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Author SHA1 Message Date
mvdbeek 858593a8ba Fix transfer of $_TOOL_DIRECTORY subdirectories 
Goes together with https://github.com/galaxyproject/pulsar/pull/385
 2025-03-13 16:19:10 +01:00
John Davis bd75278ef9 Merge pull request #19679 from jdavcs/24.2_role_name_displayed_name_description 
[24.2] Fix private role name performance issue
 2025-03-11 15:03:48 -04:00
John Davis b69a736a35 Fix notifications 2025-03-11 13:06:52 -04:00
Nicola Soranzo cc18d879c4 Merge pull request #19783 from nsoranzo/release_24.2_prm_format 
[24.2] Add rDock prm datatype
 2025-03-11 11:14:37 +00:00
John Davis ef092809ab Fix groups create/edit permissions 2025-03-11 00:34:26 -04:00
John Davis a03673be98 Fix append vs add in dataset controller 2025-03-11 00:34:26 -04:00
John Davis 5251d94fab Ensure user's email is stored in user_context as their private role name 2025-03-11 00:34:26 -04:00
John Davis d128682abc Fix dataset manager: serialize_dataset_association_roles 2025-03-11 00:34:26 -04:00
John Davis f5da759245 Fix api/group_roles::index 2025-03-11 00:34:26 -04:00
John Davis 8de7851611 Fix library_datasets::show_roles() 2025-03-11 00:34:26 -04:00
John Davis 5c143ef75a Fix controllers/dataset::get_edit 2025-03-11 00:34:26 -04:00
John Davis 3c2244bd50 Fix library_folders::get_permissions() 2025-03-11 00:34:26 -04:00
John Davis 3b35f1f58f Fix api/users::get_permissions() 2025-03-11 00:34:26 -04:00
John Davis 5beeb96f92 Fix history permissions 2025-03-11 00:34:26 -04:00
John Davis e878d57029 Fix manage library permissions 
Display associated user email as role name for private roles, and role
name for non-private roles.
 2025-03-11 00:34:25 -04:00
John Davis e050229fdd Add displayed_name to /api/roles endpoint 2025-03-11 00:34:25 -04:00
John Davis 104a375ea4 Add get_private_role_user_emails_dict, test 
Retrieves a mapping of private role ids to associated users' emails.
Used to lookup a user's email when generating a displayed_name for
private roles.
 2025-03-11 00:34:22 -04:00
Nicola Soranzo 6c69897035 Add rDock prm datatype 2025-03-10 17:39:05 +00:00
John Davis c4c66078d8 Factor out get_displayable_roles, add test 2025-03-10 11:13:13 -04:00
John Davis f2f55131b2 Fix unit tests 2025-03-10 11:13:13 -04:00
John Davis dfe1536a5d Update test fixture 
Specify correct role name for private roles. See comment in make_role
definition for why this must be set.
 2025-03-10 11:13:13 -04:00
John Davis 3d2eb9fd8e Remove hybrid property from model 2025-03-10 11:13:13 -04:00
Marius van den Beek 43a696e353 Merge pull request #19774 from mvdbeek/fix_anndata_with_integer_observations 
[24.2] Fix anndata metadata setting for data with integer indexes
 2025-03-10 10:13:09 +01:00
Marius van den Beek a1a133f655 Merge pull request #19764 from dannon/fix-webhooks-242 
[24.2] Fix masthead webhook click/nav.
 2025-03-08 13:20:30 +01:00
mvdbeek 7ad18a9d78 Start work on 24.2.3.dev0 2025-03-08 11:44:06 +01:00
mvdbeek c80d7d92a1 Create version 24.2.2 v24.2.2 2025-03-08 11:44:03 +01:00
Marius van den Beek 54de00e2cf Merge pull request #19694 from mvdbeek/bwa_index_directory_datatype 
[24.2] Add bwa_mem2_index directory datatype, framework enhancements for testing directories
 2025-03-08 11:14:52 +01:00
Marius van den Beek a2e598b106 Merge pull request #19568 from nuwang/overridable_k8s_user_group_ids 
[24.2] Make k8s user and group ids overriddable per job
 2025-03-08 11:14:00 +01:00
Marius van den Beek 2832585a34 Merge pull request #19672 from jmchilton/fix_actions_recording 
[24.2] Fix recording transform action name.
 2025-03-08 11:12:57 +01:00
Marius van den Beek e42da37486 Merge pull request #19707 from bernt-matthias/set-linter 
[24.2] add missing linter name argument to linter report function calls
 2025-03-08 11:11:11 +01:00
Marius van den Beek 5fcc4585fe Merge pull request #19715 from jmchilton/assertion_linter_fixes 
[24.2] Assertion linter fixes
 2025-03-08 11:09:51 +01:00
Marius van den Beek bcb5d55b77 Merge pull request #19746 from jdavcs/24.2_followup_19651 
[24.2] Follow-up to #19651: Do not reassign: method modifies object in-place
 2025-03-08 11:08:34 +01:00
Marius van den Beek 8818885481 Merge pull request #19761 from davelopez/24.2_move_workflow_save_button 
[24.2] Move Workflow Editor save button
 2025-03-08 11:06:51 +01:00
mvdbeek 15bec21bd2 Print more useful traceback 2025-03-08 09:51:56 +01:00
mvdbeek eb95601f32 Fix path resolution for composite test data upload 2025-03-08 09:51:55 +01:00
mvdbeek 3ce6b60152 Fix anndata metadata setting for data with integer indexes 2025-03-08 09:32:54 +01:00
Marius van den Beek 47ec11e572 Merge pull request #19768 from davelopez/24.2_fix_rdm_token_access 
[24.2] Fix RDM token access for user-defined file sources
 2025-03-07 21:23:06 +01:00
davelopez 7719a5e38d Update save button assertion in workflow editor tests to check for disabled state 2025-03-07 18:58:55 +01:00
davelopez 044338280c Fix RDM token access for user-defined file sources 
The user context was needed in the old admin-provided file sources to evaluate templated values.
However, the user context is not needed when using user-defined file sources as the templated values are already resolved when instancing the file source.
 2025-03-07 17:30:25 +01:00
davelopez 28feab5313 Adapt selenium tests for workflow editor 
Do not expect the save button to disappear when the workflow is saved
 2025-03-07 17:06:14 +01:00
Dannon Baker f2f21a62f1 Add extensionTabClick function to handle webhook tab clicks in Masthead 
component; this fixes the scope and context issues preventing webhooks
from functioning previously.
 2025-03-07 10:47:20 -05:00
davelopez 7f30afffa7 Disable save button when there are no changes 2025-03-07 15:07:09 +01:00
davelopez 161146284e Refactor save button placement in workflow editor 
- Move the save button to the top right corner of the editor and make it always visible
 2025-03-07 14:19:52 +01:00
davelopez baf70fd476 Add "Save" workflow activity in editor 2025-03-07 14:13:25 +01:00
Marius van den Beek c142228ecc Merge pull request #19757 from bernt-matthias/fix-dataypes-linter-auto 
[24.2] Fix dataypes linter: allow auto for output tags
 2025-03-07 13:44:22 +01:00
M BerntandNicola Soranzo 188a922e78 Apply suggestions from code review 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2025-03-06 18:30:49 +01:00
Matthias Bernt 9f86a7db62 linter allow datatype auto in output tags 2025-03-06 17:25:05 +01:00
John Davis fc88f6fec4 Do not reassign: method modified object in-place 2025-03-05 14:01:49 -05:00
Marius van den Beek a209a8b950 Merge pull request #19744 from jdavcs/24.2_skip_dbscript_tests 
[24.2] Skip slow tests for manage_db, db_dev scripts
 2025-03-05 17:56:36 +01:00
John Davis 0d81abe114 Skip slow tests for manage_db, db_dev scripts 2025-03-05 10:57:19 -05:00