[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 #6 from biopython-bugzilla at maubp.freeserve.co.uk  2009-06-04 17:11 EST -------
(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.

Maybe we simply can't do a drop database with the pygb driver for PostgreSQL.
Perhaps instead we can just empty all the tables in this case? That might fix
(at least part of) test_BioSQL.py

Does test_BioSQL_SeqIO.py work?

Does simple use of BioSQL with pgdb work?


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