[Biopython-dev] [Bug 2616] BioSQL support for Psycopg2

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http://bugzilla.open-bio.org/show_bug.cgi?id=2616





------- Comment #6 from biopython-bugzilla at maubp.freeserve.co.uk  2008-10-15 09:42 EST -------
(In reply to comment #5)
> OK, so a clean install from CVS seemed to do the trick and now both tests pass
> from within the test suite after applying the patch (attached)

OK, good.  I guess you had CVS tests against old Biopython or something like
that happening.

I've had a quick look at the patch - it looks fine to me, but I have not
actually tested it.

In BioSQL/BioSeqDatabase.py there is a comment about building a DSN being
required for older releases of psycopg - do we still need this for psycopg2?  I
guess it doesn't hurt.

> (NB: the buglet in preserving qualifier order - sorted the lists in
> test_BioSQL_SeqIO.py in order to pass test).

I suggest you check in this patch, plus the tweak to test_BioSQL_SeqIO.py
(conditional on the database driver) with a "TODO" comment next to it about
checking why the order wasn't preserved.

Peter


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