cellxgene-schema CLI must update validation for uns['spatial']

[brianraymor]

Changelog

• uns (Dataset Metadata)
  • Updated the requirements for spatial to include descendants of Visium Spatial Gene Expression.
  • Updated the requirements for spatial['is_single'] to include descendants of Visium Spatial Gene Expression.
  • Updated the requirements for spatial[library_id] to include descendants of Visium Spatial Gene Expression.
  • Updated the requirements for spatial[library_id]['images'] to include descendants of Visium Spatial Gene Expression.
  • Updated the requirements for spatial[library_id]['images']['fullres'] to include descendants of Visium Spatial Gene Expression.
  • Updated the requirements for spatial[library_id]['images']['hires'] to include descendants of Visium Spatial Gene Expression. Added requirements for Visium CytAssist Spatial Gene Expression, 11mm.
  • Updated the requirements for spatial[library_id]['scalefactors'] to include descendants of Visium Spatial Gene Expression.
  • Updated the requirements for spatial[library_id]['scalefactors']['spot_diameter_fullres'] to include descendants of Visium Spatial Gene Expression.
  • Updated the requirements for spatial[library_id]['scalefactors']['tissue_hires_scalef'] to include descendants of Visium Spatial Gene Expression.

Design

spatial

Key	spatial
Annotator	Curator MUST annotate if assay_ontology_term_id is descendant of "EFO:0010961" for Visium Spatial Gene Expression or "EFO:0030062" for Slide-seqV2; otherwise, this key MUST NOT be present.
Value	dict. The requirements for the key-value pairs are documented in the following sections: spatial['is_single'] spatial[library_id] spatial[library_id]['images'] spatial[library_id]['images']['fullres'] spatial[library_id]['images']['hires'] spatial[library_id]['scalefactors'] spatial[library_id]['scalefactors']['spot_diameter_fullres'] spatial[library_id]['scalefactors']['tissue_hires_scalef'] Additional key-value pairs MUST NOT be present.

is_single

Key	is_single
Annotator	Curator MUST annotate if assay_ontology_term_id is a descendant of "EFO:0010961" for Visium Spatial Gene Expression or "EFO:0030062" for Slide-seqV2; otherwise, this key MUST NOT be present.
Value	bool. This MUST be True: if assay_ontology_term_id is a descendant of "EFO:0010961" for Visium Spatial Gene Expression and the dataset represents one Space Ranger output for a single tissue section if assay_ontology_term_id is "EFO:0030062" for Slide-seqV2 and the dataset represents the output for a single array on a puck Otherwise, this MUST be False.

spatial[library_id]

Key	Identifier for the Visium library
Annotation	Curator MUST annotate if assay_ontology_term_id is a descendant of "EFO:0010961" for Visium Spatial Gene Expression and uns['spatial']['is_single'] is True; otherwise, this key MUST NOT be present.
Value	dict. There MUST be only one library_id.

spatial[library_id]['images']

Key	images
Annotation	Curator MUST annotate if assay_ontology_term_id is a descendant of "EFO:0010961" for Visium Spatial Gene Expression and uns['spatial']['is_single'] is True; otherwise, this key MUST NOT be present.
Value	dict

spatial[library_id]['images']['fullres']

Key	fullres
Annotation	Curator MAY annotate if assay_ontology_term_id is a descendant of "EFO:0010961" for Visium Spatial Gene Expression and uns['spatial']['is_single'] is True; otherwise, this key MUST NOT be present.
Value	The full resolution image MUST be converted to anumpy.ndarray with the following requirements: The length of numpy.ndarray.shape MUST be 3 The numpy.ndarray.dtype MUST be numpy.uint8 The numpy.ndarray.shape[2] MUST be either 3 (RGB color model for example) or 4 (RGBA color model for example)

spatial[library_id]['images']['hires']

Key	hires
Annotation	Curator MUST annotate if assay_ontology_term_id is a descendant of "EFO:0010961" for Visium Spatial Gene Expression and uns['spatial']['is_single'] is True; otherwise, this key MUST NOT be present.
Value	tissue_hires_image.png MUST be converted to anumpy.ndarray with the following requirements: The length of numpy.ndarray.shape MUST be 3 The numpy.ndarray.dtype MUST be numpy.uint8 If assay_ontology_term_id is "EFO:0022860" for Visium CytAssist Spatial Gene Expression, 11mm, the largest dimension in numpy.ndarray.shape[:2] MUST be 4000pixels; otherwise, the largest dimension in numpy.ndarray.shape[:2] MUST be 2000pixels. See Space Ranger Spatial Outputs The numpy.ndarray.shape[2] MUST be either 3 (RGB color model for example) for 4 (RGBA color model for example)

spatial[library_id]['scalefactors']

Key	scalefactors
Annotation	Curator MUST annotate if assay_ontology_term_id is a descendant of "EFO:0010961" for Visium Spatial Gene Expression and uns['spatial']['is_single'] is True; otherwise, this key MUST NOT be present.
Value	dict

spatial[library_id]['scalefactors']['spot_diameter_fullres']

Key	spot_diameter_fullres
Annotation	Curator MUST annotate if assay_ontology_term_id is a descendant "EFO:0010961" for Visium Spatial Gene Expression and uns['spatial']['is_single'] is True; otherwise, this key MUST NOT be present.
Value	float. This must be the value of the spot_diameter_fullres field from scalefactors_json.json. See Space Ranger Spatial Outputs.

spatial[library_id]['scalefactors']['tissue_hires_scalef']

Key	tissue_hires_scalef
Annotation	Curator MUST annotate if assay_ontology_term_id is a descendant of "EFO:0010961" for Visium Spatial Gene Expression and uns['spatial']['is_single'] is True; otherwise, this key MUST NOT be present.
Value	float. This must be the value of the tissue_hires_scalef field from scalefactors_json.json. See Space Ranger Spatial Outputs.