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AIRR Community Data Standards
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contains_single_cell is no longer a study keyword? #660

Closed schristley closed 1 year ago

schristley commented 1 year ago

I didn't see this mentioned in the release notes. Was it removed because it's redundant with something else, or was it replaced by a different keyword?

javh commented 1 year ago

Replaced by contains_schema_cell. Need to update patch notes.

schristley commented 1 year ago

Ok, so there are two concepts here, one is what the experimental protocol was attempting, that is the single_cell flag in the sample processing. When contains_single_cell was removed, I was thinking it was ok, it's redundant because you can just iterate over the repertoires and test the single_cell flag.

But the second is if the study contains AIRR Cell objects, is that the intent of contains_schema_cell? Will it be invalid to have a repertoire with single_cell: true but no Cell objects?

scharch commented 1 year ago

Will it be invalid to have a repertoire with single_cell: true but no Cell objects?

I think it should at least be strongly discouraged, but I guess making it invalid might go against our general strategy of allowing people to be jerks if they so insist...

schristley commented 1 year ago

Will it be invalid to have a repertoire with single_cell: true but no Cell objects?

I think it should at least be strongly discouraged, but I guess making it invalid might go against our general strategy of allowing people to be jerks if they so insist...

I'm fine with it being invalid, though this is a form a validation that we aren't performing yet, i.e. cross-object validation. Users probably won't check the single_cell: true flag anyways then, they'll just look for contains_schema_cell flag to see if there is single cell data.

javh commented 1 year ago

Looks like the changes to Study.keywords_study are already in the v1.4.1 Study Schema patch notes. Are we okay to close this?