InformaticsGenomicMedicine / DraftCoreDataModel

Draft of CoreDataModel
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Genome build syntax is too strict #12

Closed rrfreimuth closed 11 months ago

rrfreimuth commented 1 year ago

https://github.com/InformaticsGenomicMedicine/DraftCoreDataModel/blob/79450932a44ee677816f9c02e6f5660ea03e5ec1/src/core_variant.py#L200C14-L200C14

The genome build regex must allow: GRCh38.p14 GRCh38 T2T-CHM13 NCBI Build 36.1 (and probably others)

It might be easier to just check for empty/non-empty for now. If we get to a point where we try to normalize it then we can try to work through the details.

SalemBajjali commented 1 year ago

I removed the regular expression in the validation step and just allowed it for the user to input a string or None. If we plan to change this as you noted above we can come and revisit it at a later time.

https://github.com/InformaticsGenomicMedicine/DraftCoreDataModel/blob/6d7818ca238167fc604b02917775c482f5af7490/src/core_variant.py#L346-L365

SalemBajjali commented 11 months ago

@rrfreimuth reviewed via zoom.