[Biopython-dev] BioSQL buglets

[Cymon Cox]

All,

Selects on the seqfeature_qualifier_value and dbxref tables were not being
ordered by rank. This caused multiple qualifier values to be out of order
which in turn caused the tests to fail - see comment in
http://bugzilla.open-bio.org/show_bug.cgi?id=2616

This also solves a TODO in the test_BioSQL_SeqIO.py:

 85 +#TODO - Pin down the "Duplicate entry" IntegrityError from this:
 86 +#    ("genbank",False, 'GenBank/cor6_6.gb', 6),

This test now works and Ive generated new output.

In test_BioSQL.py create_database(), postgres returns an error string that
'find's on index 0 when the the database doesnt exist. The comparision
therefore needs to be >= 0 rather than >0.

All tests now pass OK with postgresql/psycopg2.
Patch attached.

Cheers, C.
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