build UTA REST interface / refactor UTA client packaging

[reece]

Originally reported by Reece Hart (Bitbucket: reece, GitHub: reece) in biocommons/uta #164 Migrated by bitbucket-issue-migration on 2016-09-09 15:15:07

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Data in UTA would be more accessible if it were accessible through REST interface.

The REST interface should be rich enough to obviate the psycopg2 dependency in the hgvs package.

Deploy as docker image.

TBC: Unclear whether sequence lookup should be part of UTA -- it's both necessary (e.g., for md5 validation) and difficult/inefficient to store in a database (e.g., genomic NC sequences).

TBC: Package structure could be with uta clients as separate package. If separate, psycopg2/pq dependency should be optional.

[davmlaw]

Hi, I've written a REST service for cdot - data provider I announced in a HGVS issue

If you ever make your REST service, I'd love to collaborate to agree on a standard for JSON representation (in fact, proposing a GA4GH standard may be worth doing)

Feel free to use any of the code etc I've written (all under MIT)

[davmlaw]

I copied then modified the cdot_rest server to work with UTA as a backend: https://github.com/SACGF/uta_rest

[davmlaw]

Hi @reece - I have made a start on the UTA REST service

https://github.com/SACGF/uta_rest

It's super minimal - it runs SQL on the UTA server and then caches the API call in Redis (ie doesn't have local Postgres)

There are a few API endpoints not done, but it does HGVS resolution and conversion already OK (it has the same JSON as cdot) server

The VM isn't up yet, but I can spin it up again easily, or perhaps just run it on the cdot VM

I am happy for you to take any of this code, or make it a biocommons project etc, then work on it there under your direction