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

[bugzilla-daemon at portal.open-bio.org]

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





------- Comment #14 from biopython-bugzilla at maubp.freeserve.co.uk  2009-05-22 08:06 EST -------
(In reply to comment #13)
> (In reply to comment #12)
> > After deleting the RULES in the BioSQL schema, all the new unittests pass.
> > 
> > (All the RULES can be deleted as they are all there to circumvent the
> > problem in Bioperl-db described by Hilmar Lapp on the biopython-dev list:
> > 
> > http://lists.open-bio.org/pipermail/biopython-dev/2009-May/006084.html
> > 
> > See also the comment in the schema.)
> > 
> > C.

Well spotted Cymon - I'd missed that.

> I've deleted the two rules, 
> rule_bioentry_i1
> rule_bioentry_i2
> 
> ...
> with pythhon2.4, python2.5, psycopg, psycopg2.
> Everything seems to be ok.
> ...
> After removing the rules i've run my own tests:
> .....
> >>> ## LOAD INTO DB
> >>> db.load([s1])
> 1
> >>> db.load([s2])
> 1
> >>> db.load([s3])
> Traceback (most recent call last):
>   File "<console>", line 1, in ?
>   File "../BioSQL/BioSeqDatabase.py", line 442, in load
>   File "../BioSQL/Loader.py", line 50, in load_seqrecord
>   File "../BioSQL/Loader.py", line 550, in _load_bioentry_table
>   File "../BioSQL/BioSeqDatabase.py", line 301, in execute
> IntegrityError: duplicate key value violates unique constraint
> "bioentry_accession_key"
> 
> And i've got the error, that is what it is expected as a normal behaviour.
> So now i've only to trap the exception or pre-check duplications.

Great.

It will be down to BioSQL to change the schema (in conjunction with BioPerl),
but Hilmar seems to be looking into this:
http://lists.open-bio.org/pipermail/biopython-dev/2009-May/006084.html

I suppose in the short term we could change our local copy of the schema used
in the Biopython unit tests...

Peter


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