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543 Commits
Author SHA1 Message Date
davelopez 6a7bf2454b Fix file source initialization by converting root LocalPath to string 
As the TestPosixConfiguredFileSources expects a string as root argument as well as the pydantic model for PosixFilesSource
 2025-08-18 11:21:05 +02:00
mvdbeek ec7929c742 Construct CTEs using sqlalchemy core 2025-08-11 17:17:15 +02:00
mvdbeek 2924f29a1e Use NamedTupe for collection state summary 2025-08-11 17:17:13 +02:00
mvdbeek c2ddea2217 Implement touch collection update time CTE 2025-08-11 17:17:10 +02:00
mvdbeek e83e6b72a1 Return states and deleted status with HDCA 2025-08-11 10:32:11 +02:00
Nicola Soranzo 7f89e0eab9 Code cleanups from pyupgrade 
Found by running:

```
make pyupgrade
ruff check --fix .
ruff check --preview --unsafe-fixes --select=F401 --fix .
make format
make update-client-api-schema
```

The bulk of the changes are replacements of typing deprecated aliases
such as `Dict` and `List` with the standard library classes. These
aliases became redundant in Python 3.9 when the corresponding
pre-existing classes were enhanced to support `[]`, see
https://docs.python.org/3/library/typing.html#deprecated-aliases

Also:
- Update the `pyupgrade` Makefile target to use `--py38-plus` for the
  packages needed by Pulsar, including the new galaxy-tool-util-models
  package.
 2025-07-31 11:17:22 +01:00
Nicola Soranzo e2777065eb Merge branch 'release_25.0' into dev 2025-07-30 17:45:20 +01:00
John Chilton 5447f98289 Rework sample sheets to use POSTs instead of GETs. 
Marius outlines why in the review of the PR.
 2025-07-28 13:43:14 -04:00
John Chilton d26605517e Implement sample sheets. 2025-07-25 11:46:59 -04:00
John Chilton 8947cf8051 Generalize fetch workbook parsing on backend. 
Can now read a bunch of CSV/TSV files as easily as excel files.
 2025-07-25 11:46:24 -04:00
John Chilton 316d9817a8 Validate workflow inputs more directly on the backend. 2025-07-25 11:46:24 -04:00
Leonid Kostrykin 65e5ed0d12 Revert "Merge pull request #20464 from mvdbeek/drop_num_unique_values" 
This reverts commit 6fe8a7bf6d, reversing
changes made to 8903af6964.
 2025-07-17 14:38:18 +02:00
Nicola Soranzo 99e352a3d0 Merge branch 'release_25.0' into dev 2025-06-22 15:26:46 +01:00
John Chilton 85d634ae9f Implement fetch workbooks. 2025-06-19 22:54:56 -04:00
mvdbeek 6231f4feb0 Remove `num_unique_values` tiff metadata element 
This was added in https://github.com/galaxyproject/galaxy/pull/18951 but
it's memory consumption scales with input size. On a 5.5GB TIFF file
this consumed a peak of 18GB of memory.

@kostrykin added a workaround for the memory consumption in
https://github.com/galaxyproject/galaxy/pull/19830, but this now very
slow.

Besides improving the efficient, Perhaps there is a more gentle way to approach

> Many tools assume that images are binary, or label maps, for example, and it makes no sense to run those tools on other images.

?

Could those tools just error out, and/or consume a different datatype ?
Do we need the full unique values, or is it ok to just check if it's
more than `n` unique values ?
 2025-06-15 11:44:10 +02:00
John Chilton b18f0708f7 Implement DatasetSource.requested_transform. 
Should be distinct from transforms apply.
 2025-06-12 18:01:30 +02:00
John Chilton cb2d5cc611 Implement nested collection test in test_model_discovery. 2025-05-14 12:57:29 -04:00
John Chilton 219796f049 Implement paired_or_unpaired collections, list wizards. 2025-05-09 17:39:38 -04:00
John Chilton 9c7770d3aa More dataset collection unit testing... 2025-05-09 16:38:20 -04:00
John Chilton 0b3b408b50 Migrate doctests to unit tests. 2025-05-09 16:38:19 -04:00
Eli Chadwick 70cd4511b0 avoid caching in python 3.9 2025-05-07 10:45:12 +01:00
Eli Chadwick f9688c43a7 isort 2025-05-07 10:45:11 +01:00
Eli Chadwick 09458577b2 linting 2025-05-07 10:45:10 +01:00
Eli Chadwick 007541d1e3 add version check to xfail 2025-05-07 10:45:10 +01:00
Eli Chadwick a4fbf706b4 fix version check 2025-05-07 10:45:09 +01:00
Eli Chadwick bd4da7a339 fix problem with non-existent files failing validation 2025-05-07 10:45:08 +01:00
Eli Chadwick d1906cbf54 work around dependency issues 2025-05-07 10:45:08 +01:00
Eli Chadwick 419930627b work around dependency issues 2025-05-07 10:45:08 +01:00
Eli Chadwick 5cf1dde60c checked tests 2025-05-07 10:45:07 +01:00
Eli Chadwick ed36c907b7 add tests using roc_validator 2025-05-07 10:45:06 +01:00
John Chilton 4e4017c1be Merge pull request #20152 from jmchilton/collection_cleanup_2 
Fix certain cases of collection parameter handling during workflow execution.
 2025-05-05 15:45:36 -04:00
John Chilton 576ed97001 Refactor history_query.py for typing, clarity, testing. 
Could use some more work to be sure but a first step toward cleaning it up.
 2025-05-03 10:21:17 -04:00
mvdbeek c03d179db0 Implement dataset collection support in workflow landing requests 
and tweak request models to make them compatible with workflow test format
 2025-04-22 14:18:47 +02:00
mvdbeek 95dd47fb3a cast MockObjectStore to BaseObjectStore 2025-03-31 18:55:20 +02:00
Marius van den Beek 346ba3d674 Merge pull request #19854 from bernt-matthias/fix-is_over_quota 
Fix Galaxy ignoring job object_store_id for quota check
 2025-03-26 09:58:37 +01:00
Leonid Kostrykin b638beb39e Add tests for Image base class (without PyPng) 2025-03-25 14:36:44 +01:00
Leonid Kostrykin 98f21aea20 Add Png.set_meta 2025-03-25 14:36:44 +01:00
Leonid Kostrykin f3ded28c03 Rename im9_multipage.tif -> im9_multiseries.tif 2025-03-25 14:36:42 +01:00
Matthias Bernt d6990b0707 add more complex unit test 2025-03-25 14:31:54 +01:00
Matthias Bernt 3613811030 pass quota source map instead of whole app 
makes testing also a lot easier I think
 2025-03-25 14:31:54 +01:00
Nicola Soranzo b7591a0872 Improve type annotations of `ModelPersistenceContext` and derived classes 2025-03-20 12:46:35 +00:00
Nicola Soranzo 05b9467c35 Merge branch 'release_24.2' into dev 2025-03-13 00:37:29 +00:00
John Davis 104a375ea4 Add get_private_role_user_emails_dict, test 
Retrieves a mapping of private role ids to associated users' emails.
Used to lookup a user's email when generating a displayed_name for
private roles.
 2025-03-11 00:34:22 -04:00
John Davis c4c66078d8 Factor out get_displayable_roles, add test 2025-03-10 11:13:13 -04:00
John Davis f2f55131b2 Fix unit tests 2025-03-10 11:13:13 -04:00
John Davis dfe1536a5d Update test fixture 
Specify correct role name for private roles. See comment in make_role
definition for why this must be set.
 2025-03-10 11:13:13 -04:00
Marius van den Beek 2df4acb8c5 Merge pull request #19666 from jmchilton/api_typing_dataset_source_transform_actions 
Generate correct types for Dataset source transformations on backend.
 2025-03-04 10:29:47 +01:00
Nicola Soranzo 49fa860647 Merge pull request #19706 from nsoranzo/type_annot_model 
Use model classes from ``galaxy.model`` instead of ``app.model`` object - Part 1
 2025-02-26 16:15:21 +00:00
Nicola Soranzo 9477c7773e Use model classes from `galaxy.model instead of app.model` object 
for proper type annotation of query results.

Also:
- Drop unused code from `lib/tool_shed/webapp/controllers/user.py`
- Drop Galaxy model code from
  `lib/tool_shed/util/admin_util.py:Admin.purge_user()`
 2025-02-26 12:41:40 +00:00
Nicola Soranzo edd8bccf4f Drop support for Python 3.8 2025-02-25 19:20:46 +00:00