5b2c3d7725
Using bridgehead user for performing git pull
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Otherwise problems can arise with authentication.
2024-07-16 16:06:10 +02:00
a8a15aaad8
Update repos on start
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When Bridgehead is started, make sure that all repositories are up to
date first.
2024-07-12 09:04:08 +02:00
2e8b1dc96c
Deal with multiple data files
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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
105495d6cd
Made compatible with ehds2 branch
2024-07-10 14:51:16 +02:00
93e73838c6
Made comments compatible with ehds2 branch
2024-07-10 14:39:46 +02:00
9e72b04824
Added instructions to stop and start Bridgehead
2024-07-10 14:25:21 +02:00
fbe68bc778
Adding more detail to EHDS2-specific installation tasks
2024-07-10 14:18:03 +02:00
17f372b06c
Implement a gentler way of handling clock skew
2024-07-10 14:02:04 +02:00
a250d52998
Pinned Blaze version, increased Focus retry count
2024-07-02 14:05:38 +02:00
e309dc495a
Improved docker-compose for transFAIR
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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
53cdd49fd7
Improved docs, turned off obfuscation
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ECDC does not want obfuscated results.
2024-03-28 11:04:08 +01:00
36a97ecc20
Removed ECDC URLs and certificates from dev branch
2024-03-27 16:04:25 +01:00
1b82207934
Migrated TransFAIR start logic from launch file to docker-compose
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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
4880c5cc9b
Remove dependancy on local blazectl image
2024-03-20 11:43:43 +01:00
b9b44d2530
Using standardized conditions for starting transfair
2024-03-19 09:07:56 +01:00
0d1f425df0
Auto-build focus and transfair
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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
7a33b54416
Merge branch 'ehds2' of https://github.com/samply/bridgehead into ehds2
2024-03-15 09:48:46 +01:00
40e15f4d84
Added extra stuff for EHDS2
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This includes docker-compose files that include transfair plus
configuration variables specific to EHDS2.
2024-03-15 09:35:49 +01:00
99956f3477
Added instructions to get latest TransFAIR
2024-02-14 13:10:07 +01:00
d73e6ee7a3
Merge branch 'ehds2' of https://github.com/samply/bridgehead into ehds2
2024-02-14 11:18:37 +01:00
b6bfaba855
Removed unnecessary chown
2024-02-14 11:17:28 +01:00
5bd9baaff7
Corrected things that led to errors during install
2024-02-14 11:16:39 +01:00
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
4abe193c58
Made the file type more explicit.
2024-02-13 14:08:53 +01:00
5e8db39e2a
Data needs to be readable
2024-02-13 14:05:48 +01:00
b28a48da0a
Needed sudo
2024-02-13 14:02:19 +01:00
7c2e9af947
Set up sensible volumes for TransFAIR
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Also gave instructions to copy over data file.
2024-02-13 14:00:21 +01:00
81e5a6ea3f
Explained the file edits for EHDS2
2024-02-13 13:42:55 +01:00
a364a4b3f8
Added instructions for getting EHDS2 branch
2024-02-13 13:35:52 +01:00
9459e1a979
Inserted ECDC-specific URLs and certificates
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Also updated README to include instructions for manual Beam
registration.
2024-02-13 13:19:41 +01:00
d5760ed3d0
Modified instructions for ECDC
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Also included a template configuration file.
2024-02-12 16:40:32 +01:00
8af5cf3f01
Changes made for EHDS2
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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
f3abde1dfd
Merge pull request #138 from samply/documentation/blaze_resources
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Added Blaze performance info to README
2024-02-09 11:07:24 +01:00
6550c0cdab
Merge pull request #147 from samply/fix/set-focus-version-to-main
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fix: set focus version to main
2024-02-08 13:42:10 +01:00
2d5b6e6932
fix: set focus version to main
2024-02-08 12:30:42 +01:00
40d991d94e
Merge pull request #124 from samply/documentation/gba_additions
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Mentioned data protection concept and added GBA Firewall change
2024-01-25 13:42:39 +01:00
ae02526baf
Merge pull request #142 from samply/addTestInstancesForBbmri
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Tested for test GBN and ERIC BHs
2024-01-16 13:03:12 +01:00
0fd2481425
Merge pull request #143 from samply/mtba-hotfix
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Hotfix Pierre: Use version 1.0.0 for MTBA
2024-01-09 12:50:34 +01:00
5ba1a1a820
Fix variable visibility
2024-01-09 11:47:02 +01:00
ea51fc5910
Hotfix Pierre: Use version 1.0.0 for MTBA
2024-01-09 11:32:01 +01:00
c4018aae08
fixed gbn broker url
2024-01-09 07:53:44 +01:00
417c158435
GBN broker IDs
2024-01-08 16:26:07 +01:00
00030a6141
GBN variable names
2024-01-08 16:15:46 +01:00
29fb0e7099
Use focus tag depending on ENVIRONMENT
2024-01-08 15:49:46 +01:00
00cae67fa1
Add missing switch-case for gbn
2024-01-08 15:49:28 +01:00
2074461ee7
Use new variable ENVIRONMENT in /etc/bridgehead; defaults to "production".
2024-01-08 13:03:12 +01:00
954d46efb1
Added test root certs and logic for beam to use test brokers
2024-01-05 11:58:42 +01:00
48558812aa
Merge pull request #141 from samply/feature/nngm-module-in-minimal
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Add nngm module to minimal project
2023-12-18 10:53:53 +01:00
a80a980cea
Merge pull request #140 from samply/feature/dnpm-node
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Feature/dnpm node
2023-12-18 10:53:39 +01:00
2606c62b1c
Merge pull request #139 from samply/fix/dnpm-connect
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Cleanup dnpm connect module
2023-12-18 10:53:25 +01:00
