opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity
71,200 Commits 69 Branches 243 Tags
02b99b7478992c392bc9190c94de1dec49aef7bc
Commit Graph
35812 Commits
Author SHA1 Message Date
Nuwan Goonasekera f9cecae62e Merge pull request #16497 from uwwint/refactor/oidc-custos 
Refactor/OIDC custos
 2023-10-21 19:33:17 +05:30
galaxybot 7f57ed0b98 Update Python dependencies 2023-10-21 03:13:39 +00:00
Uwe Winter 0ae47b7dba Refactoring of the whole OIDC code: move IDP specifics to subclass, create factory, build cache 2023-10-21 01:30:59 +05:30
Dannon 6954aa1252 Merge pull request #16758 from assuntad23/16556/time-wf-invoked 
WF Report Enhancement: Converting ISO to UTC for Invocation Date/Time
 2023-10-20 11:06:22 -04:00
Marius van den Beek cdcadb1357 Merge pull request #16737 from hexylena/minerva-fixes 
MINERVA display application: enable cors, add for tabular
 2023-10-20 16:12:23 +02:00
Marius van den Beek eecaeb7fad Merge pull request #15313 from pcm32/patch-14 
Update cellxgene interactive tool to 1.1.1
 2023-10-20 15:48:14 +02:00
John Chilton 96aa7b400a Merge pull request #16872 from ahmedhamidawan/restore_old_tools_api_route 
Restore ToolsApi and create new api route for new panel structure
 2023-10-20 09:36:18 -04:00
Marius van den Beek 8bac65faaa Merge pull request #16825 from nsoranzo/toolshed_wf_fixes 
Tool Shed 2.0 fixes
 2023-10-20 15:33:30 +02:00
Lucille Delisle 5de6d40f73 Update relabel_from_file.xml 2023-10-20 13:48:34 +02:00
Nicola Soranzo 048d79242f Configure temporary whoosh_index_dir for tests 
Otherwise a `<GALAXY_ROOT>/database/toolshed_whoosh_indexes` would
be reused, leading to failing tests when running tests locally.
 2023-10-20 12:04:59 +01:00
Nicola Soranzo bdcc33195a Remove unused test config option 2023-10-20 12:04:58 +01:00
Nicola Soranzo e340895134 Type annotation fixes 2023-10-20 12:04:58 +01:00
Nicola Soranzo bab9753aeb Fix another typo 
Introduced in commit 68831ddcfc .
 2023-10-20 12:04:58 +01:00
Nicola Soranzo b5013aa57a Fix another typo 
Introduced in commit 70c7f03be9 .
 2023-10-20 12:04:57 +01:00
Nicola Soranzo e5bec6ad71 Fix typo in query 
Introduced in commit 3238b21280 .
 2023-10-20 12:04:57 +01:00
Nicola Soranzo 806dfae4b3 Fix index_repositories() method 
Broken in commit 77df9c9a73 .
 2023-10-20 12:04:56 +01:00
Nicola Soranzo 4e7763d846 Add type annotations. Drop unused functions and re-exports. 2023-10-20 11:14:31 +01:00
Nicola Soranzo b85f2f10fa Fix get_users_with_repo_alert() call 
Introduced in commit 1711e96dac .
 2023-10-20 11:14:31 +01:00
Nicola Soranzo 14e3ae32ed Restore GET /api/categories/<encoded_id> in ToolShed 2.0 
and the deleted field in the response.

Rationale: it is not particularly useful, but both:
GET /api/categories
GET /api/categories/<encoded_id>/repositories
work on TS 2.0, so it's weird that this one is missing.

Also, it was breaking BioBlend's
https://bioblend.readthedocs.io/en/latest/api_docs/toolshed/all.html#bioblend.toolshed.categories.ToolShedCategoryClient.show_category
 2023-10-20 11:14:30 +01:00
Nicola Soranzo 219bd20320 Fix imports 
Broken in commit 3238b21280 .
 2023-10-20 11:14:29 +01:00
Nicola Soranzo ed0c72e3c4 Make owner and name parameters of `get_or_create_repository()` not optional 2023-10-20 11:14:29 +01:00
Nicola Soranzo b1d86d4bad Check that TOOL_SHED_TEST_BROWSER is a valid value 2023-10-20 11:14:28 +01:00
Nicola Soranzo 9a5a552ca7 Fix issues reported by `yarn build` 
Introduced in https://github.com/galaxyproject/galaxy/pull/16787 .
 2023-10-20 11:14:27 +01:00
Martin Cech 5134f2f69d Merge pull request #16887 from jdavcs/dev_ts_fix_sort_order 
Fix bug in SA statement: desc() applied to column, not statement
 2023-10-19 19:19:40 +02:00
Nicola Soranzo 245b4dc18d Merge pull request #16884 from nsoranzo/ruff_flake8_fixes 
Ruff and flake8 fixes
 2023-10-19 15:42:48 +01:00
John Davis 9c8d18fc2c Fix bug in SA statement: desc() applied to column, not statement 2023-10-19 10:39:25 -04:00
Nicola Soranzo b2cbe517ec Fix new UP032 errors from ruff 0.1.0 2023-10-19 12:59:31 +01:00
Nicola Soranzo 5aa7328896 Fix new linting errors from flake8 6.1.0 2023-10-19 12:53:59 +01:00
John Davis f791516421 Drop unused HistoryContentManager code and related tests 2023-10-18 13:01:10 -04:00
John Davis aba81f8eb0 Fix bug 2023-10-18 12:29:37 -04:00
Aysam Guerler d8d27e8e86 Merge pull request #16834 from guerler/remaining_form_inputs 
Remove remaining legacy backbone form input elements
 2023-10-18 10:54:39 +03:00
Ahmed Awan a739f88aa6 Restore deprecated ToolsApi and create new api route for new panel structure 
- restore `api/tools` that had the older (list of tool sections
  with `.elems`) structure
- but use the new `api/tool_panel` structure in the client
 2023-10-17 13:58:43 -05:00
Assunta DeSanto a7c111b88f fixing tests to use iso-like string format 2023-10-17 14:15:13 -04:00
John Chilton 9798e9d949 Merge pull request #16833 from jdavcs/dev_ts20_sa20_3 
Another batch of SA2.0 edits in TS2.0 (part 3)
 2023-10-17 13:52:12 -04:00
Assunta DeSanto 8384c315a7 Update lib/galaxy/managers/markdown_util.py 
changing format of string time to more closely match iso format
 2023-10-17 12:28:31 -04:00
mvdbeek 5b928e4d73 Drop library_data from schema 2023-10-17 18:14:24 +02:00
guerler bf02dc9948 Drop library_data input type 2023-10-17 10:29:26 +03:00
John Davis c3208363a5 Refactor get user by email 2023-10-16 11:31:14 -04:00
John Davis 189a9b373c Fix SA2.0 usage in managers.users 2023-10-16 11:31:14 -04:00
John Davis 02a2ee9b39 Fix SA2.0 usage in managers.roles 2023-10-16 11:31:14 -04:00
John Davis bbb02532d8 Fix SA2.0 usage in managers.model_stores 2023-10-16 11:31:14 -04:00
John Davis 48fe6a7d97 Fix SA2.0 usage in managers.quotas 2023-10-16 11:31:14 -04:00
John Davis 80b5adabb3 Refactor + fix SA2.0 in model.UserAuthnzToken 2023-10-16 11:31:14 -04:00
John Davis 57f26a13fd Fix SA2.0 usage in model.UserAuthnzToken 2023-10-16 11:31:14 -04:00
John Davis 94625dddbc Fix bug (needs commit) + SA2.0 usage in model.PSAPartial 2023-10-16 11:31:14 -04:00
John Davis abd672450c Fix SA2.0 usage in PSANonce 2023-10-16 11:31:14 -04:00
John Davis cb5bd5d2a3 Fix SA2.0 usage in model.PSACode 2023-10-16 11:31:14 -04:00
John Davis d577b17385 Fix SA2.0 usage in model.PSAAssociation 2023-10-16 11:31:14 -04:00
John Davis 9508463252 Fix SA2.0 usage in model.WorkflowInvocation.poll_unhandled... 2023-10-16 11:31:14 -04:00
John Davis 0545b3ed14 Fix SA2.0 usage in model.StoredWorkflow.show_in_tool_panel 2023-10-16 11:31:14 -04:00