monarch-initiative / genophenocorr

Genotype Phenotype Correlation
https://monarch-initiative.github.io/genophenocorr/stable
MIT License
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user-friendly error messages #52

Closed pnrobinson closed 7 months ago

pnrobinson commented 9 months ago

When loading phenopackets like this:

patient = patient_creator.create_patient(pp)

I get these error warnings:

No proteins found for ID NP_001361354.1. Please verify refseq ID.
No proteins found for ID NP_001361355.1. Please verify refseq ID.
No proteins found for ID NP_001361356.1. Please verify refseq ID.
ID NP_002608.1 did not match
ID NP_002608.1 did not match
ID NP_002608.1 did not match
Protein ID NP_002608.1 got 1 results
ID NP_008964.3 did not match
ID NP_008964.3 did not match
Protein ID NP_008964.3 got 1 results
ID NP_722540.1 did not match
ID NP_722540.1 did not match
ID NP_722540.1 did not match
Protein ID NP_722540.1 got 1 results

This looks like something really bad because the background is read. However, the warnings are redundant and maybe we do not care about some of them. It would be better to create one message about whether we have successfully created the objects and try to decide if we think it is an error that UniProt cannot find NP_001361354.1 (if that is what is going on). I do not think this should be an error