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Author SHA1 Message Date
Marius van den Beek cb93c7b976 Merge pull request #20502 from davelopez/add_redis_conditional_dependency 
[25.0] Add redis conditional dependency
 2025-07-01 10:58:00 -04:00
Marius van den Beek 89b37a6701 Merge pull request #20545 from mvdbeek/fix_user_defined_tool_extension 
[25.0] Fix restricting user defined tool input datasets extensions
 2025-06-23 09:22:50 -04:00
mvdbeek 462955599b Fix extension parsing for yaml tools 2025-06-22 19:22:59 -04:00
Marius van den Beek 6fe8a7bf6d Merge pull request #20464 from mvdbeek/drop_num_unique_values 
[25.0] Remove ``num_unique_values`` tiff metadata element
 2025-06-22 08:32:30 +02:00
mvdbeek 43feb0efb3 Merge branch 'release_24.2' into release_25.0 2025-06-19 10:17:22 +02:00
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
davelopez 53ace94468 Add unit test for conditional Redis configuration 2025-06-18 14:50:01 +02:00
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
Nicola Soranzo 90fad91813 Merge branch 'release_24.2' into release_25.0 2025-06-08 21:47:42 +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
mvdbeek a4bad06a06 Merge branch 'release_24.2' into dev 2025-05-16 16:24:49 +02:00
mvdbeek 3eaa78b745 Fix job rerun for dynamic tools 
Fixes https://github.com/galaxyproject/galaxy/issues/20255
 2025-05-16 12:17:42 +02:00
John Chilton 631e33f5bd Merge pull request #19716 from jmchilton/fix_citation_handling 
[24.2] Fix #19515 - invalid citation handling changed with 24.2.
 2025-05-13 13:04:22 -04:00
mvdbeek 73c72b8fc7 Fix unit test import 2025-05-12 12:29:43 +02:00
mvdbeek e6b0783194 Enable (Javascript) requirements on frontend/backend 2025-05-12 10:54:42 +02:00
mvdbeek 152bc2ffa5 Add runtime model to API 
Like job_internal but replaces dataset and dataset collection with file
and array / object of files.
 2025-05-12 10:54:30 +02:00
mvdbeek a6d6477122 Bypass global toolbox for unprivileged tools 2025-05-12 10:54:23 +02:00
mvdbeek eb38fd8ec9 Merge branch 'release_24.2' into dev 2025-05-12 09:05:28 +02:00
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
John Chilton 518fa136d9 [WIP] Implement records - heterogenous dataset collections. 
Existing dataset colleciton types are meant to be homogenous - all datasets of the same time. This introduces CWL-style record dataset collections.
 2025-05-09 16:38:19 -04:00
John Chilton 8e3e86a706 Option for add_column_regex to be unmatched, improved testing. 
Can easily be combined concatenate and such to get conditionals on rewriting values. Used for new tests in new collection types branch that mirror I think useful, real-world examples. Also extends the test framework a bit to allow testing errors during evaluation and not just errors that can be caught statically by inspecting the rule itself.
 2025-05-09 16:38:18 -04:00
Marius van den Beek 9fb00287e4 Merge pull request #20054 from davelopez/explore_rocrate_import 
Add ZIP explorer to import individual files from local or remote ZIP archives
 2025-05-09 12:07:14 +02:00
Marius van den Beek de1e356e35 Merge pull request #18628 from rhpvorderman/singularity_settings 
Isolate singularity containers more thoroughly for better reproducibility.
 2025-05-09 11:39:50 +02:00
Ruben Vorderman 9eb9274cb5 fix tests for singularity 2025-05-09 09:27:53 +02:00
davelopez e73723b3e2 Add test to ensure local file access is restricted 2025-05-08 23:57:55 +02:00
davelopez f080d5d73e Add basic test for remote zip extractor file source 2025-05-08 23:51:48 +02:00
pauldg d1ac29c049 a basic template and an ssl template 2025-05-08 23:40:03 +02:00
pauldg 2b5d35ffc5 added unit test 2025-05-08 23:40:01 +02:00
John Davis 421d43eabb Merge pull request #16696 from natefoo/clean-working 
Run the tool working dir backup/restore on Pulsar
 2025-05-08 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
mvdbeek b99112c337 Fix DataCollectionParameterModel factory 2025-05-06 14:23:23 +02:00
Marius van den Beek 2266a09e68 Merge pull request #20158 from mvdbeek/yaml_parser_fixes 
Yaml parser fixes and improvements (part 1)
 2025-05-06 09:25:58 +02:00
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
Marius van den Beek 48423962ca Merge pull request #20004 from mvdbeek/dataset_collection_support_in_landing_request 
Implement dataset collection support in workflow landing requests
 2025-05-05 19:24:53 +02:00
mvdbeek bd05b3d0e1 Settle on type instead of reftyp inside xref 
We could also make it an alias, but it seems muich simpler to not refer
to the same attribute with different names. So far this has used
internally only.
 2025-05-05 19:07:27 +02:00
mvdbeek 073acf5801 Add typing around get_tool / has_tool 2025-05-05 15:16:31 +02:00
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