Re: [Treebase-devel] can't delete aborted submission

[Hilmar L. <hl...@ne...>]

That's a known issue. We delete those "by hand" mostly, where by hand  
is running a script.

	-hilmar

On Oct 22, 2010, at 9:14 AM, Arlin Stoltzfus wrote:

> Dear TB developers--
>
> In the past month I have uploaded several test files in order to  
> test the TB submission process.   Overall, I'm very impressed with  
> the process!
>
> However,  I find that I can't delete any of the aborted entries.   I  
> press the "X" (end of row in the study table) to delete, then the  
> "Are you sure?" page loads and I press the "delete study" button.   
> But then I get an error message.   I tried it again this morning and  
> got the error message below.
>
> I also tried it with a very large submission (720 OTUs, 6309 aa  
> characters).  The server has not yet responded, after about 10  
> minutes.
>
> Arlin
>
> Data Access Failure
>
> Batch update returned unexpected row count from update [0]; actual  
> row count: 0; expected: 1; nested exception is  
> org.hibernate.StaleStateException: Batch update returned unexpected  
> row count from update [0]; actual row count: 0; expected: 1
>
> org 
> .springframework 
> .orm.hibernate3.HibernateOptimisticLockingFailureException: Batch  
> update returned unexpected row count from update [0]; actual row  
> count: 0; expected: 1; nested exception is  
> org.hibernate.StaleStateException: Batch update returned unexpected  
> row count from update [0]; actual row count: 0; expected: 1 Caused  
> by: org.hibernate.StaleStateException: Batch update returned  
> unexpected row count from update [0]; actual row count: 0; expected:  
> 1 at org.hibernate.jdbc.Expectations 
> $BasicExpectation.checkBatched(Expectations.java:61) at  
> org.hibernate.jdbc.Expectations 
> $BasicExpectation.verifyOutcome(Expectations.java:46) at  
> org 
> .hibernate 
> .jdbc.NonBatchingBatcher.addToBatch(NonBatchingBatcher.java:24) at  
> org 
> .hibernate 
> .persister 
> .entity.AbstractEntityPersister.delete(AbstractEntityPersister.java: 
> 2525) at  
> org 
> .hibernate 
> .persister 
> .entity.AbstractEntityPersister.delete(AbstractEntityPersister.java: 
> 2702) at  
> org 
> .hibernate.action.EntityDeleteAction.execute(EntityDeleteAction.java: 
> 77) at org.hibernate.engine.ActionQueue.execute(ActionQueue.java: 
> 279) at  
> org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java: 
> 263) at  
> org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java: 
> 172) 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.springframework.orm.hibernate3.HibernateTemplate 
> $27.doInHibernate(HibernateTemplate.java:811) at  
> org 
> .springframework 
> .orm.hibernate3.HibernateTemplate.execute(HibernateTemplate.java: 
> 372) at  
> org 
> .springframework 
> .orm.hibernate3.HibernateTemplate.flush(HibernateTemplate.java:809)  
> at org.cipres.treebase.dao.AbstractDAO.flush(AbstractDAO.java:158)  
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at  
> sun 
> .reflect 
> .NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)  
> at  
> sun 
> .reflect 
> .DelegatingMethodAccessorImpl 
> .invoke(DelegatingMethodAccessorImpl.java:43) at  
> java.lang.reflect.Method.invoke(Method.java:616) at  
> org 
> .springframework 
> .aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java: 
> 304) at  
> org 
> .springframework 
> .aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java: 
> 198) at $Proxy53.flush(Unknown Source) at  
> org 
> .cipres 
> .treebase 
> .service 
> .study 
> .SubmissionServiceImpl.deleteSubmission(SubmissionServiceImpl.java: 
> 428) at  
> org 
> .cipres 
> .treebase 
> .service 
> .study 
> .SubmissionServiceImpl.deleteSubmission(SubmissionServiceImpl.java: 
> 900) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)  
> at  
> sun 
> .reflect 
> .NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)  
> at  
> sun 
> .reflect 
> .DelegatingMethodAccessorImpl 
> .invoke(DelegatingMethodAccessorImpl.java:43) at  
> java.lang.reflect.Method.invoke(Method.java:616) at  
> org 
> .springframework 
> .aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java: 
> 304) at  
> org 
> .springframework 
> .aop 
> .framework 
> .ReflectiveMethodInvocation 
> .invokeJoinpoint(ReflectiveMethodInvocation.java:182) at  
> org 
> .springframework 
> .aop 
> .framework 
> .ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java: 
> 149) at  
> org 
> .springframework 
> .transaction 
> .interceptor 
> .TransactionInterceptor.invoke(TransactionInterceptor.java:106) at  
> org 
> .springframework 
> .aop 
> .framework 
> .ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java: 
> 171) at  
> org 
> .springframework 
> .aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java: 
> 204) at $Proxy81.deleteSubmission(Unknown Source) at  
> org 
> .cipres 
> .treebase 
> .web 
> .controllers 
> .DeleteStudyController.onSubmit(DeleteStudyController.java:71) at  
> org.springframework.web.servlet.mvc.SimpleFormController.processFormSubmission 
> (SimpleFormController.java:267) at org.springframework.web.servlet.mvc.CancellableFormController.processFormSubmission 
> (CancellableFormController.java:140) at org.springframework.web.servlet.mvc.AbstractFormController.handleRequestInternal 
> (AbstractFormController.java:265) at org.springframework.web.servlet.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.doPost 
> (FrameworkServlet.java:441) at  
> javax.servlet.http.HttpServlet.service(HttpServlet.java:647) 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.urlrewrite.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 
> .web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java: 
> 70) 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(ApplicationFilterChain.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.acegisecurity.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 
> .apache 
> .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.Http11Processor.process(Http11Processor.java: 
> 873) 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:689) at  
> java.lang.Thread.run(Thread.java:636) « Back
>
>
> -------
> Arlin Stoltzfus (ar...@um...)
> Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST
> IBBR, 9600 Gudelsky Drive, Rockville, MD
> tel: 240 314 6208; web: www.molevol.org
>
> ------------------------------------------------------------------------------
> Nokia and AT&T present the 2010 Calling All Innovators-North America  
> contest
> Create new apps & games for the Nokia N8 for consumers in  U.S. and  
> Canada
> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in  
> marketing
> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi  
> Store
> http://p.sf.net/sfu/nokia-dev2dev_______________________________________________
> Treebase-devel mailing list
> Tre...@li...
> https://lists.sourceforge.net/lists/listinfo/treebase-devel

-- 
===========================================================
: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
===========================================================