Nicola Soranzo
e5bec6ad71
Fix typo in query
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Introduced in commit 3238b21280
2023-10-20 12:04:57 +01:00
Nicola Soranzo
14e3ae32ed
Restore GET /api/categories/<encoded_id> in ToolShed 2.0
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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
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Broken in commit 3238b21280
2023-10-20 11:14:29 +01:00
Nicola Soranzo
9a5a552ca7
Fix issues reported by `yarn build`
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Introduced in https://github.com/galaxyproject/galaxy/pull/16787 .
2023-10-20 11:14:27 +01:00
John Davis
68831ddcfc
Fix SA2.0 usage in tool_shed.metadata, refactor
2023-10-12 14:56:58 -04:00
John Davis
f553b757c0
Fix SA2.0 usage in tool_shed.webapp.controllers.repository
2023-10-12 10:57:59 -04:00
John Davis
3238b21280
Fix SA2.0 usage in tool_shed.webapp.controllers.repository
2023-10-12 10:57:59 -04:00
John Davis
c4e1c9bc89
Fix SA2.0 usage in tool_shed.webapp.controllers.user
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Also, add case_sensitive parameter to shared function in galaxy user manager
2023-10-12 10:57:59 -04:00
John Davis
49cafd053e
Fix SA2.0 usage in tool_shed.webapp.api.groups
2023-10-12 10:57:59 -04:00
John Davis
852cb9f00b
Fix SA2.0 usage, refactor tool_shed.webapp.api.repository_revisions
2023-10-12 10:57:59 -04:00
John Davis
248b8bb90e
SA2.0: Replacde flush with commit
2023-10-06 10:17:58 -04:00
John Davis
7e7cbf1463
Refactor, fix bug, SA2.0 in tool_shed.webapp.app2.users
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Bug: check if prev session is not None before accessing its user attr.
2023-10-06 10:07:48 -04:00
John Davis
8acdc891fa
Fix SA2.0 usage in tool_shed.webapp.util.shed_statistics
2023-10-06 10:07:23 -04:00
John Davis
9d17792e97
Fix SA2.0 usage in tool_shed.webapp.security
2023-10-06 10:06:43 -04:00
John Chilton
76c560fc95
Initial bug fixes for tool shed 2.
2023-10-04 14:02:01 -04:00
John Chilton
bb4558102f
Remove incorrect auto-generated readme for frontend.
2023-09-27 14:30:42 -04:00
John Chilton
7dc0b1378b
WIP: modern tool shed frontend
2023-09-27 14:30:42 -04:00
John Chilton
c98fa8c981
Category reworking..
2023-09-26 13:46:59 -04:00
John Chilton
dd58bfcfe6
Implement the GA4GH TRS API in the new tool shed.
2023-09-26 13:46:59 -04:00
John Chilton
b04c3264ab
Refactor tool shed tests for injection of browser.
2023-09-26 13:46:59 -04:00
John Chilton
d1d629074b
ToolShed API 2.0
2023-09-26 13:46:58 -04:00
John Chilton
85100edff0
Tool Shed API Modernization ahead of FastAPI
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- Use the controller base that allow DI.
- Move a bunch functionality we want to port to FastAPI into manage layer.
- Some typing enhancements.
2023-09-26 13:46:57 -04:00
John Chilton
9e7fafb8a5
Remove contact owner functionality from the tool shed - use github please.
2023-09-26 13:46:57 -04:00
John Chilton
55564b67d7
Remove upload_point upload logic in tool shed.
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Not used by planemo and not tested by any tests.
2023-09-26 13:46:56 -04:00
John Chilton
e7353b78b9
Remove upload controller - everything should come through the API now.
2023-09-26 13:46:56 -04:00
John Chilton
8852f0733b
Progress toward exercising less of the tool shed upload API.
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So we can kill it.
2023-09-26 13:46:56 -04:00
John Chilton
2fa165781b
Use repository manager to capture more of the upload process.
2023-09-26 13:46:55 -04:00
John Chilton
904a6006c5
Additional debugging when handling API errors during repository upload.
2023-09-26 13:46:54 -04:00
John Davis
7a06b006c6
Refactor get_user_by_username, get_user_by_email; use across code base
2023-09-25 09:23:08 -04:00
Nicola Soranzo
d258e5791e
Fix new E721 errors from ruff 0.0.290
2023-09-20 01:43:40 +01:00
mvdbeek
913182fac9
Merge branch 'release_23.1' into dev
2023-08-31 13:04:47 +02:00
mvdbeek
73b1a48057
Drop RecursiveMiddleware
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It isn't used AFAICT and makes 3 copies of the request environ each,
without ever being used.
Shows up in a memray trace, though this also shouldn't cause a memory
leak ...
2023-08-27 12:04:54 +02:00
John Davis
bc60013c30
Only pass the objects that are used by the function
2023-08-08 13:29:10 -04:00
John Davis
e43761b355
Move dbkeys to managers
2023-08-08 00:53:03 -04:00
John Davis
7a0e66e96c
Move get_user_by_username function to managers.users
2023-08-08 00:52:59 -04:00
Tillman
20bd0bceb3
Move get_or_create_remote_user method to UserManager
2023-07-31 11:00:11 +02:00
claudiofr
17f22c28f3
Add new config parameters for citation database beaker cache in tool_shed yaml file
2023-06-21 22:45:12 +02:00
John Davis
51938220a9
Wrap session.flush in TS webapp.controllers.admin
2023-06-09 13:05:26 -04:00
John Davis
e93752436e
Wrap session.flush in TS webapp.controllers.hg
2023-06-09 13:05:26 -04:00
John Davis
cc2e274bf0
Wrap session.flush in TS webapp.controllers.user
2023-06-09 13:05:26 -04:00
John Davis
c512c2f8b4
Wrap session.flush in TS webapp.controllers.repository
2023-06-09 13:05:26 -04:00
John Davis
13b84744ac
Wrap session.flush in TS webapp.api
2023-06-09 13:05:26 -04:00
John Davis
680348eafa
Wrap session.flush in TS webapp.util.ratings_util
2023-06-09 13:05:26 -04:00
John Davis
5baa4765fc
Wrap session.flush in TS webapp.security
2023-06-09 13:05:26 -04:00
mvdbeek
fd0ff0bf58
Wrap TS and reports apps with RequestIDMiddleware
2023-06-09 15:04:38 +02:00
John Davis
9eb1b1b98d
Replace "unknown" str with a constant across code base
2023-06-08 17:14:24 -04:00
John Chilton
83c85d79da
Fix reset_metadata_on_repositories to not break everything.
2023-05-12 13:21:15 -04:00
Nicola Soranzo
c210257e0d
Fix new UP031 errors raised by ruff 0.0.262
2023-05-03 17:57:06 +01:00
guerler
c1ae0c420f
Remove unused styles, adjust reports app
2023-04-20 17:30:18 +03:00
guerler
ca9aafdd35
Add padding to toolshed side panel, continue decoupling from global styles
2023-04-20 15:26:46 +03:00
Nicola Soranzo