[BioPython] Biopython support for BioSQL on PostgreSQL

[Brad Chapman]

Hi Cymon;

> What is the status of Biopythons support of BioSQL on PostGreSQL?

I don't think it's been worked on it at all. Theoretically, you should
just be able to give the current codebase a postgres driver and make
things work, but I doubt if that would actually work (as you describe
below :-).

> Ive tried a few DB-API2.0 compliant PostGres drivers with the current
> BioSQL code without much success, so I'm figuring the code is still
> under development (- or perphaps I'm doing something mindless). Also, I
> see from (http://obda.open-bio.org/performance.html)

The code is always under development :-). Seriously, I haven't worked on
postgres at all, but it would be something good to see. I developed what
is there now from what Andrew started and everything was done on MySQL.
I didn't purposely use any MySQL specific code, but I'm no SQL expert by
far, so who knows.

For kicks (okay, not really kicks :-), I gave a shot at getting things
to work with the psycopg database adaptor. It looks like it's not really
easy (of course!) to get things working with postgresql -- there are
some issues with how things are returned and what parameters are passed
in during connection and eventually I had to give up.

If you want to work on this, that would be great. I'd be happy to help
with problems, etc -- I'm still learning postgres and don't even know
which driver is "best" (I found 3 of them out there; too much confusion
for my small brain) but I can try to help out.

Good luck; hope all that rambling answered your questions!
Brad