[Biopython-dev] BioSQL and PostgreSQL

Brad Chapman chapmanb at arches.uga.edu
Wed Nov 20 11:09:35 EST 2002


> I've adapted BioSQL/*.py to work with PostgreSQL.  Well, at least the 
> tests pass... Patch attached, comments are welcome.

Thanks much! I have committed these. The MySQL still seems to work fine
for me, although the PostgreSQL does give me errors in the sql schema I

IntegrityError: ERROR:  pg_ownercheck: class "bioentry_entry" not found

 CREATE INDEX bioentryentry ON bioentry_entry ( entry_id )

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.

That being said, if the postgres works for you and MySQL doesn't break,
I'm happy :-).

> * I've made utility classes for nonstandard SQL/DBAPI operations, e.g. 
> retrieving the id of the last inserted record.  (The implementation is 
> so-so, I know :).  There are Generic_dbutils, Mysql_dbutils and 
> Pg_dbutils.  The choice is made according to the DBAPI module's name; 
> only MySQLdb and psycopg are currently recognised.

Sure. Sounds find to me as this is cleaner then my implementation.
Thanks. I am no database expert, so I appreciate anything making this

> (Done but not included in the patch: adaptations to the current 
> biosql-schema CVS.)

Hmmmm, so maybe you understand better than I do what is going on with
the current schema :-). I guess the best place to talk about this is the
BioSQL list:


I wish I knew what was going on so I could offer more advice, but
mostly I am a simpleton when it comes to designing SQL schemas so I just
let the smart folks figure out what is best and then implement it.
Certaintly we do want to stay up to date whenever they have something

What do you think about talking up your patches over there?

Thanks again for this work; much appreciated!


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