[Biopython-dev] [Bug 2849] PyGresql PostgreSQL driver support for BioSQL is broken

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2849





------- Comment #7 from cymon.cox at gmail.com  2009-06-04 17:26 EST -------
(In reply to comment #6)
> (In reply to comment #5)
> > Psycopg defaults to a "read committed" isolation level that psycopg wraps
> > in a translation block. So, I think the only way not to be in a translation
> > block is to autocommit.
> 
> Presumably PyGresql/pgdb is similar in this regard? Given the apparent lack of
> any documentation on line at http://www.pygresql.org/pgdb.html this might be
> tricky to resolve, but from looking at the CVS repository I don't think they
> support autocommit.

They dont.

> 
> Maybe we simply can't do a drop database with the pygb driver for PostgreSQL.

I had myself convinced this was the case for quite a while, but you can "trick"
the cursor with a "COMMIT" and then execute a non-transactional query. I have
it working and passing all the tests.

Unfortunately, the driver spews forth "NOTICE"'s each time the database is
built, ie for each CREATE in the schema, which ruins the unittest output. Ive
yet to find a way to silence this.

I'll submit a patch forthwith...

C.


-- 
Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.