cellxgene-schema CLI must update validation for feature_is_filtered

[pablo-gar]

Design (@brianraymor and @jahilton)

See the Design in The requirements for feature_is_filtered must be clarified

Context

@jychien mentioned:

I'm currently thinking about what can be done to make sure that feature_is_filtered is being filled in correctly. The specific case I am thinking about is if the contributor have actually filtered genes from the normalized matrix as compared to the raw, but have not correctly filled out feature_is_filtered accordingly and is incorrectly set to False. After chatting with @pgarcia-nieto offline a little, it understandable that a complete check of the raw.X vs X matrices would be too computationally expensive. So, was wondering if it would be manageable to have a check to make sure that the number of features which have all zeros expression values is the same for raw.X and X.

Feature request
In the validator:

1. Count the number of columns (genes) that are filled with 0s in both adata.X and adata.raw.X.
2. If the count is different raise a warning

Why
A data contributor may have filtered out genes in X but did not flag them in adata.var["feature_is_filtered"]

Risks of new feature

1. May be computationally expensive, as this will iterate over all genes in both X and raw.X
2. The meaning of 0 in X is ambiguous -- it could mean the gene was filtered out or it could be a direct output of normalization

[brianraymor]

@jychien notes that this field has not been used very much.

[metakuni]

@pablo-gar / @jychien : Given @brianraymor 's comment above, could we close this issue as "won't fix" or would you prefer that it added to a future round of cellxgene-schema validation enhancements?

[jahilton]

Pretty sure this validation would have prevented #693

[pablo-gar]

@pablo-gar / @jychien : Given @brianraymor 's comment above, could we close this issue as "won't fix" or would you prefer that it added to a future round of cellxgene-schema validation enhancements?

I don't have much say on this. Will defer to the curation team for utility