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Author SHA1 Message Date
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
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
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 ca9c9175ac Merge pull request #14758 from dannon/drop-loglevel-version 
Improve galaxy version extra file loading.
 2022-10-07 10:06:40 -04:00
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
Matthias Bernt 83a141086a do not split "." but the path 2022-10-06 18:14:21 +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
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
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
John Chilton 13adeb3749 Rev pulsar-galaxy-lib to 0.14.16. 
CI caught another bug.
 2022-10-04 09:00:34 -04:00
Marius van den Beek 196301c058 Merge pull request #14747 from dannon/fix-a11y-workflow-list 
Accessibility issue fixes in workflow list/import interfaces
 2022-10-04 09:40:05 +02:00
John Chilton 72b319c442 Update pulsar-galaxy-lib to 0.14.15. 
Minted today.
 2022-10-03 16:19:28 -04:00
Dannon Baker c41ebc50bb Assorted lint fixes. 2022-10-03 12:30:47 -04:00
Dannon Baker bc64a1bd07 Add aria-label for workflow import URL 2022-10-03 12:21:02 -04:00
Dannon Baker 0d1a245b04 Add keypress handlers for nav in workflow dropdown (vue-a11y) 2022-10-03 11:37:15 -04:00
Dannon Baker da67f0904c Fix reused id in workflow dropdown 2022-10-03 11:20:01 -04:00
John Chilton 79a3ac12e1 Cleanup installed_repository_manager.py and related code a bit more. 
- Remove unused code and mako.
- Use more direct imports for better typing and static checking.
- Reuse existing abstractions a bit better.
 2022-10-03 09:04:00 -04:00
Dannon Baker 3387b80830 Add text for advanced tool search toggle link 2022-10-02 21:24:16 -04:00
Aysam Guerler dd25dde39e Merge pull request #14737 from dannon/drop-tools-view 
Drop ToolsView
 2022-10-02 00:17:14 -04:00
David López 1037334d54 Merge pull request #14719 from jmchilton/ts_service_models 
Outline modernizing tool shed repositories API.
 2022-10-01 23:10:38 +02:00
John Chilton 3f5f7b18e7 Cleanup more utility imports to reduce dependency requirements. 2022-10-01 11:32:42 -04:00
John Chilton 94c8218d48 setup service and fastapi layer for tool shed APIs... 2022-10-01 09:14:03 -04:00
John Chilton fe83d9e083 Move repository_util function into legacy code in only place used. 
Eliminates a galaxy -> tool shed import and centralizes legacy code.
 2022-09-30 14:04:26 -04:00
Dannon 0d25e83049 Merge pull request #14741 from ElectronicBlueberry/minimal-tsconfig 
Add minimal tsconfig for type completion
 2022-09-30 10:51:35 -04:00
Laila Los ce5487362f add minimal tsconfig 2022-09-30 15:30:53 +02:00
John Chilton 2ed83560cb Merge pull request #14693 from jmchilton/cleanup_ts_test_3 
Migrate more tool shed functional testing to Galaxy API
 2022-09-29 14:05:52 -04:00
John Chilton 9bc6c1815b Merge pull request #14695 from natefoo/tailscale-container-monitor 
Configurable get IP method for container monitor
 2022-09-29 14:05:32 -04:00
John Chilton 957a7df96a Sychronize job runner utils with fixes from and for Pulsar's version. 2022-09-29 13:53:44 -04:00
Aysam Guerler 7bcda0ac51 Merge pull request #14716 from guerler/remove_workflow_sharing_mako 
Remove workflow export mako
 2022-09-29 10:35:11 -04:00
mvdbeek 8dc765713d Drop extra newline 2022-09-29 09:45:48 +02:00
Marius van den Beek 2672f5c6a7 Merge pull request #14729 from dannon/no-hide-panel-on-multiview 
Disable multi-view create hook hiding toolbox.
 2022-09-29 09:39:48 +02:00
Marius van den Beek cc8fa200bc Merge pull request #14720 from jmchilton/cleanup_job_files_1 
Cleanup hack in job files API for very old versions of Galaxy.
 2022-09-29 09:34:06 +02:00
Marius van den Beek 687385a68d Merge pull request #14728 from nsoranzo/fix_validation_dataset_metadata_in_file_testing 
Fix ``validation_dataset_metadata_in_file`` framework test
 2022-09-29 09:26:19 +02:00
Dannon Baker 088bdfdd66 Drop vueisotope dependency (unused now) 2022-09-28 22:27:29 -04:00
Dannon Baker cb9723b150 Drop ToolsView, which is be superseded by the advanced search results view. The central panel search result view has a similar display but improved loading/filtering characteristics and we could use it in a 'show all the tools' display like this as well. 2022-09-28 22:25:16 -04:00
Dannon Baker 3694764622 Disable multi-view create hook hiding toolbox. We may want to reconsider doing this reactively (and at the panel/route level in a generic way) based on breakpoints or some other behavior in the future. 2022-09-28 21:58:42 -04:00
Nicola Soranzo 5c68bba05c Merge pull request #14717 from nsoranzo/wf_type_annot 
Add some type annotations to workflow-related code
 2022-09-29 01:54:14 +01:00
Nicola Soranzo ea4461751c Use loc file that actually exists in the param validators of test tool 
Previously, the ``validation_dataset_metadata_in_file`` test tool was failing
to load and was not tested at all during framework tests on GitHub Actions.
 2022-09-29 01:50:33 +01:00
Nicola Soranzo 5abee634b0 Cleanup 2022-09-29 01:50:33 +01:00
Nicola Soranzo 4ee1a102fb Improve error messages when parsing param validators 2022-09-29 01:50:32 +01:00