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2c19e16994b7612fb8886fb18aed83802d7c044c
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42265 Commits
Author SHA1 Message Date
mvdbeek 2c19e16994 Assert dynamic tool error message specificity 2025-09-01 17:36:10 +02:00
mvdbeek 60d12acb7d Serialize step tool_uuid as string, not UUID class instance 2025-09-01 17:36:10 +02:00
mvdbeek 4cf80afcaa Fix invocation step view with custom tools 2025-09-01 17:36:09 +02:00
mvdbeek ec186820cc Rebuild openapi schema 2025-09-01 17:36:09 +02:00
mvdbeek 4d75e3b066 Default to skip if data style unspecified 2025-09-01 17:36:08 +02:00
mvdbeek 0308f25b43 Implement templatable configfiles for yaml tools 2025-09-01 17:36:08 +02:00
mvdbeek b801dfe94b Fix tool form loading 2025-09-01 17:36:08 +02:00
galaxybot d49bc365c4 Update Python dependencies 
by running `make update-dependencies`.
 2025-08-30 03:16:24 +00:00
mvdbeek 30af8fb6ea Merge branch 'release_25.0' into dev 2025-08-29 20:00:19 +02:00
mvdbeek 4225e4b0fa Merge branch 'release_24.2' into release_25.0 2025-08-29 19:59:33 +02:00
Marius van den Beek 4ea216f0e1 Merge pull request #20836 from mvdbeek/include_user_agent 
[24.2] Include galaxy user agent in data source tools
 2025-08-29 19:40:44 +02:00
mvdbeek 541d70acf6 Include galaxy user agent in data source tools 
Closes https://github.com/galaxyproject/galaxy/issues/20833
 2025-08-29 17:22:28 +02:00
Nicola Soranzo dcd415a293 Merge pull request #20834 from bernt-matthias/bump-directory-converters 
Bump requirement of directory converters
 2025-08-29 16:55:41 +02:00
Matthias Bernt d76747df7d bump requirement of directory converters 
with conda I get

```
Traceback (most recent call last):
  File "<string>", line 1, in <module>
    from galaxy.util.compression_utils import CompressedFile; CompressedFile('/tmp/tmp3v2nuot4/files/a/9/7/dataset_a97aebb4-46f7-47a9-b418-11ff1deeed74.dat').extract('.')
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/berntm/miniforge3/envs/__galaxy-util@23.2.1/lib/python3.13/site-packages/galaxy/util/compression_utils.py", line 29, in <module>
    from .checkers import (
    ...<2 lines>...
    )
  File "/home/berntm/miniforge3/envs/__galaxy-util@23.2.1/lib/python3.13/site-packages/galaxy/util/checkers.py", line 20, in <module>
    from galaxy.util.image_util import image_type
  File "/home/berntm/miniforge3/envs/__galaxy-util@23.2.1/lib/python3.13/site-packages/galaxy/util/image_util.py", line 3, in <module>
    import imghdr
ModuleNotFoundError: No module named 'imghdr'
```
 2025-08-29 13:03:00 +02:00
John Chilton fcb5e414da Merge pull request #20805 from davelopez/add_huggingface_file_source 
Add Hugging Face 🤗 file source and user-defined template
 2025-08-28 09:36:32 -04:00
Nicola Soranzo 1a721fbc22 Get tool versions instead of the whole tool panel to check tool presence 2025-08-27 19:51:39 +01:00
Nicola Soranzo 2293a085bc Log exception if converting toolbox to dict fails 2025-08-27 19:51:38 +01:00
Ahmed Awan 3fd9b12f44 cache tours to make runTour also work 
This exists solely for the `tour_generator` webhook as of now. We are going to be refactoring and changing that from a webhook to core functionality, so we have also commented out the selenium that tests "Tool Describing Tours".
 2025-08-26 14:05:24 -05:00
davelopez 77c4bba02d Add method to extract timestamp from Hugging Face file info 2025-08-26 16:50:42 +02:00
davelopez f37b087918 Refactor timestamp extraction in FsspecFilesSource 
To allow sub-class customization
 2025-08-26 16:50:41 +02:00
davelopez 612f57a351 Refactor HuggingFaceFilesSource to use DEFAULT_SORT_BY constant 2025-08-26 16:50:41 +02:00
davelopez 7956bf028f Fix type for entries_list in HuggingFaceFilesSource 2025-08-26 16:50:40 +02:00
davelopez bcab312d58 Add Hugging Face Hub file source template 2025-08-26 16:50:39 +02:00
davelopez fd1caa8c13 Use _to_filesystem_path in huggingface file source 2025-08-26 16:50:39 +02:00
davelopez 5f75f8ff7d Add filesystem path conversion to FsspecFilesSource methods 
Some plugins may need to transform from the galaxy remote file path to the actual file system path when listing, fetching or writing files.
 2025-08-26 16:50:38 +02:00
davelopez 8779e9ee5c Add Hugging Face Hub file source plugin using fsspec 2025-08-26 16:50:37 +02:00
davelopez b18f733df2 Add huggingface_hub to conditional requirements 2025-08-26 16:50:36 +02:00
davelopez 9fdf747953 Add method to adapt entry path by removing S3 bucket name 
This was the behavior pre-fsspec refactoring. The bucket should not be displayed in the uri if it is the default bucket for this file source.
 2025-08-25 09:55:10 +02:00
davelopez 9c1a9f65f7 Refactor S3FsFilesSource to use fsspec 2025-08-25 09:55:10 +02:00
davelopez 3f50c8a9d8 Fix path handling in TempFilesSource to ensure consistent leading slashes 2025-08-25 09:48:30 +02:00
davelopez 7e4879e4d4 Adapt TempFilesSource path handling 
To improve virtual path conversion
 2025-08-25 09:48:29 +02:00
davelopez a38591df7b Refactor FsspecFilesSource to improve path handling 
And timestamp extraction
 2025-08-25 09:48:28 +02:00
galaxybot f2e03d248b Update Python dependencies 
by running `make update-dependencies`.
 2025-08-23 03:21:06 +00:00
Nicola Soranzo 7a65393d4b Merge branch 'release_25.0' into dev 2025-08-21 16:25:52 +01:00
Ahmed Hamid Awan d26ddf3ff2 Merge pull request #20744 from itisAliRH/history-list-g-card-refactor 
New History List Using GCard
 2025-08-20 18:35:36 -05:00
John Davis e6b4cb69a5 Run case-insensitive search by email regardless of provided email's casing 
Previous version did not work if the submitted email was all lowercase,
but the stored user email was non-lowercase.
 2025-08-20 13:34:45 -04:00
John Davis 536720948e Edit docstring for the validate_email function 2025-08-20 13:34:35 -04:00
Alireza Heidari 0c10ea5cca Consolidates sharing and access actions into one button 
Simplifies the history card UI by merging sharing, publishing, and permission management into a single "Share & Manage Access" action for consistency.
Updates related test selectors to match the new action identifier.
 2025-08-20 19:03:56 +02:00
Marius van den Beek c3262fa0db Merge pull request #20795 from mvdbeek/add_tool_id_tool_version_column 
Add tool_id and tool_version column to tool_landing_request table
 2025-08-20 18:18:52 +02:00
mvdbeek 26766f3e72 Add with_transaction 2025-08-20 16:56:11 +02:00
mvdbeek a6d13d6850 Add tool_id and tool_version column to tool_landing_request table 
Fixes https://github.com/galaxyproject/galaxy/issues/20793
 2025-08-20 11:03:30 +02:00
Marius van den Beek fed092fe46 Merge pull request #20698 from davelopez/add_fsspec_support 
Add `fsspec` base implementation for File Source plugins
 2025-08-20 10:58:47 +02:00
Marius van den Beek 41a72b2ab9 Merge pull request #20592 from jmchilton/tool_landing 
Implement Data Landing Requests
 2025-08-19 14:55:55 +02:00
mvdbeek b5add075cb Directly init Workflow Invocation as new 2025-08-19 14:49:37 +02:00
Marius van den BeekandNicola Soranzo 8e181aa465 Add type hint for flush argument 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2025-08-19 14:49:36 +02:00
mvdbeek 7c077846f5 Ensure that workflow invocations are persisted with state 2025-08-19 14:49:36 +02:00
davelopez 9d58f6add5 Add template and resolved config classes to MemoryFilesSource 2025-08-19 12:03:55 +02:00
davelopez 8fa412b728 Fix typo 2025-08-19 12:03:38 +02:00
Alireza Heidari aa63a12b29 Add wait for UX render in test_tags method before asserting history sort order 2025-08-19 11:51:43 +02:00
Alireza Heidari 916cb079d0 Add wait for UX render before inserting a tag in test_tags method 2025-08-19 11:51:42 +02:00