The attribute on the sample is genotype, but the way that the harmonizer was written it assigns the value to sample.gentetic_information which does match the docs. We should either change the docs to say genotype instead and update the harmonizer (which I will do for now) or make a migration on the DB to change the name of the column to genetic_information.
Context
We currently use
genotype
as the attribute on theSample
model. This should have been changed to the more appropriately namedgenetic_information
.https://github.com/AlexsLemonade/refinebio-admin/pull/116#issuecomment-1605154840
Problem or idea
Updating this should be pretty straightforward.
One caveat is that the harmonizer. For the accompanying PR for this issue lets not rewrite the harmonizer and instead rename the
genotype_fields
,self.genotype_fields
, and the string that is passed in here: https://github.com/AlexsLemonade/refinebio/blob/dev/foreman/data_refinery_foreman/surveyor/harmony.py#L800 to matching versions ofgenetic_information
.Solution or next step
genotype
togenetic_information
genotype_fields
togenetic_information_fields
Sample
attribute names and output ofto_metadata_dict
match what we describe in the docs.