11:43:43 +01:00
Gerhard Salvini b9b44d2530 Using standardized conditions for starting transfair 2024-03-19 09:07:56 +01:00
Gerhard Salvini 0d1f425df0 Auto-build focus and transfair 
This auto-build functionality is a workaround for a bug, described in README.

The README now has additional documentation for EHDS2.

The root certificate files have been expanded to contain certificates for
both the ECDC and the DKFZ setup.
 2024-03-18 11:03:50 +01:00
Gerhard Salvini 7a33b54416 Merge branch 'ehds2' of https://github.com/samply/bridgehead into ehds2 2024-03-15 09:48:46 +01:00
Gerhard Salvini 40e15f4d84 Added extra stuff for EHDS2 
This includes docker-compose files that include transfair plus
configuration variables specific to EHDS2.
 2024-03-15 09:35:49 +01:00
Croft 5bd9baaff7 Corrected things that led to errors during install 2024-02-14 11:16:39 +01:00
Croft 7c2e9af947 Set up sensible volumes for TransFAIR 
Also gave instructions to copy over data file.
 2024-02-13 14:00:21 +01:00
Croft 9459e1a979 Inserted ECDC-specific URLs and certificates 
Also updated README to include instructions for manual Beam
registration.
 2024-02-13 13:19:41 +01:00
Croft d5760ed3d0 Modified instructions for ECDC 
Also included a template configuration file.
 2024-02-12 16:40:32 +01:00
Croft 8af5cf3f01 Changes made for EHDS2 
The EHDS2 project has initiated a use case for antibiotic resistance
under the control of the ECDC. This branch caters for the ECDC
requirements.

Specifically, it contains the ETL to transform the ECDC CSV format to
FHIR, plus additional configuration options that have been packaged into
the bbmri project.
 2024-02-12 16:07:57 +01:00
Martin Lablans 5ba1a1a820 Fix variable visibility 2024-01-09 11:47:02 +01:00
Patrick Skowronek c4018aae08 fixed gbn broker url 2024-01-09 07:53:44 +01:00
Enola Knezevic 417c158435 GBN broker IDs 2024-01-08 16:26:07 +01:00
Enola Knezevic 00030a6141 GBN variable names 2024-01-08 16:15:46 +01:00
Martin Lablans 29fb0e7099 Use focus tag depending on ENVIRONMENT 2024-01-08 15:49:46 +01:00
Martin Lablans 00cae67fa1 Add missing switch-case for gbn 2024-01-08 15:49:28 +01:00
Martin Lablans 2074461ee7 Use new variable ENVIRONMENT in /etc/bridgehead; defaults to "production". 2024-01-08 13:03:12 +01:00
Patrick Skowronek 954d46efb1 Added test root certs and logic for beam to use test brokers 2024-01-05 11:58:42 +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 d28a3ac889 Add dnpm node module to bbmri project 2023-12-15 09:46:40 +00:00
Tobias Kussel c02da838c7 Cleanup dnpm connect module 2023-12-15 09:41:11 +00:00
patrickskowronekdkfz 6b1ea4c74e
Update gbn-setup.sh 2023-09-04 15:54:22 +02:00
Patrick Skowronek 8c8ebb9298 Added gbn broker url and e-mail 2023-09-04 15:30:44 +02:00
patrickskowronekdkfz 0536023ceb
Merge pull request #117 from samply/feature/bbmri_de 
Added broker.bbmri.de root cert
 2023-09-04 14:44:38 +02:00
Patrick Skowronek 3a3a9d09a9 Added broker.bbmri.de root cert 2023-09-04 14:30:52 +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
Martin Lablans 54d83736c3 Move BBMRI-ERIC, GBN to modules 2023-08-07 15:19:41 +02:00
Martin Lablans b32a19a7b5 Make Directory Sync a module 2023-08-07 13:00:24 +02:00
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 f0d423fcf7 Adapt to new beam app syntax 2023-06-28 11:48:47 +02:00
Tobias Kussel f02587d9fa Change DNPM broker id 2023-05-25 11:20:18 +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
Tobias Kussel c9806ad874 Adapt DNPM configuration 2023-05-15 13:43:01 +02:00
Tobias Kussel 3e1659a38d Modularize DNPM components 2023-05-10 10:54:05 +00:00