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Author SHA1 Message Date
Nicola Soranzo 414019da34 Fix docs versioning 
for Galaxy releases (e.g. 24.2 and 25.0) that have only tags with
2 dots.
 2025-06-21 20:16:29 +01:00
John Chilton 5b8aa60aa4 Merge pull request #20539 from nsoranzo/release_24.2_fix_pydantic 
[24.2] Move definition of ``DatasetCollectionDescriptionT`` before its use
 2025-06-21 12:52:20 -04:00
Nicola Soranzo 4b1558b284 Move definition of DatasetCollectionDescriptionT before its use 
Fix the following error on py37-test_galaxy_packages_for_pulsar tests:

```
FAILED tests/tool_util/test_input_models.py::test_input_collection_type - pydantic.errors.PydanticUserError: `ParsedTool` is not fully defined; you should define `DatasetCollectionDescriptionT`, then call `ParsedTool.model_rebuild()`.
```

Backport of commit bb87560d8f .
 2025-06-21 17:37:26 +01:00
Nicola Soranzo 36ef67be1f Merge branch 'release_24.1' into release_24.2 2025-06-20 13:00:05 +01:00
Nicola Soranzo c96792693c Merge branch 'release_24.0' into release_24.1 2025-06-20 12:55:50 +01:00
Marius van den Beek a55b61c5b4 Merge pull request #20524 from bernt-matthias/users 
[24.2] Do not expose user info to non authenticated users
 2025-06-20 12:21:33 +02:00
Nicola Soranzo fdf931b954 Fix new `test_index_anon` API test 2025-06-19 20:01:47 +01:00
Matthias Bernt 98ddca1e11 fixup 2025-06-19 19:34:52 +02:00
Matthias Bernt 79d08a4d2f Merge branch 'users' of https://github.com/bernt-matthias/galaxy into users 2025-06-19 19:09:02 +02:00
Matthias Bernt b71eaaf437 try to add test 2025-06-19 18:58:01 +02:00
M BerntandNicola Soranzo 14ab0e22b8 Raise exception for unauthenicated users 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2025-06-19 18:27:34 +02:00
Matthias Bernt 4b7afea7da never exopose user info to non authenticated users 
fixes https://github.com/galaxyproject/galaxy/issues/20505

should be fine is non-authenticated users can't share anything
(not sure about this)
 2025-06-19 16:21:35 +02:00
John Davis 6f182d7de5 Merge pull request #20519 from mvdbeek/fix_npm_publishing 
[24.2] Add id-token: write for npm publishing
 2025-06-19 09:09:19 -04:00
Marius van den Beek 044442bdfb Merge pull request #20511 from mvdbeek/fix_too_strict_validation 
[24.2] Relax validation of XML test assertion parsing
 2025-06-19 10:15:16 +02:00
mvdbeek d499501ab0 Add id-token: write for npm publishing 2025-06-19 10:12:10 +02:00
John Chilton 9523afb100 Linting fix. 2025-06-18 13:36:05 -04:00
John Chilton 0eeb71e169 Revise assertion relaxation to use better test models. 
This was supposed to be part of https://github.com/galaxyproject/galaxy/pull/19715 but clearly I missed the last mile as always.
 2025-06-18 13:22:52 -04:00
mvdbeek fdafb0655d Relax validation of XML test assertion parsing 
when tool source is XML. We can't really encode these attributes as JSON
in XML, and while we could make it work it doesn't feel great to force
tool authors to use such a hypothetical syntax.

I think we still keep all the nice validation here, it's just a little
more lenient.
 2025-06-18 18:55:10 +02:00
Marius van den Beek e61a74b4fb Merge pull request #20438 from mvdbeek/fix_single_data_json_wrap 
[24.0] Fix single data element identifier to be a regular string
 2025-06-18 12:33:21 +02:00
Nate Coraor dcd4cdca08 Start work on 24.2.5.dev0 2025-06-17 12:17:28 -04:00
Nate Coraor 7b1e4465bf Create version 24.2.4 v24.2.4 2025-06-17 12:17:16 -04:00
John Chilton e6a3dea50a Merge pull request #20492 from natefoo/optional-edam 
[24.2] Make optional edam-ontology in datatypes registry optional
 2025-06-17 09:03:24 -04:00
Marius van den Beek 957ccca59d Fall back to empty edam dict 2025-06-17 10:58:21 +02:00
Nate Coraor 8838912356 Make optional edam-ontology in datatypes registry optional 2025-06-16 16:48:10 -04:00
Marius van den Beek 539441ddd6 Merge pull request #20485 from mvdbeek/fix_workflow_invocation_import_link_outputs 
[24.2] Link workflow invocation outputs upon importing invocation
 2025-06-16 19:33:40 +02:00
mvdbeek 6d0a0b53aa Link workflow invocation outputs upon importing invocation 2025-06-16 15:02:47 +02:00
Marius van den Beek 876fdf0b24 Merge pull request #20475 from mvdbeek/header_string 
[24.2] Make response header values strings
 2025-06-16 13:41:47 +02:00
Marius van den Beek c7acfe7bea Merge pull request #20477 from mvdbeek/fix_legacy_metadata_get_file 
[24.2] Fix legacy get_metadata_file controller route
 2025-06-16 13:41:35 +02:00
Marius van den Beek 446c8deb68 Merge pull request #20479 from mvdbeek/prevent_launching_autodetect_on_purged_dataset 
[24.2] Prevent running datatype autodetect on purged datasets
 2025-06-16 13:41:00 +02:00
mvdbeek a7eaf5f74a Prevent running datatype autodetect on purged datasets 
Fixes https://github.com/galaxyproject/galaxy/issues/20478
 2025-06-16 11:16:09 +02:00
mvdbeek 4620f0716e Fix legacy get_metadata_file controller route 
Fixes https://github.com/galaxyproject/galaxy/issues/20476
 2025-06-16 11:09:25 +02:00
mvdbeek f508330d03 Make response header values strings 2025-06-16 11:02:46 +02:00
mvdbeek 4b55ecd2a0 Update documentation on staging_path_and_source_path 2025-06-16 10:14:56 +02:00
Ahmed Hamid Awan 6176b007ab Merge pull request #20107 from natefoo/fix-mulled-search-quay 
[24.2] Fix `mulled-search --destination quay`, add index reuse
 2025-06-13 12:41:49 -05:00
Nate CoraorandNicola Soranzo f66a9419a7 Update lib/galaxy/tool_util/deps/mulled/mulled_search.py 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2025-06-13 11:45:38 -04:00
mvdbeek 2bfd283f94 Fix single data element identifier to be a regular string 
These must adhere to the input parameter they belong to.
 2025-06-11 20:02:54 +02:00
John Davis 09e30616f8 Fix linting 2025-06-11 11:08:56 -04:00
John Chilton ddc07c9075 Merge pull request #20412 from mvdbeek/fix_validators_from_expression_json 
[24.2] Skip validation of expression.json input in workflow parameter validator
 2025-06-09 14:50:54 -04:00
Marius van den Beek 323d47e827 Merge pull request #20416 from nsoranzo/release_24.2_fix_mull_targets_mamba 
[24.2] Fix ``mull_targets()`` with mamba 2.x
 2025-06-08 20:51:56 +02:00
Nicola Soranzo 252a7fd72c Fix type annotation for NumPy 2.3.0 
Fix the following issues in py313-test_galaxy_packages :

```
galaxy/tool_util/verify/asserts/image.py:763: error: Incompatible types in
assignment (expression has type "list[Any]", variable has type
"ndarray[tuple[Any, ...], dtype[Any]]")  [assignment]
            present_labels = [label for label in present_labels if label i...
                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~...
galaxy/tool_util/verify/asserts/image.py:770: error: Incompatible types in
assignment (expression has type "list[Any]", variable has type
"ndarray[tuple[Any, ...], dtype[Any]]")  [assignment]
        present_labels = [label for label in present_labels if label not i...
                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~...
galaxy/tool_util/verify/asserts/image.py:773: error: Incompatible return value
type (got
"tuple[ndarray[tuple[Any, ...], dtype[Any]], ndarray[tuple[Any, ...], dtype[Any]]]",
expected "tuple[ndarray[tuple[Any, ...], dtype[Any]], list[Any]]")
[return-value]
        return im_arr, present_labels
               ^~~~~~~~~~~~~~~~~~~~~~
```
 2025-06-08 14:04:56 +01:00
Nicola Soranzo 162fe28318 Fix `mull_targets()` with mamba 2.x 
Fix mulled unit test test/unit/tool_util/mulled/test_mulled_build.py::test_mulled_build_files_cli[True] :

```
use_mamba = True
tmpdir = local('/tmp/pytest-of-runner/pytest-0/test_mulled_build_files_cli_Tr0')

    @pytest.mark.parametrize("use_mamba", [False, True])
    @external_dependency_management
    def test_mulled_build_files_cli(use_mamba: bool, tmpdir) -> None:
        singularity_image_dir = tmpdir.mkdir("singularity image dir")
        target = build_target("zlib", version="1.2.13", build="h166bdaf_4")
        involucro_context = InvolucroContext(involucro_bin=os.path.join(tmpdir, "involucro"))
        exit_code = mull_targets(
            [target],
            involucro_context=involucro_context,
            command="build-and-test",
            singularity=True,
            use_mamba=use_mamba,
            singularity_image_dir=singularity_image_dir,
        )
>       assert exit_code == 0
E       assert 1 == 0

...

[Jun  7 08:40:09] SERR error    libmamba Expected environment not found at prefix: /usr/local
[Jun  7 08:40:09] SERR critical libmamba Aborting.
```

Upstream issue: https://github.com/mamba-org/mamba/issues/3845 .
Fixed upstream in https://github.com/mamba-org/mamba/pull/3919 ,
released in mamba 2.2.0 .

Also:
- Improve type annotations
- Replace `FALLBACK_LINE_TUPLE` namedtuple with `Target` dataclass
 2025-06-07 23:06:31 +01:00
Nicola Soranzo bc0acd7f98 Merge pull request #20413 from nsoranzo/fix_package_tests 
[24.2] Fix unit tests returning values
 2025-06-07 09:30:14 +01:00
Nicola Soranzo 6eaf865073 Fix unit tests returning values 
These break with pytest 8.4.0, see
https://docs.pytest.org/en/stable/changelog.html#pytest-8-4-0-2025-06-02

Fix the following errors in test_galaxy_packages tests:

```
FAILED tests/tool_shed/test_hg_util.py::test_add_file_and_commmit_changeset - Failed: Expected None, but test returned local('/tmp/pytest-of-runner/pytest-7/test_add_file_and_commmit_chan0/test.txt'). Did you mean to use `assert` instead of `return`?
FAILED tests/tool_shed/test_hg_util.py::test_add_dir_and_commit_changeset - Failed: Expected None, but test returned local('/tmp/pytest-of-runner/pytest-7/test_add_dir_and_commit_change0/abc'). Did you mean to use `assert` instead of `return`?
```

Also:
- Replace legacy `tmpdir` fixtures with `tmp_path`.
- Improve type annotations.
 2025-06-06 20:25:39 +01:00
mvdbeek a50f890bd5 Skip validation of expression.json input in workflow parameter validator 2025-06-06 18:19:34 +02:00
Marius van den Beek 968ef13132 Merge pull request #20394 from jdavcs/24.2_role_name_bug 
[24.2] Fix searching roles in admin UI
 2025-06-03 19:41:52 +02:00
John Davis 75ab368118 Use Role.name 
Fixes bug: the `name` hybrid property has been removed and the field has
been renamed back to `_name`

Ref:
https://github.com/galaxyproject/galaxy/pull/19679/commits/3d2eb9fd8e6281d665ead0e18eb2f3ebde866196
https://github.com/galaxyproject/galaxy/pull/18966/commits/3e6191fbe3b5b1f18c6de2dfd413e9c2a6e34b19
https://github.com/galaxyproject/galaxy/pull/18966/commits/62a8b90f8aab45441b5f6922351b8a5a20cc0848
 2025-06-03 11:57:21 -04:00
David López e3e767d24a Merge pull request #20305 from davelopez/24.2_fix_wfrun_rocrate_logo_width 
[24.2] Fix WF Run RO-Crate logo width in Firefox
 2025-05-20 15:05:06 +02:00
davelopez 2bf1b96bb0 Fix WF Run RO-Crate logo width in Firefox 2025-05-20 14:03:05 +02:00
mvdbeek 957f6f5475 Merge branch 'release_24.1' into release_24.2 2025-05-19 16:54:19 +02:00
Marius van den Beek c4605dad00 Merge pull request #20239 from natefoo/fix-ucsc-display-as 
[24.1] Refactor display_as URL generation for UCSC links and fix to remove double slashes in URL
 2025-05-19 16:52:44 +02:00