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Author SHA1 Message Date
Marius van den Beek 4fa0403fed Merge pull request #17227 from mvdbeek/fix_display_applications 
[23.2] Fix Display Application link generation
 2023-12-23 15:13:08 +01:00
Marius van den Beek cca0affafe Merge pull request #17226 from mvdbeek/fix_job_param_display 
[23.2] Fix job parameter display
 2023-12-23 10:24:36 +01:00
mvdbeek 94ce87cf13 Fix Display Application link generation 
for metadata files and use same interface also for datasets,
which should effectively give us test coverage?

Fixes:
```
Stack Trace(most recent call first)

AttributeError: 'Bunch' object has no attribute 'get_file_name'
  File "starlette/applications.py", line 122, in __call__
    await self.middleware_stack(scope, receive, send)
  File "starlette/middleware/errors.py", line 184, in __call__
    raise exc
  File "starlette/middleware/errors.py", line 162, in __call__
    await self.app(scope, receive, _send)
  File "starlette_context/middleware/raw_middleware.py", line 93, in __call__
    await self.app(scope, receive, send_wrapper)
  File "starlette/middleware/base.py", line 109, in __call__
    await response(scope, receive, send)
  File "starlette/responses.py", line 270, in __call__
    async with anyio.create_task_group() as task_group:
  File "anyio/_backends/_asyncio.py", line 597, in __aexit__
    raise exceptions[0]
  File "starlette/responses.py", line 273, in wrap
    await func()
  File "starlette/middleware/base.py", line 134, in stream_response
    return await super().stream_response(send)
  File "starlette/responses.py", line 262, in stream_response
    async for chunk in self.body_iterator:
  File "starlette/middleware/base.py", line 98, in body_stream
    raise app_exc
  File "starlette/middleware/base.py", line 70, in coro
    await self.app(scope, receive_or_disconnect, send_no_error)
  File "starlette/middleware/exceptions.py", line 79, in __call__
    raise exc
  File "starlette/middleware/exceptions.py", line 68, in __call__
    await self.app(scope, receive, sender)
  File "fastapi/middleware/asyncexitstack.py", line 20, in __call__
    raise e
  File "fastapi/middleware/asyncexitstack.py", line 17, in __call__
    await self.app(scope, receive, send)
  File "starlette/routing.py", line 718, in __call__
    await route.handle(scope, receive, send)
  File "starlette/routing.py", line 443, in handle
    await self.app(scope, receive, send)
  File "a2wsgi/wsgi.py", line 157, in __call__
    return await responder(scope, receive, send)
  File "a2wsgi/wsgi.py", line 198, in __call__
    raise self.exc_info[0].with_traceback(
  File "galaxy/web/framework/middleware/error.py", line 165, in __call__
    app_iter = self.application(environ, sr_checker)
  File "galaxy/web/framework/middleware/statsd.py", line 29, in __call__
    req = self.application(environ, start_response)
  File "/cvmfs/main.galaxyproject.org/venv/lib/python3.11/site-packages/paste/httpexceptions.py", line 640, in __call__
    return self.application(environ, start_response)
  File "galaxy/web/framework/base.py", line 173, in __call__
    return self.handle_request(request_id, path_info, environ, start_response)
  File "galaxy/web/framework/base.py", line 262, in handle_request
    body = method(trans, **kwargs)
  File "galaxy/web/framework/decorators.py", line 138, in set_nocache_headers
    return func(self, trans, *args, **kwargs)
  File "galaxy/webapps/galaxy/controllers/dataset.py", line 677, in display_application
    file_name = value.get_file_name()
  File "galaxy/datatypes/display_applications/parameters.py", line 256, in __getattr__
    return getattr(self.value, key)
```
from https://sentry.galaxyproject.org/share/issue/c68d4f4d94f941c09e6eb5f62b163a69/
 2023-12-22 16:06:59 +01:00
mvdbeek b3fd9146f7 Fix job parameter display 
Fixes

```
7 validation errors for JobDisplayParametersSummary
response -> parameters -> 6 -> value
  field required (type=value_error.missing)
response -> parameters -> 9 -> value
  field required (type=value_error.missing)
response -> parameters -> 11 -> value
  field required (type=value_error.missing)
response -> parameters -> 15 -> value
  field required (type=value_error.missing)
response -> parameters -> 19 -> value
  field required (type=value_error.missing)
response -> parameters -> 23 -> value
  field required (type=value_error.missing)
response -> parameters -> 25 -> value
  field required (type=value_error.missing)
```
 2023-12-22 15:34:39 +01:00
Marius van den Beek 02f44b4c71 Merge pull request #17199 from ahmedhamidawan/single_item_selector_placeholder_bug 
[23.2] Remove `SingleItemSelector` deselect label, fix history filters hidden on smaller screen
 2023-12-22 10:42:51 +01:00
Marius van den Beek b65be82c7f Merge pull request #17224 from jdavcs/23.2_cardinality_error_2 
[23.2] Fix cardinality violation error: subquery returns multiple results
 2023-12-21 21:08:20 +01:00
John Davis c8012df503 Fix cardinality violation error: subquery returns multiple results 
Do not use scalary subquery, delete all selected jobs instead
 2023-12-21 13:08:20 -05:00
John Chilton 0887ec956e Merge pull request #17218 from nsoranzo/release_23.2_fix_TS_API_create_repo_categories 
[23.2] Fix categories in ToolShed repo create API
 2023-12-20 10:28:42 -05:00
Nicola Soranzo a8e96c9bca Fix categories in ToolShed repo create API 
Fix https://github.com/galaxyproject/galaxy/issues/17215 .

Also:
- Add API test for creation of TS repo with multiple categories.
 2023-12-19 20:56:50 +00:00
Dannon 04f1bde6b6 Merge pull request #17213 from ahmedhamidawan/tool_search_panel_view_bug 
[23.2] Fix `ToolSearch` bug for `StaticToolPanelView`s
 2023-12-19 10:02:55 -05:00
Ahmed Awan b12e72529e [23.2] Fix ToolSearch bug for StaticToolPanelViews 
The function `getPanelSectionsForTool` was outdated and not needed.
It was only working for the `default` and ontology views, and it
was only used to prevent looking at each section in
`createSortedResultObject` - which was looking at all panel
sections anyways, so the function wasn't really needed at all.
 2023-12-19 17:09:28 +05:00
mvdbeek 3a2e673e68 Merge branch 'release_23.1' into release_23.2 2023-12-19 12:00:54 +01:00
Marius van den Beek 1ffcf8e334 Merge pull request #17210 from davelopez/23.1_partial_backport_of_#17058 
[23.1] Fix `url_for` in tool error reports
 2023-12-19 12:00:33 +01:00
davelopez af9ad6037d Remove web dependency from tools/error_reports 2023-12-19 10:59:06 +01:00
davelopez 10e3dcddcb Remove web dependency from tools/errors.py 2023-12-19 10:58:49 +01:00
Ahmed Awan e87c9ee2c9 [23.2] Remove SingleItemSelector deselect label, fix history filters scroll 
In this PR:
- removed the `deselectLabel` for `SingleItemSelector`, since it
is used to only select 1 item
- added `overflow-auto` class to History `Index` to prevent filters
in advanced menu from being hidden on smaller/zoomed-in screen
- fixed `PanelViewMenu` when advanced filters are shown in tool
panel; currently it can be confusing as it shows panel views even
when filter menu is toggled
 2023-12-16 00:20:04 +05:00
David López 392c8e1be7 Merge pull request #17197 from ahmedhamidawan/modal_selector_overflow_bug 
[23.2] Fix Multiselect in BModal overflows out of view bug
 2023-12-15 17:06:49 +01:00
Ahmed Awan fa6e64b934 [23.2] Fix Multiselect in BModal overflows out of view bug 
Use `overflow: initial` to fix make sure the multiselect goes
beyond the modal.
 2023-12-15 19:35:01 +05:00
Marius van den Beek ad7fccb4ba Merge pull request #17149 from assuntad23/bug/16922/wf-report-disable-button 
[23.2] Disable Workflow Report and Generate PDF buttons unless workflow is successful
 2023-12-15 12:56:07 +01:00
Martin Cech c4c8d7b74b Merge pull request #17192 from ahmedhamidawan/fix_tool_panel_missing_tools_bug 
[23.2] Fix tools missing in panel bug
 2023-12-14 22:24:48 +01:00
Nate Coraor faaff5ee2e Merge pull request #17169 from natefoo/cgroupsv2 
[23.2] Add support for Cgroupsv2
 2023-12-14 16:05:50 -05:00
Ahmed Awan 54865cebaa [23.2] Fix tools missing in panel bug 
Some tools would be filtered out from the tool panel needlessly
when organizing the `ToolPanel` in `Panels/utilities.ts`.
 2023-12-14 23:35:33 +05:00
Nate Coraor c650007360 Cgroupsv2 metrics instrumenter tests 2023-12-14 13:29:19 -05:00
Nate Coraor ebe12aa10a Separate cgroup metrics default params from titles 2023-12-14 13:29:11 -05:00
mvdbeek 1fd9cf33c0 Merge branch 'release_23.1' into release_23.2 2023-12-14 11:43:04 +01:00
Marius van den Beek f6c06f600c Merge pull request #17176 from davelopez/23.1_fix_workflow_index_total_matches 
[23.1] Fix workflow index total matches counting
 2023-12-14 09:26:49 +01:00
Marius van den Beek 144919021c Merge pull request #17186 from dannon/fix-job-destination-params 
[23.2] Fix job destination extra params
 2023-12-14 09:10:44 +01:00
Dannon Baker 6ae573d18d Allow JobDestinationParams return to include extra admin-defined fields instead of trimming to just the defined 3. This is admin-only anyway, it's safe. 2023-12-13 23:26:51 -05:00
Nate Coraor 79da25435a Support Cgroupsv2 2023-12-13 15:27:41 -05:00
Marius van den Beek 2daff048dd Merge pull request #17182 from mvdbeek/add_rerun_and_info_button_collection_operations 
[23.2] Add rerun and show details buttons in expanded collection
 2023-12-13 15:22:45 +01:00
mvdbeek 386759b0ed Add rerun and show details buttons in expanded collection 2023-12-13 09:55:28 +01:00
John Davis 3e0b093d48 Merge pull request #17178 from natefoo/metrics-config-inline 
[23.2] Support configuring job metrics inline, update documentation
 2023-12-12 17:40:15 -05:00
Nate Coraor 0598a4be81 Document falsey values of job_metrics 2023-12-12 16:53:54 -05:00
Nate Coraor 91ef184f39 Support configuring job metrics inline, update documentation 2023-12-12 14:56:38 -05:00
davelopez fa585e1ac7 Fix workflow index total matches wrong count 2023-12-12 19:08:10 +01:00
davelopez 75c11225c6 Add test to check workflow index total matches 2023-12-12 19:08:02 +01:00
Assunta DeSanto fd36deddfb changing disabled tooltip to be more detailed for users 2023-12-08 19:31:22 -05:00
Assunta DeSantoandMarius van den Beek fe5966c0d9 Update client/src/components/WorkflowInvocationState/WorkflowInvocationSummary.vue 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2023-12-08 09:40:27 -05:00
Marius van den Beek 43b6d727cb Merge pull request #17146 from ElectronicBlueberry/fix-multiselect-dropdown-shown 
[23.2] Fix select option appears for single select
 2023-12-08 11:16:27 +01:00
Assunta DeSanto 65454e01f7 disable wf report and generate PDF buttons if WF is not complete or failed 2023-12-07 20:30:41 -05:00
Nicola Soranzo 8072dc88fe Merge pull request #17144 from nsoranzo/release_23.2_fix_create_tag 
[23.2] Make payload optional again for create tag API
 2023-12-07 14:30:22 +00:00
Laila Los 5b74f37746 hide select preference bar 2023-12-07 15:10:55 +01:00
Nicola Soranzo 71be4875e3 Make payload optional again for create tag API 
Before https://github.com/galaxyproject/galaxy/pull/17064 it was
possible to create a tag by simply making a POST request like
`/api/histories/911dde3ddb677bcd/tags/tag1` , this restores the
previous behaviour.

Fix BioBlend test failure:

https://github.com/galaxyproject/bioblend/actions/runs/7094150509/job/19308900670#step:10:3029
 2023-12-07 12:58:47 +00:00
Nicola Soranzo 295934b125 Refactor item tag API tests 
to create only necessary items.
 2023-12-07 12:26:00 +00:00
Marius van den Beek 149e8d3387 Merge pull request #17134 from mvdbeek/workflow_test_schema_support 
[23.2] Enhance xsd schema and allow simpler assertion lists
 2023-12-06 17:00:47 +01:00
mvdbeek 0f76e6ada7 Add int to Bytes, bool to PermissiveBoolean schema 2023-12-06 13:23:18 +01:00
mvdbeek 68a8608e16 Allow parsing lists of simple test assertions 2023-12-06 13:23:17 +01:00
mvdbeek dca591437f Merge branch 'release_23.1' into release_23.2 2023-12-06 11:29:33 +01:00
mvdbeek ac8cc32b30 Merge branch 'release_23.0' into release_23.1 2023-12-06 11:29:03 +01:00
Marius van den Beek f9be1a4344 Merge pull request #17133 from mvdbeek/tusuploader_fix 
[23.0] Assert that tus uploader instance has URL
 2023-12-06 11:28:40 +01:00