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biocommons / biocommons.seqrepo

non-redundant, compressed, journalled, file-based storage for biological sequences
Apache License 2.0
39 stars 35 forks source link

Working on adding support for dataproxy #98

Closed andreasprlic closed 2 years ago

andreasprlic commented 2 years ago

Working on adding support for the vrs-python derived dataproxy for SeqRepo. (Thanks @reece !)

The goal is to enable seqrepo-rest-service communication for clients, such as the hgvs library (see related feature request there).

bmrobin commented 2 years ago

how are pull requests tested (were the tests running locally?)

andreasprlic commented 2 years ago

@bmrobin I believe there was an update in the meanwhile in the original https://github.com/ga4gh/vrs-python/blob/main/src/ga4gh/vrs/dataproxy.py which probably should get propagated back to in here. (see this commit https://github.com/ga4gh/vrs-python/commit/def64f9d8404ce4903993822c3db3a085e7311a8 )

bmrobin commented 2 years ago

@bmrobin I believe there was an update in the meanwhile in the original which probably should get propagated back to in here

https://github.com/andreasprlic/biocommons.seqrepo/pull/1

bmrobin commented 2 years ago

what is the release process like when you merge this? wondering how i can help next.

reece commented 2 years ago

I'll look at this PR this weekend. Thanks to both of you!

bmrobin commented 2 years ago

i suppose you could put it into bioutils, but honestly it seems to me that the seqrepo repo itself should be responsible for providing the dataproxy for itself.

andreasprlic commented 2 years ago

I can't think of a better place for this code either.

andreasprlic commented 2 years ago

I'll merge this since we are in agreement to move this forward.