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

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

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





------- Comment #1 from biopython-bugzilla at maubp.freeserve.co.uk  2008-10-14 13:25 EST -------
Supporting psycopg2 sounds good :)

What version of Biopython do you have? 1.48 or CVS as there have been some
BioSQL changes recently (mostly to do with the taxonomy tables).

I'm surprised the order of the qualifiers isn't being preserved - I think we
should fix that rather than tweaking test_BioSQL_SeqIO.py to ignore this.

Which version of the BioSQL schema do you have?  It is possible that this is a
BioSQL issue/difference in the PostgreSQL schema compared to the BioSQL schema
which I have been using when running the tests.

Also your problem about the two tests failing when run via run_tests.py is
concerning.  What happens if you do this:

python run_tests.py -g test_BioSQL
python run_tests.py -g test_BioSQL_SeqIO
python run_tests.py test_BioSQL test_BioSQL_SeqIO
cvs diff output/test_BioSQL output/test_BioSQL_SeqIO

Thanks

Peter


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