> >> 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. >>
This was the case, and it was very simple to find once I went looking for it. One of the data values included a superscript that was causing the error. Thank for the tips and help, I am grateful. Marie~ >>> >>> 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] > -- 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]
