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41652 Commits
Author SHA1 Message Date
mvdbeek 29088af250 Update pulsar-galaxy-lib to 0.15.8 
Fixes https://github.com/galaxyproject/pulsar/issues/392
 2025-06-09 19:41:29 +02:00
mvdbeek 4f545f424d Fix job rerun with tool version change 
Fixes https://github.com/galaxyproject/galaxy/issues/20337, broken in https://github.com/galaxyproject/galaxy/pull/20259
 2025-06-09 12:16:26 +02:00
Nicola Soranzo 90fad91813 Merge branch 'release_24.2' into release_25.0 2025-06-08 21:47:42 +01:00
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 2c41fefdce Merge branch 'release_24.2' into release_25.0 2025-06-07 18:00:47 +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
Marius van den Beek 8db845b7ca Merge pull request #20397 from ahmedhamidawan/no_waiting_for_ok_state 
[25.0] Prevent waiting for history item state to be ok in uploader
 2025-06-06 13:15:32 +02:00
Martin Cech 93e1446e4c Merge pull request #20400 from bernt-matthias/fix_20395 
[25.0] Add job config variable for singularity `--contain`
 2025-06-06 08:42:21 +02:00
Ahmed Awan 04602c3b84 wait for add items button to enable; no need to switch to create tab 
The test would fail because the add items to collection button's disabled/enabled state was not being detected, and hence, we would manually switch tabs and the items would not even have been added to the list yet. Now, we wait for the button to enable, and then adding the items automatically switches tab to Create.
 2025-06-05 14:09:23 -05:00
Ahmed Awanandmvdbeek 58561002d5 No need to wait for item hids, waiting for the button itself is better 
Co-authored-by: mvdbeek <m.vandenbeek@gmail.com>
 2025-06-05 11:40:03 -05:00
M Bernt 0ed6442318 Add missing comments 2025-06-05 09:33:11 +02:00
M BerntandNicola Soranzo 704f0620f5 Doc improvements 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2025-06-05 09:31:28 +02:00
M BerntandNate Coraor a71d4dd0db Fix sample config 
Co-authored-by: Nate Coraor <nate@bx.psu.edu>
 2025-06-04 21:03:38 +02:00
Matthias Bernt 964a62bb2c add job config for singularity --contain 
also move doc to yaml config job config file
 2025-06-04 18:53:10 +02:00
Dannon Baker 7ee1d3c480 Add tests for tool icon endpoint handling simple and toolshed tool IDs 2025-06-04 12:10:48 -04:00
Ahmed Awan c2974fe61c remove wait for upload state alert 2025-06-04 10:38:54 -05:00
Dannon Baker 97fb170e82 Fix tool icon endpoint to handle toolshed tool IDs with slashes 
Changed the FastAPI route parameter from {tool_id} to {tool_id:path} to
properly capture complex tool identifiers containing forward slashes.
 2025-06-04 11:06:16 -04:00
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
Chris Grams ffb51f7821 Fix conda_link to use platform.machine() for architecture detection 2025-05-30 12:48:50 -05:00
Dannon Baker 270ba9cb14 Generate a tenant-unique UID for tapis. 2025-05-29 10:43:19 -04:00
Marius van den Beek 5e8d771a74 Merge pull request #20363 from mvdbeek/log_invalid_path_exception 
[25.0] Log invalid vault paths
 2025-05-28 17:02:52 +02:00
mvdbeek 25e5b2e01b Log invalid path exceptions 2025-05-28 15:07:17 +02:00
Marius van den Beek 8c45d86108 Merge pull request #20326 from ahmedhamidawan/fix_workflow_rerun_version_TESTS 
[25.0] Add test for workflow instance download fix
 2025-05-22 21:28:58 +02:00
Ahmed Awanandmvdbeek db234a29ee fix (expression has type "bool", target has type "str") mypy err 
Co-authored-by: mvdbeek <m.vandenbeek@gmail.com>
 2025-05-22 10:48:22 -05:00
Ahmed Awan 909b8d9c73 [25.0] Add test for workflow instance download fix 
Test for the change in https://github.com/galaxyproject/galaxy/pull/20313
 2025-05-22 10:35:10 -05:00
mvdbeek 146ae6bc69 Enable retrieving contents from extra file paths with leading / 
by stripping all leading `/` in filename.

I don't think there's a legitimate reason that we should treat this as
an absolute path marker. Addresses @luke-c-sargent's comment in
https://github.com/goeckslab/tools-mti/pull/99#issuecomment-2864667012
 2025-05-22 16:36:33 +02:00
Marius van den Beek ac78028d6b Merge pull request #20313 from ahmedhamidawan/fix_workflow_rerun_version 
[25.0] Rerun workflows for the correct version/instance
 2025-05-21 20:04:07 +02:00
Marius van den Beek 7515f053af Merge pull request #20325 from davelopez/25.0_fix_wf_bookmark_filter 
[25.0] Fix workflow bookmark filtering
 2025-05-21 20:03:47 +02:00
Marius van den Beek 2e1534aa2e Merge pull request #20311 from davelopez/25.0_increase_proxy_api_robustness 
[25.0] Increase proxy API robustness by validating URL before use
 2025-05-21 17:20:38 +02:00
davelopez f7f643c683 Fix workflow bookmark filtering 
We need to specify the `onclause` for the join explicitly, so SQLAlchemy knows which columns to use for the join.
 2025-05-21 16:41:52 +02:00
davelopez 46168bfa5a Add workflow bookmarking selenium test 2025-05-21 16:39:00 +02:00
davelopez 4964660e50 Move test for local files to invalid urls 
Only https and http schemes are allowed so any other scheme will be considered invalid.
 2025-05-20 23:38:25 +02:00
davelopez c2fb2547a6 Refactor URL validation to use a constant for allowed schemes 2025-05-20 23:32:00 +02:00
Dannon 12396d09f4 Merge pull request #20290 from guerler/adjust_dataset_view 
[25.0] Touch up Dataset View
 2025-05-20 15:44:24 -04:00
Ahmed Awanandmvdbeek 4084e75837 decode id earlier 
Co-authored-by: mvdbeek <m.vandenbeek@gmail.com>
 2025-05-20 14:25:57 -05:00
Ahmed Awan 11d4a9165a [25.0] Rerun workflows for the correct version/instance 
In `GET /api/workflows/{encoded_workflow_id}/download`, for the case when `instance = True`, we were correctly obtaining the stored workflow.

However, then in `WorkflowContentsManager.workflow_to_dict` we were not considering the case that when `instance = True`, we need to not return the `latest_workflow.workflow_to_dict`, and instead return the specific workflow instance which has been specified.

We did handle the case when `version` is explicitly provided here, but not instance.

Fixes https://github.com/galaxyproject/galaxy/issues/20223
 2025-05-20 13:46:51 -05:00
davelopez 59fef1f7b5 Add test for invalid URL formats in proxy endpoint 2025-05-20 17:39:39 +02:00
davelopez 47bc0f0f1c Add URL validation function to proxy endpoint 2025-05-20 17:39:28 +02:00
guerler 894f97d121 Adjust for selenium tests 2025-05-19 19:07:13 -04:00
mvdbeek a92286ba8e Merge branch 'release_24.2' into release_25.0 2025-05-19 17:00:12 +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
Marius van den Beek e5af55199b Merge pull request #20281 from mvdbeek/httpx 
[25.0] Add non-dev httpx dependency
 2025-05-19 16:08:16 +02:00
mvdbeek 50ec064838 Add non-dev httpx dependency 2025-05-19 15:19:33 +02:00
Martin Cech 3df96589c9 Merge branch 'release_24.2' into release_25.0 2025-05-19 12:44:44 +02:00
Martin Cech 1f7f2e7845 Merge branch 'release_24.1' into release_24.2 2025-05-19 12:44:19 +02:00
Martin Cech 4e1acd06ce Merge branch 'release_24.0' into release_24.1 2025-05-19 12:43:58 +02:00
Martin Cech faa7442ee7 Merge branch 'release_23.2' into release_24.0 2025-05-19 12:43:20 +02:00
Martin Cech 7d4b3de58f Merge branch 'release_23.1' into release_23.2 2025-05-19 12:32:42 +02:00