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Author SHA1 Message Date
John Davis 16e18d404e Merge pull request #19395 from mvdbeek/alternative_format_source_fix 
Alternative `format_source` fix
 2025-01-23 10:54:03 -05:00
Nicola Soranzo e2636d774f Merge pull request #19442 from nsoranzo/type_annot 
Type annotations improvements
 2025-01-23 13:53:58 +00:00
Nicola Soranzo a79f518f49 Proper subclassing of `ModelManager` generic class 2025-01-22 23:18:53 +00:00
Nicola Soranzo 345d7a588b Add type annotations 2025-01-22 23:18:53 +00:00
Nicola Soranzo 8797f1e4ef Make `InstallationTarget` a runtime-checkable protocol 
Also:
- Reuse its `installed_repository_manager` attribute instead of
  instantiating a `InstalledRepositoryManager` in several places.
 2025-01-22 23:14:48 +00:00
Nicola Soranzo 0f3a870be5 Fix typos 2025-01-22 23:14:48 +00:00
Aysam Guerler 42f190ea43 Merge pull request #19227 from guerler/vitessce 
Add Vitessce Viewer
 2025-01-22 10:32:16 -05:00
Nicola Soranzo 4a2bdac98b Merge branch 'release_24.2' into dev 2025-01-22 09:33:23 +00:00
Martin Cech d1ea6dd3a2 Merge pull request #19308 from guerler/fix_winbox_style 
[24.2] Fixes window manager scrolling and resizing
 2025-01-22 09:30:27 +01:00
Ahmed Awan 3baafc2477 Merge remote-tracking branch 'upstream/release_24.1' into HEAD 2025-01-21 10:24:32 -06:00
Marius van den Beek b0fe8c9dbf Merge pull request #19423 from ahmedhamidawan/catch_errors_in_toolStore 
[24.1] Catch errors in `toolStore` and `ToolPanel`
 2025-01-21 14:55:56 +01:00
Laila Los f3e9ff4eef Merge pull request #19426 from ElectronicBlueberry/fix-ref-sync 
[24.2] Fix Activity Bar state lost on page reload
 2025-01-21 14:14:04 +01:00
Laila Los 34d127254a fix synced ref resets empty values 2025-01-21 13:04:38 +01:00
Ahmed Awan 5ebece7168 [24.1] Catch errors in toolStore and ToolPanel 
Fixes https://github.com/galaxyproject/galaxy/issues/19422
 2025-01-20 13:17:56 -06:00
Laila Los 5f484fca62 Merge pull request #19420 from ElectronicBlueberry/duplicate-subworkflows-button 
Enable cloning subworkflows
 2025-01-20 18:30:58 +01:00
John Chilton a7fcdd3046 Merge pull request #19393 from ahmedhamidawan/hide_upload_help_after_one_view 
[24.2] Display upload help highlight only once and include Rule-based upload info
 2025-01-20 10:14:00 -05:00
David López 28e5f7d84b Merge pull request #19154 from kysrpex/file_sources_assign_paths 
Let file sources choose a path for uploaded files
 2025-01-20 16:11:57 +01:00
José Manuel DomínguezandDavid López 3b1516c0c5 Remove remark concerning ExportObjectResultMetadata model validation 
`ExportObjectResultMetadata.validate_uri()` includes commented out code as a remark for the reader that short term exports need not to have a URI as part of their result metadata. Remove this remark.

Co-authored-by: David López <46503462+davelopez@users.noreply.github.com>
 2025-01-20 15:14:15 +01:00
Laila Los 9d0ce932ef remove test counting i elements 2025-01-20 14:55:14 +01:00
Laila Los e1c9e7fb2e enable cloning 2025-01-20 13:58:59 +01:00
Nicola Soranzo 42bf463829 Merge pull request #19406 from nsoranzo/TarFile.extraction_filter 
Set safe default extraction filter for tar archives
 2025-01-18 16:48:01 +00:00
Nicola Soranzo 54df792117 Use CompressedFile.open_tar() to open tar files 2025-01-18 15:03:02 +00:00
Nicola Soranzo aa49793ecf Make CompressedFile a context manager 
to ensure that the archive is closed.
 2025-01-18 14:40:30 +00:00
Nicola Soranzo ccebdcb1f2 Set safe default extraction filter for tar archives 
[PEP 706](https://peps.python.org/pep-0706/), first implemented in Python
3.11.4, mitigates some of the security issues of `TarFile.extract()` and
`TarFile.extractall()` by allowing to specify a `filter` keyword-only
parameter.
Set a safe default (`data_filter`) for the filter if available,
reverting to Python 3.11 behavior ('fully_trusted') otherwise, see
https://docs.python.org/3/library/tarfile.html#supporting-older-python-versions

Also:
- Remove unused `tar` parameter from `upload_tar()`
 2025-01-18 14:40:29 +00:00
Nicola Soranzo 371242cbf7 Merge pull request #19418 from galaxybot/dev_auto_update_dependencies 
Update Python dependencies
 2025-01-18 12:27:48 +00:00
galaxybot b0ce7ccfa9 Update Python dependencies 
by running `make update-dependencies`.
 2025-01-18 03:06:32 +00:00
John Davis d18ab5495f Merge pull request #19414 from davelopez/24.1_fix_config_templates_validation 
[24.1] Fix config template validation for file sources and object store templates
 2025-01-17 09:41:00 -05:00
davelopez eef942a240 Add number coercion to string in StrictModel configuration 
This will workaround an issue with jinja templates rendering a field composed only by numbers to be considered a number when the field is of type string, causing the config model validation to fail. Trying to cast the value to string using the jinja template itself did not work.
 2025-01-17 11:22:27 +01:00
Martin Cech 4e781cd02e Merge pull request #19409 from jdavcs/dev_pagination_fix 
Prevent negative offset
 2025-01-16 11:12:02 +01:00
Martin Cech 2411fb8887 Merge pull request #19402 from jdavcs/dev_user_email_api_help 
Display email activation help only if user activation is enabled
 2025-01-16 11:10:27 +01:00
John Davis 75cf57adbc Prevent negative offset 2025-01-15 15:16:40 -05:00
José Manuel Domínguez 7a9a52af67 Add new field uri to ExportObjectResultMetadata model 
Write the actual URIs where files are saved to by file sources to a new `uri` field of the `ExportObjectResultMetadata` model. Restore behavior before commit 53012bf, namely setting the history export request metadata before attempting the export.

---

Before applying the set of changes from 53012bf, the method `ModelStoreManager.set_history_export_request_metadata()` instantiates a `ExportObjectMetadata` Pydantic model and dumps it to the database in the form of JSON as the field `StoreExportAssociation.export_metadata`. After the export is complete, the method `set_history_export_result_metadata()` takes the same instance of `ExportObjectMetadata`, instantiates a `ExportObjectResultMetadata` Pydantic model, sets it as the `result_data` of the `ExportObjectMetadata` instance, and then saves the `ExportObjectMetadata` Pydantic model in the form of JSON to the database again.

After applying the set of changes, the call to `ModelStoreManager.set_history_export_request_metadata()` is delayed until the file has already been saved to the file source, as the actual URI that the file source assigns to the file is otherwise unknown.

The URI assigned by the file source overwrites the original target URI in the request. This involves a slight deviation from the previous behavior: if for example, power gets cut at the right time, `StoreExportAssociation.export_metadata` may not exist despite the history having been already saved to the file source, because database writes happen within the `finally:` block.

Moreover, overwriting the original target URI from the request is formally wrong, because the actual URI assigned by the file source should be part of the export result metadata, as it becomes known when the export completes.

This commit addresses these issues by adding a new field `uri` to the `ExportObjectResultMetadata` model, where the actual URI the file has been saved to by the file source is written. Backwards compatibility is ensured via `HistoriesService._get_export_record_data()`, which retrieves the new field when available and otherwise uses `ExportObjectRequestMetadata.payload.target_uri` (given that `ExportObjectRequestMetadata.payload` is of type `WriteStoreToPayload`).
 2025-01-14 17:02:01 +01:00
John Davis 9fc0f05935 Merge pull request #19366 from galaxybot/dev_auto_update_dependencies 
Update Python dependencies
 2025-01-13 11:25:46 -05:00
Nicola Soranzo 39bb35bebc Merge branch 'release_24.2' into dev 2025-01-13 16:10:31 +00:00
Marius van den Beek 2d629d0f44 Merge pull request #19208 from bernt-matthias/OutputsFilterExpression-fixes 
[24.2]  Outputs filter linter fixes
 2025-01-13 18:09:06 +02:00
Nicola Soranzo bb438e1e8d Merge branch 'release_24.1' into release_24.2 2025-01-13 16:02:22 +00:00
John Davis c11908ff8b Merge pull request #19399 from nsoranzo/release_24.2_backport_19396 
[24.2] Backport fix from #19396
 2025-01-13 10:28:41 -05:00
John Davis 93b684e913 Display api help based on config 2025-01-13 10:13:52 -05:00
Nicola Soranzo e61121acab Use id entity attribute when setting exampleOfWork property 
Fix the following error in 3 unit tests when using rocrate 0.13.0 :

```
______________________ test_export_invocation_to_ro_crate ______________________

tmp_path = PosixPath('/tmp/pytest-of-runner/pytest-5/test_export_invocation_to_ro_c0')

    def test_export_invocation_to_ro_crate(tmp_path):
        app = _mock_app()
        workflow_invocation = _setup_invocation(app)
        crate_directory = tmp_path / "crate"
        with store.ROCrateModelExportStore(crate_directory, app=app) as export_store:
            export_store.export_workflow_invocation(workflow_invocation)
>       validate_invocation_crate_directory(crate_directory)

tests/data/model/test_model_store.py:627:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/data/model/test_model_store.py:564: in validate_invocation_crate_directory
    validate_create_action(crate)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

ro_crate = <rocrate.rocrate.ROCrate object at 0x7fb4673c2520>

    def validate_create_action(ro_crate: ROCrate):
        workflow = ro_crate.mainEntity
        actions = [_ for _ in ro_crate.contextual_entities if "CreateAction" in _.type]
        assert len(actions) == 1
        wf_action = actions[0]
        assert wf_action["instrument"]
        assert wf_action["instrument"] is workflow
        wf_objects = wf_action["object"]
        wf_results = wf_action["result"]
        assert len(wf_objects) == 1
        assert len(wf_results) == 1
        for entity in wf_results:
            if entity.id.endswith(".txt"):
                assert "File" in entity.type
                wf_output_file = entity
                assert wf_output_file["encodingFormat"] == "text/plain"
>               assert wf_output_file["exampleOfWork"] is workflow["output"][0]
E               AssertionError: assert '#d2ed04ef-36f8-49ae-86ce-47cb03a856c0' is <d2ed04ef-36f8-49ae-86ce-47cb03a856c0 FormalParameter>

tests/data/model/test_model_store.py:540: AssertionError
```

Also:
- Remove unused `_add_step_tool_pv` method.
 2025-01-13 13:04:45 +00:00
Björn Grüning 5c28aaf10b Merge pull request #19232 from guerler/update_visualizations_24.2 
[24.2] Update visualizations package versions
 2025-01-13 14:02:00 +01:00
Nicola Soranzo f799a996e1 Ignore mypy unused-ignore error on Python >=3.10 2025-01-13 12:00:55 +00:00
galaxybot 8dc0cf55cb Update Python dependencies 
by running `make update-dependencies`.
 2025-01-13 11:58:32 +00:00
Nicola Soranzo 0858e07821 Merge pull request #19396 from nsoranzo/ro_crate 
Use ``id`` entity attribute when setting ``exampleOfWork`` property
 2025-01-13 11:55:43 +00:00
mvdbeek f28ea20d46 Fix unit test 2025-01-10 23:37:11 +02:00
mvdbeek 7566674baa Fix type annotation resulting from annotating HDCA.collection 2025-01-10 23:37:10 +02:00
mvdbeek a0919d1117 Evaulate format_source (again) just before job submission 
At this point the inputs are ready, so expession.json has been replaced
with the true extension.
 2025-01-10 19:19:56 +02:00
mvdbeek 20dc7b7eae Simplify determine_output_format 2025-01-10 18:55:08 +02:00
mvdbeek f65b754dd0 Add regression test for https://github.com/galaxyproject/galaxy/issues/19245 2025-01-10 18:55:08 +02:00
Nicola Soranzo dad7c26a83 Use id entity attribute when setting exampleOfWork property 
Fix the following error in 3 unit tests when using rocrate 0.13.0 :

```
______________________ test_export_invocation_to_ro_crate ______________________

tmp_path = PosixPath('/tmp/pytest-of-runner/pytest-5/test_export_invocation_to_ro_c0')

    def test_export_invocation_to_ro_crate(tmp_path):
        app = _mock_app()
        workflow_invocation = _setup_invocation(app)
        crate_directory = tmp_path / "crate"
        with store.ROCrateModelExportStore(crate_directory, app=app) as export_store:
            export_store.export_workflow_invocation(workflow_invocation)
>       validate_invocation_crate_directory(crate_directory)

tests/data/model/test_model_store.py:627:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/data/model/test_model_store.py:564: in validate_invocation_crate_directory
    validate_create_action(crate)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

ro_crate = <rocrate.rocrate.ROCrate object at 0x7fb4673c2520>

    def validate_create_action(ro_crate: ROCrate):
        workflow = ro_crate.mainEntity
        actions = [_ for _ in ro_crate.contextual_entities if "CreateAction" in _.type]
        assert len(actions) == 1
        wf_action = actions[0]
        assert wf_action["instrument"]
        assert wf_action["instrument"] is workflow
        wf_objects = wf_action["object"]
        wf_results = wf_action["result"]
        assert len(wf_objects) == 1
        assert len(wf_results) == 1
        for entity in wf_results:
            if entity.id.endswith(".txt"):
                assert "File" in entity.type
                wf_output_file = entity
                assert wf_output_file["encodingFormat"] == "text/plain"
>               assert wf_output_file["exampleOfWork"] is workflow["output"][0]
E               AssertionError: assert '#d2ed04ef-36f8-49ae-86ce-47cb03a856c0' is <d2ed04ef-36f8-49ae-86ce-47cb03a856c0 FormalParameter>

tests/data/model/test_model_store.py:540: AssertionError
```

Also:
- Remove unused `_add_step_tool_pv` method.
 2025-01-10 15:13:14 +00:00
Nicola Soranzo 944450aa38 Uniform use of tmp_path in ro-crate tests 2025-01-10 15:12:17 +00:00