[Biojava-l] ontology exception, addSequence & BioSQLSequenceDB

[Frederik Decouttere]

Hi,

Anybody knows why I'm getting this exception:

*** Importing a core ontology -- hope this is okay
org.biojava.bio.BioError: Unexpected ontology duplication error
	at
org.biojava.bio.seq.db.biosql.OntologySQL.addCore(OntologySQL.java:215)
	at
org.biojava.bio.seq.db.biosql.OntologySQL.<init>(OntologySQL.java:337)
	at
org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.<init>(BioSQLSequenceDB.java:
176)
Caused by: org.biojava.ontology.AlreadyExistsException: Ontology
__core_ontology already contains instance_of(and, predicate)
	at org.biojava.ontology.Ontology$Impl.addTerm(Ontology.java:333)
	at
org.biojava.ontology.Ontology$Impl.createTriple(Ontology.java:483)
	at
org.biojava.bio.seq.db.biosql.OntologySQL.addCore(OntologySQL.java:198)
	... 4 more


the code:

Sequence seq = DNATools.createDNASequence("atgctgatgatgatg", "my_dna_1") ;
BioSQLSequenceDB db = new BioSQLSequenceDB(url, user, pass, biodatabase,
false);
db.addSequence(seq) ;

the database:
I'm using hsqldb 1.7.1 with the schema found in biosqldb-hsqldb.sql
(biojava-live Main branch from cvs)


Thanx
Frederik