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Add XML based vtk datatype #19104

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merged 17 commits into from
Nov 17, 2024
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tStehling
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@tStehling tStehling commented Nov 4, 2024

Added the datatype VTK Unstructured Grid / VTU so the VTU files can be processed by Galaxy tools.
Also added test data for the sniff method.

How to test the changes?

(Select all options that apply)

  • I've included appropriate automated tests.
  • This is a refactoring of components with existing test coverage.
  • Instructions for manual testing are as follows:
    1. Use a tool that processes VTU files

License

  • I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.

@bgruening
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Is it possible to reduce the test data size to a bare minimum?

Thanks a lot @tStehling!

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lib/galaxy/datatypes/test/output.vtu Outdated Show resolved Hide resolved
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Can you remove this TODO:

TODO: only legacy formats are currently supported and support for XML formats

Would be great if we would have also tests for set_meta. Maybe analogous to:

def test_qzv_set_meta():

The datatype needs to be added here as well https://github.com/galaxyproject/galaxy/blob/8f22c937894c718f513401279a55bddf40ba79cb/lib/galaxy/config/sample/datatypes_conf.xml.sample

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@mvdbeek mvdbeek marked this pull request as draft November 12, 2024 15:14
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I think a unit test along the lines of

def test_qza_set_meta():
would be great.

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@bernt-matthias bernt-matthias changed the title Vtu datatype Add XML based vtk datatype Nov 13, 2024
@bernt-matthias bernt-matthias marked this pull request as ready for review November 15, 2024 08:06
@bernt-matthias bernt-matthias merged commit 2d4d883 into galaxyproject:dev Nov 17, 2024
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This PR was merged without a "kind/" label, please correct.

@tStehling tStehling deleted the vtu-datatype branch November 17, 2024 10:04
@bernt-matthias
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Thanks a lot @tStehling

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4 participants