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Author SHA1 Message Date
mvdbeek bc5259f5d2 Merge branch 'release_23.1' into release_23.2 2024-01-04 16:02:16 +01:00
Marius van den Beek d0a7562ad7 Merge pull request #17236 from mvdbeek/fix_schema_integrity 
[23.1] Separate collection and non-collection data element
 2024-01-02 20:41:31 +02:00
Marius van den Beek 2b90dec2c1 Merge pull request #17233 from mvdbeek/display_application_fixes_and_tests 
[23.2] Display application fixes and tests
 2024-01-02 20:40:34 +02:00
mvdbeek 4027c99350 Skip test when ftp.gnu.org not available 2024-01-01 10:07:30 +02:00
mvdbeek b1361c8e79 Separate collection and non-collection data element 
in tool schema. New lxml is more strict when validating
the xml schema and fails with

```
lxml.etree.XMLSchemaParseError: complex type 'Output': The content model is not determinist., line 5329
```

this is because `filter` and `discover_datasets` are present in
OutputDataElement and OutputCollectionElement, making

```
     <xs:sequence>
       <xs:group ref="OutputDataElement" minOccurs="0" maxOccurs="unbounded" />
       <xs:group ref="OutputCollectionElement" minOccurs="0" maxOccurs="unbounded" />
     </xs:sequence>
```

not deterministic.

In any case this isn't an accurate model of what is allowed and parsed,
as you can't use collection-specific discover_datasets options outside
of a dataset collection.

I **think** that the reason for adding
OutputCollectionElement to the sequence is that you can have a `data`
element nested in a `collection` element.

To continue allowing this and making it more precise I've added an
additional `OutputCollectionDataElement` type that is allowed within
`collection`. This then should allow us to remove
`OutputCollectionElement` from the `OutputData` type.

A quick test against IUC and devteam revealed no problem with this
approach per se, however it showed that https://github.com/galaxyproject/tools-iuc/blob/aa8360cb3ec9faf1488938a430855977632706ff/tools/krakentools/extract_kraken_reads.xml#L145
uses `change_format` which is not implemented for collections.
 2023-12-31 19:59:17 +02:00
mvdbeek ccdd733121 Commit and legacy backpopulate pattern from unit test 2023-12-25 10:59:05 +01:00
mvdbeek 8bab912a7f Move display application link test to integration test 2023-12-25 10:38:21 +01:00
mvdbeek 0b951643f4 Don't fail CONVERTER_fasta_to_fai with stderr contents 2023-12-25 10:35:43 +01:00
mvdbeek 21bfb0c490 Test and fix display application link handling 2023-12-25 09:37:19 +01:00
mvdbeek f7b7409ea8 Add dbkey to DatasetLikeObject 2023-12-24 10:30:41 +01:00
mvdbeek 7105af4917 Merge branch 'release_23.1' into release_23.2 2023-12-23 15:17:49 +01:00
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
Björn Grüning 687bcf9d01 Merge pull request #17231 from mvdbeek/convert_test_backport 
[23.1] Backport #17188: Fix for converter tests
 2023-12-23 12:43:56 +01:00
Björn Grüning 4d07aa974d Merge pull request #17232 from mvdbeek/session_order_fix 
[23.1] Fix User.current_galaxy_session
 2023-12-23 12:43:26 +01:00
mvdbeek 1113f4c744 Fix User.current_galaxy_session 2023-12-23 10:34:11 +01:00
Matthias Bernt 07bf0d6955 Also fix test of the vcf_to_vcf_bgzip_converter 2023-12-23 10:27:01 +01:00
Matthias Bernt dc8275cb86 slighly more intrusive fix 2023-12-23 10:27:01 +01:00
Matthias Bernt e4993e6d88 unintrusive fix for converter tests 2023-12-23 10:27:00 +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