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645 Commits

Author SHA1 Message Date
DavidCroftDKFZ 353fc010cb Cherry picked the stop/start files from ehds2_develop branch 2024-07-17 09:28:40 +02:00
DavidCroftDKFZ c15c3962a7 Switched to bridgehead user for git to avoid auth problems 2024-07-17 09:24:37 +02:00
DavidCroftDKFZ e0fe39ab83 Perform git actions with the bridgehead user, to prevent authentication issues 2024-07-16 16:58:13 +02:00
DavidCroftDKFZ cce76bab84 Updated README for the new run/stop scripts 2024-07-16 16:55:08 +02:00
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