John Davis
68831ddcfc
Fix SA2.0 usage in tool_shed.metadata, refactor
2023-10-12 14:56:58 -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 Chilton
c98fa8c981
Category reworking..
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
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
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
Nicola Soranzo
d258e5791e
Fix new E721 errors from ruff 0.0.290
2023-09-20 01:43:40 +01:00
John Davis
13b84744ac
Wrap session.flush in TS webapp.api
2023-06-09 13:05:26 -04:00
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
Nicola Soranzo
c655360e4e
Merge branch 'release_23.0' into dev
2023-04-05 12:39:43 +01:00
Nicola Soranzo
bee3d2e7ac
Merge branch 'release_22.05' into release_23.0
2023-04-03 16:31:48 +01:00
davelopez
682da9f24e
Remove IDs from error messages
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Simplifies encoding/decoding of IDs and prevents exposure issues
2023-03-31 12:35:00 +02:00
John Chilton
e9832bfbfb
Some typing for api/categories.py
2023-02-03 13:47:39 -05:00
John Chilton
e0887dce68
Improved type signature for repository_util.
2023-02-03 13:47:38 -05:00
John Davis
38afccd780
Fix linting
2023-01-21 11:13:36 -05:00
John Davis
fe7bf27658
Join/load: replace strings with attrs (toolshed-related)
2023-01-21 10:59:59 -05:00
Michael R. Crusoe
75ba9cfd13
Even more typing
2022-11-28 04:50:00 +00:00
Nicola Soranzo
8b461d2639
Merge branch 'release_22.05' into dev
2022-11-04 09:37:23 +00:00
mvdbeek
a02d407f4c
Fix server errors when querying for invalid repos or repos without valid tools
2022-11-03 10:18:52 +01:00
mahendrapaipuri
9b8024bff2
Add new HTTP request arg to get_api_key method
2022-10-12 09:32:00 +02:00
John Chilton
808eca05bd
Use API repository object instead of database object in dozens of spots in tool shed functional tests.
2022-09-24 08:42:23 -04:00
John Chilton
02d34ea341
Merge pull request #14656 from jmchilton/shed_app_2
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ToolShedApp for more correct typing in tool shed code.
2022-09-19 18:17:15 -04:00
John Chilton
23b27f0dfa
ToolShedApp for more correct typing in tool shed code.
2022-09-19 10:50:07 -04:00
John Chilton
44d6a34178
Remove repository review functionality from tool shed.
2022-09-16 20:25:37 -04:00
John Chilton
f8c1c11016
API tests for tool shed search APIs.
2022-09-14 09:31:27 -04:00
Björn Grüning
78960c6fc6
Merge pull request #14553 from jmchilton/more_ts_api_tests
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More API tests for the tool shed.
2022-09-10 20:01:15 +02:00
David López
e6fba1ec89
Merge pull request #14562 from jmchilton/ts_cleanup_2
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Remove broken tool shed API endpoint.
2022-09-07 15:26:20 +02:00
John Chilton
735993ca33
Remove broken tool shed API endpoint.
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It has been broken since https://github.com/galaxyproject/galaxy/commit/5ecec9514a7c4f46fa2af1008ef39d9c1567daf9 .
2022-09-01 15:26:10 -04:00
John Chilton
2020b756a6
Remove no longer useful API endpoint in the toolshed.
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Was added in https://github.com/galaxyproject/galaxy/commit/c90c0e503b362f838ca4b39cb8c52228befca436 to control the order reset happens in when doing that in batch, but that underlying API does that now the corresponding script has been simplified.
2022-08-31 13:55:23 -04:00
John Chilton
fc8938fb67
More API tests for the tool shed.
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Continue working toward a set of pydantic models to rapidly move toward FastAPI/OpenAPI also.
2022-08-31 13:32:00 -04:00
John Chilton
12b34ff47c
API tests for the tool shed.
2022-08-29 09:51:20 -04:00
John Chilton
02d240efed
Remove unused code...
2022-08-29 09:51:19 -04:00
John Chilton
f4078b1f96
Fix authenticate controller in tool shed for #13967 .
2022-08-29 09:51:19 -04:00
Nicola Soranzo
14b1730eb2
Combine "as" imports with other "from" imports
2022-06-20 20:06:30 +01:00
John Chilton
5c807f6b6b
Remove tool shed tool_dependencies.xml handling on the client side.
2022-05-27 10:57:44 -04:00
Nicola Soranzo
0c80836c34
Upgrade syntax to Python 3.7
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using `ack --type=python -f | grep -v '^tools/' | xargs pyupgrade --py37-plus`
Also more refactoring of Python files in `packages/` .
2022-03-14 14:57:43 +00:00
Dannon Baker
623a5e165a
Apply black formatting.
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Apply isort.
2022-02-03 07:42:20 -05:00
Simon Bray
ee62798b0c
fix error getting toolshed repo metadata when no repo found
2022-01-19 17:54:31 +01:00
Dannon Baker
22e7601653
First pass fstring conversion
2021-05-11 13:47:00 -04:00
davelopez
4c9ffef89c
Remove redundant decode_id exception checks
2021-04-16 13:57:56 +02:00
Nicola Soranzo
d26b3d9848
Fix all E203, E741 and W504 flake8 errors
2021-01-18 10:35:41 +00:00
John Chilton
f405c61596
Various sphinx fixes.
2021-01-12 09:29:54 -05:00
John Chilton
6fd6100285
Various sphinx warning fixes.
2021-01-11 12:58:45 -05:00
Nicola Soranzo
9d74bba7fb
Drop support for retired Python 3.5
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Upgrade syntax using `pyupgrade --py36-plus` .
Manually drop several `six` imports.
Also:
- Remove broken pr_cache in scripts/bootstrap_history.py
- Fix broken prefix removal in lib/galaxy/tool_util/deps/mulled/mulled_build.py
2020-10-07 11:52:13 +01:00
John Davis