John Chilton
5b08e9b9bb
Integrate some new Pydantic models into Planemo lint.
2024-10-30 10:58:35 -04:00
John Chilton
078ad6114b
Fix param models for dynamic options and truevalue/falsevalue
2024-10-22 07:49:37 -04:00
John Chilton
730ea2ee03
Pydantic models for parameter validators.
2024-10-22 07:49:37 -04:00
John Chilton
c198c7cb97
models for tool landing request state...
2024-10-22 07:49:37 -04:00
John Chilton
7ef5cc22e4
Refactor for reuse in galaxy.tool_util.parameters.
2024-10-22 07:49:37 -04:00
John Chilton
f27b202500
Spelling error.
2024-10-22 07:49:37 -04:00
Nicola Soranzo
4e56b47d5d
Merge branch 'release_24.1' into dev
2024-10-16 11:26:07 +01:00
mvdbeek
a42496e8ec
Disable locking when opening h5 files, add missing with
2024-10-12 09:26:54 +02:00
Björn Grüning
d18bc6855d
Merge pull request #18919 from jmchilton/biotools
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Fix commas that shouldn't be in biotools_mappings.tsv
2024-10-04 11:06:06 +02:00
John Chilton
beb4842b8d
Allow multiple xrefs in biotools_mappings.tsv.
2024-10-02 00:10:44 -04:00
John Chilton
ad73e9e838
Tool Request models.
2024-09-30 13:25:02 -04:00
John Chilton
675c9670e2
Models for YAML test format.
2024-09-24 12:47:07 -04:00
John Chilton
0863221237
Merge pull request #18743 from jmchilton/parameter_models_rework_test_case_xml
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Improvements to parameter models for test case inputs
2024-09-19 11:02:56 -04:00
John Chilton
b70d83d8b2
Modeling from assertions.
2024-09-13 16:23:10 -04:00
John Chilton
67b4a69c1b
Merge pull request #18722 from jmchilton/markdown_help_2
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Improvements to help terms & tool help.
2024-09-03 12:41:05 -04:00
John Chilton
fd4b182317
Rework test case validation schema.
2024-08-27 19:02:19 -04:00
John Chilton
b45c58a258
Integrate tool test validation into upgrade advisor.
2024-08-24 16:12:32 -04:00
John Chilton
7b294fcaaa
Implement tool upgrade assistant script.
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Inspect a tool's XML file and provide advice on upgrading to new tool versions. It is implemented as a library in tool_util for integration with Planemo in the future but I've added a script here to run it on the command-line directly. It can also output in JSON for integration with external tools such as the galaxy language server.
2024-08-24 11:22:43 -04:00
John Chilton
701c6f552d
Improvements to help terms & tool help.
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- Allow tools to declare markdown help.
- Allow tools to reference help terms from their Markdown tools.
- Auto generate help terms for each datatype from values in datatypes_conf.xml
- Add permenant links for each help term - both the auto generated ones and the YAML specified
ones.
- Add some initial help terms for collection operations.
- Use new help term for "map over" from tool form.
2024-08-23 11:03:13 -04:00
John Chilton
0a35eea309
Tool test case parameter models.
2024-08-23 09:46:44 -04:00
John Chilton
da220efd23
First pass at workflow step models - linked and unlinked.
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Work scoped out in 18536.
2024-08-23 09:46:44 -04:00
John Chilton
e475003830
Disable unqualified parameters in test cases for new tools.
2024-08-23 09:46:44 -04:00
John Chilton
b919f21c47
Parameter models for optional data columns.
2024-08-11 17:19:21 -04:00
John Chilton
67dc43f4e1
Parameter models for multiple=true data column data parameters.
2024-08-11 17:19:21 -04:00
John Chilton
95da14738e
Parmaeter models for multiple=true group tags.
2024-08-11 17:19:21 -04:00
John Chilton
c18bfa3475
Tool parameter models for optional group tags.
2024-08-10 10:30:20 -04:00
John Chilton
7dc12dfe27
Clarify behavior around unspecified hidden parameters.
2024-08-09 12:47:55 -04:00
John Chilton
384a30728c
Validate wild static select with no options.
2024-08-09 12:47:55 -04:00
John Chilton
ed720332b9
Parameter models for directory_uri parameters.
2024-08-09 11:54:19 -04:00
John Chilton
aa569ae71b
Parameter models for genomebuild parameters
2024-08-09 11:54:19 -04:00
John Chilton
38b1a07f0c
More clarification of current advanced select behavior.
2024-08-09 11:54:19 -04:00
John Chilton
53a1ee520f
Update parameter models for required integers.
2024-08-09 11:54:19 -04:00
John Chilton
d41544db70
Group tag parameter models.
2024-08-09 11:54:19 -04:00
John Chilton
e0b6532a82
Merge pull request #18641 from jmchilton/model_parameter_improvements_1
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Parameter Model Improvements
2024-08-06 11:07:25 -04:00
John Chilton
e8e569f820
Work toward data column support in tool parameter meta models.
2024-08-05 18:37:24 -04:00
John Chilton
a9343f336b
Refactor parameter unit testing to be more general.
2024-08-05 18:37:24 -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
5bb6804045
Parameter specification reference testing - conditionals with selects.
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
c5c4ba39b8
Simplify test_parameter_specification a bit.
2024-08-05 09:44:43 -04:00
John Chilton
139e00ccc2
Fix #18554 .
2024-08-05 09:43:15 -04:00
Nicola Soranzo
359bcfeec8
Fixes for errors reported by mypy 1.11.0
2024-08-01 18:13:27 +01:00
John Chilton
9695ccc3c4
More typing of test case parsing - again.
2024-07-23 08:56:36 -04:00
John Chilton
7d4c9f43f3
More typing of test case parsing.
2024-07-18 13:36:48 -04:00
John Chilton
071c376773
Drop old Tool test parsing logic in favor of ToolSource logic.
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Add to tool_util, drop all the Galaxy mocking required using the older tool based logic.
2024-07-18 13:30:42 -04:00
John Chilton
22709b416c
Abstraction for finding functional test tools.
2024-07-18 10:48:18 -04:00
John Chilton
5359f8ba74
Input parameter schema.
2024-07-15 09:46:13 -04:00
John Chilton
3eb03c0c1e
Pydantic models for tool outputs.
2024-07-15 09:46:13 -04:00
John Chilton
301e1fc3fc
Remove duplication in test_parsing.py.
2024-07-15 09:46:13 -04:00
John Chilton