Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add XML based vtk datatype #19104

Draft
wants to merge 17 commits into
base: dev
Choose a base branch
from
Draft

Conversation

tStehling
Copy link

@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
Copy link
Member

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

Thanks a lot @tStehling!

Copy link
Contributor

@bernt-matthias bernt-matthias left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

lib/galaxy/datatypes/test/output.vtu Outdated Show resolved Hide resolved
lib/galaxy/datatypes/xml.py Outdated Show resolved Hide resolved
Copy link
Contributor

@bernt-matthias bernt-matthias left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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

lib/galaxy/datatypes/constructive_solid_geometry.py Outdated Show resolved Hide resolved
lib/galaxy/datatypes/constructive_solid_geometry.py Outdated Show resolved Hide resolved
lib/galaxy/datatypes/constructive_solid_geometry.py Outdated Show resolved Hide resolved
lib/galaxy/datatypes/constructive_solid_geometry.py Outdated Show resolved Hide resolved
lib/galaxy/datatypes/constructive_solid_geometry.py Outdated Show resolved Hide resolved
@mvdbeek mvdbeek marked this pull request as draft November 12, 2024 15:14
Copy link
Contributor

@bernt-matthias bernt-matthias left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I think a unit test along the lines of

def test_qza_set_meta():
would be great.

lib/galaxy/config/sample/datatypes_conf.xml.sample Outdated Show resolved Hide resolved
lib/galaxy/config/sample/datatypes_conf.xml.sample Outdated Show resolved Hide resolved
lib/galaxy/config/sample/datatypes_conf.xml.sample Outdated Show resolved Hide resolved
lib/galaxy/datatypes/constructive_solid_geometry.py Outdated Show resolved Hide resolved
lib/galaxy/datatypes/constructive_solid_geometry.py Outdated Show resolved Hide resolved
lib/galaxy/datatypes/constructive_solid_geometry.py Outdated Show resolved Hide resolved
lib/galaxy/datatypes/constructive_solid_geometry.py Outdated Show resolved Hide resolved
lib/galaxy/datatypes/constructive_solid_geometry.py Outdated Show resolved Hide resolved
lib/galaxy/datatypes/xml.py Outdated Show resolved Hide resolved
@bernt-matthias bernt-matthias changed the title Vtu datatype Add XML based vtk datatype Nov 13, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
Development

Successfully merging this pull request may close these issues.

3 participants