[BioSQL-l] Error loading ontology terms

[Yi-Feng Chang]

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