[Biopython-dev] [Bug 2833] Features insertion on previous bioentry_id

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http://bugzilla.open-bio.org/show_bug.cgi?id=2833





------- Comment #8 from biopython-bugzilla at maubp.freeserve.co.uk  2009-05-21 07:36 EST -------
(In reply to comment #7)
> However, the unit test doesn't reproduce your original issue. Hopefully
> your pickled SeqRecord objects will help there...

Based on your example script in comment 6 with the pickled SeqRecord objects,
but using MySQL, I get an IntegrityError as expected:

Traceback (most recent call last):
...
IntegrityError: (1062, "Duplicate entry 'ENST00000334859-2-0' for key 2")

I get the same error with simplified records lacking any annotation or features
(I just saved your three records to a FASTA file and reloaded them). So what
ever is going wrong seems to be PostgreSQL specific (or at least, does not
affect MySQL).

I have updated test_BioSQL.py in CVS to cover more variations (revision 1.33),
and hopefully the error message check should work on PostgreSQL as well. It
would be very helpful if you could test that.

Part of the new tests is a slight variation on your original example.  Could
you try this:

db.load([s1])
server.commit()
db.load([s2])
server.commit()
db.load([s3])
server.commit()

This might tell us if the issue is with PostgreSQL not checking the key
constraints until the commit.

Peter


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