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openvax / pyensembl

Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl
Apache License 2.0
374 stars 65 forks source link

Allow pyensembl to use any DB-API backend #91

Closed tavinathanson closed 9 years ago

tavinathanson commented 9 years ago

cc @arahuja

Intimately related to https://github.com/hammerlab/datacache/pull/25; see that PR for more details.

Review on Reviewable

timodonnell commented 9 years ago

Thanks for doing this, @tavinathanson and sorry for my slow turnaround. Overall looks good to me.

Especially since this code is generating SQL queries directly instead of using the sqlalchemy expression library (a choice I generally agree with -- I've found the expression library to often be pretty troublesome), I think we need to have some sort of test that this works on postgres and whatever other databases we're targeting. Is there a way to add an easy way for the user to configure the unit tests to run on a local postgres database? (Apologies if you've already done this and I missed it. It might just need to be documented more obviously.)

tavinathanson commented 9 years ago

This is way out of date, so closing it for now.