FactorValueValue objects are not fully populated for experimentalFactors for getDatasetDifferentialExpressionAnalyses endpoint

[oganm]

According to the API specification, getDatasetDifferentialExpressionAnalyses endpoint is supposed to return ExperimentalFactorValueObjects as values of experimentalFactors of the returned resultSets

However an actual call to the endpoint would show that the output is missing experimentalFactorId and experimentalFactorCategory fields. I assume this was removed since these fields are redundant with the parent but not having such changes reflected in the specification causes invisible failures on occasion

[arteymix]

I'll add a flag to trigger the old behavior. In general, when a ExperimentalFactor is rendered, I omit the EF inside its FVs because that is redundant.

[oganm]

Pushed a fix to the packages to work with this form but is there anything we can do so the specification matches what is actually going on?

[arteymix]

Unless indicated by a required property in the JSON schema, no fields are guaranteed to be present. I think I will consider adding a few required fields to the spec.

[arteymix]

I can restore the fields, but mark them as deprecated in the context of an EFVO.

[oganm]

gemmapy and gemma.R currently work without those specific fields. but it's good to have the specification give a heads up when things vanish.

oh can you do context specific deprecations?

[arteymix]

Hmm, not really because the models are shared. I can document individual fields though.

[oganm]

ah, just something akin to "pst i just removed this bit in this context" would be enough