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635 Commits

Author SHA1 Message Date
Gerhard Salvini 5b2c3d7725 Using bridgehead user for performing git pull 
Otherwise problems can arise with authentication.
 2024-07-16 16:06:10 +02:00
DavidCroftDKFZ a8a15aaad8 Update repos on start 
When Bridgehead is started, make sure that all repositories are up to
date first.
 2024-07-12 09:04:08 +02:00
Bridgehead User 2e8b1dc96c Deal with multiple data files 
The original TransFAIR logic was only able to handle a single CSV file
and broke if there were more. This commit fixes that.
 2024-07-12 08:45:17 +02:00
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
DavidCroftDKFZ 9e72b04824 Added instructions to stop and start Bridgehead 2024-07-10 14:25:21 +02:00
DavidCroftDKFZ fbe68bc778 Adding more detail to EHDS2-specific installation tasks 2024-07-10 14:18:03 +02:00
Gerhard Salvini 17f372b06c Implement a gentler way of handling clock skew 2024-07-10 14:02:04 +02:00
Gerhard Salvini a250d52998 Pinned Blaze version, increased Focus retry count 2024-07-02 14:05:38 +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 99956f3477 Added instructions to get latest TransFAIR 2024-02-14 13:10:07 +01:00
Croft d73e6ee7a3 Merge branch 'ehds2' of https://github.com/samply/bridgehead into ehds2 2024-02-14 11:18:37 +01:00
Croft b6bfaba855 Removed unnecessary chown 2024-02-14 11:17:28 +01:00
Croft 5bd9baaff7 Corrected things that led to errors during install 2024-02-14 11:16:39 +01:00
Patrick Skowronek a629d87a5f Inserted right urlInserted right urlInserted right urlInserted right urlInserted right urlInserted right urlInserted right urlInserted right urlInserted right url 2024-02-14 10:19:19 +01:00
Croft 4abe193c58 Made the file type more explicit. 2024-02-13 14:08:53 +01:00
Croft 5e8db39e2a Data needs to be readable 2024-02-13 14:05:48 +01:00
Croft b28a48da0a Needed sudo 2024-02-13 14:02:19 +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 81e5a6ea3f Explained the file edits for EHDS2 2024-02-13 13:42:55 +01:00
Croft a364a4b3f8 Added instructions for getting EHDS2 branch 2024-02-13 13:35:52 +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
DavidCroftDKFZ f3abde1dfd
Merge pull request #138 from samply/documentation/blaze_resources 
Added Blaze performance info to README
 2024-02-09 11:07:24 +01:00
Martin Lablans 6550c0cdab
Merge pull request #147 from samply/fix/set-focus-version-to-main 
fix: set focus version to main
 2024-02-08 13:42:10 +01:00
Torben Brenner 2d5b6e6932
fix: set focus version to main 2024-02-08 12:30:42 +01:00
DavidCroftDKFZ 40d991d94e
Merge pull request #124 from samply/documentation/gba_additions 
Mentioned data protection concept and added GBA Firewall change
 2024-01-25 13:42:39 +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
Pierre Delpy 0fd2481425
Merge pull request #143 from samply/mtba-hotfix 
Hotfix Pierre: Use version 1.0.0 for MTBA
 2024-01-09 12:50:34 +01:00
Martin Lablans 5ba1a1a820 Fix variable visibility 2024-01-09 11:47:02 +01:00
Martin Lablans ea51fc5910
Hotfix Pierre: Use version 1.0.0 for MTBA 2024-01-09 11:32:01 +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 48558812aa
Merge pull request #141 from samply/feature/nngm-module-in-minimal 
Add nngm module to minimal project
 2023-12-18 10:53:53 +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 2606c62b1c
Merge pull request #139 from samply/fix/dnpm-connect 
Cleanup dnpm connect module
 2023-12-18 10:53:25 +01:00