opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-10-31 10:32:11 +08:00
Code Issues Packages Projects Releases Wiki Activity
84,057 Commits 64 Branches 246 Tags
543b395a432c195e0efce1d8f94deaba61ebafae
Commit Graph
21929 Commits
Author SHA1 Message Date
davelopez bf39fe242a Fix error handling in workflow load function 2025-07-03 14:00:16 +02:00
Alireza Heidari 8cc3267c0a Adds route name for dataset details view 
Adds a name property ("DatasetDetails") to the dataset view route to use reference in router.
 2025-06-25 19:44:29 +02:00
David López cd40df30f2 Merge pull request #20558 from itisAliRH/fix-25-workflow-invocation-report-pdf 
[25.0] Fix workflow invocation report pdf generate
 2025-06-25 15:53:45 +02:00
Alireza Heidari e20dd61634 Refactors workflow report PDF download 
Replaces `StsDownloadButton` with a conditional `GButton` for direct PDF downloads.
Removes unused `directDownloadLink` prop and related logic from `StsDownloadButton`.

Use `outline` prop in `AsyncButton`.
 2025-06-25 14:22:34 +02:00
Alireza Heidari a5557a7579 Adds support for direct download links in markdown exports 
Adds a `directDownloadLink` prop to enable direct file downloads without an intermediate storage API call.
Fix WF invocation report pdf download
 2025-06-25 12:56:14 +02:00
Martin Cech 655da84087 Merge pull request #20550 from dannon/activity-bar-order-fix 
[25.0] Fix activity bar reordering persistence
 2025-06-25 09:16:54 +02:00
Dannon Baker 60ebeb7781 Fix PDF preview functionality in dataset view 
This is a quick fix for 25.0, but I want to think more about the right
way to annotate these more cleanly moving froward.  PDFs were being
caught by auto-download logic instead of rendering inline due to their
display_behavior setting, now explicitly handle PDFs before
auto-download check to restore browser-based PDF viewing.
 2025-06-24 09:51:38 -04:00
Dannon Baker dabbe3359b Fix activity bar reordering persistence 
Activity bar reordering was broken when the activities computed property
was changed from a direct store reference to a read-only computed
property with filtering.

Fixes #20499
 2025-06-24 09:20:36 -04:00
Marius van den Beek 8903af6964 Merge pull request #20534 from ahmedhamidawan/fix_can_rename_nested_pair 
[25.0] Prevent DCE collections from being renamed
 2025-06-22 08:31:56 +02:00
Ahmed Awan 97aa3a3add fix AXE error 2025-06-21 17:31:54 -05:00
Nate Coraor 751b52f1ec Start work on 25.0.2.dev0 2025-06-20 16:37:11 -04:00
Nate Coraor 5915a88342 Create version 25.0.1 2025-06-20 16:37:07 -04:00
Ahmed Awan a90c1c3d04 adds a title to the click to edit component to make enter to save obvious 2025-06-20 12:20:57 -05:00
Ahmed Awan bfd1f3347a [25.0] Prevent DCE collections from being renamed 
Fixes https://help.galaxyproject.org/t/how-can-i-rename-a-paired-fastq-file/15784

Adds a `renameable` prop to `DetailsLayout` in addition to the existing `writeable` prop, because this way, we allow anonymous user histories to still be renamed (https://github.com/galaxyproject/galaxy/issues/20197) and in the case of the collection layout, DCEs are made not-renamaeable and unwriteable.
 2025-06-20 12:18:27 -05:00
Ahmed Awan 0d223a99b2 Start work on 25.0.1.dev0 2025-06-18 11:59:57 -05:00
Ahmed Awan b15565d03e Create version 25.0.0 2025-06-18 11:59:32 -05:00
davelopez a74b71b6ed Allow workflow description to show full text 2025-06-18 10:10:03 +02:00
Ahmed Awan 0a97c8d580 remove save button from ClickToEdit; add a enter/return key icon instead 2025-06-17 13:40:42 -05:00
Ahmed Awan ddc01be984 fix selenium selector for adding item to list in multiselect 
It keeps clicking the click to edit somehow, so I had to scope the selector to the hid span.
 2025-06-17 13:40:42 -05:00
Ahmed Awan ede0271056 align the input field for changing identifier better 2025-06-17 13:40:41 -05:00
Ahmed Awan 6849af3ef6 allow rename in workingElements and inListElements 2025-06-17 13:40:41 -05:00
Ahmed Awan 385acddbf8 Follow up to 20442 
https://github.com/galaxyproject/galaxy/pull/20442 contained an unresolved comment for reverting the renaming of elements to the multiselect, and also removing the Rename/Reordering modal entirely. Here are the changes proposed in that comment.
 2025-06-17 13:40:41 -05:00
Dannon Baker 72568a72f9 Add click-to-toggle fluid scaling for DatasetAsImage 
Users can now click on images in DatasetView to switch between scaled
and actual size. This helps deal with browser scaling weirdness while
keeping things simple.
 2025-06-16 16:34:05 -04:00
Dannon Baker 23d2e0520c Replaces iframe-based display with DatasetAsImage component for image 
datasets in the preview tab. This provides better image scaling control
and consistent display behavior across browsers, addressing Chrome's
automatic image scaling in iframes.
 2025-06-16 11:14:25 -04:00
Marius van den Beek 8fb5418bcd Merge pull request #20480 from mvdbeek/fix_workflow_graph_fit 
[25.0] Don't fit workflow if it doesn't have steps
 2025-06-16 13:55:35 +02:00
Marius van den Beek 8b9de36a30 Merge pull request #20246 from guerler/replace_bootstrap_popper 
[25.0] Replace Bootstrap Popover with Popper wrapper
 2025-06-16 13:53:11 +02:00
Marius van den Beek 1d8b6247e7 Merge pull request #19900 from ahmedhamidawan/form_data_various_fixes 
[25.0] More fixes to `FormData` drag and drop and typing
 2025-06-16 13:47:57 +02:00
mvdbeek 390f25bb18 Fix handling of step.workflow_outputs, which might be undefined 
Fixes https://github.com/galaxyproject/galaxy/issues/20316
 2025-06-16 12:07:13 +02:00
mvdbeek 6be802563e Don't fit workflow if it doesn't have steps 
Fixes https://github.com/galaxyproject/galaxy/issues/19667 and
https://github.com/galaxyproject/galaxy/issues/20242
 2025-06-16 11:56:52 +02:00
Marius van den Beek c71e529cd1 Merge pull request #20468 from mvdbeek/extra_files_path 
[25.0] Add ``/api/datasets/{dataset_id}/extra_files/raw/{filename:path}``
 2025-06-16 10:17:31 +02:00
Ahmed Awan 0e7596d496 show loading span for dataset error details view 2025-06-15 20:40:32 -05:00
Ahmed Awan ee88f52d73 [25.0] Fix dataset error button not using router 
Fixes https://github.com/galaxyproject/galaxy/issues/20471
 2025-06-15 20:39:46 -05:00
mvdbeek f928b08fa7 Add `/api/datasets/{dataset_id}/extra_files/raw/{filename:path}` 
We need this for the vitessce visualization, that will build urls based
on the path of the current url. In practice, to get the file expected at `obs/.zattrs` the
visualization will build
https://usegalaxy.org/api/datasets/f9cad7b01a4721358531a44ecfb1aff6/display/obs/.zattrs?filename=A/1/bdbd683b-1870-4c11-ae29-b35ff0be59b2.adata.zarr,
because it reasonably assumes the query parameter is independent of the
path.
With this change we can access the file in question via
https://usegalaxy.org/api/datasets/f9cad7b01a4721358531a44ecfb1aff6/extra_files/raw/A/1/bdbd683b-1870-4c11-ae29-b35ff0be59b2.adata.zarr/obs/.zattrs.
 2025-06-15 16:10:49 +02:00
Ahmed Hamid Awan df51b26889 Merge pull request #20459 from jmchilton/auto_pairing_fix 
[25.0] Fix bug with handling compressed file names while auto-pairing.
 2025-06-14 17:31:36 -05:00
John Chilton 5194738cb5 Fix auto pairing for compressed file handling. 2025-06-13 16:59:12 -04:00
John Chilton 5268cb855e Declarative testing of auto-pairing code. 2025-06-13 16:59:09 -04:00
John Chilton 337678769c Bug fix: paired_or_unpaired also endswith paired. 2025-06-13 16:46:01 -04:00
Marius van den Beek 514c169e0c Merge pull request #20442 from ahmedhamidawan/list_collection_creator_style_fixes 
[25.0] Fix inconsistent styling in List Collection Builder selector
 2025-06-13 21:19:01 +02:00
Marius van den Beek 8e27ecae10 Merge pull request #20457 from davelopez/25.0_update_tiffviewer 
[25.0] Update tiffviewer to latest version supporting more formats
 2025-06-13 21:16:57 +02:00
Marius van den Beek f667ce8d08 Merge pull request #20456 from ahmedhamidawan/fix_remote_file_upload_in_collection 
[25.0] Fix multiple remote file upload to collection creator
 2025-06-13 20:37:49 +02:00
davelopez 29c2c11c72 Update TIFF viewer to latest installable version 2025-06-13 20:02:04 +02:00
Ahmed Awan e18910f19c fix duplicates being pushed to uploadedDatasets from upload values 
In the case of remote file uploads, for each upload value, we have the entire set of uploads in the `model.outputs` object, which would cause the same dataset to appear multiple times in the `uploadedHistoryItems` object.

For other, non-remote uploads, we typically only have the matching output for the upload value in the `model.outputs` object.
 2025-06-13 12:32:39 -05:00
Ahmed Awan 2ccc5851cc [25.0] Fix multiple file upload to collection creator 
Fixes https://github.com/galaxyproject/galaxy/issues/20454

The `if` condition in `addUploadedFiles` in `ListCollectionCreator` was incorrectly flagging uploaded items as invalid if they've already been added to the list once, and the function is called again.
 2025-06-13 11:59:33 -05:00
Dannon Baker ca8d869b5e Refactor, cleanup. 2025-06-13 12:47:40 -04:00
Dannon Baker 39ad160d7c Use persistentRef instead 2025-06-13 12:00:41 -04:00
Ahmed Awan 464e1f4aa4 show the hid and extension (if applicable) to the rename modal elements 2025-06-13 10:50:14 -05:00
Dannon Baker ae52282ed3 persist library entries per page to localstorage 2025-06-13 11:39:55 -04:00
Alireza Heidari 4eab3488cc Fix pagination state in FilesDialog 
Remember last page when navigating back
 2025-06-13 15:25:28 +02:00
Ahmed Awan 8c51407ae9 allow list elements to be reordered as well 2025-06-12 23:12:48 -05:00
Ahmed Awan a9a9f4a649 change "dataset name" to "element identifier"; only show identifiers 
(no `hid` or `extension`)
 2025-06-12 23:12:48 -05:00