John Chilton
96aa7b400a
Merge pull request #16872 from ahmedhamidawan/restore_old_tools_api_route
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Restore ToolsApi and create new api route for new panel structure
2023-10-20 09:36:18 -04:00
Nicola Soranzo
048d79242f
Configure temporary whoosh_index_dir for tests
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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
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Introduced in commit 68831ddcfc
2023-10-20 12:04:58 +01:00
Nicola Soranzo
b5013aa57a
Fix another typo
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Introduced in commit 70c7f03be9
2023-10-20 12:04:57 +01:00
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
806dfae4b3
Fix index_repositories() method
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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
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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
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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
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`
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Introduced in https://github.com/galaxyproject/galaxy/pull/16787 .
2023-10-20 11:14:27 +01:00
John Davis
9c8d18fc2c
Fix bug in SA statement: desc() applied to column, not statement
2023-10-19 10:39:25 -04:00
Ahmed Awan
a739f88aa6
Restore deprecated ToolsApi and create new api route for new panel structure
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- 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
John Chilton
9798e9d949
Merge pull request #16833 from jdavcs/dev_ts20_sa20_3
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Another batch of SA2.0 edits in TS2.0 (part 3)
2023-10-17 13:52:12 -04:00
Ahmed Awan
8809476a17
fix all tests to work with the new GET 'api/tools' structure
2023-10-13 19:29:18 -05:00
Heinz-Alexander Fuetterer and Nicola Soranzo
347e7b8301
chore: fix typos
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Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2023-10-13 16:29:27 +02:00
John Davis
3c52785dab
Ignore typing error (see note)
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RepositoryMetadata is mapped imperatively, so until the mapper creates
attributes based on Column definitions, the attribute does not exist on
the class. This class is mapped imperatively due to the complications
triggered by mapping the "metadata" attribute.
2023-10-12 15:30:23 -04:00
John Davis
b0684fa9ff
Import models
2023-10-12 15:14:59 -04:00
John Davis
68831ddcfc
Fix SA2.0 usage in tool_shed.metadata, refactor
2023-10-12 14:56:58 -04:00
John Davis
bf919c049c
Fix SA2.0 usage in tool_shed.util.repository_util
2023-10-12 13:12:23 -04:00
John Davis
43500cf656
Fix SA2.0 usage in tool_shed.util.commit_util
2023-10-12 10:57:59 -04:00
John Davis
b064064387
Fix SA2.0 usage in tool_shed.util.search_util
2023-10-12 10:57:59 -04:00
John Davis
d4a0cce034
Fix SA2.0 usage in tool_shed.util.shed_index
2023-10-12 10:57:59 -04:00
John Davis
1711e96dac
Fix SA2.0 usage in tool_shed.util.shed_util_common
2023-10-12 10:57:59 -04:00
John Davis
a5a7d0675d
Fix SA2.0 usage in tool_shed.util.metadata_util
2023-10-12 10:57:59 -04:00
John Davis
4db5e31563
Fix SA2.0 usage in tool_shed.managers.groups
2023-10-12 10:57:59 -04:00
John Davis
77df9c9a73
Fix SA2.0 usage in tool_shed.managers.repositories
2023-10-12 10:57:59 -04:00
John Davis
ff8f6292bd
Fix SA2.0 usage in tool_shed.managers.users
2023-10-12 10:57:59 -04:00
John Davis
08b5a433e6
Fix SA2.0 usage in tool_shed.managers.categories
2023-10-12 10:57:59 -04:00
John Davis
5a70f2f690
Fix SA2.0 usage in tool_shed.test.base.test_db_util; refactor
2023-10-12 10:57:59 -04:00
John Davis
a5110bcf1d
Drop unused functions from tool_shed.test.base.test_db_util
2023-10-12 10:57:59 -04:00
John Davis
70c7f03be9
Fix SA2.0 usage in tool_shed.test.base.twilltestcase
2023-10-12 10:57:59 -04:00
John Davis
6a6e5bf3e6
Fix SA2.0 formatting in tool_shed.repository_registry + refactor
2023-10-12 10:57:59 -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 Davis
a127685205
Improve function names for current users, groups, roles
2023-10-04 23:43:38 -04:00
John Davis
fa07e87eae
Optimize checking existing group by name
2023-10-04 23:43:38 -04:00
John Davis
316afb0b1d
Optimize checking for existing role by name
2023-10-04 23:43:38 -04:00
John Davis
ce9cdc9c29
Optimize email autocomplete string
2023-10-04 23:43:38 -04:00
John Chilton