[Biojava-l] 2 problems found in org.biojava.bio.seq.db.biosql code

mark.schreiber at group.novartis.com mark.schreiber at group.novartis.com
Sun Feb 8 20:26:17 EST 2004

Hi Len -

I think it's probably worth committing the tests. It will serve as a 
warning that we know something doesn't work as advertised until someone 
gets around to fixing it.

- Mark

Mark Schreiber
Principal Scientist (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
1 Science Park Road
#04-14 The Capricorn
Singapore 117528

phone +65 6722 2973
fax  +65 6722 2910

Len Trigg <len at reeltwo.com>
Sent by: biojava-l-bounces at portal.open-bio.org
02/09/2004 09:09 AM

        To:     "Frederik Decouttere" <sherpa at coresoft.be>
        cc:     biojava-l at biojava.org
        Subject:        Re: [Biojava-l] 2 problems found in org.biojava.bio.seq.db.biosql code

"Frederik Decouttere" <sherpa at coresoft.be> wrote:
> After doing some tests with the biojava - biosql code I think there are
> 2 (little) bugs in there:
> - when persisting a Sequence which contains a Feature with
> BetweenLocation this Location gets converted to a RangeLocation upon
> retrieval
> - when persisting a Sequence which contains (a) Feature(s) in 2
> different biodatabases an exception is thrown in the ontology code part
> of biojava

I have got as far as inserting your example code into the BioSQL JUnit
test and it replicates the problem perfectly. I think I know what's
going on with the ontology bug, but haven't looked into the Location
one. I probably won't be able to look at it in more detail for a
couple more days though (if anyone wants to jump the gun, I can commit
the test so the tests start failing :-)).


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