Commit Graph
20059 Commits
Author SHA1 Message Date
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
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
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
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
Nicola Soranzo 39bb35bebc Merge branch 'release_24.2' into dev 2025-01-13 16:10:31 +00:00
Dannon e453ca1da5 Merge pull request #19389 from dannon/chatgxy-fixes
[24.2] Fix to only show ChatGXY when available.
2025-01-09 15:08:18 -05:00
Ahmed Awan 89baf0bdc2 hide upload help after one viewing and add Rule-based info to it
Fixes https://github.com/galaxyproject/galaxy/issues/19334
2025-01-09 13:11:34 -06:00
John Chilton fed368f394 Merge pull request #19373 from jmchilton/upload_tab_optional
[24.2] Fix to not display upload when creating collections from existing datasets.
2025-01-09 11:34:02 -05:00
John ChiltonandAhmed Hamid Awan 9023ef3aed Update client/src/components/Collections/common/CollectionCreator.vue
Co-authored-by: Ahmed Hamid Awan <qe66653@umbc.edu>
2025-01-09 09:39:33 -05:00
mvdbeek 01e912ae3c Adjust client unit tests to conditional console rendering 2025-01-09 10:56:39 +02:00
Dannon Baker 1349d27610 Only show error wizard when llm api is configured 2025-01-08 23:21:00 -05:00
Nicola Soranzo cd999d2a86 Merge branch 'release_24.2' into dev 2025-01-07 22:27:15 +00:00
John Chilton 22bae10ec3 Fixes for console logging. 2025-01-07 12:21:59 -05:00
John Chilton 4ded93df09 Merge pull request #19378 from mvdbeek/node_22_fixes
Node 22 unreachable fixes
2025-01-07 11:41:41 -05:00
Ahmed Hamid Awan 6d0bff4b25 Merge pull request #19350 from guerler/fix_activity_panel_24.2
[24.2] Fix simple activity panel item style
2025-01-07 10:35:49 -06:00
mvdbeek 78af185a36 Node 22 unreachable fixes
Just some minor stuff that gets the client to compile
2025-01-07 16:53:36 +02:00
Nicola Soranzo 25d7ab42b4 Merge branch 'release_24.2' into dev 2025-01-03 13:09:06 +00:00
John Chilton b2e2053431 Don't show upload files option when selecting datasets. 2025-01-02 16:21:04 -05:00
John Chilton 1bbe39c57a Refactor no items message out of collection creator for reuse. 2025-01-02 16:21:04 -05:00
John Chilton d20672096c Refactor collection creator footer buttons into a component. 2025-01-02 16:21:04 -05:00
John Chilton df03361852 Refactor showing of extensions into own component. 2025-01-02 16:21:04 -05:00
John Chilton 40eb1d9aab Refactor collection creator help out to simplify. 2025-01-02 16:21:04 -05:00
John Chilton e6742ed4e1 Refactor the source options out of collection creator. 2025-01-02 16:21:04 -05:00
John Chilton 5229449c95 Refactor collection name input out of CollectionCreator. 2024-12-30 19:17:57 -05:00
Laila Los 1015134c0c Merge pull request #19351 from ElectronicBlueberry/fix-id-assignment
[24.2] Fix handling of step id offsets when duplicating selections
2024-12-20 22:14:19 +01:00
mvdbeek b88a792b93 Merge branch 'release_24.2' into dev 2024-12-20 11:19:56 +01:00
Nicola Soranzo 4fa092c860 Merge branch 'release_24.1' into release_24.2 2024-12-19 15:45:08 +00:00
Nicola Soranzo 8f0465f0ca Merge branch 'release_24.0' into release_24.1 2024-12-19 15:18:45 +00:00
Laila Los 09fb715a66 fix link assignment 2024-12-19 14:29:27 +01:00
Laila Los 4fac7daae3 fix stepIdOffset handling 2024-12-19 13:40:27 +01:00
guerler fa30172938 Fix styling of visualization items 2024-12-19 09:27:44 +03:00
guerler c159aa4da2 Remove unused no-highlight class, since item is a button 2024-12-19 09:27:36 +03:00
guerler 15115ffa04 Remove unused styles from activity settings panel 2024-12-19 09:27:30 +03:00
davelopez 173f170736 Fix reactive reference for selection change warning dismissal 2024-12-18 18:33:45 +01:00
Marius van den Beek 4684800641 Merge pull request #19340 from guerler/consistent_help_popper
Use popper wrapper for help text popover
2024-12-18 14:45:55 +01:00
guerler eda3b0e0c8 Adjust margin 2024-12-18 13:05:30 +03:00
Nicola Soranzo 9e2a3ccfab Replace deprecated `example parameter of fastapi.Path()`
See https://fastapi.tiangolo.com/reference/parameters/#fastapi.Path
2024-12-17 19:58:32 +00:00
guerler 8347fc55c5 Add margin to popper 2024-12-17 20:47:15 +03:00
guerler f415007ec0 Fix type warning in help term wrapper 2024-12-17 20:47:14 +03:00
guerler 0adae47772 Use popper to show help text items 2024-12-17 20:47:14 +03:00
John Chilton 16ec912385 Merge pull request #19337 from guerler/consistent_popper
Refactor and add tests for Popovers
2024-12-17 12:10:57 -05:00