[BioSQL-l] Error loading ontology terms

[Hilmar Lapp]

The specific solution is in the biojava list archives, not the biosql  
list. If I remember correctly, you need to either upgrade biojava or  
biosql or both to the latest revision.

	-hilmar

On May 31, 2006, at 10:39 AM, Yi-Feng Chang wrote:

> 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
>
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-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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