John Davis
89f753767b
Fix packages tests: script is one level up
2022-09-16 00:39:03 -04:00
John Davis
ac6b0ceee0
Fix linting
2022-09-16 00:39:03 -04:00
John Davis
de856e825a
Add init command
2022-09-16 00:39:03 -04:00
John Davis
e247afd8d7
Set dburl in alembic config
2022-09-16 00:39:03 -04:00
John Davis
0a798ea536
Test against 1 or 2 databases
2022-09-16 00:39:03 -04:00
John Davis
b30e4e14ae
Add inline testing documentation
2022-09-16 00:39:03 -04:00
John Davis
811392b468
Add logging to script
2022-09-16 00:39:03 -04:00
John Davis
a69ab407a6
Add initial draft
2022-09-16 00:39:03 -04:00
John Davis
6abc9dc1c5
Refactor get_alembic_cfg: make available to other code
2022-09-16 00:39:03 -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
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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
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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
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[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
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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
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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
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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
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More Tool Shed Cleanup
2022-09-15 09:04:39 -04:00
davelopez and Marius van den Beek
07b38ba429
Fix toolbox access in invocation export
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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
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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
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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
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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
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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
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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
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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
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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 Davis