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Merged
merged 11 commits into from
Apr 19, 2025
Merged

Add VTK Visualization Toolkit Plugin #20028

merged 11 commits into from
Apr 19, 2025

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guerler
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@guerler guerler commented Apr 16, 2025 •
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Add VTK as Visualization plugin, supporting ply and vtp files. This PR also add the vtpascii and vtpbinary datatypes to the registry.

Test data available at:
http://cdn.jsdelivr.net/gh/galaxyproject/galaxy-test-data/square.plyascii
http://cdn.jsdelivr.net/gh/galaxyproject/galaxy-test-data/horse.plybinary
http://cdn.jsdelivr.net/gh/galaxyproject/galaxy-test-data/square.vtpascii
http://cdn.jsdelivr.net/gh/galaxyproject/galaxy-test-data/human.vtpbinary

vtk

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. [add testing steps and prerequisites here if you didn't write automated tests covering all your changes]

License

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

@guerler guerler added this to the 25.0 milestone Apr 16, 2025
@guerler guerler marked this pull request as ready for review April 16, 2025 22:37
@guerler guerler requested review from bgruening and removed request for bgruening April 17, 2025 20:35
@guerler guerler mentioned this pull request Apr 17, 2025
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bgruening
bgruening reviewed Apr 18, 2025
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The VIS is great! I have a few questions about the datatype.

Thanks Sam!

lib/galaxy/datatypes/constructive_solid_geometry.py Outdated
subtype = ""

# Add metadata elements (sorted alphabetically by name).
MetadataElement(name="file_format", default=None, desc="File format", readonly=True, optional=True, visible=True)
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What are those file_formats? Should we have subclasses of this for each of the file_format? E.g. can there be tools or Vis that require one of the specific sub-types?

Is unusual to encode file_formats this way I think.

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file_format here refers to type in the VTP-file, commonly its PolyData. I used file_format because it is used in VTK and PLY but I switched it to type so it aligns with actual attribute name in the VTP-file.

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@guerler guerler Apr 18, 2025 •
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I followed up one more time, and removed file_format/type, instead the blurb is now showing any of the other metadata attributes collected from the dataset e.g.
image

bgruening
bgruening reviewed Apr 19, 2025
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Works nicely. The test data really helps to test, thanks @guerler!

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bgruening approved these changes Apr 19, 2025
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Thanks @guerler works great! The test data in the PR description are helping a lot :)

@guerler guerler merged commit d41d9d3 into galaxyproject:dev Apr 19, 2025
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@guerler guerler deleted the vtk.000 branch April 19, 2025 17:10
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mvdbeek commented Apr 20, 2025

Test failure is relevant: https://github.com/galaxyproject/galaxy/actions/runs/14542428601/job/40802807530#step:15:3038

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guerler commented Apr 20, 2025

Thank you @mvdbeek, followed-up with #20051 to add the missing new line.

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