ga4gh / vrs-python

GA4GH Variation Representation Python Implementation
https://github.com/ga4gh/vrs
Apache License 2.0
50 stars 27 forks source link

Where and how to define the `data_proxy` interface #390

Open jsstevenson opened 5 months ago

jsstevenson commented 5 months ago

https://github.com/ga4gh/vrs-python/blob/main/src/ga4gh/vrs/dataproxy.py (always a tell when the code references "VR" and not "VRS")

Most of this is copy-pasted from SeqRepo. This seems less than ideal, but I think we probably didn't want to depend on SeqRepo for the dataproxy if it could be avoided.

jsstevenson commented 4 months ago

Didn't think much of it at the time, but the new derive_refget_accession method that was added to the VRS DataProxy class does mean you have to be careful about how you're constructing it in cases where you need a singleton instance shared across multiple resources (e.g. Cool Seq Tool, Variation Normalizer, etc)