DavidCroftDKFZ
013d6d219b
Provided more detailed instructions on uploading data to a Bridgehead
2024-07-15 10:28:21 +02:00
DavidCroftDKFZ
cc228e20d9
Reordered the Bridgehead restart instructions
...
Ordered them so that first a stop is performed, then a start. This
reflects what administrators will be doing in real life. Also included a
git pull for the Bridgehead, since this will normally also be part of
the regular administrative tasks.
Also removed a bunch of instructions for the installation, since these
steps are now performed automatically by the bridgehead script.
2024-07-15 09:20:18 +02:00
DavidCroftDKFZ
153f654397
Deal with multiple data files, update repos
...
The check for the presence of data in the TransFAIR updating function
only worked for single CSV files. Tis commit corrects that.
Now also do a git pull on the various repos, to keep things up to date.
2024-07-12 11:07:06 +02:00
DavidCroftDKFZ
70aca8e99c
Wait longer for Blaze to start
2024-07-10 14:34:14 +02:00
DavidCroftDKFZ
f925c27791
Suggested more robust Bridgehead start
2024-07-10 14:26:46 +02:00
DavidCroftDKFZ
350a4c84af
Added extra detail relating to EHDS2
2024-07-10 14:20:40 +02:00
DavidCroftDKFZ
b52931e46c
Pinned Blaze version
2024-07-02 14:11:34 +02:00
DavidCroftDKFZ
eb0f392e3c
Croatia is having problems with a slow starting Blaze, increase Focus retry count
2024-06-13 09:25:57 +02:00
Croft
a738f1468f
Fixed bug in CVS test logic
...
The -f test with a wildcard works OK if there is 0 or 1 CSV files but
breaks if there are 2 or more. The replacement uses ls to check if
there are any CSV files.
2024-06-07 16:08:16 +02:00
Croft
aa122d0bff
Shortened national node names in config
...
For ECDC, the Beam broker URL is very long, so the resulting Beam ID
can be longer than 64 characters, which is too much for the CSR
generation algorithm.
2024-05-17 11:44:37 +02:00
Croft
ec4e91fade
Corrected data target directory
2024-05-17 09:59:33 +02:00
Croft
c5f82bf93c
Removed outdated steps relating to transFAIR
2024-05-17 09:57:31 +02:00
Croft
eb563113e0
Merge branch 'ehds2' of https://github.com/samply/bridgehead into ehds2
2024-05-17 09:50:59 +02:00
Croft
a10d0f9605
Added instructions for starting/stopping ECDC Bridgeheads
2024-05-17 09:49:39 +02:00
Patrick Skowronek
994b0a4124
remove time
2024-04-25 14:03:39 +02:00
Gerhard Salvini
593f93fffc
Turned off obfuscation, because ECDC does not want this feature
2024-03-28 11:06:10 +01:00
Gerhard Salvini
b2b9865e8c
Improved documentation for EHDS2/ECDC
2024-03-28 09:22:41 +01:00
Gerhard Salvini
4588960e19
Removed DKFZ URLs and certificates from EHDS2 branch
2024-03-27 16:08:32 +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
