Dannon Baker
8111f85ab2
Don't load top-level visualization_mappings in datatypes_conf -- we pushed these to indivdual datatypes.
2025-05-14 08:50:34 -04:00
Dannon Baker
6bbf6321fa
Swap configuration of default dataset viz to be specified inline with the datatype.
2025-05-14 08:50:34 -04:00
Dannon Baker
f8c739efde
Adds a new /api/datatypes/{datatype} endpoint
...
provides comprehensive information about a specific datatype in a single
response, consolidating information previously spread across multiple
endpoints, and adds a bit new.
2025-05-14 08:50:33 -04:00
Dannon Baker
47ca870ae4
Adjust datatypes preferred viz API /datatypes/{type}/visualizations
2025-05-14 08:50:33 -04:00
Dannon Baker
a1ce48a282
Preferred viz rough sketch
2025-05-14 08:50:33 -04:00
Dannon Baker
959b8bd00b
Sketch out initial dataset view component
2025-05-14 08:32:21 -04:00
Dannon
eac679df74
Merge pull request #20100 from ahmedhamidawan/enhance_external_login
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Enhance external login interface styling
2025-05-14 08:20:25 -04:00
Dannon
8e3501aff7
Merge pull request #19786 from ahmedhamidawan/make_private_make_history_inaccessible
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Add history sharing and accessibility management view
2025-05-14 07:54:36 -04:00
Bjoern Gruening
b2340aa66e
fix NFDI auth
2025-05-13 21:21:22 +02:00
Marius van den Beek
546aee0a58
Merge pull request #20166 from simonbray/replacement-dataset-filter-collection
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Add replacement_dataset option to collection filter tools
2025-05-13 19:28:31 +02:00
Marius van den Beek
d832488dd9
Merge pull request #20194 from nsoranzo/type_annot_galaxy.model.dataset_collections
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Improve type annotation of ``galaxy.model.dataset_collections``
2025-05-13 17:48:28 +02:00
mvdbeek
665269ce66
Add tools to tool config
2025-05-13 17:47:33 +02:00
Marius van den Beek
9dbe398e82
Merge pull request #19996 from dannon/it-panel
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IT Activity Panel
2025-05-13 16:22:28 +02:00
Marius van den Beek
30bedf3787
Merge pull request #20165 from martenson/aai-updates
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add three AAI providers
2025-05-13 16:18:15 +02:00
Marius van den Beek
2ed928ec6e
Merge pull request #20210 from guerler/allow_anon_viz
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Enable visualizations for anonymous user
2025-05-13 16:09:17 +02:00
Nicola Soranzo
b9a273925b
Improve type annotation of `galaxy.model.dataset_collections`
2025-05-13 15:07:47 +01:00
mvdbeek
490766e539
Keep old and new version
2025-05-13 15:47:48 +02:00
Marius van den Beek
6ecb8f2770
Merge pull request #20058 from bgruening/markdown_tool_help_lint
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fix linting with markdown in tool help
2025-05-13 15:20:38 +02:00
guerler
965d83e039
Add a grid to display visualizations shared with me
2025-05-12 21:19:40 -04:00
guerler
dc1b870893
Allow access to shared visualizations
2025-05-12 21:00:57 -04:00
guerler
6cf1f5bff4
Enable visualizations for anonymous user
2025-05-12 20:47:54 -04:00
Nicola Soranzo
61075f1ee9
Merge pull request #20208 from nsoranzo/missing_pkg_deps
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Package fixes
2025-05-12 21:51:06 +01:00
Marius van den Beek and Nicola Soranzo
7d53bd61c0
Fix import order
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Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2025-05-12 19:37:52 +02:00
Nicola Soranzo
bb87560d8f
Move definition of `DatasetCollectionDescriptionT` before its use
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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()`.
```
Also:
- Removed unused types:
- `IncomingNotRequiredDatasetCollectionDescriptionT`
- `IncomingNotRequiredDatasetCollectionDescription`
- `IncomingToolOutputBaseModel`
2025-05-12 17:31:36 +01:00
mvdbeek
634ddce7de
Move UnprivilegedToolResponse into api
2025-05-12 18:02:06 +02:00
Dannon Baker
f2852f0406
Add icon to the tool dict -- already loaded, no extra cost other than minor data over the wire
2025-05-12 10:07:24 -04:00
mvdbeek
d2597738cb
Make to_cwl compatible with pulsar
2025-05-12 10:54:56 +02:00
mvdbeek
259bee364b
Don't set tool if we don't have a tool dir
2025-05-12 10:54:55 +02:00
mvdbeek
e73ec140ca
Rebuild client schema
2025-05-12 10:54:54 +02:00
mvdbeek
b007fc1341
Subclass generic for readable model title
2025-05-12 10:54:53 +02:00
mvdbeek
7c52e9fc79
Skip unprivileged tool resolution if we don't have appropriate permissions
2025-05-12 10:54:53 +02:00
mvdbeek
74a6f31f4f
Implement roles to restrict custom tool permissions
2025-05-12 10:54:52 +02:00
mvdbeek
40e1be1632
Fix up tool source display for user tools
2025-05-12 10:54:52 +02:00
mvdbeek
9815e8204c
Move dynamic_tool_models to tool_util_models
2025-05-12 10:54:50 +02:00
mvdbeek
fde572dfc0
Update import path
2025-05-12 10:54:50 +02:00
mvdbeek
86e823304f
Add missing `Literal` import
2025-05-12 10:54:49 +02:00
mvdbeek
1ea07735c2
Don't require validators for select parameters
2025-05-12 10:54:49 +02:00
mvdbeek
1c8090e7ad
Fix local import in __resolvers_dict
2025-05-12 10:54:47 +02:00
mvdbeek
c3e167bba4
Move dynamic tool models to tool_util
2025-05-12 10:54:47 +02:00
mvdbeek
ddaf5d3021
Fix linting issues with new API routes
2025-05-12 10:54:46 +02:00
mvdbeek
22d111e0ac
Add required name and version to embedded tool
2025-05-12 10:54:45 +02:00
mvdbeek
4ae1ea2010
Fix toolbox.get_tool return type annotation
2025-05-12 10:54:45 +02:00
mvdbeek
ef409b27c2
Fix admin tool deactivation, dynamic tool endpoint mixup
2025-05-12 10:54:45 +02:00
mvdbeek
280208f777
Fix duplicate import
2025-05-12 10:54:44 +02:00
mvdbeek
d9ea2fde61
Type fixes for workflow_run_dict
2025-05-12 10:54:44 +02:00
mvdbeek
a52b78bf16
Add a few annotations to test out schema info rendering
2025-05-12 10:54:44 +02:00
mvdbeek
e6b0783194
Enable (Javascript) requirements on frontend/backend
2025-05-12 10:54:42 +02:00
mvdbeek
791ab043ff
Exclude defaults from unprivileged tool api response
2025-05-12 10:54:32 +02:00
mvdbeek
301bb62974
Use native type discriminator for UserToolSource model
2025-05-12 10:54:32 +02:00
mvdbeek
152bc2ffa5
Add runtime model to API
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Like job_internal but replaces dataset and dataset collection with file
and array / object of files.
2025-05-12 10:54:30 +02:00
Dannon Baker