[Biojava-l] ontology exception, addSequence & BioSQLSequenceDB

[Matthew Pocock]

Hi Frederik,

Well, I'm still plugging away at this error. Yours is gone, but my old 
error is back. I have modified java.utils.JDBCConnectionPool to test 
existing connections using SELECT 1, which as removed the exceptions 
about roll-backs. However, now it appears that postgresql does not 
maintain the value of currval(sequence) between sessions (and sometimes 
even when you just call preparedStatement.close() ).

More news when I have it.


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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