Add support for pulling from seqrepo-rest-service.

[andreasprlic]

Summary It would be nice to be able to connect hgvs to pull sequence data from an instance of seqrepo-rest-service, rather than a local copy of the data (or NCBI). Happy to provide a PR for that.

Implementation Sketch:

Make the vrs-python data proxy more re-usable. Where is the best location for this? Should this be directly in seqrepo? Alternatively, this could also reside in bioutils. Any recommendations? (otherwise I'll just create a PR in seqrepo for this), and then a PR in hgvs to update the SeqFetcher to use this new proxy as a 3rd mechanism for sequence access.

[reece]

@andreasprlic Awesome that you're working on this. It's been needed for a long time. (See #199)

Architectural question: Would it be better (and do we have time) to implement something more like seqrepo-rest-service as a biocommons-rest-service, which would encapsulate UTA and seqrepo? hgvs would then need a new biocommons-rest data provider. And, we'd have to replumb hgvs to standardize responses from both sources. I think this route is better, but also larger, which is why I haven't done it. :-/

[andreasprlic]

@reece yes I totally agree. It would be better to have a service layer also on top of UTA. Having said that, I don't think I have time right now to work on that. Perhaps we should write this up as a ticket (or an epic).

In the meanwhile I was hoping that https://github.com/biocommons/biocommons.seqrepo/pull/98 could be a first step in the right direction.

[bmrobin]

Would it be better (and do we have time) to implement something more like...

@reece - andreas created this github issue after a conversation he & i had about how a requirement has arisen at Invitae with a project i'm working on that requires this now, and ultimately may be of use architecturally for future projects at Invitae.

i intend to investigate what can be done right now to satisfy the immediate need, unless y'all object

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This issue was closed because it has been stalled for 7 days with no activity.

[reece]

This issue was closed by stalebot. It has been reopened to give more time for community review. See biocommons coding guidelines for stale issue and pull request policies. This resurrection is expected to be a one-time event.