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Author SHA1 Message Date
Nicola Soranzo d266eb7f80 Add missing package requirements 
Packages that are imported directly in galaxy-tool-util that were already
required through the galaxy-util dependency.
 2022-10-12 18:13:46 +01:00
Nicola Soranzo c810ebf9e1 Make 2 test decorators usable on both functions and methods 2022-10-12 18:13:45 +01:00
David López f733734299 Merge pull request #14736 from jmchilton/ts_service_models_2 
Migrate index and show tool shed repositories endpoints to Pydantic and FastAPI
 2022-10-12 18:25:14 +02:00
Nicola Soranzo a81d680cca Merge branch 'release_22.05' into dev 2022-10-11 21:34:31 +01:00
Dannon bbac935f50 Merge pull request #14769 from martenson/admin-jobs-page 
improve UX of admin job page
 2022-10-11 14:17:11 -04:00
Dannon a6acbffee1 Merge pull request #14549 from ElectronicBlueberry/tool-form-improvements 
Tool form improvements
 2022-10-11 11:54:32 -04:00
Dannon 1221904383 Merge pull request #14703 from itisAliRH/store-multi-view-selected-list 
Storing selected histories in multiple view into local storage
 2022-10-11 09:30:22 -04:00
Dannon 15364b72c7 Merge pull request #14752 from guerler/safe_path_upgrade 
Align url handling for more consistency
 2022-10-11 09:15:25 -04:00
Dannon 3574b08d5b Merge pull request #14766 from xtrojak/visualisation_visjs_transition_system 
[Visualization] visjs-based transition system visualization
 2022-10-11 09:06:59 -04:00
Nicola Soranzo b31e2f02f2 Merge branch 'release_22.01' into release_22.05 2022-10-11 13:28:32 +01:00
Dannon 577a7d198a Merge pull request #14773 from nsoranzo/release_22.01_fix_provenance_follow 
[22.01] Fix dataset provenance API when ``follow=False``
 2022-10-11 08:01:10 -04:00
Dannon Baker d0bebf23ba Minor stop job message tweak 2022-10-11 07:53:31 -04:00
Nicola Soranzo bb3006df87 Fix dataset provenance API when `follow=False` 2022-10-11 00:45:37 +01:00
Martin Cech 79d3ce3ffb Merge pull request #14665 from itisAliRH/scroll-shadow-in-multiple-view 
add scroll shadow on the right and left sides
 2022-10-11 00:41:24 +02:00
Martin Cech 11ac6cd7c6 Merge pull request #14755 from jdavcs/dev_config_file 
Do not load sample config file; assign correct config paths
 2022-10-10 20:29:10 +02:00
John Chilton 552f0cfd61 Migrate index and show install repository endpoints to Pydantic+FastAPI. 2022-10-10 11:19:18 -04:00
John Chilton 84005605c8 Extend tool shed install testing to include index API. 2022-10-10 11:19:18 -04:00
John Chilton 649c9913f6 Typing for uses_shed_api.py 2022-10-10 10:45:08 -04:00
John Chilton b827f0be6c Reuse a constant in uses_shed_api.py. 2022-10-10 10:45:08 -04:00
Marius van den Beek 595e8f1479 Merge pull request #14701 from davelopez/fix_subworkflow_tool_version_update 
[22.05] Fix tool version inconsistency when downloading workflows with missing outdated tools
 2022-10-10 12:51:54 +02:00
Nicola Soranzo c4a317a974 Merge pull request #14745 from galaxybot/dev_auto_update_dependencies 
Update Python dependencies
 2022-10-08 14:06:56 +01:00
galaxybot ccb03950a3 Update Python dependencies 2022-10-08 03:40:06 +00:00
Martin CechandAysam Guerler 6afebbc38b Apply suggestions from code review 
Co-authored-by: Aysam Guerler <aysam.guerler@gmail.com>
 2022-10-08 02:41:02 +02:00
Martin Cech 5f2a704ade prtr 2022-10-07 14:46:08 -07:00
Martin Cech fb1a41db70 improve UX of admin job page 
- remove the label-for attribute which was the cause of the UX bug when
the switch would be triggered by click on the form-group label
- deduplicate and reorder the interface
- clarify some language

fixes #13774
 2022-10-07 14:03:35 -07:00
John Davis aa0f4707fe Merge pull request #14712 from bernt-matthias/topic/format-incorrect-number-of-outputs 
Minor reformatting of verification error
 2022-10-07 16:44:28 -04:00
John Davis 17a68cd587 Merge pull request #14727 from jmchilton/pulsar_manager_utils_updates 
Synchronize job runner utils with fixes from and for Pulsar's version.
 2022-10-07 11:30:01 -04:00
John Davis b1c912f179 Merge pull request #14744 from jmchilton/cleanup_ts_dependency_structure 
Small cleanups to shed package dependency structures
(integration test failure unrelated)
 2022-10-07 11:26:42 -04:00
John Davis 0a6604a6ec Merge pull request #14751 from abretaud/fix_recommendations 
[22.05] Fix tool recommendations display
 2022-10-07 11:23:47 -04:00
Matej Trojak eb0bfbd98b polish the code in mako template 2022-10-07 16:30:39 +02:00
John Davis ca9c9175ac Merge pull request #14758 from dannon/drop-loglevel-version 
Improve galaxy version extra file loading.
 2022-10-07 10:06:40 -04:00
Matej Trojak 95c80b4e27 Clean up code & get it working properly 2022-10-07 15:57:17 +02:00
Nicola Soranzo 898eac3e19 Merge pull request #14760 from bernt-matthias/topic/fix-ext 
do not split "." but the path
 2022-10-07 02:03:28 +02:00
Matthias Bernt 3b4900830a more of don't split "." but the string 2022-10-06 21:57:32 +02:00
Matej Trojak e007ba2cb3 Complete ts_visjs package build 2022-10-06 21:49:21 +02:00
Matej Trojak 7370253244 Separated mako template to JS script and CSS styles 2022-10-06 21:43:56 +02:00
Matej Trojak f4b366c8c9 Add static icons 2022-10-06 21:42:05 +02:00
John Davis 333c8c82fa Add type annotation; check value before os.path.join 2022-10-06 13:27:22 -04:00
Matthias Bernt 83a141086a do not split "." but the path 2022-10-06 18:14:21 +02:00
Matej Trojak 2d2f268346 Init files 2022-10-06 17:13:29 +02:00
Dannon Baker de3d81e8c2 Separate exception handling for granularity -- file not existing will be DEBUG and will state it; an actual error loading a galaxy extra version JSON will remain an error. 2022-10-06 10:11:27 -04:00
Dannon Baker 4829d1edcb Drop loglevel to debug for checking for and loading extra version json // this isn't likely an actual error. 2022-10-06 10:00:10 -04:00
Aysam Guerler 39ea7d7a24 Merge pull request #14746 from jmchilton/installed_repository_manager_cleanup 
Cleanup installed_repository_manager.py and related code a bit more.
 2022-10-06 07:39:02 -04:00
John Davis 48d54f57f5 Do not patch config file 2022-10-06 02:54:27 -04:00
John Davis cf5d846703 Do not load sample config; set correct paths 
1. We should not be loading galaxy.yml.sample if no config file is
   provided
2. If a config file is provided and config_dir is not set, config_dir
   should be the parent dir of the provided config file.
 2022-10-06 01:12:21 -04:00
guerler 2f06c940a6 Align url handling for more consistency 2022-10-05 11:47:11 -04:00
Nicola Soranzo 4a158f7cdd Merge pull request #14748 from jmchilton/pulsar_lib_0_14_15 
Update pulsar-galaxy-lib to 0.14.16.
 2022-10-05 13:49:43 +02:00
Anthony Bretaudeau 3cbecdeb6a Fix tool recommendations display 2022-10-05 11:18:29 +02:00
David López 6dafb07e5f Merge pull request #14749 from dannon/tooltip-tweak-historysize 
Update history size tooltip
 2022-10-05 09:37:25 +02:00
Dannon Baker 4d5923b142 Change history tooltip to indicate what the contents are, not what the link target is. 2022-10-04 22:38:01 -04:00