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

[Michael Griffith]

Michael, 

Well, that could be the problem?  I don't have a table called ontology_term.
I do have a table called ontology that looks like this:

  4   __core_ontology   BioSQL core ontology (imported by BioJava)
  5   __biojava_guano   Namespace for old, but still useful, shit imported
from ontology-less BioJava data models

The version of my schema was created from:
biosql-schema/sql/biosqldb-mysql.sql Version 1.38.  Is this correct?

Cheers!

MG



On 8/3/04 12:18 PM, "Michael Heuer" <heuermh at acm.org> wrote:

> 
> 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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>> 
> 
>