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[Treebase-guts] [ treebase-Bugs-2981217 ] Ghost records cause Exception
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From: SourceForge.net <no...@so...> - 2010-04-08 19:11:35
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Bugs item #2981217, was opened at 2010-04-02 13:21 Message generated for change (Comment added) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2981217&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None >Status: Closed Priority: 8 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: youjun guo (youjun) Summary: Ghost records cause Exception Initial Comment: Here's a weird bug. 1. Start by uploading the two attached matrices to a new submission (attached to this bug report). 2. Run "select count(*) from sub_taxonlabel where submission_id = <sub_id>" or "select count(*) from taxonlabel where study_id = <study_id>" and the result is 48 taxon labels in both cases. 3. Delete the matrix called "concatenated" 4. Run the count(*) queries again, and you get 37 taxa (so far so good) 5. Go to the taxaList.html page and click the edit tool for the "Asterochloris italiana ex cf Xanthoria parietina CCAP 519 5B" taxon. 6. Choose "I did a uBio lookup..." item and enter "3530703" as the namebankid 7. Click "Update" and you get the Exception (below). The weird thing is that I was asking to edit taxonlabelid 277197, but the exception says that taxonlabel 277205 does not exist. And that is correct: Taxonlabel 277205 was deleted when the concatenated matrix was deleted, however, here I'm trying to update taxonlabelid 277197, so I don't know why it is trying to update 277205 -- especially since 277205 does not exist. For some reason the software has a "ghost memory" of this taxonlabel still existing, even though it has been deleted along with the deleted matrix using pure Hibernate (no direct SQL). Likewise, if I try to delete the whole submission (http://treebasedb-dev.nescent.org/treebase-web/user/deleteStudy.html?submissionid=10324), I also get an exception with a very similar result (see below). So there's some sort of ghost memory for deleted records that's preventing deletion of submissions or update of taxon labels after having deleted a matrix (and I think a tree too). regards, Bill ******** Error when editing taxonlabel: Uncaught Exception Encountered org.hibernate.ObjectNotFoundException: No row with the given identifier exists: [org.cipres.treebase.domain.taxon.TaxonLabel#277205] at org.hibernate.impl.SessionFactoryImpl$1.handleEntityNotFound(SessionFactoryImpl.java:377) at org.hibernate.event.def.DefaultLoadEventListener.load(DefaultLoadEventListener.java:145) at org.hibernate.event.def.DefaultLoadEventListener.proxyOrLoad(DefaultLoadEventListener.java:195) at org.hibernate.event.def.DefaultLoadEventListener.onLoad(DefaultLoadEventListener.java:103) at org.hibernate.impl.SessionImpl.fireLoad(SessionImpl.java:878) at org.hibernate.impl.SessionImpl.internalLoad(SessionImpl.java:846) at org.hibernate.type.EntityType.resolveIdentifier(EntityType.java:557) at org.hibernate.type.ManyToOneType.assemble(ManyToOneType.java:196) at org.hibernate.collection.PersistentSet.initializeFromCache(PersistentSet.java:124) at org.hibernate.cache.entry.CollectionCacheEntry.assemble(CollectionCacheEntry.java:35) at org.hibernate.event.def.DefaultInitializeCollectionEventListener.initializeCollectionFromCache(DefaultInitializeCollectionEventListener.java:133) at org.hibernate.event.def.DefaultInitializeCollectionEventListener.onInitializeCollection(DefaultInitializeCollectionEventListener.java:51) at org.hibernate.impl.SessionImpl.initializeCollection(SessionImpl.java:1716) at org.hibernate.collection.AbstractPersistentCollection.initialize(AbstractPersistentCollection.java:344) at org.hibernate.collection.AbstractPersistentCollection.read(AbstractPersistentCollection.java:86) at org.hibernate.collection.PersistentSet.toArray(PersistentSet.java:171) at java.util.ArrayList.addAll(ArrayList.java:497) at org.cipres.treebase.domain.study.Submission.getSubmittedTaxonLabelsReadOnly(Submission.java:279) at org.cipres.treebase.web.validators.TaxonLabelValidator.validate(TaxonLabelValidator.java:48) at org.springframework.validation.ValidationUtils.invokeValidator(ValidationUtils.java:63) at org.springframework.web.servlet.mvc.BaseCommandController.bindAndValidate(BaseCommandController.java:373) at org.springframework.web.servlet.mvc.AbstractFormController.handleRequestInternal(AbstractFormController.java:263) 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.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$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148) at org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) at org.apache.coyote.http11.Http11AprProcessor.process(Http11AprProcessor.java:837) at org.apache.coyote.http11.Http11AprProtocol$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: itemToHighlight=[http%3A//treebasedb-dev.nescent.org/treebase-web/user/taxaList.html] JSESSIONID=[7D0D4BAD900FBD0DE51EE36BAE354FF1] __utma=[53240375.1924499357.1236724314.1268887193.1269487089.61] __utmz=[53240375.1269487089.61.11.utmccn] ******** Error when trying to delete entire submission: Uncaught Exception Encountered org.hibernate.ObjectNotFoundException: No row with the given identifier exists: [org.cipres.treebase.domain.taxon.TaxonLabel#277205] at org.hibernate.impl.SessionFactoryImpl$1.handleEntityNotFound(SessionFactoryImpl.java:377) at org.hibernate.event.def.DefaultLoadEventListener.load(DefaultLoadEventListener.java:145) at org.hibernate.event.def.DefaultLoadEventListener.proxyOrLoad(DefaultLoadEventListener.java:195) at org.hibernate.event.def.DefaultLoadEventListener.onLoad(DefaultLoadEventListener.java:103) at org.hibernate.impl.SessionImpl.fireLoad(SessionImpl.java:878) at org.hibernate.impl.SessionImpl.internalLoad(SessionImpl.java:846) at org.hibernate.type.EntityType.resolveIdentifier(EntityType.java:557) at org.hibernate.type.ManyToOneType.assemble(ManyToOneType.java:196) at org.hibernate.collection.PersistentSet.initializeFromCache(PersistentSet.java:124) at org.hibernate.cache.entry.CollectionCacheEntry.assemble(CollectionCacheEntry.java:35) at org.hibernate.event.def.DefaultInitializeCollectionEventListener.initializeCollectionFromCache(DefaultInitializeCollectionEventListener.java:133) at org.hibernate.event.def.DefaultInitializeCollectionEventListener.onInitializeCollection(DefaultInitializeCollectionEventListener.java:51) at org.hibernate.impl.SessionImpl.initializeCollection(SessionImpl.java:1716) at org.hibernate.collection.AbstractPersistentCollection.initialize(AbstractPersistentCollection.java:344) at org.hibernate.collection.AbstractPersistentCollection.read(AbstractPersistentCollection.java:86) at org.hibernate.collection.PersistentSet.toArray(PersistentSet.java:171) at java.util.ArrayList.addAll(ArrayList.java:497) at org.cipres.treebase.domain.study.Submission.getSubmittedTaxonLabelsReadOnly(Submission.java:279) at org.cipres.treebase.service.study.SubmissionServiceImpl.deleteSubmittedData(SubmissionServiceImpl.java:482) at org.cipres.treebase.service.study.SubmissionServiceImpl.deleteSubmission(SubmissionServiceImpl.java:374) 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.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$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148) at org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) at org.apache.coyote.http11.Http11AprProcessor.process(Http11AprProcessor.java:837) at org.apache.coyote.http11.Http11AprProtocol$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: itemToHighlight=[http%3A//treebasedb-dev.nescent.org/treebase-web/user/submissionList.html] JSESSIONID=[7D0D4BAD900FBD0DE51EE36BAE354FF1] __utma=[53240375.1924499357.1236724314.1268887193.1269487089.61] __utmz=[53240375.1269487089.61.11.utmccn] ---------------------------------------------------------------------- >Comment By: William Piel (sfrgpiel) Date: 2010-04-08 15:11 Message: Fixed by no longer making use of the sub_taxonlabel table (in standby). Ultimately, this is not a desirable solution but to solve it requires major surgery. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2981217&group_id=248804 |
