DavidCroftDKFZ
ca93451357
Added ECDC Beam Broker site to list of Firewall exceptions
2024-07-26 09:49:13 +02:00
Gerhard Salvini
892e2c2cf1
Removed misleading text from stop.sh
...
This command no longer disables the Bridgehead in systemctl, it
only stops it.
2024-07-18 12:56:42 +02:00
Gerhard Salvini
520c560be0
Got systemctl restart to work locally
...
There were problems on my Ubuntu VM with the target run level that I was
using, so I went for the default. Now, if I restart my VM, the Bridgehead
is successfully started automatically.
Also added some status-generating commands to the run.sh and stop.sh
scripts, so that it looks like they are doing something.
2024-07-18 12:31:42 +02:00
Gerhard Salvini
bb81617873
Replaced tabs with spaces
2024-07-17 09:34:46 +02:00
Gerhard Salvini
c27536b566
Cherry picked from ehds2 and updated data upload for new scripts
2024-07-16 16:47:57 +02:00
Gerhard Salvini
f213e6909a
Started adding the new scripts to the README
2024-07-16 16:17:30 +02:00
Gerhard Salvini
6887264a5b
Added infrastructure for running ECDC-Bridgehead under systemctl
...
This comprises of the service file to be copied into the systemctl directory,
plus Bridgehead start and stop scripts for both systemctl and for the
administrator on the command line.
2024-07-16 16:08:08 +02:00
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
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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
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
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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
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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
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
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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
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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
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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
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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
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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
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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
