The error happens because we get 'null' for the RawDataType for (at least) one raw bioassay. The page displays correctly some times because the 'bad' raw bioassay is not on it. The RawDataType is a required property and it should never be null. I can think of two reasons for it to happen:
1. There is a problem with the upgrade between 2.4 --> 2.5. The upgrade changed the way Affymetrix data is handled. We are not aware of any problems, but since we are not Affymetrix users ourselves we have only been able to do tests with a few data sets. To check this you need to find out which raw bioassay that is causing the problem and then manually check in the database the value of the 'rawdatatype' column. The hard part may be to find which raw bioassay is causing it. If you hide the 'Raw data type' column the page should be able to display correctly. 2. A raw data type definition has been removed from the raw-data-types.xml file. If you have made modifications to this file, check that you did'nt accidentaly overwite it during the upgrade. In any case, we'll try to fix the BASE code to handle this error better. /Nicklas Reha Yildirimman wrote: > Didn't realize that I didn't copy the complete error message: > > ERROR [jsp]:253 - Servlet.service() for servlet jsp threw exception > java.lang.NullPointerException > at > org.apache.jsp.views.rawbioassays.list_005frawbioassays_jsp._jspService(list_005frawbioassays_jsp.java:1295) > > > at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:97) > at javax.servlet.http.HttpServlet.service(HttpServlet.java:802) > at > org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:332) > > > at > org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:314) > at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:264) > at javax.servlet.http.HttpServlet.service(HttpServlet.java:802) > at > org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252) > > > at > org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173) > > > at > net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:72) > > > at > org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202) > > > at > org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173) > > > at > org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) > > > at > org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:178) > > > at > org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:126) > > at > org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:105) > > at > org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:107) > > > at > org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:148) > at > org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:869) > at > org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:664) > > > at > org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:527) > > > at > org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:80) > > > at > org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:684) > > > at java.lang.Thread.run(Thread.java:595) > > Thanks in advance > > Reha > > Nicklas Nordborg wrote: >> Reha Yildirimman wrote: >> >>> Hello, >>> >>> I recently updated our BASE system from 2.2 > 2.5.0 > 2.5.1 and now >>> have the following problem. >>> >>> When I try to view rawbioassays (we currently have ~2000, >>> view-setting is 99 assays per page) and I click on any page number >>> the page wont be completely displayed , i.e. just until item 12 (the >>> number is always different). >>> When I reset the view by selecting a saved profile (showing name, raw >>> data type, array design, has data) the current page is displayed >>> properly. >>> Checking the log file (catalina.out) I get the following message: >>> >>> ERROR [jsp]:253 - Servlet.service() for servlet jsp threw exception >>> java.lang.NullPointerException >>> >> >> Can you send the complete stacktrace? It is hard to do anything >> without knowing were in the code the error happens. Since the error >> doesn't happen every time, I guess there is some special case that is >> not handled properly in the BASE code. >> >> /Nicklas >> >> ------------------------------------------------------------------------- >> This SF.net email is sponsored by: Microsoft >> Defy all challenges. Microsoft(R) Visual Studio 2008. >> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >> _______________________________________________ >> The BASE general discussion mailing list >> basedb-users@lists.sourceforge.net >> unsubscribe: send a mail with subject "unsubscribe" to >> [EMAIL PROTECTED] >> > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > > > ------------------------------------------------------------------------ > > _______________________________________________ > The BASE general discussion mailing list > basedb-users@lists.sourceforge.net > unsubscribe: send a mail with subject "unsubscribe" to > [EMAIL PROTECTED] ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
