Howdy all, I have a fresh brand new a brand new installation of Base 2.16.1, on MySQL 5.1.41, on Ubuntu 10.04.1, with Tomcat 6.0.24, and 1.6 of the illumina plugin installed. When attempting to import the BGX file it fails with error could not execute query on line 10 in file 'MouseWG-6_V2_0_R0_11278593_A.bgx': Mus musculus RefS...
I'm pretty sure I've got most everything installed and configured properly. Any help would be greatly appreciated. Thanks in advance, Thomas Stack trace is: net.sf.basedb.core.BaseException: could not execute query on line 10 in file 'MouseWG-6_V2_0_R0_11278593_A.bgx': Mus musculus RefS... at net.sf.basedb.plugins.AbstractFlatFileImporter.doImport(AbstractFlatFileImporter.java:731) at net.sf.basedb.plugins.AbstractFlatFileImporter.run(AbstractFlatFileImporter.java:468) at net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:116) at net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:510) at java.lang.Thread.run(Thread.java:662) Caused by: net.sf.basedb.core.BaseException: could not execute query at net.sf.basedb.core.HibernateUtil.loadData(HibernateUtil.java:1384) at net.sf.basedb.core.ReporterBatcher.getByExternalId(ReporterBatcher.java:269) at net.sf.basedb.core.ReporterBatcher.getByExternalId(ReporterBatcher.java:242) at net.sf.basedb.plugins.ReporterFlatFileImporter.handleData(ReporterFlatFileImporter.java:619) at net.sf.basedb.plugins.AbstractFlatFileImporter.doImport(AbstractFlatFileImporter.java:699) ... 4 more Caused by: org.hibernate.exception.SQLGrammarException: could not execute query at org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:92) at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:66) at org.hibernate.loader.Loader.doList(Loader.java:2452) at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2192) at org.hibernate.loader.Loader.list(Loader.java:2187) at org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:452) at org.hibernate.hql.ast.QueryTranslatorImpl.list(QueryTranslatorImpl.java:363) at org.hibernate.engine.query.HQLQueryPlan.performList(HQLQueryPlan.java:196) at org.hibernate.impl.StatelessSessionImpl.list(StatelessSessionImpl.java:515) at org.hibernate.impl.QueryImpl.list(QueryImpl.java:102) at net.sf.basedb.core.hibernate.QueryWrapper.list(QueryWrapper.java:109) at net.sf.basedb.core.HibernateUtil.loadData(HibernateUtil.java:1378) ... 8 more Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Unknown column 'reporterda0_.source' in 'field list' at sun.reflect.GeneratedConstructorAccessor105.newInstance(Unknown Source) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27) at java.lang.reflect.Constructor.newInstance(Constructor.java:513) at com.mysql.jdbc.Util.handleNewInstance(Util.java:409) at com.mysql.jdbc.Util.getInstance(Util.java:384) at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1054) at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3566) at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3498) at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1959) at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2113) at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2568) at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2113) at com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:2275) at com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeQuery(NewProxyPreparedStatement.java:76) at org.hibernate.jdbc.AbstractBatcher.getResultSet(AbstractBatcher.java:208) at org.hibernate.loader.Loader.getResultSet(Loader.java:1869) at org.hibernate.loader.Loader.doQuery(Loader.java:718) at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:270) at org.hibernate.loader.Loader.doList(Loader.java:2449) ... 17 more ________________________________ UT Southwestern Medical Center The future of medicine, today. ------------------------------------------------------------------------------ The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE: Pinpoint memory and threading errors before they happen. Find and fix more than 250 security defects in the development cycle. Locate bottlenecks in serial and parallel code that limit performance. http://p.sf.net/sfu/intel-dev2devfeb _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
