[Biopython-dev] Re: BioSQL and PostgreSQL

Brad Chapman chapmanb at arches.uga.edu
Thu Nov 21 14:47:05 EST 2002

Hi Yves;

> > I know that there is tons happening on the BioSQL development front that
> > I just plain haven't been following, so I am really out of the loop on
> > what the current schema is or what schema we should be working with or
> > if anything is stable.
> Hmm, you must have a weird version of the schema :) (this said, the
> current one in CVS doesn't work with the corresponding bioperl-db)

I'm absolutely positive I was using a weird version :-). Wait, are there
versions. I think the most important thing for this release is to have a
SQL schema that works with the code we release. When the BioSQL decision
making has settled down to a new "for sure" schema, then we can migrate
over to that.

Do you have an "almost official" version that works with both Postgres
and MySQL? If so, I vote for including that.

> Yep.  But my implementation is a hack: it hardcodes the name of two
> adaptors, MySQLdb and psycopg -- while there are at least 3 ones for
> postgresql.

No worries on that front from me -- psycopg is a semi-official Postgres
driver, I reckon, since it's used in Zope. My only beef with it is that
the name is damn hard to type properly.

For right now, having one working driver with Postgres makes me happy,
so the hack is right on as far as I'm concerned.

> For discussing about the schema itself: you're right.  But at the
> moment, I suppose you would prefer to stick to its old version, since
> the new biopython release is slated for next week while I think a new
> BioSQL won't come out before December...

Yup. This sounds good. I would like Postgres to work for this release,
though -- do you want to send the schema you used that works and I can
check it into CVS? 

There will be another hacking session going on and I imagine BioSQL will
get beat around hard there, so for right now it's good to have something
that works for people who want a relational database.

> Hmm, not sure the perl and java guys are interested a lot in biopython's
> biosql guts :)

Well, they should be :-).


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