Marius van den Beek
1e2737a4bc
Merge pull request #20650 from jmchilton/deferred_multiple_25_0
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[25.0] Fix deferred datasets in multiple dataset parameters.
2025-08-01 08:26:09 +02:00
John Chilton
7769f6379d
Merge pull request #20553 from mvdbeek/live_fix_cry_emoji
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[25.0] Propagate cached job output replacement to copies of outputs
2025-07-29 10:26:42 -04:00
Arash
b5d27075fb
Add tests for copying datasets with copied_from fields in history and library
2025-07-25 15:28:27 +02:00
mvdbeek
d1543b7be3
Assert output copies are correctly replaced
2025-07-21 18:37:51 +02:00
John Chilton
da575fe2d0
Fix deferred datasets in multi-data parameters.
2025-07-11 13:44:27 -04:00
John Chilton
505ac8d8d5
Migrate some tool-on-deferred tests to newer style execute tests.
2025-07-11 13:44:26 -04:00
mvdbeek
76823c5b67
Fix optional unspecified input to conditional step
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Fixes https://github.com/galaxyproject/galaxy/issues/20182
2025-07-11 15:59:36 +02:00
David López and Nicola Soranzo
1708721eab
Refactor test to simplify assertion
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Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2025-07-03 14:07:42 +02:00
davelopez
7318b85469
Add test for invalid UUID v4 format in workflow steps
2025-07-03 13:33:06 +02:00
Nicola Soranzo
cc26ab7834
Merge branch 'release_24.2' into release_25.0
2025-06-20 13:00:45 +01:00
Nicola Soranzo
fdf931b954
Fix new `test_index_anon` API test
2025-06-19 20:01:47 +01:00
Matthias Bernt
98ddca1e11
fixup
2025-06-19 19:34:52 +02:00
Matthias Bernt
b71eaaf437
try to add test
2025-06-19 18:58:01 +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
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
Ahmed Hamid Awan
1241ab4450
Merge pull request #20436 from mvdbeek/fix_job_metric_copy
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[25.0] Fix copying of job metrics for cached jobs
2025-06-13 13:36:55 -05:00
mvdbeek
32914f2e07
Add test that confirms element sorting must match
2025-06-11 20:54:15 +02:00
mvdbeek
9d3268e721
Ensure query columns are unique
2025-06-11 20:54:14 +02:00
mvdbeek
711923a3b3
Fix copying of job metrics for cached jobs
2025-06-11 17:52:59 +02:00
Ahmed Awan
80530acc67
add API test for DCEs being acceptable as mapped over inputs on drop
2025-06-09 12:37:04 -05:00
mvdbeek
4f545f424d
Fix job rerun with tool version change
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Fixes https://github.com/galaxyproject/galaxy/issues/20337 , broken in https://github.com/galaxyproject/galaxy/pull/20259
2025-06-09 12:16:26 +02:00
Marius van den Beek
8db845b7ca
Merge pull request #20397 from ahmedhamidawan/no_waiting_for_ok_state
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[25.0] Prevent waiting for history item state to be ok in uploader
2025-06-06 13:15:32 +02:00
Ahmed Awan
04602c3b84
wait for add items button to enable; no need to switch to create tab
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The test would fail because the add items to collection button's disabled/enabled state was not being detected, and hence, we would manually switch tabs and the items would not even have been added to the list yet. Now, we wait for the button to enable, and then adding the items automatically switches tab to Create.
2025-06-05 14:09:23 -05:00
Ahmed Awan and mvdbeek
58561002d5
No need to wait for item hids, waiting for the button itself is better
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Co-authored-by: mvdbeek <m.vandenbeek@gmail.com >
2025-06-05 11:40:03 -05:00
Dannon Baker
7ee1d3c480
Add tests for tool icon endpoint handling simple and toolshed tool IDs
2025-06-04 12:10:48 -04:00
Ahmed Awan
c2974fe61c
remove wait for upload state alert
2025-06-04 10:38:54 -05:00
Marius van den Beek
8c45d86108
Merge pull request #20326 from ahmedhamidawan/fix_workflow_rerun_version_TESTS
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[25.0] Add test for workflow instance download fix
2025-05-22 21:28:58 +02:00
Ahmed Awan and mvdbeek
db234a29ee
fix (expression has type "bool", target has type "str") mypy err
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Co-authored-by: mvdbeek <m.vandenbeek@gmail.com >
2025-05-22 10:48:22 -05:00
Ahmed Awan
909b8d9c73
[25.0] Add test for workflow instance download fix
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Test for the change in https://github.com/galaxyproject/galaxy/pull/20313
2025-05-22 10:35:10 -05:00
mvdbeek
146ae6bc69
Enable retrieving contents from extra file paths with leading /
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by stripping all leading `/` in filename.
I don't think there's a legitimate reason that we should treat this as
an absolute path marker. Addresses @luke-c-sargent's comment in
https://github.com/goeckslab/tools-mti/pull/99#issuecomment-2864667012
2025-05-22 16:36:33 +02:00
Marius van den Beek
7515f053af
Merge pull request #20325 from davelopez/25.0_fix_wf_bookmark_filter
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[25.0] Fix workflow bookmark filtering
2025-05-21 20:03:47 +02:00
davelopez
46168bfa5a
Add workflow bookmarking selenium test
2025-05-21 16:39:00 +02:00
davelopez
4964660e50
Move test for local files to invalid urls
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Only https and http schemes are allowed so any other scheme will be considered invalid.
2025-05-20 23:38:25 +02:00
davelopez
59fef1f7b5
Add test for invalid URL formats in proxy endpoint
2025-05-20 17:39:39 +02:00
mvdbeek
fd392b805a
Fix test_charts_h5web, drop test_charts_nvd3_bar since there's no nvd3_bar anymore
2025-05-15 14:19:13 +02:00
mvdbeek
93f081d1c2
Selenium test fixes
2025-05-15 14:19:13 +02:00
mvdbeek
f628ee230e
Wait for ... to disappear
2025-05-14 20:37:30 +02:00
mvdbeek
0e7ee07cac
Keep using history panel item edit button in selenium
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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
mvdbeek
74a6f31f4f
Implement roles to restrict custom tool permissions
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
c3e167bba4
Move dynamic tool models to tool_util
2025-05-12 10:54:47 +02:00
mvdbeek
22d111e0ac
Add required name and version to embedded tool
2025-05-12 10:54:45 +02:00
mvdbeek
152bc2ffa5
Add runtime model to API
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Like job_internal but replaces dataset and dataset collection with file
and array / object of files.
2025-05-12 10:54:30 +02:00
mvdbeek
bfaad0773c
Enable unprivileged tool preview endpoint
2025-05-12 10:54:28 +02:00
mvdbeek
841e19d4ad
Fix admin-only dynamic tools
2025-05-12 10:54:26 +02:00
mvdbeek
746935b7fc
Return unprivileged tool api return types
2025-05-12 10:54:23 +02:00
mvdbeek
1767ad21a9
Test tool run
2025-05-12 10:54:22 +02:00
mvdbeek
a234ec565a
Add separate unprivileged tools endpoint
2025-05-12 10:54:22 +02:00
Marius van den Beek