[Treebase-devel] can't delete aborted submission

[Arlin S. <ar...@um...>]

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