[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 #2 from cymon.cox at gmail.com  2008-10-14 14:09 EST -------
(In reply to comment #1)
> Supporting psycopg2 sounds good :)
> 
> What version of Biopython do you have? 1.48 or CVS

1.48

> as there have been some
> BioSQL changes recently (mostly to do with the taxonomy tables).

I loaded taxonomy in with the Pg driver and load_ncbi_taxonomy.pl with no
problem.

> 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.

Sure, that's probably a better approach :)

> Which version of the BioSQL schema do you have?

biosql-1.0.1

>  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

It really is broken when using run_tests.py, after running with the -g flag:
$ cat output/test_BioSQL
test_BioSQL
Load SeqRecord objects into a BioSQL database. ... ERROR
Get a list of all items in the database. ... ERROR
Test retrieval of items using various ids. ... ERROR
Make sure Seqs from BioSQL implement the right interface. ... ERROR
Check SeqFeatures of a sequence. ... ERROR
Make sure SeqRecords from BioSQL implement the right interface. ... ERROR
Check that slices of sequences are retrieved properly. ... ERROR
Make sure all records are correctly loaded. ... ERROR
Indepth check that SeqFeatures are transmitted through the db. ... ERROR
etc...

Probably not the solution we're looking for...

The problem is that run_test.py is not picking up the psycopg2 adapter and is
deferring to the generic adapter, consequently it throws on "InternalError:
DROP DATABASE cannot run inside a transaction block". Why that's the case when
individually the test work OK is something I tried to track this down but just
couldn't figure it...

Cheers, C.


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