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2490 Commits
Author SHA1 Message Date
Marius van den Beek 4251715943 Merge pull request #19047 from jmchilton/toolshed_fixes 
Better search stuff in Tool Shed 2.0.
 2024-11-06 17:08:13 +01:00
Björn Grüning d11d8930a3 Merge pull request #19027 from jmchilton/parameter_model_enhancements 
A variety of improvements around tool parameter modeling (second try)
 2024-10-29 07:57:12 +01:00
John Chilton 251410b20e Better search stuff in Tool Shed 2.0. 2024-10-23 12:34:45 -04:00
John Chilton 93df8de0e8 Tool shed sort repositories by name instead of time. 2024-10-23 09:41:32 -04:00
John Chilton e053eee52a Update tool shed schema for parameter model changes. 2024-10-22 07:49:38 -04:00
Nicola Soranzo 9f780658e7 Fixes for mypy 1.12.0 2024-10-21 18:11:23 +01:00
Nicola Soranzo 4e56b47d5d Merge branch 'release_24.1' into dev 2024-10-16 11:26:07 +01:00
Nicola Soranzo ceef7caad2 Merge branch 'release_24.0' into release_24.1 2024-10-16 11:03:57 +01:00
Nicola Soranzo cfc31bcb40 Merge branch 'release_23.2' into release_24.0 2024-10-16 11:03:03 +01:00
Nicola Soranzo 63b92e717d Merge branch 'release_23.1' into release_23.2 2024-10-16 11:01:44 +01:00
mvdbeek 3f2b2ba294 Use dev-all and yarn in instructions 2024-10-14 17:16:24 +02:00
mvdbeek 6e6e04cd27 Make vite tool shed client proxy configurable 2024-10-14 16:01:11 +02:00
Nicola Soranzo 136747e766 Type annotations and fixes 
- Use `galaxy.util.path.StrPath` everywhere
 2024-09-30 21:33:44 +01:00
mvdbeek 9da413cf7b Merge branch 'release_24.1' into dev 2024-09-19 11:39:11 +02:00
mvdbeek 2b4b7ed37f Maybe fix flaky navigation in v2 ts tests 
The stack trace is this:
```
__ TestSimplePriorInstallation.test_0005_create_convert_repository[chromium] ___

self = <tool_shed.test.functional.test_1170_prior_installation_required.TestSimplePriorInstallation object at 0x7f87c33834c0>

    def test_0005_create_convert_repository(self):
        """Create and populate convert_chars_0150."""
        global running_standalone
        category = self.create_category(name=category_name, description=category_description)
>       self.login(email=common.test_user_1_email, username=common.test_user_1_name)

lib/tool_shed/test/functional/test_1170_prior_installation_required.py:50:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
lib/tool_shed/test/base/twilltestcase.py:776: in login
    previously_created, username_taken, invalid_username = self.create(
lib/tool_shed/test/base/twilltestcase.py:714: in create
    self.visit_url("/user/create", params)
lib/tool_shed/test/base/twilltestcase.py:850: in visit_url
    return self._browser.visit_url(url, allowed_codes=allowed_codes)
lib/tool_shed/test/base/playwrightbrowser.py:31: in visit_url
    response = self._page.goto(url)
.venv/lib/python3.8/site-packages/playwright/sync_api/_generated.py:8851: in goto
    self._sync(
.venv/lib/python3.8/site-packages/playwright/_impl/_page.py:524: in goto
    return await self._main_frame.goto(**locals_to_params(locals()))
.venv/lib/python3.8/site-packages/playwright/_impl/_frame.py:145: in goto
    await self._channel.send("goto", locals_to_params(locals()))
.venv/lib/python3.8/site-packages/playwright/_impl/_connection.py:59: in send
    return await self._connection.wrap_api_call(
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

self = <playwright._impl._connection.Connection object at 0x7f873c8bebe0>
cb = <function Channel.send.<locals>.<lambda> at 0x7f87af067550>
is_internal = False

    async def wrap_api_call(
        self, cb: Callable[[], Any], is_internal: bool = False
    ) -> Any:
        if self._api_zone.get():
            return await cb()
        task = asyncio.current_task(self._loop)
        st: List[inspect.FrameInfo] = getattr(task, "__pw_stack__", inspect.stack())
        parsed_st = _extract_stack_trace_information_from_stack(st, is_internal)
        self._api_zone.set(parsed_st)
        try:
            return await cb()
        except Exception as error:
>           raise rewrite_error(error, f"{parsed_st['apiName']}: {error}") from None
E           playwright._impl._errors.Error: Page.goto: Navigation to "http://127.0.0.1:8723/user/create?cntrller=user&use_panels=False" is interrupted by another navigation to "http://127.0.0.1:8723/logout_success"
E           Call log:
E           navigating to "http://127.0.0.1:8723/user/create?cntrller=user&use_panels=False", waiting until "load"
```
 2024-09-17 17:17:04 +02:00
John Chilton 67b4a69c1b Merge pull request #18722 from jmchilton/markdown_help_2 
Improvements to help terms & tool help.
 2024-09-03 12:41:05 -04:00
John Chilton 701c6f552d Improvements to help terms & tool help. 
- Allow tools to declare markdown help.
- Allow tools to reference help terms from their Markdown tools.
- Auto generate help terms for each datatype from values in datatypes_conf.xml
- Add permenant links for each help term - both the auto generated ones and the YAML specified
ones.
- Add some initial help terms for collection operations.
- Use new help term for "map over" from tool form.
 2024-08-23 11:03:13 -04:00
John Chilton 0a35eea309 Tool test case parameter models. 2024-08-23 09:46:44 -04:00
John Chilton aaff1ee20b Merge pull request #18678 from jmchilton/parameter_models_3 
Another round of parameter model enhancements and tool tests
 2024-08-23 09:46:18 -04:00
John Chilton 7f4bb4f390 Restore session free acccess broken with... 
https://github.com/galaxyproject/galaxy/commit/12b34ff47c3e4bb86e2ba5d8813a050c44b506baf
 2024-08-20 14:53:09 -04:00
Marius van den Beek 19fa41c93a Merge pull request #16894 from jmchilton/ts_bug 
Fix "Latest Updates" order in tool shed 2.0
 2024-08-16 15:10:43 +02:00
davelopez 30e39ea64c Handle errors consistently in Tool Shed client 2024-08-13 14:39:38 +02:00
davelopez 1e5639a7a5 Remove unused axios dependency 2024-08-13 13:48:47 +02:00
davelopez df6ced6305 Refactor current user API call to use ToolShedApi 
And remove unnecessary code
 2024-08-13 13:48:47 +02:00
davelopez 25053096c6 Refactor error handling in Tool Shed client 
To use errorMessageAsString consistently
 2024-08-13 13:47:57 +02:00
davelopez bd53019b0e Refactor schema imports and API calls to use ToolShedApi 
This will avoid import side effects and will enable easy API mocking in unit tests in the future.
 2024-08-13 13:23:57 +02:00
davelopez e49dee7b60 Include specific error messages in Tool Shed ManageApiKey.vue 2024-08-13 13:23:56 +02:00
davelopez 00faba3509 Refactor Tool Shed ManageApiKey.vue to use async/await syntax 2024-08-13 13:23:55 +02:00
davelopez f7ad8e4d55 Update error handling in CitableRepositoryPage.vue 2024-08-13 13:23:55 +02:00
davelopez 672cabdcc8 Update openapi-fetch and openapi-typescript dependencies 2024-08-13 13:23:44 +02:00
davelopez 9aefbd1701 Add middleware for error handling in Toolshed API client 2024-08-13 13:22:52 +02:00
davelopez 8867f90d67 Replace openapi-typescript-fetch with openapi-fetch in Toolshed 2024-08-13 13:22:52 +02:00
davelopez d73af2258b Rebuild client API schema 2024-08-13 13:22:46 +02:00
Marius van den Beek ac0bf8daae Merge pull request #18655 from jmchilton/restore_repository_update 
Restore repository update in the tool shed 2.0.
 2024-08-13 11:17:15 +02:00
John Chilton 7011a3a94c Rebuild ts schema for recent changes. 2024-08-11 17:19:22 -04:00
John Chilton 39cb7f2ed5 Rebuild schema for parameter model changes... 2024-08-09 12:47:55 -04:00
John Chilton 1a7e5d1df9 Restore repository update in the tool shed 2.0. 
I guess somehow this critical API endpoint had no tests.
 2024-08-08 12:30:53 -04:00
mvdbeek 5f635a3917 Merge branch 'release_24.1' into dev 2024-08-07 12:59:25 +02:00
mvdbeek dfea749b6c Merge branch 'release_24.0' into release_24.1 2024-08-07 12:58:32 +02:00
John Chilton e0b6532a82 Merge pull request #18641 from jmchilton/model_parameter_improvements_1 
Parameter Model Improvements
 2024-08-06 11:07:25 -04:00
John Chilton a8a8199771 Rebuild schema... 2024-08-05 18:37:24 -04:00
John Chilton fd2425fb37 Do not initialize a full repository registry in ToolShed 2.0. 
It seems like it is only used by repository_grids - which I think are unused by the new tool shed. I don't recall writing any client side grid framework code and my PR description did claim it was mako free.
 2024-08-05 13:53:14 -04:00
John Chilton efe76b53e0 Skip buggy hgweb_config_manager to find tool sources. 2024-08-05 12:24:45 -04:00
John Chilton 3f21193bc4 Improve tool shed API error messages for repo path bug. 2024-08-05 12:24:45 -04:00
mvdbeek d20b3331f0 Use get_app_with_request_session as dependency resolver 2024-08-02 12:31:13 +02:00
Nicola Soranzo 359bcfeec8 Fixes for errors reported by mypy 1.11.0 2024-08-01 18:13:27 +01:00
John Chilton 4103cbb2ac Fix bugs in tool shed tool API. 2024-07-17 11:11:52 -04:00
John Chilton fc57099fc6 Rebuild tool shed 2.0 API schema... 2024-07-15 09:47:42 -04:00
John Chilton ae6464e610 Rework ParsedTool for reuse outside of the tool shed. 2024-07-15 09:46:13 -04:00
John Chilton bcb25383c8 Improved tool API. 2024-07-15 09:46:13 -04:00