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Commit Graph
37065 Commits
Author SHA1 Message Date
guerler ccf2e13235 Attempt to combine typing by reusing HistoryDetailed 2024-02-08 15:46:05 -05:00
guerler 7a2eb798a0 Determine qqv mode by availability of search term 2024-02-08 15:46:05 -05:00
guerler 406b697c34 Combine legacy and modern history endpoint pattern 2024-02-08 15:46:05 -05:00
mvdbeek 39bfc6ab78 Merge branch 'release_23.2' into dev 2024-02-08 12:23:28 +01:00
mvdbeek 2d702a7402 Merge branch 'release_23.1' into release_23.2 2024-02-08 12:22:32 +01:00
mvdbeek 0008b4d7cc Merge branch 'release_23.0' into release_23.1 2024-02-08 12:21:53 +01:00
Marius van den Beek 4c1c8e227f Merge pull request #17384 from ahmedhamidawan/fix_genome_build_filter_postgres 
[23.0] Fix History contents `genome_build` filter postgresql bug
 2024-02-08 12:20:32 +01:00
mvdbeek b278d8a2aa Merge branch 'release_23.2' into dev 2024-02-08 11:35:49 +01:00
mvdbeek 327dfa0056 Merge branch 'release_23.1' into release_23.2 2024-02-08 11:08:15 +01:00
Marius van den Beek 62ee88db55 Merge pull request #17433 from davelopez/23.1_fix_bulk_operations_menu 
[23.1] Fix history bulk operations menu conditions
 2024-02-08 11:04:07 +01:00
Marius van den Beek 5f25655096 Merge pull request #17346 from jmchilton/model_store_fixes 
Fix model store exports that include implicit conversions.
 2024-02-08 10:59:36 +01:00
Nicola Soranzo 5e14d03779 Merge branch 'release_23.1' into release_23.2 2024-02-07 22:50:08 +00:00
Nicola Soranzo 52933ed5fd Merge branch 'release_23.0' into release_23.1 2024-02-07 22:48:53 +00:00
Martin Cech af169f711e Merge pull request #17398 from jmchilton/typed_testing 
Some additional typing for test interactor stuff.
 2024-02-07 18:23:08 +01:00
Marius van den Beek 47926baac6 Merge pull request #17155 from guerler/grids_tool_versions 
Remove legacy tool versions list from admin panel
 2024-02-07 15:41:17 +01:00
davelopez f60f0ae6e3 Fix new edge case where all items might be already deleted 
This case was previously prevented at the UI level but should be considered here.
 2024-02-07 14:58:52 +01:00
Nicola Soranzo de8d4562b6 Add missing Werkzeug test requirement 
Used in `test/unit/util/test_get_url.py` since commit
69ebbb761a .

Pin Werkzeug in `lib/galaxy/dependencies/dev-requirements.txt`
to latest version compatible with pytest-httpserver 1.0.6 .

Fix unit test collection error on Python 3.11:
```
  File "/home/runner/work/galaxy/galaxy/galaxy root/.tox/unit-coverage/lib/python3.11/site-packages/pytest_httpserver/httpserver.py", line 26, in <module>
    from werkzeug.http import parse_authorization_header
ImportError: cannot import name 'parse_authorization_header' from 'werkzeug.http' (/home/runner/work/galaxy/galaxy/galaxy root/.tox/unit-coverage/lib/python3.11/site-packages/werkzeug/http.py)
```
 2024-02-07 05:44:42 +00:00
Nicola Soranzo 10ace7bd10 Update python-multipart to 0.0.7 
xref: https://github.com/tiangolo/fastapi/security/advisories/GHSA-qf9m-vfgh-m389
 2024-02-06 17:33:21 +00:00
Marius van den Beek bbfc0425c4 Merge pull request #17411 from davelopez/purge_groups_and_roles_from_db 
Purge `groups` and `roles` from DB (for real)
 2024-02-02 16:39:21 +01:00
Marius van den Beek beea9fa832 Merge pull request #17390 from davelopez/cancel_deleted_user_jobs 
Cancel all active jobs when the user is deleted
 2024-02-02 11:01:28 +01:00
davelopez b9e40f8fa6 Make group update API test rerunnable in same instance 2024-02-01 17:40:45 +01:00
davelopez fd01ab96f2 Delete role from DB after purge 2024-02-01 17:29:35 +01:00
davelopez 34a7b00e04 Refactor sa_session variable 2024-02-01 17:28:59 +01:00
davelopez ad2c7d352e Add tests for purged roles DB deletion 2024-02-01 17:27:18 +01:00
davelopez df56f8a1db Fix small API error code inconsistencies 
Use specific error codes instead of 400. Results in more consistency with other API like groups.
 2024-02-01 17:24:08 +01:00
davelopez 2a1caef076 Refactor explicitly import galaxy exceptions 2024-02-01 17:16:50 +01:00
davelopez 46282362f4 Add API test coverage for roles deletion/purge 2024-02-01 16:57:19 +01:00
davelopez 4c86d0032b Delete groups from DB after purge 2024-02-01 16:55:24 +01:00
davelopez 0a80772d0b Add tests for purged groups DB deletion 2024-02-01 16:54:57 +01:00
davelopez 7f0d5ba2d3 Add API test coverage for groups deletion/purge 2024-02-01 16:53:28 +01:00
John Chilton 4847ef6241 Some additional typing for test stuff. 2024-02-01 10:28:29 -05:00
Wolfgang Maier dcb20450a0 Fix IUC best practices links, mention data_source_async 2024-02-01 16:05:13 +01:00
David LópezandMarius van den Beek c0a3b298d0 Use correct job ID in test 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2024-02-01 12:11:56 +01:00
davelopez 5218c626bb Wait for the job to be ready in test 2024-02-01 12:11:56 +01:00
davelopezandmvdbeek 6248086ea0 Let the job queue handle the jobs deletion 
Co-authored-by: mvdbeek <m.vandenbeek@gmail.com>
 2024-02-01 12:11:56 +01:00
davelopez ffe354a523 Add API test for cancelling jobs for deleted users 2024-02-01 12:11:56 +01:00
davelopez bd79ab453e Cancel all active jobs when the user is deleted 2024-02-01 12:11:56 +01:00
John Davis a354d12a4e Merge branch 'release_23.2' into dev 2024-01-31 18:19:54 -05:00
John Davis 8732e0d14c Update version to 24.0.dev0 2024-01-31 10:54:07 -05:00
David López 29290dea0c Merge pull request #17391 from nsoranzo/black_2024 
Update to black 2024 stable style
 2024-01-31 13:45:01 +01:00
davelopezandmvdbeek 7d27634879 Give webdav plugin a clean temp directory 
Co-authored-by: mvdbeek <m.vandenbeek@gmail.com>
 2024-01-31 11:25:46 +01:00
mvdbeek fbad571b13 Respect `upstream_gzip` config setting when streaming dataset collection archive 
Which means archives won't be compressed when this setting is activated.
This is about 20 times faster than the current default.
 2024-01-31 11:22:09 +01:00
Marius van den Beek fa670f8f13 Merge pull request #17381 from nsoranzo/17367_followup 
More specific type annotation for ``BaseJobExec.parse_status()``
 2024-01-31 10:54:49 +01:00
Aysam Guerler da12de9702 Merge pull request #17282 from guerler/grids_batchoperation 
Adds delete, purge and undelete batch operations to History Grid
 2024-01-30 15:56:53 -05:00
Ahmed Hamid AwanandJohn Davis 5ffa9e153b move database_connection assignment after super()... 
Co-authored-by: John Davis <jdavcs@gmail.com>
 2024-01-30 13:57:09 -06:00
Nicola Soranzo e975ca3754 Update to black 2024 stable style 2024-01-30 18:09:51 +00:00
Marius van den BeekandNicola Soranzo d08044c50b Define variables 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2024-01-30 17:32:49 +01:00
Aysam Guerler 34fab93f75 Merge pull request #17338 from ahmedhamidawan/upload_modal_loses_content 
[23.2] Fix upload modal loses its content when closed
 2024-01-30 10:50:21 -05:00
Aysam GuerlerandDavid López 4407ef981c Update lib/galaxy/webapps/galaxy/api/histories.py 
Co-authored-by: David López <46503462+davelopez@users.noreply.github.com>
 2024-01-30 10:45:21 -05:00
mvdbeek e9d7b18d41 Adapt to upstream FileResponse logic 
The ``send_header_only`` attribute has been removed in starlette
(https://github.com/encode/starlette/pull/2366), and replaced with
`scope["method"].upper() == "HEAD"`
 2024-01-30 16:39:22 +01:00