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monarch-initiative / genophenocorr

Genotype Phenotype Correlation
https://monarch-initiative.github.io/genophenocorr/stable
MIT License
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Formalize handling and reporting of input errors #128

Closed ielis closed 5 months ago

ielis commented 5 months ago

Create an Auditor API to formalize recording and reporting errors in the input data, while preserving the context of the hierarchical data.

Auditor is implemented on the following APIs:

Note, we introduce CohortCreator as the top-level API for creating cohort e.g. from a phenopacket folder. We provide a new convenience method for configuring the cohort creator:

from genophenocorr.preprocessing import configure_caching_cohort_creator

The errors and warnings are handled depending on the validation policy. See the docs for more info.

fixes #56 fixes #120 fixes #84 fixes #113 fixes #79

ielis commented 5 months ago

@lnrekerle please have a look, please check the notebooks as we discussed, and give it a :+1: if looks good.