[Biojava-l] Error loading ontology terms

[Richard Holland]

Hi there.

I looked through your stack trace, and the line numbers don't match up
with the current code. I have a strong feeling you may have an out-of-
date version of biojava.

Could you double-check that you have the latest biojava-1.4 version, or
are using the biojava-live version built from CVS?

If you can confirm that you are using the latest 1.4 or biojava-live
then it'd be easier to solve this.

Alternatively, you could have an out-of-date version of the BioSQL
schema. 

The reason I suspect that your BioSQL or BioJava are out of date is
because in the last stack trace you mention, this exception arises:

	java.sql.SQLException: Unknown column 'name' in 'field list'

This shows that BioJava has expected to find a column called 'name' in
some table in BioSQL, but that column is not there. This would only
happen if your BioSQL version did not match the version of BioSQL that
your version of BioJava was expecting.

cheers,
Richard

On Thu, 2006-06-01 at 21:32 +0800, Yi-Feng Chang wrote:
> Leif, this looks more like a biojava or biojava-x related problem, so  
> I'm resending it to the Biojava list. -hilmar
> ======================================================================== 
> ==
> Dear All,
> I've checked biosql archives, and found a similar thread
> (http://lists.open-bio.org/pipermail/biojava-l/2005-November/ 
> 005151.html)
> however, it did not give specific solution. So I post here again, and
> hope there are someone could help me.
> I'm using JDK1.5.0_05, Biojava 1.4, Biosql 1.41, and Mysql 5.0 with
> My_connectJ 3.1
> I was following the demo source that provide by biojava-in-anger except
> for the database connection
> the exceptions were listed in following:
> In first connection there would be a connection error
> *** Importing a core ontology -- hope this is okay
> *** Importing terms
> Exception in thread "main" org.biojava.bio.BioException: Error
> connecting to BioSQL database: Connection is closed.
> at
> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.initDb 
> (BioSQLSequenceDB.java:276)
> at
> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.<init> 
> (BioSQLSequenceDB.java:194)
> at genevote.BioSQLTest.loadSeq(BioSQLTest.java:31)
> at genevote.BioSQLTest.main(BioSQLTest.java:70)
> Caused by: java.sql.SQLException: Connection is closed.
> at
> org.apache.commons.dbcp.PoolingDataSource 
> $PoolGuardConnectionWrapper.checkOpen(PoolingDataSource.java:219)
> at
> org.apache.commons.dbcp.PoolingDataSource 
> $PoolGuardConnectionWrapper.createStatement(PoolingDataSource.java:248)
> at
> org.biojava.bio.seq.db.biosql.MySQLDBHelper.getInsertID 
> (MySQLDBHelper.java:68)
> at
> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.initDb 
> (BioSQLSequenceDB.java:268)
> ... 3 more
> Then I tried again, it works, and I put all sequences in genbank format
> into biosql db without error.
> But, while I tried to extract sequences, exception comes again.
> org.biojava.bio.BioException: Error loading ontology terms
> at
> org.biojava.bio.seq.db.biosql.OntologySQL.loadOntology 
> (OntologySQL.java:444)
> at
> org.biojava.bio.seq.db.biosql.OntologySQL.getOntology 
> (OntologySQL.java:116)
> at org.biojava.bio.seq.db.biosql.OntologySQL.<init>(OntologySQL.java: 
> 413)
> at
> org.biojava.bio.seq.db.biosql.OntologySQL.getOntologySQL 
> (OntologySQL.java:72)
> at
> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.initDb 
> (BioSQLSequenceDB.java:240)
> at
> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.<init> 
> (BioSQLSequenceDB.java:194)
> at genevote.test.loadSeq(test.java:25)
> at genevote.test.main(test.java:76)
> Caused by: java.sql.SQLException: Unknown column 'name' in 'field list'
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2851)
> at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1534)
> at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1625)
> at com.mysql.jdbc.Connection.execSQL(Connection.java:2297)
> at com.mysql.jdbc.Connection.execSQL(Connection.java:2226)
> at
> com.mysql.jdbc.PreparedStatement.executeInternal 
> (PreparedStatement.java:1812)
> at
> com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java: 
> 1657)
> at
> org.apache.commons.dbcp.DelegatingPreparedStatement.executeQuery 
> (DelegatingPreparedStatement.java:205)
> at
> org.apache.commons.dbcp.DelegatingPreparedStatement.executeQuery 
> (DelegatingPreparedStatement.java:205)
> at org.biojava.bio.seq.db.biosql.OntologySQL.loadTerms 
> (OntologySQL.java:339)
> at
> org.biojava.bio.seq.db.biosql.OntologySQL.loadOntology 
> (OntologySQL.java:441)
> ... 7 more
> 
> yi-feng chang
> 
> 
> _______________________________________________
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-- 
Richard Holland (BioMart Team)
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
UNITED KINGDOM
Tel: +44-(0)1223-494416