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feat: update validation for uns['spatial'] #1129

Merged
merged 15 commits into from
Nov 26, 2024
Merged

feat: update validation for uns['spatial'] #1129

merged 15 commits into from
Nov 26, 2024

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ejmolinelli
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@ejmolinelli ejmolinelli commented Nov 25, 2024 •
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Reason for Change

Changes

  • add test cases for Visium siblings, descendants and ancestors to validate uns
  • added custom image max resolution for 11m Visium

Testing

  • test__validate_spatial_required_if_visium
  • test__validate_is_single_required_visium_error
  • test__validate_library_id_required_if_visium
  • test__validate_images_hires_max_dimension_greater_than_error
  • test__validate_images_hires_max_dimension_less_than_error
pip install git+https://github.com/chanzuckerberg/single-cell-curation/@main#subdirectory=cellxgene_schema_cli

Notes for Reviewer

  • here is a fix unrelated to this ticket, in which the schema was mutated in place, causing order dependent results when running tests.

@ejmolinelli ejmolinelli requested a review from joyceyan November 25, 2024 19:43
@ejmolinelli ejmolinelli requested a review from joyceyan November 25, 2024 20:15
joyceyan
joyceyan requested changes Nov 25, 2024
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cellxgene_schema_cli/tests/test_validate.py
# if spatial, MUST specify `is_single`
assert "uns['spatial'] must contain the key 'is_single'." in validator.errors[0]
else:
# if not spatial, MUST NOT speciffy `is_single`
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nit: specify

cellxgene_schema_cli/tests/test_validate.py Outdated Show resolved Hide resolved
nayib-jose-gloria
nayib-jose-gloria reviewed Nov 26, 2024
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couple of small rename suggestions + one test idea, but overall this looks good! thanks!

@ejmolinelli ejmolinelli merged commit 478648e into main Nov 26, 2024
7 of 8 checks passed
@ejmolinelli ejmolinelli deleted the ejmolinelli/visium-vldt-uns branch November 26, 2024 16:41
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@nayib-jose-gloria nayib-jose-gloria nayib-jose-gloria approved these changes

@joyceyan joyceyan Awaiting requested review from joyceyan

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@ejmolinelli @joyceyan @nayib-jose-gloria