John Chilton
2bee911ce4
Add max length to pydantic models - not sure this makes sense.
2025-06-19 22:55:54 -04:00
John Chilton
85d634ae9f
Implement fetch workbooks.
2025-06-19 22:54:56 -04:00
John Chilton
7efe923b4c
Sharper exception handling in apply rules test.
2025-06-19 22:54:55 -04:00
John Chilton
05ecc12d96
Test case for rule builder backend errors.
2025-06-19 22:54:55 -04:00
John Chilton
a776836dba
Update rule builder to allow list:paired_or_unpaired creation.
2025-06-19 22:54:55 -04:00
Marius van den Beek
e839cb7cd5
Merge pull request #20509 from jmchilton/input_by_url_to_conversion
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Test case for using URL-based workflow inputs with implicit conversions.
2025-06-19 10:41:11 +02:00
mvdbeek
cafd0c8c62
Merge branch 'release_25.0' into dev
2025-06-19 10:18:46 +02:00
mvdbeek
43feb0efb3
Merge branch 'release_24.2' into release_25.0
2025-06-19 10:17:22 +02:00
Marius van den Beek
044442bdfb
Merge pull request #20511 from mvdbeek/fix_too_strict_validation
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[24.2] Relax validation of XML test assertion parsing
2025-06-19 10:15:16 +02:00
John Chilton
9523afb100
Linting fix.
2025-06-18 13:36:05 -04:00
John Chilton
0eeb71e169
Revise assertion relaxation to use better test models.
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This was supposed to be part of https://github.com/galaxyproject/galaxy/pull/19715 but clearly I missed the last mile as always.
2025-06-18 13:22:52 -04:00
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
mvdbeek
fdafb0655d
Relax validation of XML test assertion parsing
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when tool source is XML. We can't really encode these attributes as JSON
in XML, and while we could make it work it doesn't feel great to force
tool authors to use such a hypothetical syntax.
I think we still keep all the nice validation here, it's just a little
more lenient.
2025-06-18 18:55:10 +02:00
John Chilton
3190de2a07
Test case for using workflow inputs with implicit conversions.
2025-06-18 11:46:37 -04:00
John Davis
a015157789
Add merge migration
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Migrations were added to both branches which resulted in 2 heads on dev
after 25.0 was merged into dev. This merges the two lineages.
2025-06-18 09:43:19 -04:00
John Davis
e82b35602c
Revert "Fix alembic migrations"
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This reverts commit a41a3c93a6
2025-06-18 09:33:11 -04:00
mvdbeek
a41a3c93a6
Fix alembic migrations
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Broken on merging 25.0 into dev
2025-06-18 12:24:23 +02:00
David López
22b7f14f1a
Merge pull request #20372 from guerler/remove_common_templates
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Install visualizations directly to static path, avoid duplication
2025-06-18 09:42:19 +02:00
Nate Coraor
dcd4cdca08
Start work on 24.2.5.dev0
2025-06-17 12:17:28 -04:00
Nate Coraor
7b1e4465bf
Create version 24.2.4
2025-06-17 12:17:16 -04:00
Nate Coraor
22e73db9c0
Merge remote-tracking branch 'upstream/release_25.0' into dev
2025-06-17 11:36:14 -04:00
Marius van den Beek
a8c53d29f0
Merge pull request #20473 from mvdbeek/vitessce.json_instead_of_vitessce_json
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[25.0] Rename vitessce_json file_ext to vitessce.json
2025-06-17 17:04:06 +02:00
Nate Coraor
ccaa419418
Merge remote-tracking branch 'upstream/release_25.0' into dev
2025-06-17 10:23:03 -04:00
Nate Coraor
bba5cc7448
Merge remote-tracking branch 'upstream/release_24.2' into release_25.0
2025-06-17 10:21:51 -04:00
John Chilton
e6a3dea50a
Merge pull request #20492 from natefoo/optional-edam
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[24.2] Make optional edam-ontology in datatypes registry optional
2025-06-17 09:03:24 -04:00
Marius van den Beek
957ccca59d
Fall back to empty edam dict
2025-06-17 10:58:21 +02:00
Nate Coraor
8838912356
Make optional edam-ontology in datatypes registry optional
2025-06-16 16:48:10 -04:00
John Davis
0a2aeb6424
Update migration release tags
2025-06-16 14:27:53 -04:00
davelopez
58a7a9adef
Merge branch 'release_25.0' into dev
2025-06-16 20:14:12 +02:00
John Davis
5c1506a202
Recreate triggers
2025-06-16 14:11:49 -04:00
mvdbeek
03fb43a00d
Merge branch 'release_24.2' into release_25.0
2025-06-16 19:34:41 +02:00
Marius van den Beek
6dd2a45e74
Merge pull request #20484 from davelopez/merge_25.0_into_dev
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Merge `release_25.0` into `dev`
2025-06-16 15:47:19 +02:00
mvdbeek
6d0a0b53aa
Link workflow invocation outputs upon importing invocation
2025-06-16 15:02:47 +02:00
davelopez
fdac8820a6
Merge release_25.0 into dev
2025-06-16 14:12:30 +02:00
Marius van den Beek
1d8b6247e7
Merge pull request #19900 from ahmedhamidawan/form_data_various_fixes
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[25.0] More fixes to `FormData` drag and drop and typing
2025-06-16 13:47:57 +02:00
mvdbeek
9c165bb054
Merge branch 'release_24.2' into release_25.0
2025-06-16 13:42:10 +02:00
Marius van den Beek
876fdf0b24
Merge pull request #20475 from mvdbeek/header_string
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[24.2] Make response header values strings
2025-06-16 13:41:47 +02:00
Marius van den Beek
c7acfe7bea
Merge pull request #20477 from mvdbeek/fix_legacy_metadata_get_file
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[24.2] Fix legacy get_metadata_file controller route
2025-06-16 13:41:35 +02:00
Marius van den Beek
446c8deb68
Merge pull request #20479 from mvdbeek/prevent_launching_autodetect_on_purged_dataset
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[24.2] Prevent running datatype autodetect on purged datasets
2025-06-16 13:41:00 +02:00
mvdbeek
a7eaf5f74a
Prevent running datatype autodetect on purged datasets
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Fixes https://github.com/galaxyproject/galaxy/issues/20478
2025-06-16 11:16:09 +02:00
mvdbeek
4620f0716e
Fix legacy get_metadata_file controller route
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Fixes https://github.com/galaxyproject/galaxy/issues/20476
2025-06-16 11:09:25 +02:00
mvdbeek
f508330d03
Make response header values strings
2025-06-16 11:02:46 +02:00
Marius van den Beek
c71e529cd1
Merge pull request #20468 from mvdbeek/extra_files_path
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[25.0] Add ``/api/datasets/{dataset_id}/extra_files/raw/{filename:path}``
2025-06-16 10:17:31 +02:00
mvdbeek
5b796aa402
Rename vitessce_json file_ext to vitessce.json
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Pretty sure this hasn't been used yet, added in
https://github.com/galaxyproject/galaxy/pull/20027/files . A proper json
extension allows json tooling to work with this file.
2025-06-16 09:37:21 +02:00
John Chilton
41fee0a742
Collection API related spelling fix.
2025-06-15 10:14:35 -04:00
mvdbeek
f928b08fa7
Add `/api/datasets/{dataset_id}/extra_files/raw/{filename:path}`
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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
Marius van den Beek
972b5abe21
Merge pull request #20465 from bgruening/aladin_fits
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[25.0] Add Aladin as standard FITS viewer
2025-06-15 15:11:45 +02:00
Bjoern Gruening
39f1b267ae
add molstar as standard viewer for a bunch of Molecule files
2025-06-15 14:01:51 +02:00
Bjoern Gruening
71ff613248
add aladin as standard viewer for FITS
2025-06-15 11:47:14 +02:00
John Chilton