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
Dannon Baker
747c6d0b2b
Consolidate loading states, fix API imports.
2025-06-10 10:19:06 -04:00
Dannon Baker
75212d09d0
Swap datatypes info request to fetch client
2025-06-10 10:19:06 -04:00
Dannon Baker
3e9d1a9e97
Rebuild api schema
2025-06-10 10:19:05 -04:00
Dannon Baker
a92a3e3b48
Enhance API response for datatypes to include extra display information so the client can account for direct download vs preview, etc.
2025-06-10 10:19:05 -04:00
Laila Los
4e7f8dd32a
remove type import side-effects
2025-05-21 15:11:02 +02:00
mvdbeek
0e13bacee5
Provide more field annotations
2025-05-17 18:58:15 +02:00
Marius van den Beek
e807b0ff7c
Merge pull request #20190 from dannon/preferred-viz
...
Visualization-First Display functionality
2025-05-15 15:46:53 +02:00
Dannon Baker
2f306fa2c4
rebuild api schema
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
dabb154347
Remove viz default params linkage. Update datasetview loading state
...
handling of viz frame.
2025-05-14 08:50:34 -04:00
Dannon Baker
5701a1307a
Update client-api-schema
2025-05-14 08:50:33 -04:00
Dannon Baker
a673b2c4a8
rebase into endpoint adjustment
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
mvdbeek
da7498c144
Display invocation inputs and outputs in workflow report
...
As opposed to just the label as we've been doing before.
2025-05-14 12:17:43 +02:00
mvdbeek
e73ec140ca
Rebuild client schema
2025-05-12 10:54:54 +02:00
mvdbeek
74a6f31f4f
Implement roles to restrict custom tool permissions
2025-05-12 10:54:52 +02:00
mvdbeek
9c2f81e279
Add UserToolPanel
2025-05-12 10:54:24 +02:00
John Chilton
15757c7e4a
Rework type imports for collection stuff.
...
Didn't fix circular import but it simplifies it a bit.
2025-05-09 17:39:39 -04:00
John Chilton
219796f049
Implement paired_or_unpaired collections, list wizards.
2025-05-09 17:39:38 -04:00
John Chilton
17de736ccb
record ui.
2025-05-09 16:38:19 -04:00
John Chilton
518fa136d9
[WIP] Implement records - heterogenous dataset collections.
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Existing dataset colleciton types are meant to be homogenous - all datasets of the same time. This introduces CWL-style record dataset collections.
2025-05-09 16:38:19 -04:00
David López
bbeb1965fd
Merge pull request #20167 from kysrpex/rspace
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Implement file source to integrate Galaxy with RSpace
2025-05-09 13:56:59 +02:00
Marius van den Beek
9fb00287e4
Merge pull request #20054 from davelopez/explore_rocrate_import
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Add ZIP explorer to import individual files from local or remote ZIP archives
2025-05-09 12:07:14 +02:00
José Manuel Domínguez
10de12c5f1
Implement file source to integrate Galaxy with RSpace
...
This commit implements a FilesSource that interacts with an RSpace [1] instance and includes a file source template so that users can define their own file sources based on it.
RSpace is an electronic lab notebook
(ELN) designed for documenting, managing and sharing scientific data. The central concepts in RSpace are the Workspace,
the Inventory and the Gallery.
The Workspace's role is organizing and managing research activities. It allows creating documents, folders and research
notebooks [2]. The Inventory is a tool to keep track of laboratory resources, such as reagents, samples and equipment
[3]. The Gallery is where any research data represented as files is stored [4].
The FilesSource implemented by this module accesses the Gallery of an RSpace instance. The Gallery is organized in
categories (e.g. Images, Audio, Documents, Chemistry), where each category is itself a tree structure with folders and
files just like a regular filesystem, although there is a key difference: categories and their subfolders can only
contain files of certain types (e.g. jpeg, bmp, png, etc. for the Images category).
This implementation is based on the rspace-client-python` library [5], which provides a PyFilesystem2 [6] interface
to interact with RSpace's Gallery (available as `GalleryFilesystem` in the rspace_client.eln.fs` module). It
consists just of a minimal wrapper (based on the base `PyFilesystem2FilesSource` provided by Galaxy) around the
`GalleryFilesystem` class.
References:
- [1] https://www.researchspace.com/
- [2] https://documentation.researchspace.com/article/bzgr8ea9e3-the-workspace
- [3] https://documentation.researchspace.com/category/zpizk20kgx-inventory
- [4] https://documentation.researchspace.com/article/sl6mo1i9do-the-gallery
- [5] https://github.com/rspace-os/rspace-client-python
- [6] https://docs.pyfilesystem.org/
2025-05-09 12:04:46 +02:00
Marius van den Beek
a3bd5a0e71
Merge pull request #20032 from ahmedhamidawan/rerun_workflows
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Add rerun option for workflows
2025-05-09 09:45:24 +02:00
davelopez
e1f3b7d40c
Rename API module from remotezip to proxy
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As it doesn't have anything to do with remote zips really other that is the only use case for now
2025-05-08 23:57:46 +02:00
davelopez
c50bfb5eb1
Update client API schema
2025-05-08 23:57:43 +02:00
pauldg
f0feb755c4
fix client
2025-05-08 23:43:08 +02:00
pauldg
1d217cc10b
make client
2025-05-08 23:40:01 +02:00
Ahmed Awan
8a0b56c1d8
Add rerun option for invocations
...
Fixes https://github.com/galaxyproject/galaxy/issues/11340
2025-05-07 10:45:03 -05:00
davelopez
fc0920e065
add Rucio support to object store templates and messages
2025-05-07 16:10:49 +02:00
Yakubov, Sergey
76459116b3
update api schema
2025-05-07 16:10:48 +02:00
Ahmed Hamid Awan
d7fa1d19ce
Merge pull request #19054 from jmchilton/tool_markdown
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Implement tool markdown reports.
2025-05-06 20:49:30 +05:00
Nicola Soranzo
7861ecc73c
Rename tool "Citations" to "References"
...
and former "References" (xrefs) to "External links"
Fix https://github.com/galaxyproject/galaxy/issues/19740
2025-05-06 13:07:31 +01:00
Ahmed Awan
fc7f8bdeb8
show output collections as well on job success view
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Without this change, it wouldn't show anything after `It produces this output`
2025-05-05 13:49:52 -05:00
Ahmed Awan
e553dc6e3e
convert jobStore to composition API and type related files accordingly
2025-05-05 13:20:27 -05:00
John Chilton
9c1e7f29df
Small fixes from PR review.
2025-05-05 09:59:17 -04:00
John Chilton
00b97cb4bd
Better typing around collection API calls in client.
2025-05-02 18:36:33 -04:00
John Chilton
6440fdde22
Rebuild schema for tool markdown reports...
2025-05-02 11:25:21 -04:00
guerler
457c9471c5
Add hid to selection field in visualization creation form
2025-04-29 17:47:53 -04:00
Aysam Guerler
f2a83da66c
Merge pull request #20097 from guerler/add_visualizations.000
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Adds Example Datasets and Help Text for Visualizations
2025-04-29 16:14:28 -04:00
Ahmed Hamid Awan
5c1478ec9f
Merge pull request #20082 from jmchilton/collectionTypeTypes
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Flexible mapping from collection parameter types to collection builder components.
2025-04-29 00:27:03 +05:00
John Davis
3bd6b48f9b
Merge pull request #20033 from jdavcs/dev_wf_metadata
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Add DOI to workflow metadata
2025-04-28 10:42:37 -04:00
guerler
08fc03e744
Allow optional ftype setting for visualization xml test entries
2025-04-27 10:48:03 -04:00
guerler
75e304754f
Allow optional test data label
2025-04-26 16:38:16 -04:00
guerler
c3a7f8c648
Improve typing and naming to avoid confusion
2025-04-25 10:58:25 -04:00
guerler
61d4ab48bd
Derive extensions from serialized datasources
2025-04-25 01:24:55 -04:00
guerler
85be1b8551
Ensure prefix addition in plugin wrapper
2025-04-25 01:24:55 -04:00
mvdbeek