Arash
ce52a72ebf
Update HDASerializer test to validate copied_from_history_dataset_association_id with assertNullableEncodedId
2025-07-28 09:15:22 +02:00
Marius van den Beek
cb93c7b976
Merge pull request #20502 from davelopez/add_redis_conditional_dependency
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[25.0] Add redis conditional dependency
2025-07-01 10:58:00 -04:00
mvdbeek
462955599b
Fix extension parsing for yaml tools
2025-06-22 19:22:59 -04:00
davelopez
53ace94468
Add unit test for conditional Redis configuration
2025-06-18 14:50:01 +02:00
mvdbeek
3eaa78b745
Fix job rerun for dynamic tools
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Fixes https://github.com/galaxyproject/galaxy/issues/20255
2025-05-16 12:17:42 +02:00
mvdbeek
a6d6477122
Bypass global toolbox for unprivileged tools
2025-05-12 10:54:23 +02:00
John Davis
421d43eabb
Merge pull request #16696 from natefoo/clean-working
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Run the tool working dir backup/restore on Pulsar
2025-05-08 16:38:19 -04:00
guerler
1057c1d6b9
Properly adjust for escaping parsed content
2025-04-22 21:25:29 -04:00
Aysam Guerler
fc18093c76
Merge pull request #20022 from guerler/parse_host_to_viz
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Pass host url to visualizations
2025-04-21 13:12:14 -04:00
guerler
67e7337e10
Add test case?
2025-04-16 11:28:35 -04:00
Laila Los
33723c313e
remove tags used from api
2025-04-16 13:07:05 +02:00
John Chilton
bfc612e1ed
Merge pull request #19962 from mvdbeek/job_cache_allow_different_names_when_possible
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Job cache allow different names when possible
2025-04-11 15:58:15 -04:00
mvdbeek
bfd3d1972a
WIP: if not accessing input.name, allow input.name to differ
2025-04-11 16:11:43 +02:00
Nicola Soranzo
47e546c4a3
Add some type annotations to `ToolParameter` classes
2025-04-11 10:04:02 +01:00
mvdbeek
ca5ea6f1e8
Fix test_execution unit tests
2025-04-07 17:26:31 +02:00
Ahmed Awan
449dcf5564
Merge remote-tracking branch 'upstream/release_24.2' into dev
2025-03-24 16:52:23 -05:00
Nicola Soranzo
b7591a0872
Improve type annotations of `ModelPersistenceContext` and derived classes
2025-03-20 12:46:35 +00:00
mvdbeek
3e767c940e
Add unit tests for queue_with_limit
2025-03-18 14:10:09 +01:00
Nicola Soranzo
4607d88509
Merge branch 'release_24.2' into dev
2025-03-17 12:00:29 +00:00
Marius van den Beek and Nicola Soranzo
c732a365e7
Improve test assertion
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Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2025-03-16 20:51:19 +01:00
mvdbeek
e2135d6e16
Mock unit test doi.org requests
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We're testing the cache, not the requests here.
2025-03-16 13:54:20 +01:00
Aysam Guerler
0d174f5ee8
Merge pull request #19721 from guerler/preserve_invocation_id
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Preserve workflow labels in final invocation reports
2025-03-09 14:51:28 -04:00
mvdbeek
eb1709fcbb
Merge branch 'release_24.2' into dev
2025-03-08 11:20:03 +01:00
guerler
09d69e4fb6
Adjust test case
2025-03-06 22:09:36 -05:00
John Davis
0d81abe114
Skip slow tests for manage_db, db_dev scripts
2025-03-05 10:57:19 -05:00
Nicola Soranzo
5467231fd3
Use model classes from `galaxy.model instead of app.model` object - Part 2
2025-02-28 16:20:17 +00:00
Nicola Soranzo
9477c7773e
Use model classes from `galaxy.model instead of app.model` object
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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
John Chilton
17177d45eb
Merge pull request #19642 from nsoranzo/type_annot
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Type annotation improvements
2025-02-25 12:07:07 -05:00
Nicola Soranzo
ea1f245181
Merge branch 'release_24.2' into dev
2025-02-24 15:59:51 +00:00
Nicola Soranzo
0f1bfb6839
Type annotation improvements
2025-02-21 15:46:14 +00:00
Nate Coraor
a987e3ddc6
Fix test
2025-02-19 13:09:00 -05:00
mvdbeek
8c4149b094
Fix dependency structure for ParameterOption
2025-02-19 17:57:49 +01:00
mvdbeek
c3cf80fc75
Fix data table filters that operate on `value` field
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This is a little cleaner. Also replaces the `list[tuple[str, str,
bool]]` return type of get_options with a NamedTuple.
Fixes https://github.com/galaxyproject/galaxy/issues/19609
2025-02-19 15:05:35 +01:00
Nicola Soranzo
7ce76af796
Format code with black 25.1.0
2025-02-16 18:07:51 +00:00
mvdbeek
2e6841680c
Merge branch 'release_24.1' into release_24.2
2025-01-28 15:55:05 +01:00
mvdbeek
57b8311b8b
Fix unit test
2025-01-27 16:14:16 +01:00
John Davis
dee88049f5
Remove transaction helper from test.unit.app.tools
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Note: app.model.context.current == app.model.context. The `current` attr
may have been a very legacy attribute still silently supported.
2025-01-23 11:39:24 -05:00
John Davis
1ce27e3fcb
Remove transaction helper from test.unit.app.managers
2025-01-23 11:39:24 -05:00
John Davis
a26cd0f359
Remove transaction helper from test.unit.app.jobs
2025-01-23 11:39:24 -05:00
John Davis
16e18d404e
Merge pull request #19395 from mvdbeek/alternative_format_source_fix
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Alternative `format_source` fix
2025-01-23 10:54:03 -05:00
Nicola Soranzo
8797f1e4ef
Make `InstallationTarget` a runtime-checkable protocol
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Also:
- Reuse its `installed_repository_manager` attribute instead of
instantiating a `InstalledRepositoryManager` in several places.
2025-01-22 23:14:48 +00:00
David López
28e5f7d84b
Merge pull request #19154 from kysrpex/file_sources_assign_paths
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Let file sources choose a path for uploaded files
2025-01-20 16:11:57 +01:00
Nicola Soranzo
f799a996e1
Ignore mypy unused-ignore error on Python >=3.10
2025-01-13 12:00:55 +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
José Manuel Domínguez
6fe92643af
Merge branch 'dev' into file_sources_assign_paths
2024-11-28 13:11:29 +01:00
Nicola Soranzo
26a4e146e0
Fix UP031 errors
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reported by ruff 0.8.0 .
2024-11-24 21:35:23 +00:00
José Manuel Domínguez
53012bf059
Let file sources choose a path for uploaded files
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The method `write_from()` of `SingleFileSource` and `BaseFilesSource` reads a local file from `native_path` and saves it to `target_path` on a file source.
This commit allows the service backing the file source to choose which will be the path of the saved file, meaning that `target_path` and the actual path where the file can be recovered later do not have to match. The latter is the return value of `write_from()`.
Therefore, all usages of `write_from()` have also been refactored to consider the paths chosen by the file source's backing service. In addition, when exporting a history, the URI that the service backing the file source assigns to it will be saved to the history export result metadata object.
2024-11-18 17:02:29 +01:00
John Chilton
b3f68a366d
Fixes for rebase of 18781 (workflow regex validators).
2024-11-13 09:50:21 -05:00
mvdbeek
0d5c5116db
Fix unit tests
2024-11-13 09:50:20 -05:00
Arash