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41575 Commits
Author SHA1 Message Date
mvdbeek 0e7ee07cac Keep using history panel item edit button in selenium 
New tab needs to be disabled if dataset is running, can follow up later.
 2025-05-14 20:37:29 +02:00
mvdbeek ce0e0f6b24 Selenium fixes 2025-05-14 20:37:28 +02:00
Dannon Baker a0220694ee Drop all-datatypes visualization mapping endpoint 
We have this for edam data, formats, sniffers, etc., though.  It's a
pattern we should make a decision on -- these may be better implemented
as a set of requested keys on the main datatypes summary and exposed
independently on the datatype detail endpoint that has been added.
 2025-05-14 08:50:34 -04:00
Dannon Baker 85c55ac094 Drop unused import 2025-05-14 08:50:34 -04:00
Dannon Baker 764dbcde8f Add default visualization plugins for GeoJSON and VitessceJSON datatypes; include TIFF viewer for TIFF datatype 2025-05-14 08:50:34 -04:00
Dannon Baker 4d5d834327 Drop 'default_params' concept for preferred viz, for now -- this is extra admin/configuration burden without much benefit at this point 2025-05-14 08:50:34 -04:00
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 
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 
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 
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 
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 
IT Activity Panel
 2025-05-13 16:22:28 +02:00
Marius van den Beek 30bedf3787 Merge pull request #20165 from martenson/aai-updates 
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 
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 
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 
Package fixes
 2025-05-12 21:51:06 +01:00
Marius van den BeekandNicola Soranzo 7d53bd61c0 Fix import order 
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 
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