Re-index after upgrade from 5.0.6 to 5.2.5.
Asked by Ievgen Aleinikov:

Hello,

We are going to upgrade our Jira.

In order to test functionality I have upgraded our development/testing sandbox.

However, after upgrade I faced following error during re-index:

{code}

java.util.concurrent.ExecutionException: java.lang.NullPointerException

Task completed in 1 minute, 20 seconds with unexpected error.

Started Today 4:24 PM.

Finished Today 4:26 PM.

java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.NullPointerException

at com.atlassian.jira.index.FutureResult.await(FutureResult.java:35)

at com.atlassian.jira.index.CompositeResultBuilder$CompositeResult.await(CompositeResultBuilder.java:82)

at com.atlassian.jira.issue.index.DefaultIndexManager.doIndexIssuesInBatchMode(DefaultIndexManager.java:855)

at com.atlassian.jira.issue.index.DefaultIndexManager.doStopTheWorldReindex(DefaultIndexManager.java:825)

at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexAll(DefaultIndexManager.java:335)

at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexAll(DefaultIndexManager.java:301)

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:81)

at com.atlassian.jira.config.component.SwitchingInvocationHandler.invoke(SwitchingInvocationHandler.java:28)

at $Proxy160.reIndexAll(Unknown Source)

at com.atlassian.jira.util.index.CompositeIndexLifecycleManager.reIndexAll(CompositeIndexLifecycleManager.java:54)

at com.atlassian.jira.web.action.admin.index.ReIndexAsyncIndexerCommand.doReindex(ReIndexAsyncIndexerCommand.java:28)

at com.atlassian.jira.web.action.admin.index.AbstractAsyncIndexerCommand.call(AbstractAsyncIndexerCommand.java:54)

at com.atlassian.jira.web.action.admin.index.ReIndexAsyncIndexerCommand.call(ReIndexAsyncIndexerCommand.java:16)

at com.atlassian.jira.web.action.admin.index.AbstractAsyncIndexerCommand.call(AbstractAsyncIndexerCommand.java:23)

at com.atlassian.jira.task.TaskManagerImpl$TaskCallableDecorator.call(TaskManagerImpl.java:366)

at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)

at java.util.concurrent.FutureTask.run(Unknown Source)

at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)

at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)

at java.util.concurrent.FutureTask.run(Unknown Source)

at com.atlassian.multitenant.impl.DefaultMultiTenantManager.runForTenant(DefaultMultiTenantManager.java:61)

at com.atlassian.multitenant.juc.MultiTenantExecutors$WrappedRunnable.run(MultiTenantExecutors.java:160)

at com.atlassian.jira.task.ForkedThreadExecutor$ForkedRunnableDecorator.run(ForkedThreadExecutor.java:249)

at java.lang.Thread.run(Unknown Source)

Caused by: java.util.concurrent.ExecutionException: java.lang.NullPointerException

at java.util.concurrent.FutureTask$Sync.innerGet(Unknown Source)

at java.util.concurrent.FutureTask.get(Unknown Source)

at com.atlassian.jira.index.FutureResult.await(FutureResult.java:31)

... 27 more

Caused by: java.lang.NullPointerException

at java.util.ArrayList.addAll(Unknown Source)

at com.atlassian.jira.issue.index.DefaultChangeHistoryRetriever.filterChangeItems(DefaultChangeHistoryRetriever.java:120)

at com.atlassian.jira.issue.index.DefaultChangeHistoryRetriever.createChangeGroupsFromChangeItems(DefaultChangeHistoryRetriever.java:61)

at com.atlassian.jira.issue.index.DefaultChangeHistoryRetriever.get(DefaultChangeHistoryRetriever.java:54)

at com.atlassian.jira.issue.index.DefaultChangeHistoryRetriever.get(DefaultChangeHistoryRetriever.java:30)

at com.atlassian.jira.issue.index.DefaultIssueIndexer$ChangeHistoryDocumentBuilder.get(DefaultIssueIndexer.java:567)

at com.atlassian.jira.issue.index.DefaultIssueIndexer$IssueLockDocumentCreationStrategy$2.get(DefaultIssueIndexer.java:597)

at com.atlassian.jira.issue.index.DefaultIssueIndexer$IssueLockDocumentCreationStrategy$2.get(DefaultIssueIndexer.java:593)

at com.atlassian.util.concurrent.ManagedLocks$ManagedLockImpl.withLock(ManagedLocks.java:315)

at com.atlassian.jira.issue.index.DefaultIssueIndexer$IssueLockDocumentCreationStrategy.get(DefaultIssueIndexer.java:592)

at com.atlassian.jira.issue.index.DefaultIssueIndexer$IndexIssuesOperation.perform(DefaultIssueIndexer.java:446)

at com.atlassian.jira.issue.index.DefaultIssueIndexer$4$1.get(DefaultIssueIndexer.java:284)

at com.atlassian.jira.issue.index.DefaultIssueIndexer$4$1.get(DefaultIssueIndexer.java:280)

at com.atlassian.jira.index.SimpleIndexingStrategy.get(SimpleIndexingStrategy.java:9)

at com.atlassian.jira.index.SimpleIndexingStrategy.get(SimpleIndexingStrategy.java:5)

at com.atlassian.jira.index.MultiThreadedIndexingStrategy$1.call(MultiThreadedIndexingStrategy.java:38)

at com.atlassian.jira.index.MultiThreadedIndexingStrategy$1.call(MultiThreadedIndexingStrategy.java:35)

at com.atlassian.jira.util.concurrent.BoundedExecutor$2.call(BoundedExecutor.java:70)

at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)

at java.util.concurrent.FutureTask.run(Unknown Source)

at com.atlassian.multitenant.impl.DefaultMultiTenantManager.runForTenant(DefaultMultiTenantManager.java:61)

at com.atlassian.multitenant.juc.MultiTenantExecutors$WrappedRunnable.run(MultiTenantExecutors.java:160)

at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)

... 1 more

{code}

I tried to uninstall all plugins and repeated procedure few times without any luck.

<br />


Answers:
author: Zul NS _Atlassian_
body: This is indeed an issue with database integrity. There is a KB in the following

\* [https://confluence.atlassian.com/pages/viewpage.action?pageId=308609418\&utm_source=SAC\&utm_medium=hercules-email\&utm_content=407632](https://confluence.atlassian.com/pages/viewpage.action?pageId=308609418&utm_source=SAC&utm_medium=hercules-email&utm_content=407632)


author: richie_gee
body: Hi there,

Have you tried using integrity checker instead, it seems have some broken link on the reference, it might not fix your problem but I think it is worth a try.

<https://confluence.atlassian.com/display/JIRA/Using+the+Database+Integrity+Checker>

After using integrity checker, you might want to clear cache to let the index build back using the correct reference.

1. Shut down Jira
2. Delete the content of {Jira installation folder}/work directory
3. Delete the content of {Jira Home}/caches directory
4. Delete the content of {Jira Home}/plugins/.bundled-plugins
5. Delete the content of {Jira Home}/plugins/.osgi-plugins
6. Restart Jira.

See if this helps :) cheers!