Re: [Treebase-devel] Null pointer Exception

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The stack trace means that there is a situation when two taxon labels  
are being compared that either one of the two TaxonLabel objects, or  
the taxonLabel property of one, is null.

Indeed, the TaxonLabel.taxonLabel property property is nullable  
(why?), so this seems to be a legitimate situation and the fact that  
the code assumes that it can never be null is a bug. I fixed this and  
committed it to trunk. I haven't had a chance to rebuild, so I'm  
hoping it compiles.

	-hilmar

On May 24, 2010, at 12:06 PM, William Piel wrote:

>
> I've been plodding through tables and records associated with  
> study_id 10526, but I have not found a spurious NULL value, yet we  
> continue to get an uncaught exception when we try to access the  
> summary page for the study.
>
> Is there someone skilled at reading the trace barfs (see below) who  
> can point me in the right direction? (or, Jon, do you have a more  
> informative error log about what is causing the  
> "NullPointerException"?)
>
> thanks,
>
> Bill
>
>
> http://treebase-stage.nescent.org/treebase-web/search/study/summary.html?id=10526
> http://treebase.nescent.org/treebase-web/search/study/summary.html?id=10526
>
> Uncaught Exception Encountered
> java.lang.NullPointerException at org.cipres.treebase.web.controllers.SearchSummaryController 
> $TaxonLabelByLabelComparator.compare(SearchSummaryController.java: 
> 550) at org.cipres.treebase.web.controllers.SearchSummaryController 
> $TaxonLabelByLabelComparator.compare(SearchSummaryController.java: 
> 548) at java.util.Arrays.mergeSort(Arrays.java:1283) at  
> java.util.Arrays.mergeSort(Arrays.java:1294) at  
> java.util.Arrays.mergeSort(Arrays.java:1294) at  
> java.util.Arrays.mergeSort(Arrays.java:1294) at  
> java.util.Arrays.mergeSort(Arrays.java:1294) at  
> java.util.Arrays.sort(Arrays.java:1223) at  
> java.util.Collections.sort(Collections.java:176) at  
> org 
> .cipres 
> .treebase 
> .web 
> .controllers 
> .SearchSummaryController.showForm(SearchSummaryController.java:415)  
> at org.springframework.web.servlet.mvc.AbstractFormController.showNewForm 
> (AbstractFormController.java:338) at org.springframework.web.servlet.mvc.AbstractFormController.handleRequestInternal 
> (AbstractFormController.java:278) at org.springframework.web.s
> ervlet.mvc.AbstractController.handleRequest(AbstractController.java: 
> 153) at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle 
> (SimpleControllerHandlerAdapter.java:48) at org.springframework.web.servlet.DispatcherServlet.doDispatch 
> (DispatcherServlet.java:858) at org.springframework.web.servlet.DispatcherServlet.doService 
> (DispatcherServlet.java:792) at org.springframework.web.servlet.FrameworkServlet.processRequest 
> (FrameworkServlet.java:476) at org.springframework.web.servlet.FrameworkServlet.doGet 
> (FrameworkServlet.java:431) at  
> javax.servlet.http.HttpServlet.service(HttpServlet.java:627) at  
> javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at  
> org 
> .apache 
> .catalina 
> .core 
> .ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java: 
> 269) at  
> org 
> .apache 
> .catalina 
> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java: 
> 188) at  
> org 
> .tuckey 
> .web.filters.urlrewrite.RuleChain.handleRewrite(RuleChain.java:164)  
> at org.tuckey.web.filters.urlrewri
> te.RuleChain.doRules(RuleChain.java:141) at org.tuckey.web.filters.urlrewrite.UrlRewriter.processRequest 
> (UrlRewriter.java:90) at org.tuckey.web.filters.urlrewrite.UrlRewriteFilter.doFilter 
> (UrlRewriteFilter.java:406) at  
> org 
> .apache 
> .catalina 
> .core 
> .ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java: 
> 215) at  
> org 
> .apache 
> .catalina 
> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java: 
> 188) at  
> org 
> .displaytag 
> .filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java: 
> 125) at  
> org 
> .apache 
> .catalina 
> .core 
> .ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java: 
> 215) at  
> org 
> .apache 
> .catalina 
> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java: 
> 188) at  
> org 
> .springframework 
> .orm 
> .hibernate3 
> .support 
> .OpenSessionInViewFilter 
> .doFilterInternal(OpenSessionInViewFilter.java:198) at  
> org 
> .springframework 
> .web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java: 
> 75) at  
> org 
> .apache 
> .catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationF
> ilterChain.java:215) at  
> org 
> .apache 
> .catalina 
> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java: 
> 188) at  
> com 
> .opensymphony 
> .module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119) at  
> com 
> .opensymphony 
> .module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55) at  
> org 
> .apache 
> .catalina 
> .core 
> .ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java: 
> 215) at  
> org 
> .apache 
> .catalina 
> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java: 
> 188) at org.acegisecurity.util.FilterChainProxy 
> $VirtualFilterChain.doFilter(FilterChainProxy.java:264) at  
> org 
> .acegisecurity 
> .intercept 
> .web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java: 
> 107) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter 
> (FilterSecurityInterceptor.java:72) at  
> org.acegisecurity.util.FilterChainProxy 
> $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at  
> org 
> .acegisecurity 
> .ui 
> .ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java: 
> 110) at org.aceg
> isecurity.util.FilterChainProxy 
> $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at  
> org 
> .acegisecurity 
> .wrapper 
> .SecurityContextHolderAwareRequestFilter 
> .doFilter(SecurityContextHolderAwareRequestFilter.java:81) at  
> org.acegisecurity.util.FilterChainProxy 
> $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at  
> org 
> .acegisecurity 
> .ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java: 
> 217) at org.acegisecurity.util.FilterChainProxy 
> $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at  
> org 
> .acegisecurity 
> .context 
> .HttpSessionContextIntegrationFilter 
> .doFilter(HttpSessionContextIntegrationFilter.java:191) at  
> org.acegisecurity.util.FilterChainProxy 
> $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at  
> org 
> .acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java: 
> 148) at  
> org 
> .acegisecurity 
> .util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) at  
> org 
> .apache 
> .catalina 
> .core 
> .ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java: 
> 215) at org.a
> pache 
> .catalina 
> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java: 
> 188) at  
> org 
> .apache 
> .catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java: 
> 213) at  
> org 
> .apache 
> .catalina.core.StandardContextValve.invoke(StandardContextValve.java: 
> 172) 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: 
> 174) at  
> org 
> .apache 
> .coyote.http11.Http11AprProcessor.process(Http11AprProcessor.java: 
> 837) at org.apache.coyote.http11.Http11AprProtocol 
> $Http11ConnectionHandler.process(Http11AprProtocol.java:640) at  
> org.apache.tomcat.util.net.AprEndpoint$Worker.run(AprEndpoint.java: 
> 1286) at java.lang.Thread.run(Thread.java:636) Cookies:  
> JSESSIONID=[708FEE6348ECE9CE1D3288CA0EE772E1]  
> __utma=[53240375.1924499357.1236724314.127
> 3464586.1273467037.78] __utmz=[53240375.1271940457.73.13.utmccn]
>
>
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>
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-- 
===========================================================
: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
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