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Commit Graph
2304 Commits
Author SHA1 Message Date
John Chilton d5eff4581f Merge pull request #14909 from jmchilton/remove_delete 
Remove ability to delete individual files from tool shed.
 2022-11-03 08:45:23 -04:00
mvdbeek a02d407f4c Fix server errors when querying for invalid repos or repos without valid tools 2022-11-03 10:18:52 +01:00
John Chilton c9caa4ef84 Remove ability to delete individual files from tool shed. 
Working toward a simplified, Planemo-used API that is just uploading archives.
 2022-11-02 16:54:03 -04:00
mvdbeek 94f23ad2c5 Use local import of sqlalchemy sessions 
If we import too early we just get the inital None. Slightly more robust
but still bad.
 2022-11-01 18:45:08 +00:00
mvdbeek ba593057c2 Use `galaxy_driver_class` to create tool shed driver 
Use ``autouse`` fixture to configure test driver
 2022-11-01 18:45:07 +00:00
John Chilton e38a5c0fae Remove more unused tool shed mako code. 2022-10-19 15:39:32 -04:00
John Chilton 9ce082a103 Remove unused makos related tool shed. 2022-10-19 15:39:32 -04:00
John Chilton 3f27895c42 Remove unused render_readme_section in common.mako templates. 2022-10-19 15:39:32 -04:00
John Chilton d61459b783 Remove unused tool shed makos. 2022-10-19 15:39:32 -04:00
John Chilton 9e51a10834 Remove reinstall_repository endpoint and just reinstall with the API. 2022-10-19 15:39:32 -04:00
Björn Grüning a1f5f4f064 Merge pull request #14810 from jmchilton/cleanup_ts_controllers_3 
More tool shed dependency and dead code cleanup.
 2022-10-19 20:11:08 +02:00
Marius van den Beek eb74a1d32e Merge pull request #14793 from jmchilton/cleanup_ts_controllers 
Cleanup More Tool Shed Admin Controllers and Makos
 2022-10-19 17:08:29 +02:00
Dannon 6caea3295e Merge pull request #14687 from guerler/remove_makos 
Remove legacy base panel makos
 2022-10-19 00:05:08 -04:00
Dannon c7216e4b85 Merge pull request #14776 from mahendrapaipuri/add_request_obj_authmanager 
Make HTTP request object available to `AuthManager`
 2022-10-18 09:23:10 -04:00
Björn Grüning 18cae9a221 Merge pull request #14735 from jmchilton/simplified_ts_tests 
Simplify tool shed tests.
 2022-10-17 23:04:53 +02:00
John Chilton ead32bcfc5 Move dependency_display to avoid Galaxy -> Tool Shed import. 2022-10-17 16:11:35 -04:00
John Chilton be49c8edd1 Rework GalaxyUtilityContainerManager to avoid a Galaxy-> Tool Shed import. 2022-10-17 16:11:35 -04:00
John Chilton 4f603d68f7 Refactor utility container stuff to avoid galaxy -> tool shed imports. 2022-10-17 16:11:35 -04:00
John Chilton f734fb8159 Remove tool dependency related folders in container dict. 2022-10-17 16:11:35 -04:00
John Chilton dea1d0e12f Remove more unused parameters to GalaxyUtilityContainerManager 2022-10-17 16:09:55 -04:00
John Chilton 25e830fa81 Remove more unused containers. 2022-10-17 16:09:55 -04:00
John Chilton 8e6fc9dcc7 Remove unused container readme files. 2022-10-17 16:09:55 -04:00
John Chilton e6519265ad Remove unused container invalid_tools. 2022-10-17 16:09:55 -04:00
John Chilton 6dfb59f9ce Simplify dependency_display now that it is used for a lot less. 2022-10-17 16:09:55 -04:00
John Chilton 401328a6dd Remove no-op Lock in utility containers. 2022-10-17 16:09:55 -04:00
John Chilton 1326745b65 Remove unused methods in dependency_display.py. 2022-10-17 16:09:55 -04:00
John Chilton fcc58d5411 Improved dependency imports for toolshed. 2022-10-17 16:09:55 -04:00
John Chilton 2dd9065926 Mark dependency_display internal-only methods as such. 2022-10-17 16:09:55 -04:00
John Chilton 6915c5c556 Cleanup up imports in dependency_display.py. 2022-10-17 16:09:55 -04:00
John Chilton 03f3f0ee0a Improved dependency imports in readme_util. 2022-10-17 16:09:55 -04:00
John Chilton 0d61a37a71 Remove now unused function from dependency_display. 2022-10-17 14:48:15 -04:00
John Chilton 8262c7d75a Simplify admin_toolshed by dropping untested logic for reactivating uninstalled repos. 2022-10-17 14:47:53 -04:00
guerler 168d4e0098 Remove masthead mako, remove custom galaxy base panels mako 2022-10-16 00:15:38 -04:00
guerler 56563fd781 Decouple login/logout toolshed from Galaxy makos 2022-10-16 00:15:38 -04:00
Nicola Soranzo 0391cd4b62 Rename FooBarTestCase test classes as TestFooBar in API, framework, performance, Selenium and ToolShed tests 
These are collected by pytest only because they are `unittest.TestCase` derived,
but normally pytest collects only test classes whose name starts with `Test`, see
https://docs.pytest.org/en/7.1.x/reference/reference.html#confval-python_classes

Also:
- Some type annotations
 2022-10-15 17:54:31 +01:00
John Chilton 729c5ca6c8 Remove now unused admin toolshed grids. 2022-10-15 11:13:23 -04:00
John Chilton bb8028a91a Remove many hits to legacy Galaxy UI during tool shed tests. 2022-10-15 11:03:21 -04:00
John Chilton 7221d0c876 Port more of the Galaxy side of tool shed tests to mako-less variants. 2022-10-14 16:41:55 -04:00
John Chilton fa184380af Simplify checking valid/invalid tools in tool shed tests. 
Operation no longer requires the target makos.
 2022-10-14 16:41:55 -04:00
Alireza Heidari aa842df560 Merge branch 'dev' into api-key-Enhancement 2022-10-13 14:38:08 +02:00
mahendrapaipuri 5e2be48822 Add missing new arg to check_registration_allowed method 2022-10-12 10:10:38 +02:00
mahendrapaipuri 9b8024bff2 Add new HTTP request arg to get_api_key method 2022-10-12 09:32:00 +02:00
John Davis b1c912f179 Merge pull request #14744 from jmchilton/cleanup_ts_dependency_structure 
Small cleanups to shed package dependency structures
(integration test failure unrelated)
 2022-10-07 11:26:42 -04:00
John Chilton 79a3ac12e1 Cleanup installed_repository_manager.py and related code a bit more. 
- Remove unused code and mako.
- Use more direct imports for better typing and static checking.
- Reuse existing abstractions a bit better.
 2022-10-03 09:04:00 -04:00
John Chilton 3f5f7b18e7 Cleanup more utility imports to reduce dependency requirements. 2022-10-01 11:32:42 -04:00
John Chilton 94c8218d48 setup service and fastapi layer for tool shed APIs... 2022-10-01 09:14:03 -04:00
John Chilton fe83d9e083 Move repository_util function into legacy code in only place used. 
Eliminates a galaxy -> tool shed import and centralizes legacy code.
 2022-09-30 14:04:26 -04:00
davelopez fd299bdf20 Cleanup unused code and mixin 2022-09-30 16:46:24 +02:00
davelopez 3f86751f89 Add deleted column to api_keys table in ToolShed 
Since the toolshed uses a duplicated `api_keys` table we sadly need to duplicate the migration too...
 2022-09-30 16:39:12 +02:00
John Chilton 9934a83cf6 Cleanup more cruft... 2022-09-28 13:03:58 -04:00