[Biojava-dev] BioJava Nightly Build + BioSQL/MySQL problem...

[Michael Heuer]

It appears you have data problems, might you be able to

select * from ontology_term;

from your biosql database and send the result?

   michael


On Tue, 3 Aug 2004, Michael Griffith wrote:

> Hi,
>
> I am trying to use the BioJava 1.4 nightly build (8.3.2004) to read a
> GeneBank File and insert it into a BIOSQL/MySQL db.
>
> My code basically is doing this:
>
> // Connecting to the BioSQL DB
> SequenceDB db = new BioSQLSequenceDB(dbDriver, dbURL, dbUser, dbPass,
> biodatabase, create);
>
> // Reading a GeneBank flat file
> SequenceIterator iter = (SequenceIterator)SeqIOTools.fileToBiojava(format,
> alpha, br);
>             while (iter.hasNext()) {
>
>                 Sequence seq = iter.nextSequence();
>
>                 try {
>                     db.addSequence(seq);
>                 }
>                 catch (Exception e) {
>                     e.printStackTrace();
>                 }
>                 ...
>                 }
>
> It progresses a little ways and I get the following error stack:
>
>  [java] Caused by: java.sql.SQLException: Couldn't create term 'ORGANISM'
> for 'ORGANISM' in legacy ontology namespace
>      [java]     at
> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.intern_ontology_term(BioSQLSe
> quenceDB.java:942)
>      [java]     at
> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.persistBioentryProperty(BioSQ
> LSequenceDB.java:894)
>      [java]     at
> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB._addSequence(BioSQLSequenceDB
> .java:485)
>      [java]     ... 2 more
>      [java] Caused by: org.biojava.bio.BioRuntimeException: Error commiting
> to BioSQL tables (rolled back successfully)
>      [java]     at
> org.biojava.bio.seq.db.biosql.OntologySQL.persistTerm(OntologySQL.java:536)
>      [java]     at
> org.biojava.bio.seq.db.biosql.OntologySQL.access$200(OntologySQL.java:61)
>      [java]     at
> org.biojava.bio.seq.db.biosql.OntologySQL$OntologyMonitor.postChange(Ontolog
> ySQL.java:503)
>      [java]     at
> org.biojava.utils.ChangeSupport.firePostChangeEvent(ChangeSupport.java:338)
>      [java]     at
> org.biojava.ontology.Ontology$Impl.addTerm(Ontology.java:349)
>      [java]     at
> org.biojava.ontology.Ontology$Impl.createTerm(Ontology.java:358)
>      [java]     at
> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.intern_ontology_term(BioSQLSe
> quenceDB.java:938)
>      [java]     ... 4 more
>      [java] Caused by: java.sql.SQLException: Failed to persist term:
> ORGANISM from ontology: ontology: __biojava_guano with error: 1062 : 23000
>      [java]     at
> org.biojava.bio.seq.db.biosql.OntologySQL.persistTerm(OntologySQL.java:562)
>      [java]     at
> org.biojava.bio.seq.db.biosql.OntologySQL.persistTerm(OntologySQL.java:524)
>      [java]     ... 10 more
>      [java] Caused by: java.sql.SQLException: Duplicate key or integrity
> constraint violation,  message from server: "Duplicate entry 'ORGANISM-5'
> for key 2"
>      [java]     at
> com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:1977)
>      [java]     at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1163)
>      [java]     at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1272)
>      [java]     at com.mysql.jdbc.Connection.execSQL(Connection.java:2236)
>      [java]     at
> com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1741)
>      [java]     at
> com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1588)
>      [java]     at
> org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(Delegating
> PreparedStatement.java:233)
>      [java]     at
> org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(Delegating
> PreparedStatement.java:233)
>      [java]     at
> org.biojava.bio.seq.db.biosql.OntologySQL.persistTerm(OntologySQL.java:554)
>      [java]     ... 11 more
>      [java] Exception in thread "main" org.biojava.bio.BioError: Error
> looking up biosqlized ID for ORGANISM
>      [java]     at
> org.biojava.bio.seq.db.biosql.OntologySQL.termID(OntologySQL.java:684)
>      [java]     at
> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.intern_ontology_term(BioSQLSe
> quenceDB.java:927)
>      [java]     at
> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.persistBioentryProperty(BioSQ
> LSequenceDB.java:894)
>      [java]     at
> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB._addSequence(BioSQLSequenceDB
> .java:485)
>      [java]     at
> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.addSequence(BioSQLSequenceDB.
> java:365)
>      [java]     at
> com.gts.genebank.GeneralReader.main(GeneralReader.java:64)
>      [java] Caused by: java.lang.NullPointerException
>      [java]     at
> org.biojava.bio.seq.db.biosql.OntologySQL.termID(OntologySQL.java:682)
>      [java]     ... 5 more
>      [java] Java Result: 1
>
>
> What am I doing wrong?  Any help would be greatly appreciated!
>
> MG
>
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