> Marie Mooney wrote: >> Here's the step by step path: >> >> 1. Go to Administrate -> Plugins -> Configurations >> 2. Click on the name of my genepix configuration with Plugin >> definition=raw data importer >> 3. Click 'Save and Configure' >> 4. Raw data type selection is GenePix, click next >> 5. I have previously entered in the regular expressions to parse the >> files, so I click 'Test with file' button >> 6. Click 'Browse' and select a .gpr file that I've imported, click ok >> and >> then 'Parse File' button >> 7. Then I get: >> >> Could not parse the file /home/admin/raw >> data/N+L3[17]_N-L3[9]_090806.gpr >> >> 1. Start of data couldn't be found. Please try again with different >> settings. >> >> And after reviewing the parsing, I recognize that my data header is on >> line 32, the first row with Type='Unknown'. So I select Use as='Data >> Header' from the dropdown options on that line and click ok. >> >> 8. Then I am put back to the screen where I can select the 'Test with >> File' button again. I do this, browse for my data file, and select >> "Parse >> File' button again. The file parses correctly, and I select ok. >> >> 9. Now, I am back at the screen where I was selecting 'Test with File', >> but now since it parses correctly I just hit 'Next'. I get this error, >> which I don't remember seeing Friday, but I am getting by doing this >> now: > > I do the same thing and it works just fine. I am using BASE 2.2.2 > though, but I don't think anything has changed that affects this. > It seems like the database is complaining about some of the values so > maybe there is something strange in your parameters that isn't taken > care of correctly. First, I don't think the 'Test with file' function > has anything to do with the problem, but you can use it for debugging. > If you don't change any other parameter values it is most probably > something in the 'Data header' value that the database doesn't like. Can > you check the value to see if there is something strange with it? Try > cutting away pieces (say 10-20 characters at a time) from the value > until the configuration can be saved correctly. Then, it should be easy > to identify the part that is problematic. > >> >> Unexpected error >> BaseException on page /base2/common/plugin/index.jsp >> >> Version BASE 2.2.1 (build #0; schema #29) >> Web server Apache Tomcat/5.5.23 >> Database Dialect org.hibernate.dialect.MySQLInnoDBDialect >> JDBC Driver com.mysql.jdbc.Driver (version 5.0) >> Java runtime Java(TM) 2 Runtime Environment, Standard Edition >> (1.5.0_11-b03), Sun Microsystems Inc. >> Operating system Linux i386 2.6.20-1.2933.fc6xen >> Memory Total: 32.4 MB >> Free: 12.6 MB >> Max: 63.6 MB >> Browser Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.7.6) >> Gecko/20050328 >> Fedora/1.7.6-1.2.5 >> Error message could not insert collection: >> [net.sf.basedb.core.data.TextParameterValueData.values#440] >> Stack trace >> >> ...at HibernateUtil.commit(HibernateUtil.java:869) >> ...at DbControl.commit(DbControl.java:383) >> ...at >> org.apache.jsp.common.plugin.index_jsp._jspService(index_jsp.java:484) >> ...at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:98) >> ...at javax.servlet.http.HttpServlet.service(HttpServlet.java:803) >> ...at >> org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:328) >> ...at >> org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:315) >> ...at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:265) >> >> ...at javax.servlet.http.HttpServlet.service(HttpServlet.java:803) >> ...at >> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) >> ...at >> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) >> ...at >> net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:71) >> ...at >> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) >> ...at >> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) >> ...at >> org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:210) >> ...at >> org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:174) >> ...at >> org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) >> ...at >> org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) >> ...at >> org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) >> ...at >> org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:151) >> ...at >> org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:870) >> ...at >> org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665) >> ...at >> org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528) >> ...at >> org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81) >> ...at >> org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:685) >> ...at java.lang.Thread.run(Thread.java:595) >> >> 45 more... > > Please submit the entire stack trace. I think (hope) there is some > important information later on.
Here is the complete stack trace: Stack trace ...at HibernateUtil.commit(HibernateUtil.java:869) ...at DbControl.commit(DbControl.java:383) ...at org.apache.jsp.common.plugin.index_jsp._jspService(index_jsp.java:484) ...at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:98) ...at javax.servlet.http.HttpServlet.service(HttpServlet.java:803) ...at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:328) ...at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:315) ...at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:265) ...at javax.servlet.http.HttpServlet.service(HttpServlet.java:803) ...at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) ...at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) ...at net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:71) ...at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) ...at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) ...at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:210) ...at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:174) ...at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) ...at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) ...at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) ...at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:151) ...at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:870) ...at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665) ...at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528) ...at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81) ...at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:685) ...at java.lang.Thread.run(Thread.java:595) Caused by: org.hibernate.exception.GenericJDBCException ...at org.hibernate.exception.SQLStateConverter.handledNonSpecificException(SQLStateConverter.java:103) ...at org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:91) ...at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43) ...at org.hibernate.persister.collection.AbstractCollectionPersister.recreate(AbstractCollectionPersister.java:1183) ...at org.hibernate.action.CollectionRecreateAction.execute(CollectionRecreateAction.java:26) ...at org.hibernate.engine.ActionQueue.execute(ActionQueue.java:248) ...at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:232) ...at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:143) ...at org.hibernate.event.def.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:298) ...at org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:27) ...at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1000) ...at org.hibernate.impl.SessionImpl.managedFlush(SessionImpl.java:338) ...at org.hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java:106) ...at HibernateUtil.commit(HibernateUtil.java:856) ...at DbControl.commit(DbControl.java:383) ...at org.apache.jsp.common.plugin.index_jsp._jspService(index_jsp.java:484) ...at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:98) ...at javax.servlet.http.HttpServlet.service(HttpServlet.java:803) ...at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:328) ...at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:315) ...at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:265) ...at javax.servlet.http.HttpServlet.service(HttpServlet.java:803) ...at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) ...at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) ...at net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:71) ...at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) ...at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) ...at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:210) ...at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:174) ...at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) ...at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) ...at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) ...at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:151) ...at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:870) ...at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665) ...at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528) ...at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81) ...at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:685) ...at java.lang.Thread.run(Thread.java:595) Caused by: com.mysql.jdbc.MysqlDataTruncation ...at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2868) ...at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1573) ...at com.mysql.jdbc.ServerPreparedStatement.serverExecute(ServerPreparedStatement.java:1169) ...at com.mysql.jdbc.ServerPreparedStatement.executeInternal(ServerPreparedStatement.java:693) ...at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1404) ...at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1318) ...at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1303) ...at com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeUpdate(NewProxyPreparedStatement.java:105) ...at org.hibernate.jdbc.NonBatchingBatcher.addToBatch(NonBatchingBatcher.java:23) ...at org.hibernate.persister.collection.AbstractCollectionPersister.recreate(AbstractCollectionPersister.java:1146) ...at org.hibernate.action.CollectionRecreateAction.execute(CollectionRecreateAction.java:26) ...at org.hibernate.engine.ActionQueue.execute(ActionQueue.java:248) ...at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:232) ...at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:143) ...at org.hibernate.event.def.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:298) ...at org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:27) ...at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1000) ...at org.hibernate.impl.SessionImpl.managedFlush(SessionImpl.java:338) ...at org.hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java:106) ...at HibernateUtil.commit(HibernateUtil.java:856) ...at DbControl.commit(DbControl.java:383) ...at org.apache.jsp.common.plugin.index_jsp._jspService(index_jsp.java:484) ...at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:98) ...at javax.servlet.http.HttpServlet.service(HttpServlet.java:803) ...at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:328) ...at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:315) ...at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:265) ...at javax.servlet.http.HttpServlet.service(HttpServlet.java:803) ...at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) ...at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) ...at net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:71) ...at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) ...at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) ...at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:210) ...at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:174) ...at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) ...at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) ...at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) ...at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:151) ...at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:870) ...at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665) ...at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528) ...at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81) ...at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:685) ...at java.lang.Thread.run(Thread.java:595) > >> >> 10. BUT if I now hit the 'Back' button, and then try the 'Next' button >> again, I get the error I was getting on Friday: > > The back button is broken. If it doesn't work the first time you have to > close the window and start over from the beginning. Normally this > wouldn't be a problem since most errors are caught and you will be taken > back to the previous page automatically. It seems however that this > error happens when everything already has been validated. It is the last > step of sending the data to the database that for some reason fails. > > The NullPointerException the second time happens because everything has > already been cleared the first time you hit the 'Next' button. > > /Nicklas > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share > your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > The BASE general discussion mailing list > basedb-users@lists.sourceforge.net > unsubscribe: send a mail with subject "unsubscribe" to > [EMAIL PROTECTED] > -- Marie Mooney [EMAIL PROTECTED] ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
