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  1. Jira Data Center
  2. JRASERVER-65052

Unexpected Entries in the nodeassociation table cause JIRA Service Upgrade to fail

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    • Icon: Bug Bug
    • Resolution: Fixed
    • Icon: Low Low
    • 7.3.5
    • 7.2.1
    • Upgrade

      Summary

      When attempting to upgrade to JIRA Service Desk 3.2.1, the exception as below is experienced. This is caused by entries in the nodeassociation table in JIRA referencing project Id's that do not exist.

      java.lang.NullPointerException
	at java.util.Comparator.lambda$comparing$77a9974f$1(Comparator.java:469)
	at java.util.TimSort.countRunAndMakeAscending(TimSort.java:355)
	at java.util.TimSort.sort(TimSort.java:234)
	at java.util.Arrays.sort(Arrays.java:1512)
	at java.util.stream.SortedOps$SizedRefSortingSink.end(SortedOps.java:348)
	at java.util.stream.Sink$ChainedReference.end(Sink.java:258)
	at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482)
	at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
	at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708)
	at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
	at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:499)
	at com.atlassian.jira.scheme.AbstractSchemeManager.getProjects(AbstractSchemeManager.java:481)
	... 3 filtered
	at java.lang.reflect.Method.invoke(Method.java:497)
	at com.atlassian.plugin.util.ContextClassLoaderSettingInvocationHandler.invoke(ContextClassLoaderSettingInvocationHandler.java:26)
	at com.sun.proxy.$Proxy551.getProjects(Unknown Source)
	... 3 filtered
	at java.lang.reflect.Method.invoke(Method.java:497)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:317)
	at org.eclipse.gemini.blueprint.service.importer.support.internal.aop.ServiceInvoker.doInvoke(ServiceInvoker.java:56)
	at org.eclipse.gemini.blueprint.service.importer.support.internal.aop.ServiceInvoker.invoke(ServiceInvoker.java:60)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
	at org.springframework.aop.support.DelegatingIntroductionInterceptor.doProceed(DelegatingIntroductionInterceptor.java:133)
	at org.springframework.aop.support.DelegatingIntroductionInterceptor.invoke(DelegatingIntroductionInterceptor.java:121)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
	at org.eclipse.gemini.blueprint.service.util.internal.aop.ServiceTCCLInterceptor.invokeUnprivileged(ServiceTCCLInterceptor.java:70)
	at org.eclipse.gemini.blueprint.service.util.internal.aop.ServiceTCCLInterceptor.invoke(ServiceTCCLInterceptor.java:53)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
	at org.eclipse.gemini.blueprint.service.importer.support.LocalBundleContextAdvice.invoke(LocalBundleContextAdvice.java:57)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
	at org.springframework.aop.support.DelegatingIntroductionInterceptor.doProceed(DelegatingIntroductionInterceptor.java:133)
	at org.springframework.aop.support.DelegatingIntroductionInterceptor.invoke(DelegatingIntroductionInterceptor.java:121)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:207)
	at com.sun.proxy.$Proxy3179.getProjects(Unknown Source)
	at com.atlassian.servicedesk.bootstrap.upgrade.tasks.SyncUpgradeTaskMigrateAgentPermission.isPermissionSchemeUsedByServiceDeskProject(SyncUpgradeTaskMigrateAgentPermission.java:182)
	at com.atlassian.servicedesk.bootstrap.upgrade.tasks.SyncUpgradeTaskMigrateAgentPermission.getPermissionSchemesUsedByServiceDesk(SyncUpgradeTaskMigrateAgentPermission.java:173)
	at com.atlassian.servicedesk.bootstrap.upgrade.tasks.SyncUpgradeTaskMigrateAgentPermission.performUpgradeAgentPermission(SyncUpgradeTaskMigrateAgentPermission.java:128)
	at com.atlassian.servicedesk.bootstrap.upgrade.tasks.SyncUpgradeTaskMigrateAgentPermission.doUpgrade(SyncUpgradeTaskMigrateAgentPermission.java:86)
	at com.atlassian.servicedesk.bootstrap.upgrade.SyncUpgradeTaskServiceImpl.runTask(SyncUpgradeTaskServiceImpl.java:71)
	at com.atlassian.servicedesk.bootstrap.upgrade.SyncUpgradeTaskServiceImpl.runAll(SyncUpgradeTaskServiceImpl.java:48)
	at com.atlassian.servicedesk.bootstrap.lifecycle.PluginLifeCycle.runSyncUpgradeTasks(PluginLifeCycle.java:319)
	at com.atlassian.servicedesk.bootstrap.lifecycle.PluginLifeCycle.checkAndRunUpgrades(PluginLifeCycle.java:272)
	at com.atlassian.servicedesk.bootstrap.lifecycle.PluginLifeCycle.runPluginStartupSideEffectsImpl(PluginLifeCycle.java:183)
	at com.atlassian.servicedesk.bootstrap.lifecycle.LifecycleLock.writeImpl(LifecycleLock.java:97)
	at com.atlassian.servicedesk.bootstrap.lifecycle.LifecycleLock.runOnStartup(LifecycleLock.java:75)
	at com.atlassian.servicedesk.bootstrap.lifecycle.PluginLifeCycle.onPluginStarted(PluginLifeCycle.java:126)
	at com.atlassian.servicedesk.bootstrap.lifecycle.Launcher.onStartCompleted(Launcher.java:75)
	at com.atlassian.servicedesk.bootstrap.lifecycle.Launcher.access$000(Launcher.java:23)
	at com.atlassian.servicedesk.bootstrap.lifecycle.Launcher$1$1.run(Launcher.java:42)
	at com.atlassian.pocketknife.api.util.runners.SealedRunner.checkSeals(SealedRunner.java:111)
	at com.atlassian.pocketknife.api.util.runners.SealedRunner.breakSeal(SealedRunner.java:68)
	at com.atlassian.servicedesk.bootstrap.lifecycle.Launcher.onStart(Launcher.java:68)
	at com.atlassian.sal.core.lifecycle.DefaultLifecycleManager$4.consume(DefaultLifecycleManager.java:277)
	at com.atlassian.sal.core.lifecycle.DefaultLifecycleManager$4.consume(DefaultLifecycleManager.java:274)
	at com.atlassian.sal.core.lifecycle.DefaultLifecycleManager.notifyLifecyleAware(DefaultLifecycleManager.java:303)
	at com.atlassian.sal.core.lifecycle.DefaultLifecycleManager.notifyOnStartIfStartedAndEnabled(DefaultLifecycleManager.java:273)
	at com.atlassian.sal.core.lifecycle.DefaultLifecycleManager.access$300(DefaultLifecycleManager.java:49)
	at com.atlassian.sal.core.lifecycle.DefaultLifecycleManager$3.evaluate(DefaultLifecycleManager.java:235)
	at com.atlassian.sal.core.lifecycle.DefaultLifecycleManager$3.evaluate(DefaultLifecycleManager.java:232)
	at com.atlassian.sal.core.lifecycle.DefaultLifecycleManager.notifyLifecycleAwares(DefaultLifecycleManager.java:258)
	at com.atlassian.sal.core.lifecycle.DefaultLifecycleManager.notifyStartableLifecycleAwares(DefaultLifecycleManager.java:231)
	at com.atlassian.sal.core.lifecycle.DefaultLifecycleManager.startIfApplicationSetup(DefaultLifecycleManager.java:219)
	at com.atlassian.sal.core.lifecycle.DefaultLifecycleManager.start(DefaultLifecycleManager.java:210)
	at com.atlassian.sal.jira.lifecycle.JiraLifecycleManager.onJiraStart(JiraLifecycleManager.java:64)
	... 3 filtered
	at java.lang.reflect.Method.invoke(Method.java:497)
	at com.atlassian.event.internal.SingleParameterMethodListenerInvoker.invoke(SingleParameterMethodListenerInvoker.java:36)
	at com.atlassian.event.internal.AsynchronousAbleEventDispatcher$1$1.run(AsynchronousAbleEventDispatcher.java:48)
	at com.google.common.util.concurrent.MoreExecutors$DirectExecutorService.execute(MoreExecutors.java:299)
	at com.atlassian.event.internal.AsynchronousAbleEventDispatcher.dispatch(AsynchronousAbleEventDispatcher.java:107)
	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:73)
	at com.atlassian.jira.upgrade.PluginUpgradeLauncher.start(PluginUpgradeLauncher.java:30)
	at com.atlassian.jira.startup.ActiveServicesLauncher.start(ActiveServicesLauncher.java:51)
	at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$postTenantArrived$4(DefaultJiraLauncher.java:178)
	at com.atlassian.jira.startup.DefaultInstantUpgradeManager$StartupTask.run(DefaultInstantUpgradeManager.java:139)
	at com.atlassian.jira.startup.DefaultInstantUpgradeManager.runTask(DefaultInstantUpgradeManager.java:55)
	at com.atlassian.jira.startup.DefaultInstantUpgradeManager.doNowOrWhenInstanceBecomesActive(DefaultInstantUpgradeManager.java:42)
	at com.atlassian.jira.startup.DefaultJiraLauncher.postTenantArrived(DefaultJiraLauncher.java:171)
	at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$postDBActivated$3(DefaultJiraLauncher.java:159)
	at com.atlassian.jira.tenancy.DefaultTenantManager.doNowOrWhenTenantArrives(DefaultTenantManager.java:55)
	at com.atlassian.jira.startup.DefaultJiraLauncher.postDBActivated(DefaultJiraLauncher.java:156)
	at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$postDbLaunch$2(DefaultJiraLauncher.java:145)
	at com.atlassian.jira.config.database.DatabaseConfigurationManagerImpl.doNowOrEnqueue(DatabaseConfigurationManagerImpl.java:298)
	at com.atlassian.jira.config.database.DatabaseConfigurationManagerImpl.doNowOrWhenDatabaseActivated(DatabaseConfigurationManagerImpl.java:194)
	at com.atlassian.jira.startup.DefaultJiraLauncher.postDbLaunch(DefaultJiraLauncher.java:135)
	at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$start$0(DefaultJiraLauncher.java:101)
	at com.atlassian.jira.util.devspeed.JiraDevSpeedTimer.run(JiraDevSpeedTimer.java:31)
	at com.atlassian.jira.startup.DefaultJiraLauncher.start(DefaultJiraLauncher.java:99)
	at com.atlassian.jira.startup.LauncherContextListener.initSlowStuff(LauncherContextListener.java:149)
	at java.lang.Thread.run(Thread.java:745)

      Environment

      An instance that is being upgraded to JIRA Service Desk 7.2.1 (Service Desk 3.2.1).

      Steps to Reproduce

      Using an XML backup that contains unexpected data in the nodeassoication table.

      Expected Results

      The Upgrade Task should be able to avoid this situation.

      Actual Results

      The upgrade fails and the JIRA Service Desk instance upgrade is blocked.

      Notes

      It is recommended that you work with Atlassian Support to determine the best path forward with this solution at this stage. To workaround this issue, attempt to detect the entries causing this issue.

      SELECT n.*
  FROM nodeassociation n
 WHERE n.sink_node_entity = 'PermissionScheme'
   AND source_node_id NOT IN (
		SELECT id
		  FROM project
       );

      If this is the case, test removing these entries from an XML Backup (these entries will look like: <NodeAssocation sourceNodeId=...) and restore this data to the instance.

              Unassigned Unassigned
              majones Matt Jones (Inactive)
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              1 Vote for this issue
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                Created:
                Updated:
                Resolved: