Details
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Bug
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Resolution: Timed out
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Medium
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None
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None
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None
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5
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Severity 2 - Major
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Description
Summary
Upgrading JIRA Agile fails with a NullPointerException, Caught an exception trying to replicate reindexed issues. The replicated index may or may not be correct.
Steps to Reproduce
- Restore an instance with dodgy data.
- Attempt to upgrade it.
Expected Results
The instance upgrades without any problems.
Actual Results
The upgrade fails and the below exception and stack trace can be found in the logs:
2014-04-24 11:50:52,516 http-bio-1523-exec-8 ERROR localadmin 710x731x1 1a3wbvp 172.22.2.218 /rest/plugins/1.0/com.pyxis.greenhopper.jira-key [jira.index.ha.DefaultReplicatedIndexManager] Caught an exception trying to replicate reindexed issues. The replicated index may or may not be correct java.lang.NullPointerException at com.atlassian.jira.index.ha.DefaultReplicatedIndexManager$1.consume(DefaultReplicatedIndexManager.java:63) at com.atlassian.jira.index.ha.DefaultReplicatedIndexManager$1.consume(DefaultReplicatedIndexManager.java:59) at com.atlassian.jira.util.collect.CollectionUtil.foreach(CollectionUtil.java:44) at com.atlassian.greenhopper.upgrade.IssueIdsIssueIterable.foreach(IssueIdsIssueIterable.java:32) at com.atlassian.jira.index.ha.DefaultReplicatedIndexManager.reindexIssues(DefaultReplicatedIndexManager.java:58) at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexIssues(DefaultIndexManager.java:504) at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexIssues(DefaultIndexManager.java:461) at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexIssues(DefaultIndexManager.java:454) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.lang.reflect.Method.invoke(Unknown Source) at com.atlassian.util.profiling.object.ObjectProfiler.profiledInvoke(ObjectProfiler.java:83) at com.atlassian.jira.config.component.SwitchingInvocationHandler.invoke(SwitchingInvocationHandler.java:28) at $Proxy10.reIndexIssues(Unknown Source) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.lang.reflect.Method.invoke(Unknown Source) at com.atlassian.plugin.osgi.hostcomponents.impl.DefaultComponentRegistrar$ContextClassLoaderSettingInvocationHandler.invoke(DefaultComponentRegistrar.java:129) at $Proxy10.reIndexIssues(Unknown Source) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.lang.reflect.Method.invoke(Unknown Source) at com.atlassian.plugin.osgi.bridge.external.HostComponentFactoryBean$DynamicServiceInvocationHandler.invoke(HostComponentFactoryBean.java:154) at $Proxy10.reIndexIssues(Unknown Source) at com.atlassian.greenhopper.upgrade.GhUpgradeTask041.reindexUpdatedIssues(GhUpgradeTask041.java:164) at com.atlassian.greenhopper.upgrade.GhUpgradeTask041.performUpgrade(GhUpgradeTask041.java:110) at com.atlassian.greenhopper.upgrade.AbstractGhUpgradeTask.doUpgrade(AbstractGhUpgradeTask.java:62) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.lang.reflect.Method.invoke(Unknown Source) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) at org.springframework.osgi.service.importer.support.internal.aop.ServiceInvoker.doInvoke(ServiceInvoker.java:58) at org.springframework.osgi.service.importer.support.internal.aop.ServiceInvoker.invoke(ServiceInvoker.java:62) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.aop.support.DelegatingIntroductionInterceptor.doProceed(DelegatingIntroductionInterceptor.java:131) at org.springframework.aop.support.DelegatingIntroductionInterceptor.invoke(DelegatingIntroductionInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.osgi.service.util.internal.aop.ServiceTCCLInterceptor.invokeUnprivileged(ServiceTCCLInterceptor.java:56) at org.springframework.osgi.service.util.internal.aop.ServiceTCCLInterceptor.invoke(ServiceTCCLInterceptor.java:39) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.osgi.service.importer.support.LocalBundleContextAdvice.invoke(LocalBundleContextAdvice.java:59) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.aop.support.DelegatingIntroductionInterceptor.doProceed(DelegatingIntroductionInterceptor.java:131) at org.springframework.aop.support.DelegatingIntroductionInterceptor.invoke(DelegatingIntroductionInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204) at $Proxy2914.doUpgrade(Unknown Source) at com.atlassian.sal.core.upgrade.PluginUpgrader.doUpgrade(PluginUpgrader.java:85) at com.atlassian.sal.core.upgrade.PluginUpgrader.upgrade(PluginUpgrader.java:66) at com.atlassian.sal.core.upgrade.DefaultPluginUpgradeManager.upgradePlugin(DefaultPluginUpgradeManager.java:204) at com.atlassian.sal.core.upgrade.DefaultPluginUpgradeManager.upgradeInternal(DefaultPluginUpgradeManager.java:194) at com.atlassian.sal.core.upgrade.DefaultPluginUpgradeManager$2.doInTransaction(DefaultPluginUpgradeManager.java:178) at com.atlassian.sal.core.transaction.HostContextTransactionTemplate$1.doInTransaction(HostContextTransactionTemplate.java:25) at com.atlassian.jira.DefaultHostContextAccessor.doInTransaction(DefaultHostContextAccessor.java:34) at sun.reflect.GeneratedMethodAccessor124.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.lang.reflect.Method.invoke(Unknown Source) at com.atlassian.plugin.osgi.hostcomponents.impl.DefaultComponentRegistrar$ContextClassLoaderSettingInvocationHandler.invoke(DefaultComponentRegistrar.java:129) at $Proxy361.doInTransaction(Unknown Source) at sun.reflect.GeneratedMethodAccessor124.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.lang.reflect.Method.invoke(Unknown Source) at com.atlassian.plugin.osgi.bridge.external.HostComponentFactoryBean$DynamicServiceInvocationHandler.invoke(HostComponentFactoryBean.java:154) at $Proxy361.doInTransaction(Unknown Source) at com.atlassian.sal.core.transaction.HostContextTransactionTemplate.execute(HostContextTransactionTemplate.java:21) at com.atlassian.sal.core.upgrade.DefaultPluginUpgradeManager.upgradeInTransaction(DefaultPluginUpgradeManager.java:174) at com.atlassian.sal.core.upgrade.DefaultPluginUpgradeManager.onPluginEnabled(DefaultPluginUpgradeManager.java:95) at sun.reflect.GeneratedMethodAccessor192.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.lang.reflect.Method.invoke(Unknown Source) at com.atlassian.event.internal.SingleParameterMethodListenerInvoker.invoke(SingleParameterMethodListenerInvoker.java:36) at com.atlassian.event.internal.AsynchronousAbleEventDispatcher$2.run(AsynchronousAbleEventDispatcher.java:66) at com.atlassian.event.internal.AsynchronousAbleEventDispatcher$1.execute(AsynchronousAbleEventDispatcher.java:32) at com.atlassian.event.internal.AsynchronousAbleEventDispatcher.dispatch(AsynchronousAbleEventDispatcher.java:60) at com.atlassian.event.internal.EventPublisherImpl.invokeListeners(EventPublisherImpl.java:160) at com.atlassian.event.internal.EventPublisherImpl.publish(EventPublisherImpl.java:79) at com.atlassian.plugin.event.impl.DefaultPluginEventManager.broadcast(DefaultPluginEventManager.java:84) at com.atlassian.plugin.manager.DefaultPluginManager.notifyPluginEnabled(DefaultPluginManager.java:1400) at com.atlassian.plugin.manager.DefaultPluginManager.enablePlugins(DefaultPluginManager.java:1370) at com.atlassian.jira.plugin.JiraPluginManager.enablePlugins(JiraPluginManager.java:91) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.lang.reflect.Method.invoke(Unknown Source) at com.atlassian.plugin.osgi.hostcomponents.impl.DefaultComponentRegistrar$ContextClassLoaderSettingInvocationHandler.invoke(DefaultComponentRegistrar.java:129) at $Proxy292.enablePlugins(Unknown Source) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.lang.reflect.Method.invoke(Unknown Source) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) at org.springframework.osgi.service.importer.support.internal.aop.ServiceInvoker.doInvoke(ServiceInvoker.java:58) at org.springframework.osgi.service.importer.support.internal.aop.ServiceInvoker.invoke(ServiceInvoker.java:62) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.aop.support.DelegatingIntroductionInterceptor.doProceed(DelegatingIntroductionInterceptor.java:131) at org.springframework.aop.support.DelegatingIntroductionInterceptor.invoke(DelegatingIntroductionInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.osgi.service.util.internal.aop.ServiceTCCLInterceptor.invokeUnprivileged(ServiceTCCLInterceptor.java:56) at org.springframework.osgi.service.util.internal.aop.ServiceTCCLInterceptor.invoke(ServiceTCCLInterceptor.java:39) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.osgi.service.importer.support.LocalBundleContextAdvice.invoke(LocalBundleContextAdvice.java:59) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.aop.support.DelegatingIntroductionInterceptor.doProceed(DelegatingIntroductionInterceptor.java:131) at org.springframework.aop.support.DelegatingIntroductionInterceptor.invoke(DelegatingIntroductionInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204) at $Proxy3809.enablePlugins(Unknown Source) at com.atlassian.upm.core.impl.PluginEnablementServiceImpl$1.doInTransaction(PluginEnablementServiceImpl.java:66) at com.atlassian.upm.core.impl.PluginEnablementServiceImpl$1.doInTransaction(PluginEnablementServiceImpl.java:58) at com.atlassian.sal.core.transaction.HostContextTransactionTemplate$1.doInTransaction(HostContextTransactionTemplate.java:25) at com.atlassian.jira.DefaultHostContextAccessor.doInTransaction(DefaultHostContextAccessor.java:34) at sun.reflect.GeneratedMethodAccessor124.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.lang.reflect.Method.invoke(Unknown Source) at com.atlassian.plugin.osgi.hostcomponents.impl.DefaultComponentRegistrar$ContextClassLoaderSettingInvocationHandler.invoke(DefaultComponentRegistrar.java:129) at $Proxy361.doInTransaction(Unknown Source) at sun.reflect.GeneratedMethodAccessor124.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.lang.reflect.Method.invoke(Unknown Source) at com.atlassian.plugin.osgi.bridge.external.HostComponentFactoryBean$DynamicServiceInvocationHandler.invoke(HostComponentFactoryBean.java:154) at $Proxy361.doInTransaction(Unknown Source) at com.atlassian.sal.core.transaction.HostContextTransactionTemplate.execute(HostContextTransactionTemplate.java:21) at sun.reflect.GeneratedMethodAccessor217.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.lang.reflect.Method.invoke(Unknown Source) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) at org.springframework.osgi.service.importer.support.internal.aop.ServiceInvoker.doInvoke(ServiceInvoker.java:58) at org.springframework.osgi.service.importer.support.internal.aop.ServiceInvoker.invoke(ServiceInvoker.java:62) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.aop.support.DelegatingIntroductionInterceptor.doProceed(DelegatingIntroductionInterceptor.java:131) at org.springframework.aop.support.DelegatingIntroductionInterceptor.invoke(DelegatingIntroductionInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.osgi.service.util.internal.aop.ServiceTCCLInterceptor.invokeUnprivileged(ServiceTCCLInterceptor.java:56) at org.springframework.osgi.service.util.internal.aop.ServiceTCCLInterceptor.invoke(ServiceTCCLInterceptor.java:39) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.osgi.service.importer.support.LocalBundleContextAdvice.invoke(LocalBundleContextAdvice.java:59) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.aop.support.DelegatingIntroductionInterceptor.doProceed(DelegatingIntroductionInterceptor.java:131) at org.springframework.aop.support.DelegatingIntroductionInterceptor.invoke(DelegatingIntroductionInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204) at $Proxy3751.execute(Unknown Source) at com.atlassian.upm.core.impl.PluginEnablementServiceImpl.enablePlugin(PluginEnablementServiceImpl.java:57) at com.atlassian.upm.core.rest.resources.PluginResource.put(PluginResource.java:126) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.lang.reflect.Method.invoke(Unknown Source) at com.atlassian.plugins.rest.common.interceptor.impl.DispatchProviderHelper$ResponseOutInvoker$1.invoke(DispatchProviderHelper.java:234) at com.atlassian.plugins.rest.common.interceptor.impl.DispatchProviderHelper$1.intercept(DispatchProviderHelper.java:100) at com.atlassian.plugins.rest.common.interceptor.impl.DefaultMethodInvocation.invoke(DefaultMethodInvocation.java:61) at com.atlassian.plugins.rest.common.expand.interceptor.ExpandInterceptor.intercept(ExpandInterceptor.java:38) at com.atlassian.plugins.rest.common.interceptor.impl.DefaultMethodInvocation.invoke(DefaultMethodInvocation.java:61) at com.atlassian.plugins.rest.common.interceptor.impl.DispatchProviderHelper.invokeMethodWithInterceptors(DispatchProviderHelper.java:132) at com.atlassian.plugins.rest.common.interceptor.impl.DispatchProviderHelper$ResponseOutInvoker._dispatch(DispatchProviderHelper.java:230) at com.sun.jersey.server.impl.model.method.dispatch.ResourceJavaMethodDispatcher.dispatch(ResourceJavaMethodDispatcher.java:75) at com.sun.jersey.server.impl.uri.rules.HttpMethodRule.accept(HttpMethodRule.java:288) at com.sun.jersey.server.impl.uri.rules.ResourceClassRule.accept(ResourceClassRule.java:108) at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147) at com.sun.jersey.server.impl.uri.rules.RootResourceClassesRule.accept(RootResourceClassesRule.java:84) at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1469) at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1400) at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1349) at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1339) at com.sun.jersey.spi.container.servlet.WebComponent.service(WebComponent.java:416) at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:537) at com.atlassian.plugins.rest.module.RestDelegatingServletFilter$JerseyOsgiServletContainer.doFilter(RestDelegatingServletFilter.java:178) at com.sun.jersey.spi.container.servlet.ServletContainer.doFilter(ServletContainer.java:795) at com.atlassian.plugins.rest.module.RestDelegatingServletFilter.doFilter(RestDelegatingServletFilter.java:73) at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74) at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42) at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:77) at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:63) at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74) at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42) at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66) at com.atlassian.plugins.rest.module.servlet.RestServletUtilsUpdaterFilter.doFilterInternal(RestServletUtilsUpdaterFilter.java:26) at com.atlassian.plugins.rest.module.servlet.RestServletUtilsUpdaterFilter.doFilter(RestServletUtilsUpdaterFilter.java:40) at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74) at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42) at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66) at com.atlassian.applinks.core.rest.context.ContextFilter.doFilter(ContextFilter.java:25) at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74) at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42) at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66) at com.atlassian.mywork.client.filter.ServingRequestsFilter.doFilter(ServingRequestsFilter.java:37) at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74) at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42) at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66) at com.atlassian.plugins.cors.CorsFilter.doFilter(CorsFilter.java:65) at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74) at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42) at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66) at com.atlassian.prettyurls.filter.PrettyUrlsDispatcherFilter.doFilter(PrettyUrlsDispatcherFilter.java:60) at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74) at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42) at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66) at com.atlassian.prettyurls.filter.PrettyUrlsSiteMeshFilter.doFilter(PrettyUrlsSiteMeshFilter.java:92) at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74) at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42) at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66) at com.atlassian.prettyurls.filter.PrettyUrlsMatcherFilter.doFilter(PrettyUrlsMatcherFilter.java:56) at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74) at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42) at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66) at com.atlassian.labs.botkiller.BotKillerFilter.doFilter(BotKillerFilter.java:36) at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74) at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42) at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:77) at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:63) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210) at com.atlassian.jira.web.filters.accesslog.AccessLogFilter.executeRequest(AccessLogFilter.java:103) at com.atlassian.jira.web.filters.accesslog.AccessLogFilter.doFilter(AccessLogFilter.java:87) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210) at com.atlassian.jira.security.xsrf.XsrfTokenAdditionRequestFilter.doFilter(XsrfTokenAdditionRequestFilter.java:54) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210) at com.atlassian.jira.web.filters.steps.ChainedFilterStepRunner.doFilter(ChainedFilterStepRunner.java:87) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210) at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:46) at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66) at com.atlassian.prettyurls.filter.PrettyUrlsCombinedMatchDispatcherFilter.doFilter(PrettyUrlsCombinedMatchDispatcherFilter.java:61) at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74) at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42) at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:77) at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:63) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210) at com.atlassian.seraph.filter.SecurityFilter.doFilter(SecurityFilter.java:234) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210) at com.atlassian.security.auth.trustedapps.filter.TrustedApplicationsFilter.doFilter(TrustedApplicationsFilter.java:100) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210) at com.atlassian.seraph.filter.BaseLoginFilter.doFilter(BaseLoginFilter.java:169) at com.atlassian.jira.web.filters.JiraLoginFilter.doFilter(JiraLoginFilter.java:70) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210) at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:46) at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66) at com.atlassian.oauth.serviceprovider.internal.servlet.OAuthFilter.doFilter(OAuthFilter.java:61) at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74) at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42) at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66) at com.atlassian.plugins.rest.module.servlet.RestSeraphFilter.doFilter(RestSeraphFilter.java:40) at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74) at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42) at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66) at com.atlassian.prettyurls.filter.PrettyUrlsCombinedMatchDispatcherFilter.doFilter(PrettyUrlsCombinedMatchDispatcherFilter.java:61) at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74) at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42) at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:77) at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:63) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210) at com.atlassian.johnson.filters.AbstractJohnsonFilter.doFilter(AbstractJohnsonFilter.java:71) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210) at org.tuckey.web.filters.urlrewrite.RuleChain.handleRewrite(RuleChain.java:176) at org.tuckey.web.filters.urlrewrite.RuleChain.doRules(RuleChain.java:145) at org.tuckey.web.filters.urlrewrite.UrlRewriter.processRequest(UrlRewriter.java:92) at org.tuckey.web.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:394) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210) at com.atlassian.gzipfilter.GzipFilter.doFilterInternal(GzipFilter.java:74) at com.atlassian.gzipfilter.GzipFilter.doFilter(GzipFilter.java:51) at com.atlassian.jira.web.filters.gzip.JiraGzipFilter.doFilter(JiraGzipFilter.java:55) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210) at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:46) at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66) at com.atlassian.prettyurls.filter.PrettyUrlsCombinedMatchDispatcherFilter.doFilter(PrettyUrlsCombinedMatchDispatcherFilter.java:61) at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74) at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42) at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:77) at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:63) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210) at com.atlassian.jira.web.filters.steps.ChainedFilterStepRunner.doFilter(ChainedFilterStepRunner.java:87) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210) at com.atlassian.core.filters.cache.AbstractCachingFilter.doFilter(AbstractCachingFilter.java:33) at com.atlassian.core.filters.AbstractHttpFilter.doFilter(AbstractHttpFilter.java:31) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210) at com.atlassian.core.filters.encoding.AbstractEncodingFilter.doFilter(AbstractEncodingFilter.java:41) at com.atlassian.core.filters.AbstractHttpFilter.doFilter(AbstractHttpFilter.java:31) at com.atlassian.jira.web.filters.PathMatchingEncodingFilter.doFilter(PathMatchingEncodingFilter.java:45) at com.atlassian.core.filters.AbstractHttpFilter.doFilter(AbstractHttpFilter.java:31) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210) at com.atlassian.jira.startup.JiraStartupChecklistFilter.doFilter(JiraStartupChecklistFilter.java:78) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210) at com.atlassian.jira.web.filters.MultipartBoundaryCheckFilter.doFilter(MultipartBoundaryCheckFilter.java:41) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210) at com.atlassian.jira.web.filters.steps.ChainedFilterStepRunner.doFilter(ChainedFilterStepRunner.java:87) at com.atlassian.jira.web.filters.JiraFirstFilter.doFilter(JiraFirstFilter.java:57) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:222) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:123) at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:502) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:100) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118) at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:953) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408) at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1041) at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:603) at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:312) at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source)
Workaround
This appears to fail due to orphaned custom field values that point to an issue that no longer exists. This can be identified with the below SQL:
SELECT * FROM customfieldvalue WHERE issue NOT IN (SELECT id FROM jiraissue);
And fixed with the following:
- Disable JIRA Agile.
- Stop JIRA.
- Backup the database.
- Execute the following:
DELETE FROM customfieldvalue WHERE issue NOT IN (SELECT id FROM jiraissue);
- Start JIRA, reindex and re-enable JIRA Agile.