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fix: check type of uns["spatial"][library_id] is dict #886

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May 8, 2024
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5 changes: 4 additions & 1 deletion cellxgene_schema_cli/cellxgene_schema/validate.py
Original file line number Diff line number Diff line change
Expand Up @@ -1662,7 +1662,10 @@ def _check_spatial_uns(self):
# Confirm shape of library_id is valid: allowed keys are images and scalefactors.
library_id_key = library_ids[0]
uns_library_id = uns_spatial[library_id_key]
if not self._has_no_extra_keys(uns_library_id, ["images", "scalefactors"]):
if not isinstance(uns_library_id, dict):
self.errors.append("uns['spatial'][library_id] must be a dictionary.")
return
elif not self._has_no_extra_keys(uns_library_id, ["images", "scalefactors"]):
self.errors.append(
"uns['spatial'][library_id] can only contain the keys 'images' and 'scalefactors'."
f"Detected keys: {list(uns_library_id.keys())}."
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12 changes: 12 additions & 0 deletions cellxgene_schema_cli/tests/test_validate.py
Original file line number Diff line number Diff line change
Expand Up @@ -521,6 +521,18 @@ def test__validate_library_id_required_if_visium(self):
in validator.errors[0]
)

@pytest.mark.parametrize("library_id", [None, "invalid", 1, 1.0, True])
def test__validate_library_id_type_error(self, library_id):
validator: Validator = Validator()
validator._set_schema_def()
validator.adata = adata_visium.copy()
validator.adata.uns["spatial"][visium_library_id] = library_id

# Confirm library_id is identified as invalid.
validator.validate_adata()
assert validator.errors
assert "uns['spatial'][library_id] must be a dictionary." in validator.errors[0]

def test__validate_library_id_allowed_keys_error(self):
validator: Validator = Validator()
validator._set_schema_def()
Expand Down
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