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
Dannon Baker
7ee1d3c480
Add tests for tool icon endpoint handling simple and toolshed tool IDs
2025-06-04 12:10:48 -04:00
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
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
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
74a6f31f4f
Implement roles to restrict custom tool permissions
2025-05-12 10:54:52 +02:00
mvdbeek
fde572dfc0
Update import path
2025-05-12 10:54:50 +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
mvdbeek
cbddc5196e
Add unprivileged tools endpoint and models
2025-05-12 09:07:57 +02:00
mvdbeek
024d688e58
Minor fix to restore admin-style dynamic tools
2025-05-12 09:07:56 +02:00
mvdbeek
5228e32a14
Create UserToolSource pydantic model
2025-05-12 09:07:54 +02:00
mvdbeek
855d359f0c
Add an experimental non-cheetah way of building command lines
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The primary benefit is that the command section does not have access the
app or any dangling reference to the database connection or any other
secrets. There are two flavors here, one uses base_command and
arguments, and allows building up an (escaped) argv list, the other is a
shortcut for writing shell scripts and feels maybe a bit more like
writing a very simple cheetah section.
base_command:
```yml
name: base_command tool
class: GalaxyTool
version: 1.0.0
base_command: cat
arguments:
- $(inputs.input.path)
- '>'
- output.fastq
inputs:
- type: data
name: input
outputs:
output:
type: data
from_work_dir: output.fastq
name: output
```
shell_command style:
```yml
name: shell_command tool
class: GalaxyTool
version: 1.0.0
shell_command: cat '$(inputs.input.path)' > output.fastq
inputs:
- type: data
name: input
outputs:
output:
type: data
from_work_dir: output.fastq
name: output
```
2025-05-12 09:07:24 +02:00
John Chilton
e3c6ea3a3e
Tweak API tests for small test tool tweaks.
2025-05-09 17:39:41 -04:00
John Chilton
be6de1273f
Apply Rules on Collection Element Index.
2025-05-09 17:39:40 -04:00
John Chilton
0c78f3a8a9
Rule builder API test case for paired/unpaired datasets.
2025-05-09 17:39:40 -04:00
John Chilton
219796f049
Implement paired_or_unpaired collections, list wizards.
2025-05-09 17:39:38 -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
John Chilton
94ead7c8df
WIP: embedded list of pairs workflow run selenium test case.
2025-05-09 16:38:18 -04:00
davelopez
7d1ccef49d
Add test to ensure users cannot access local files via proxy
2025-05-08 23:57:54 +02:00
David López and Marius van den Beek
a2bf8d3314
Remove testing leftover
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Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com >
2025-05-08 23:57:53 +02:00
davelopez
30157eb465
Add tests for proxy API including HEAD, GET, and range requests
2025-05-08 23:57:50 +02:00
Marius van den Beek
2266a09e68
Merge pull request #20158 from mvdbeek/yaml_parser_fixes
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Yaml parser fixes and improvements (part 1)
2025-05-06 09:25:58 +02:00
John Chilton
4e4017c1be
Merge pull request #20152 from jmchilton/collection_cleanup_2
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Fix certain cases of collection parameter handling during workflow execution.
2025-05-05 15:45:36 -04:00
Marius van den Beek
48423962ca
Merge pull request #20004 from mvdbeek/dataset_collection_support_in_landing_request
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Implement dataset collection support in workflow landing requests
2025-05-05 19:24:53 +02:00
mvdbeek
bd05b3d0e1
Settle on type instead of reftyp inside xref
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We could also make it an alias, but it seems muich simpler to not refer
to the same attribute with different names. So far this has used
internally only.
2025-05-05 19:07:27 +02:00
mvdbeek
fa3c19c2a4
Merge branch 'release_24.2' into dev
2025-05-05 16:52:31 +02:00
Marius van den Beek
18c68b067f
Merge pull request #20144 from mvdbeek/fix_param_value_restriction
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[24.2] Skip ``param_value`` filter if ref value is runtime value
2025-05-05 13:42:20 +02:00
mvdbeek
a53b4125aa
Skip `param_value` filter if ref value is runtime value
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Fixes https://github.com/galaxyproject/galaxy/issues/20136
2025-05-04 16:48:33 +02:00
guerler
94fef0c2f2
Fix test name
2025-05-04 09:16:33 -04:00
