cellxgene-schema CLI must update validation for obs['assay_ontology_term_id']

[brianraymor]

Context

See Visium Spatial Gene Expression must be prohibited in assay_ontology_term_id.

Design

This MUST be an EFO term and either:

• the most accurate descendant of "EFO:0002772" for assay by molecule excluding "EFO:0010961" for Visium Spatial Gene Expression while allowing its descendants

• the most accurate descendant of "EFO:0010183" for single cell library construction excluding "EFO:0010961" for Visium Spatial Gene Expression while allowing its descendants

[ejmolinelli]

would you like us to update the error messages to reflect this language? That is, instead of:

ERROR: A dict in uns['spatial'] is required when obs['assay_ontology_term_id'] is either a descendant of 'EFO:0010961' (Visium Spatial Gene Expression) or 'EFO:0030062' (Slide-seqV2)."

We would use

ERROR: A dict in uns['spatial'] is required when obs['assay_ontology_term_id'] is either a descendant of 'EFO:0010961' (Visium Spatial Gene Expression) excluding 'EFO:0010961' or 'EFO:0030062' (Slide-seqV2)."

[ejmolinelli]

In regards to previous comment

the response from the Lattice Team is:

I'd say the original comment can remain. It took me a few rereads of the updated message to parse out that the parent visium term is forbidden but the slide-seq term is allowed. I think there are other error messages/places in the schema that specify using descendant terms, so we are familiar with that kind of requirement. Thanks for checking