I'm having the same problem. Investigating now. This seems to work for me on the 1.3 releases, but not on the devel release.
Matthew
Frederik Decouttere wrote:
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
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