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Author SHA1 Message Date
John Chilton 10dcf79157 Annotate tool shed registry in structured_app. 2022-09-16 13:05:39 -04:00
John Chilton 528bd5df5a Refactor galaxy.tool_shed.tool_shed_registry -> galaxy.util.tool_shed. 
common_util makes heavy use of this implicitly so typing and designwise this will be better.
 2022-09-16 13:03:41 -04:00
John Chilton 49c990a53b Typing for tool shed registry. 2022-09-16 13:03:39 -04:00
John Chilton e1daab1768 Merge pull request #14629 from jmchilton/toolbox_typing 
Type annotations for base toolbox functionality.
 2022-09-16 09:22:33 -04:00
John Chilton b84076fa4a Merge pull request #14609 from guerler/bundle_toolshed_js 
Place Toolshed JS modules into separate bundle
 2022-09-16 09:21:58 -04:00
Björn Grüning 5d1a3e0b13 Merge pull request #14630 from guerler/remove_display_structured 
Remove outdated display structured history view
 2022-09-16 15:10:14 +02:00
John Chilton 222fb13029 Merge pull request #14626 from jmchilton/mypy_infrastructure 
Improvements to mypy setup.
 2022-09-16 08:58:13 -04:00
John Chilton cf298957e3 Toolbox typing. 2022-09-15 21:14:04 -04:00
John Chilton 1b3da85119 Merge pull request #14628 from jmchilton/cleanup_update_repo_manager 
Cleanup update_repository_manager in Galaxy repository install code.
 2022-09-15 21:09:19 -04:00
Nicola Soranzo aa4443af18 Merge pull request #14596 from jdavcs/dev_alembic_fix3 
Better + additional fix for alembic offline mode
 2022-09-16 01:02:52 +01:00
guerler bf73d4fe6e Remove corresponding client route from backend 2022-09-15 15:52:39 -04:00
guerler 0372dfc1ea Remove structure display selenium tests 2022-09-15 15:50:31 -04:00
guerler 9c504a2ca4 Run prettier 2022-09-15 14:45:07 -04:00
guerler 8806869356 Remove unused legacy history controller template helpers 2022-09-15 14:24:33 -04:00
guerler fa5d24b017 Remove unused import 2022-09-15 14:21:54 -04:00
guerler 35d4b1b6f2 Remove display structure route from central router 2022-09-15 14:11:41 -04:00
guerler 71e4d7dab5 Remove show display structure option from current history dropdown 2022-09-15 14:11:08 -04:00
guerler 2c3ace6414 Remove beta toggle feature from code base 2022-09-15 14:10:12 -04:00
guerler 9691c1dfc6 Remove legacy toggle switch to old history from current history dropdown 2022-09-15 14:08:47 -04:00
guerler 2905b87377 Remove display structured client component 2022-09-15 14:05:57 -04:00
Nicola Soranzo 331d0d2465 Merge pull request #14580 from nsoranzo/recommend_draft_instead_of_WIP 
[PROCEDURES] Recommend to use PR draft state instead of WIP title/label
 2022-09-15 19:05:40 +01:00
guerler bb10689ffe Remove display structured controller endpoint 2022-09-15 14:04:52 -04:00
John Chilton c04dd77de0 Cleanup update_repository_manager in Galaxy repository install code. 2022-09-15 13:39:25 -04:00
John Chilton b0a230b8f0 Script for finding unused mypy.ini entries. 2022-09-15 13:20:04 -04:00
John Chilton c32e736f85 Restructure mypy.ini to distinguish between "good" exclusions and "bad" ones. 2022-09-15 12:29:14 -04:00
Björn Grüning 01fffdf175 Merge pull request #14617 from jmchilton/remove_propertiary_datatypes 
Remove legacy tool shed datatype handling
 2022-09-15 18:21:43 +02:00
Björn Grüning 89803553db Merge pull request #14624 from davelopez/fix_invocation_export_with_celery 
Fix `toolbox` access in invocation export
 2022-09-15 18:20:12 +02:00
John Chilton a887fc894d Merge pull request #14616 from jmchilton/ts_tests_1 
More tool shed API tests (+fixes)
 2022-09-15 09:08:31 -04:00
John Chilton 1c6c697d55 Merge pull request #14615 from jmchilton/ts_cleanup_3 
More Tool Shed Cleanup
 2022-09-15 09:04:39 -04:00
davelopezandMarius van den Beek 07b38ba429 Fix toolbox access in invocation export 
When exporting an invocation using Celery we don't have access to the ToolBox and also don't need it so we make it optional.
Thanks Marius for the solution.

In addition:
- Fix mypy by raising a tool missing exception in the `augment` method
- Also remove unused `inputs` parameter

Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2022-09-15 14:42:50 +02:00
Dannon 705d8fbffd Merge pull request #14623 from ElectronicBlueberry/vue-jest-upgrade 
Upgrade vue2-jest to 29.1.0
 2022-09-15 07:56:48 -04:00
Laila Los 87b7085941 upgrade vue-jest to 29.1.0 2022-09-15 12:30:11 +02:00
David López 2741b20841 Merge pull request #14595 from jmchilton/ro_crate 
Implement RO Crate export of Galaxy histories and invocations.
 2022-09-15 08:55:19 +02:00
Nicola Soranzo 9a8efa6c28 Merge pull request #14614 from nsoranzo/deprecated_method_status_code 
Change HTTP status code for ``DeprecatedMethod`` exception to 410
 2022-09-14 20:07:40 +01:00
John Chilton 0f9dbb4045 Remove more datatype legacy handling code. 2022-09-14 11:51:39 -04:00
John Chilton 3b1331de51 Remove code and config option related to loading shed datatypes. 2022-09-14 11:51:38 -04:00
John Chilton f8c1c11016 API tests for tool shed search APIs. 2022-09-14 09:31:27 -04:00
John Chilton e5bbad2f36 Flush out pydantic models for tool shed metadata. 2022-09-14 09:31:25 -04:00
John Chilton b2a4cdeb82 Remove now unused function. 2022-09-14 09:24:25 -04:00
John Chilton 0869bfd17f Rename method to indicate an internal method. 2022-09-14 09:23:55 -04:00
John Chilton 9351be5c96 Refactor method name to make clear it is private. 2022-09-14 09:07:43 -04:00
John Chilton d26cade072 Remove more unused tool shed code. 2022-09-14 09:07:43 -04:00
John Chilton 90858d3137 Move create_element into the only place it is used. 2022-09-14 09:07:43 -04:00
Nicola Soranzo b4a3735999 Change HTTP status code for `DeprecatedMethod` exception to 410 
Replaced the 404 (Not Found) HTTP response status code with 410 (Gone),
which is more correct, see details at:

https://developer.mozilla.org/en-US/docs/Web/HTTP/Status#client_error_responses
 2022-09-14 13:24:24 +01:00
Marius van den Beek 2ee253cbbd Merge pull request #14612 from jmchilton/ts_unused_1 
Remove unused tool shed functions.
 2022-09-14 10:32:28 +02:00
Nicola Soranzo f3912e9135 Merge pull request #14613 from jmchilton/unused_mypy_exceptions 
Remove mypy exceptions for deleted files.
 2022-09-14 01:12:36 +01:00
Aysam Guerler 4f6fa6a18f Merge pull request #14608 from dannon/multipanel-cleanup 
Multipanel cleanup, remove dead code
 2022-09-13 19:50:57 -04:00
John Chilton 3dbe2891e7 Implement RO Crate export of Galaxy histories and invocations. 2022-09-13 19:20:48 -04:00
John Chilton d99c6f8a73 Run linting in Github actions when mypy config is updated. 2022-09-13 18:55:44 -04:00
John Chilton 506921c2d8 Remove mypy exceptions for deleted files. 2022-09-13 17:41:22 -04:00