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68b4a0c948d94de4d1002e0f16efceec8501998b
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42432 Commits
Author SHA1 Message Date
Uwe Winter 68b4a0c948 Add Config opion disable_local_accounts 2025-09-29 17:40:47 -05:00
Nicola Soranzo 2f570c46e6 Merge pull request #20963 from mvdbeek/nodejs-wheel 
Use nodejs-wheel to install node
 2025-09-30 00:07:25 +02:00
John Chilton 10991781e4 Merge pull request #20960 from mvdbeek/landing_request_tracking_2 
Track landing request with invocation
 2025-09-28 22:35:06 -04:00
mvdbeek 9f919eb5e1 Track landing request with invocation 
Contains stub for tool request tracking, once that is merged we could
start using it.
 2025-09-27 09:19:33 +02:00
mvdbeek b488cf2694 Use nodejs-wheel to install node 2025-09-27 09:17:12 +02:00
galaxybot 9fd34d7843 Update Python dependencies 
by running `make update-dependencies`.
 2025-09-27 03:14:53 +00:00
Ahmed Awan 426a1b5fd1 Move tours schema to schema directory (to fix package structure) 
Discovered in https://github.com/galaxyproject/galaxy/pull/20868#issuecomment-3338402529
 2025-09-26 12:14:27 -05:00
Marius van den Beek f0ad237301 Merge pull request #20957 from mvdbeek/landing_request_tracking 
Allow sending and tracking landing request origin
 2025-09-26 16:42:10 +02:00
mvdbeek 77f28029e5 Allow sending and tracking landing request origin 2025-09-26 16:07:24 +02:00
John Chilton 8c61eb68be Merge pull request #20912 from ahmedhamidawan/invocation_view_step_enhancements 
Improve Invocation View step display
 2025-09-26 09:36:51 -04:00
Aysam Guerler 8ec885eda0 Merge pull request #20868 from ahmedhamidawan/move_tour_generator_webhook_to_core 
Replace tour_generator webhook with internal API and frontend
 2025-09-26 07:45:08 +03:00
Marius van den Beek 7d6bce7983 Merge pull request #20851 from ksuderman/20750-ijson-parser 
Use a streaming based parser (ijson) when setting metadata for biom1 files.
 2025-09-25 21:19:45 +02:00
Marius van den Beek 8855675d09 Merge pull request #20717 from selten/patch-14 
Improve cli and slurmcli runner traceability for job status and failure reasons
 2025-09-25 20:53:42 +02:00
Marius van den Beek 8a5d749ba2 Merge pull request #20951 from mvdbeek/tool_source_schema_enhancements 
Add resource docs and tweak tool source schema title generation
 2025-09-25 20:49:47 +02:00
mvdbeek 8850857ee9 Fix sacct call 2025-09-25 17:28:41 +02:00
Nicola Soranzo ba41eefe99 Add type annotations 2025-09-25 16:22:07 +01:00
Nicola Soranzo 47acb619bb Move `Optional[] inside Annotated[]` 
Otherwise title and description are missing from the generated
TypeScript schemas.
 2025-09-25 16:21:30 +01:00
setlen e1930a1be3 Try changing return value lint 2025-09-25 16:49:04 +02:00
setlen 0c5fc067ac FIx formatting 2025-09-25 16:49:04 +02:00
selten 08bf91c5c5 Also fix linting errors 2025-09-25 16:49:03 +02:00
selten 64a1f4e5b2 Add import for subprocess 2025-09-25 16:49:03 +02:00
selten c4b643ea3a Fix indentation 2025-09-25 16:49:03 +02:00
selten 8b18fc5a39 Improve cli and slurmcli runner traceability for job status and failure reasons 2025-09-25 16:49:01 +02:00
Marius van den Beek 3481880c41 Merge pull request #20899 from jmchilton/tool_request_types_1 
Small cleanup of tool execution code.
 2025-09-25 15:15:42 +02:00
mvdbeek 7a240dc91b Don't auto-capitalize tool source field titles 2025-09-25 14:55:50 +02:00
mvdbeek 614afd2fc8 Add more documentation to cores and ram 2025-09-25 11:15:23 +02:00
Ahmed Awan 49bd6cac01 fix invocation job details selenium to open the newly added outputs tab first 
The job(s) and output(s) are in tabs now, so the selenium accounts for that.
 2025-09-24 15:47:48 -05:00
mvdbeek a1ecabdfbc Adjust API tests 
Most of the time we just want an OK status code. 202, 204, 200 should
all be OK and some of this depends on the Galaxy instance config,
so this should be more robust to future changes.
 2025-09-23 22:16:20 +02:00
mvdbeek fbadca413a Don't serialize view of item in delete/purge request 
This is a breaking change for the API, it is motivated by
https://sentry.galaxyproject.org/share/issue/3970e49a695f4600bcaeae55021555a9/:
```
Message
Unexpected error
Stack Trace

Newest

FileNotFoundError: [Errno 2] No such file or directory: ''
  File "galaxy/datatypes/interval.py", line 1326, in get_estimated_display_viewport
    with open(dataset.get_file_name()) as fh:
```
This is a purge request, which does return the entire detailed response,
including available display applications. We already check that the
dataset isn't purged, but ther celery task often executes between the
check and the deletion.

I don't think it makes sense to return any data at all here,
and there are other endpoints where we simply return 202 or 204,
like purging user file source instanes.
 2025-09-23 22:16:20 +02:00
Marius van den Beek 1ccf881190 Merge pull request #20838 from nsoranzo/pytest8 
Update pytest to v8
 2025-09-23 17:00:13 +02:00
John Chilton 248ffcde05 Merge pull request #19086 from jmchilton/markdown_embedded_directives 
Allow several Galaxy Markdown directives to be embedded.
 2025-09-23 10:48:32 -04:00
Ahmed Hamid Awan 8ca7075df5 Merge pull request #19225 from PlushZ/execute-tags 
Add tags to output datasets from tool form
 2025-09-23 09:46:02 -05:00
Ahmed AwanandBjörn Grüning e9710be048 set enable_tool_generated_tours to true by default 
Co-authored-by: Björn Grüning <469983+bgruening@users.noreply.github.com>
 2025-09-23 08:41:29 -05:00
Ahmed Awan 355cce56f6 change tool generated tour API test's tool from cat1 to random lines 
I did this because `cat1` does not have supported input types for TGTs.
 2025-09-23 08:41:28 -05:00
Ahmed AwanandJohn Davis 8b7285aba9 raise an error as soon as we find unsupported input types 
Co-authored-by: John Davis <jdavcs@gmail.com>
 2025-09-23 08:41:28 -05:00
Ahmed Awan 850d344e5a add API tests for tool generated tours 
These utilize the `performs_upload` parameter which was added for this purpose; since we do not have a valid history available to upload the datasets to.
 2025-09-23 08:41:28 -05:00
Ahmed Awan 35f7931921 add performs_upload parameter to tool generated tour api 2025-09-23 08:41:28 -05:00
Ahmed Awan f19d396a27 ensure TGTs actually textinsert for text and number inputs 2025-09-23 08:41:28 -05:00
Ahmed Awan 0dcc5cb6c5 give file an auto datatype in TGT upload data 2025-09-23 08:41:28 -05:00
Ahmed Awan 93a196ab94 end tour when clicking run tool 
Also adds `postclick` functionality to that last step which auto clicks the execute button.
 2025-09-23 08:41:28 -05:00
Ahmed Awan 3e4719f818 fix exception handling in tours manager 2025-09-23 08:41:28 -05:00
Ahmed Awan 8be3cdf113 restore/uncomment test_tool_describing_tours since TDTs work now! 2025-09-23 08:41:27 -05:00
Ahmed Awan b2a31148c6 Add /api/tours/generate that replaces the entire tour_generator webhook 
- Tool Generated Tours have an internal GET FastAPI route.
- That API uses a new `TourManager`.
- The `tour_generator` webhook has been removed entirely.
 2025-09-23 08:41:27 -05:00
Ahmed Awan 8e47e1638d add enable_tool_generated_tours config option 
Doesn't do anything yet
 2025-09-23 08:41:27 -05:00
John Chilton 28e6e2c6f8 Fix default conditional test parameters... 
... for tools using 21.01 input format.
 2025-09-22 17:04:38 -04:00
Polina Polunina 9c0cde8d34 Merge branch 'dev' into execute-tags 2025-09-22 17:05:09 +02:00
Marius van den Beek 50e39b245c Merge pull request #20932 from mvdbeek/user_defined_tool_type 
Allow addressing user defined tools in job config
 2025-09-22 15:01:11 +02:00
mvdbeek 99df41a49a Merge branch 'release_25.0' into dev 2025-09-22 09:11:38 +02:00
mvdbeek 0c09aa9e5c Add test for proposed prod-like deployment 2025-09-21 17:03:17 +02:00
mvdbeek b204902146 Discriminate user defined tools via tool_type and tool_class 2025-09-21 15:28:27 +02:00