[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 #7 from cymon.cox at gmail.com  2008-10-16 05:53 EST -------
(In reply to comment #6)
> (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?

Apparently not (tests run after editing out code...).

>  I
> guess it doesn't hurt.

I assume we want to maintain support for the older psycopg driver.
Unfortunately, I cant get the old drivers to compile on my box - they
configure, but gcc chokes on the make... I cant see why the patch should effect
the operation of the old driver, but it would be worth checking.

> > (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.

Unfortunately, I dont have direct CVS access - proxy hassles - I downloaded the
cvs tarball previously. Besides I'm not a developer. Perhaps, someone else
would check it in.

Cheers, C.


-- 
Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.