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

[Michael Griffith]

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