[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 #5 from cymon.cox at gmail.com  2008-10-15 08:31 EST -------
(In reply to comment #3)
> (In reply to comment #2)
> > (In reply to comment #1)
> > > 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).
> > 
> > 1.48
> > 
> 
> Could you update to Biopython CVS please?  This now populates the
> taxon/taxon_name tables differently when there is an NCBI taxon ID (with the
> option to fetch lineages from Entrez).
> 
> Once you're running CVS, could you attach a patch to this bug.  That should
> make it easier for me to look at this.

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)

[cymon at chara Tests]$ cat setup_BioSQL.py |grep "DBDRIVER \="
16:#DBDRIVER = 'MySQLdb'
19:DBDRIVER = 'psycopg2'
[cymon at chara Tests]$ python run_tests.py test_BioSQL.py test_BioSQL_SeqIO.py
test_BioSQL ... ok
test_BioSQL_SeqIO ... ok

----------------------------------------------------------------------
Ran 2 tests in 32.882s

OK

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

Cheers, C.


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