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143 Commits
Author SHA1 Message Date
Marius van den Beek 1e2737a4bc Merge pull request #20650 from jmchilton/deferred_multiple_25_0 
[25.0] Fix deferred datasets in multiple dataset parameters.
 2025-08-01 08:26:09 +02:00
mvdbeek d1543b7be3 Assert output copies are correctly replaced 2025-07-21 18:37:51 +02:00
John Chilton 505ac8d8d5 Migrate some tool-on-deferred tests to newer style execute tests. 2025-07-11 13:44:26 -04:00
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
Ahmed Hamid Awan 1241ab4450 Merge pull request #20436 from mvdbeek/fix_job_metric_copy 
[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
Dannon Baker 7ee1d3c480 Add tests for tool icon endpoint handling simple and toolshed tool IDs 2025-06-04 12:10:48 -04:00
mvdbeek 841e19d4ad Fix admin-only dynamic tools 2025-05-12 10:54:26 +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 
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 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
mvdbeek bd05b3d0e1 Settle on type instead of reftyp inside xref 
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 79e8a8b736 Make sure HDCAs are properly copied and populated 2025-04-12 12:48:40 +02:00
mvdbeek 00d64f74be Fix copying job output from discovered outputs 2025-04-12 10:45:52 +02:00
mvdbeek 4d0c507961 Test that nested collection map-over works fine with job cache 2025-04-11 16:11:49 +02:00
mvdbeek f55ae853ae Test cache with HDCA (renamed) input 2025-04-11 16:11:49 +02:00
mvdbeek bfd3d1972a WIP: if not accessing input.name, allow input.name to differ 2025-04-11 16:11:43 +02:00
John Chilton 5ffd5abfc3 Improved simplicity and isolation in transiently failing test. 
The test failure without any really useful context on the client is bad and indicating a problem - it is going to be some concurrency or database thing in the test environment or an issue with us hitting Github a bunch right in a row. Regardless - it isn't the job of this test case to uncover that I think - I think isolating the network and simplifying the test here will increase the test robustness and ensure it is testing what it is meant to test.
 2025-02-26 13:35:21 -05:00
mvdbeek 32ddf2ba86 Merge branch 'release_24.2' into dev 2025-01-31 17:06:52 +01:00
mvdbeek 86b449b861 Fail with error message when submitting invalid request 
This should eventually be redundant / unnecessary with
https://github.com/galaxyproject/galaxy/pull/17393 but in the meantime I
think this can help anyone trying to use the API and cleans up the logs
for admins. Fixes https://github.com/galaxyproject/galaxy/issues/19488
 2025-01-30 16:01:07 +01:00
mvdbeek b4bcfc9f5d Fix wrong id in test_combined_mapping_and_subcollection_mapping 
We weren't actually testing what we thought we did here ...
 2025-01-29 15:49:30 +01:00
Nicola Soranzo bb438e1e8d Merge branch 'release_24.1' into release_24.2 2025-01-13 16:02:22 +00:00
mvdbeek a75bca59b4 Add test 2024-12-11 12:28:39 +01:00
John Chilton 5219968faf Test fixes... 2024-11-13 09:50:21 -05:00
mvdbeek 3a6fdf24fb Allow searching jobs in public histories for job cache 2024-11-06 11:42:18 +01:00
Björn Grüning a5aaa1c1be Merge pull request #19077 from davelopez/allow_deferred_as_uri 
Allow deferred datasets to behave as URIs
 2024-11-04 23:09:12 +01:00
davelopez 2bdcec0dda Add test for gx_allow_uri_if_protocol with deferred collections 2024-11-03 12:47:15 +01:00
davelopez 678caa415f Add test for allow_uri_if_protocol with deferred input 2024-10-31 11:17:17 +01:00
John Chilton 6d7842e66f Numerous fixes for tool input format "21.01" parameters. 2024-10-30 10:52:08 -04:00
Björn Grüning d4b2b83310 Merge pull request #19002 from jmchilton/do_not_skip_ci_tests_on_missing_tools 
Do not skip CI tests on missing tools.
 2024-10-29 18:02:27 +01:00
John Chilton 951ab47f47 More tool tests. 2024-10-22 07:49:37 -04:00
John Chilton d3e0e28ce3 Do not skip CI tests on missing tools. 2024-10-15 16:02:27 -04:00
John Chilton 687f3661f1 Migrate various tool execute tests to more declarative style. 2024-10-14 09:40:22 -04:00
John Chilton 3f50b25327 pytest-y API test fixtures 2024-10-14 09:40:22 -04:00
John Chilton b367c8a5a3 More tests for various data column feature combos. 2024-09-30 13:25:02 -04:00
Matthias Bernt 7dd606a6b2 Merge branch 'release_24.1' into dev 
# Conflicts:
#	lib/galaxy/version.py
#	packages/app/HISTORY.rst
#	packages/app/setup.cfg
#	packages/auth/HISTORY.rst
#	packages/auth/setup.cfg
#	packages/config/HISTORY.rst
#	packages/config/setup.cfg
#	packages/data/HISTORY.rst
#	packages/data/setup.cfg
#	packages/files/HISTORY.rst
#	packages/files/setup.cfg
#	packages/job_execution/HISTORY.rst
#	packages/job_execution/setup.cfg
#	packages/job_metrics/HISTORY.rst
#	packages/job_metrics/setup.cfg
#	packages/navigation/HISTORY.rst
#	packages/navigation/setup.cfg
#	packages/objectstore/HISTORY.rst
#	packages/objectstore/setup.cfg
#	packages/schema/HISTORY.rst
#	packages/schema/setup.cfg
#	packages/selenium/HISTORY.rst
#	packages/selenium/setup.cfg
#	packages/test_api/HISTORY.rst
#	packages/test_api/setup.cfg
#	packages/test_base/HISTORY.rst
#	packages/test_base/setup.cfg
#	packages/test_driver/HISTORY.rst
#	packages/test_driver/setup.cfg
#	packages/tool_shed/HISTORY.rst
#	packages/tool_shed/setup.cfg
#	packages/tool_util/HISTORY.rst
#	packages/tool_util/setup.cfg
#	packages/tours/HISTORY.rst
#	packages/tours/setup.cfg
#	packages/util/HISTORY.rst
#	packages/util/setup.cfg
#	packages/web_apps/HISTORY.rst
#	packages/web_apps/setup.cfg
#	packages/web_framework/HISTORY.rst
#	packages/web_framework/setup.cfg
#	packages/web_stack/HISTORY.rst
#	packages/web_stack/setup.cfg
 2024-09-25 14:29:37 +02:00
mvdbeek d470587028 Fix data_column ref to nested collection 2024-09-23 18:27:30 +02:00
John Chilton 38b1a07f0c More clarification of current advanced select behavior. 2024-08-09 11:54:19 -04:00
John Chilton e0b6532a82 Merge pull request #18641 from jmchilton/model_parameter_improvements_1 
Parameter Model Improvements
 2024-08-06 11:07:25 -04:00
John Chilton c92f6dd47c Richer typing / models / parsing for drill down parameters. 2024-08-05 17:02:51 -04:00
John Chilton 57f9137861 Progress on repeat validation... 2024-08-05 09:44:43 -04:00
John Chilton b27d6331d4 Clarify current select behavior around null and empty selections. 2024-08-05 09:44:43 -04:00
John Chilton 3345de12f6 Typing for much of the tool execution and action plumbing. 2024-07-31 20:37:56 -04:00
John Chilton 9695ccc3c4 More typing of test case parsing - again. 2024-07-23 08:56:36 -04:00