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After creation of Sub Task no deletion possible (index error)

Andreas Karner

Hi,

I am facing a major problem with Sub Tasks. When I created a Issue (does not matter which type), I am able to delete it. If I create a sub task and it also does not matter which type and which status, I can't delete it.

In fact this I see in the atlassian-jira.log file:

2020-11-04 11:05:10,244+0100 http-nio-8080-exec-9 ERROR [o.a.c.c.C.[.[localhost].[/].[action]] Servlet.service() for servlet [action] in context with path [] threw exception [com.atlassian.jira.index.IndexingFailureException: Indexing completed with 1 errors] with root cause
com.atlassian.jira.index.IndexingFailureException: Indexing completed with 1 errors
at com.atlassian.jira.index.AccumulatingResultBuilder$CompositeResult.await(AccumulatingResultBuilder.java:189)
at com.atlassian.jira.issue.index.DefaultIndexManager.obtain(DefaultIndexManager.java:863)
at com.atlassian.jira.issue.index.DefaultIndexManager.await(DefaultIndexManager.java:843)
at com.atlassian.jira.issue.index.DefaultIndexManager.executeWithIndexLock(DefaultIndexManager.java:830)
at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexIssues(DefaultIndexManager.java:618)
at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexIssueObjects(DefaultIndexManager.java:494)
at com.atlassian.jira.issue.index.DefaultIndexManager.reIndex(DefaultIndexManager.java:540)
at com.atlassian.jira.issue.index.DefaultIndexManager.reIndex(DefaultIndexManager.java:523)
... 2 filtered
at java.lang.reflect.Method.invoke(Method.java:498)
.....

and

2020-11-04 11:05:10,327+0100 http-nio-8080-exec-9 ERROR [c.a.j.web.servlet.InternalServerErrorServlet] {errorId=b91dca6b-e2e8-4ef7-8ce2-b86872fc6002, interpretedMsg=, cause=com.atlassian.jira.index.IndexingFailureException: Indexing completed with 1 errors, stacktrace=com.atlassian.jira.index.IndexingFailureException: Indexing completed with 1 errors
at com.atlassian.jira.index.AccumulatingResultBuilder$CompositeResult.await(AccumulatingResultBuilder.java:189) [classes/:?]
at com.atlassian.jira.issue.index.DefaultIndexManager.obtain(DefaultIndexManager.java:863) [classes/:?]
at com.atlassian.jira.issue.index.DefaultIndexManager.await(DefaultIndexManager.java:843) [classes/:?]
at com.atlassian.jira.issue.index.DefaultIndexManager.executeWithIndexLock(DefaultIndexManager.java:830) [classes/:?]
at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexIssues(DefaultIndexManager.java:618) [classes/:?]
at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexIssueObjects(DefaultIndexManager.java:494) [classes/:?]
at com.atlassian.jira.issue.index.DefaultIndexManager.reIndex(DefaultIndexManager.java:540) [classes/:?]
at com.atlassian.jira.issue.index.DefaultIndexManager.reIndex(DefaultIndexManager.java:523) [classes/:?]
at sun.reflect.GeneratedMethodAccessor1742.invoke(Unknown Source) [?:?]
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) [?:1.8.0_202]
at java.lang.reflect.Method.invoke(Method.java:498) [?:1.8.0_202]
at com.atlassian.jira.config.component.SwitchingInvocationHandler.invoke(SwitchingInvocationHandler.java:38) [classes/:?]
at com.sun.proxy.$Proxy17.reIndex(Unknown Source) [?:?]
at com.atlassian.jira.issue.link.DefaultIssueLinkManager.reindexLinkedIssues(DefaultIssueLinkManager.java:122) [classes/:?]
at com.atlassian.jira.issue.link.DefaultIssueLinkManager.removeIssueLinkInternal(DefaultIssueLinkManager.java:194) [classes/:?]
at com.atlassian.jira.issue.link.DefaultIssueLinkManager.deleteIssueLinksFromIssue(DefaultIssueLinkManager.java:261) [classes/:?]
at .......

What I already tried to fix:

Restart server
Run Reindex, full (also manually deleted the content in index directory). Re-Index alsways is fine and throws no error.
Run Integrity checker (no errors).
Deactivated all 3rd party plugins.
Removed the *.bundled-plugins* and *.osgi-plugins* manually in the *<JIRA Home>/plugins* directory.

This is somehow very weird, we had no change to the system since one week.

Did anyone here saw this already?

Accepted answers

All comments

Fazila Ashraf

Hi @Andreas Karner

Have you tried all troubleshooting steps in https://confluence.atlassian.com/jirakb/troubleshoot-a-reindex-failure-in-jira-server-429917142.html ?

Andreas Karner

Yes, some minutes ago.
Unfortunately without success. I also set the logging for com.atlassian.jira.index.AccumulatingResultBuilder to DEBUG, but not really much more output yet.

none_ms3ui7

Hi @Andreas Karner ,

I observed the same thing but go this error from the error logs.

And yes I tried the suggested fixes but it doesn't make a difference

2020-11-05 08:40:46,946+0100 http-nio-8080-exec-22 INFO XXXX 520x2512x1 1wdbzpk 172.18.2.15 /secure/DeleteIssue.jspa [c.a.j.issue.index.DefaultIssueIndexer] The issue with id 21769 could not be indexed as it is marked as deleted. If you see this message rarely, this is just a result of a race condition between updating and deleting an entity. If this is not the case, the deleted flag can be cleaned on the database:
delete from issue_version where issue_id = 21769 and deleted = 'Y';
com.atlassian.jira.versioning.IncrementDeletedEntityVersionException: IssueVersion with id 21769 is marked as deleted and its version cannot be incremented.
at com.atlassian.jira.versioning.EntityVersioningManagerImpl.incrementVersion(EntityVersioningManagerImpl.java:293)
at com.atlassian.jira.versioning.EntityVersioningManagerImpl.incrementIssueVersion(EntityVersioningManagerImpl.java:75)
at com.atlassian.jira.versioning.EntityVersioningManagerWithStats.incrementIssueVersion(EntityVersioningManagerWithStats.java:118)
at com.atlassian.jira.issue.index.DefaultIssueIndexer$IssuesOperation.bumpVersion(DefaultIssueIndexer.java:954)
at com.atlassian.jira.issue.index.DefaultIssueIndexer$IssuesOperation.bumpVersion(DefaultIssueIndexer.java:904)
at com.atlassian.jira.issue.index.DefaultIssueIndexer$EntityOperation.bumpVersionIfNeeded(DefaultIssueIndexer.java:796)
at com.atlassian.jira.issue.index.DefaultIssueIndexer.lambda$perform$5(DefaultIssueIndexer.java:496)
at com.atlassian.jira.util.collect.CollectionUtil.foreach(CollectionUtil.java:39)
at com.atlassian.jira.util.collect.CollectionUtil.foreach(CollectionUtil.java:52)
at com.atlassian.jira.issue.util.IssueObjectIssuesIterable.foreach(IssueObjectIssuesIterable.java:24)
at com.atlassian.jira.issue.index.DefaultIssueIndexer.perform(DefaultIssueIndexer.java:485)
at com.atlassian.jira.issue.index.DefaultIssueIndexer.reindexIssues(DefaultIssueIndexer.java:348)
at com.atlassian.jira.issue.index.DefaultIndexManager.lambda$reIndexIssues$5(DefaultIndexManager.java:618)
at com.atlassian.jira.issue.index.DefaultIndexManager.executeWithIndexLock(DefaultIndexManager.java:830)
at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexIssues(DefaultIndexManager.java:618)
at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexIssueObjects(DefaultIndexManager.java:494)
at com.atlassian.jira.issue.index.DefaultIndexManager.reIndex(DefaultIndexManager.java:540)
at com.atlassian.jira.issue.index.DefaultIndexManager.reIndex(DefaultIndexManager.java:523)
at jdk.internal.reflect.GeneratedMethodAccessor1607.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at com.atlassian.jira.config.component.SwitchingInvocationHandler.invoke(SwitchingInvocationHandler.java:38)
at com.sun.proxy.$Proxy17.reIndex(Unknown Source)
at com.atlassian.jira.issue.link.DefaultIssueLinkManager.reindexLinkedIssues(DefaultIssueLinkManager.java:122)
at com.atlassian.jira.issue.link.DefaultIssueLinkManager.removeIssueLinkInternal(DefaultIssueLinkManager.java:194)
at com.atlassian.jira.issue.link.DefaultIssueLinkManager.deleteIssueLinksFromIssue(DefaultIssueLinkManager.java:261)
at com.atlassian.jira.issue.link.DefaultIssueLinkManager.removeIssueLinksInternal(DefaultIssueLinkManager.java:250)
at com.atlassian.jira.issue.link.DefaultIssueLinkManager.removeIssueLinksNoChangeItems(DefaultIssueLinkManager.java:230)
at com.atlassian.jira.issue.managers.DefaultIssueDeleteHelper.removeIssueLinks(DefaultIssueDeleteHelper.java:193)
at com.atlassian.jira.issue.managers.DefaultIssueDeleteHelper.deleteIssue(DefaultIssueDeleteHelper.java:145)
at com.atlassian.jira.issue.managers.DefaultIssueManager.deleteIssue(DefaultIssueManager.java:743)
at com.atlassian.jira.issue.managers.RequestCachingIssueManager.deleteIssue(RequestCachingIssueManager.java:247)
at com.atlassian.jira.bc.issue.DefaultIssueService.delete(DefaultIssueService.java:427)
at com.atlassian.jira.bc.issue.DefaultIssueService.delete(DefaultIssueService.java:403)
at com.atlassian.jira.web.action.issue.DeleteIssue.doExecute(DeleteIssue.java:23)
... 1 filtered
at com.atlassian.jira.action.JiraActionSupport.execute(JiraActionSupport.java:63)
... 7 filtered
at javax.servlet.http.HttpServlet.service(HttpServlet.java:733)
... 48 filtered
at com.atlassian.servicedesk.internal.web.ExternalCustomerLockoutFilter.doFilter(ExternalCustomerLockoutFilter.java:55)
... 4 filtered
at com.atlassian.greenhopper.jira.filters.ClassicBoardRouter.doFilter(ClassicBoardRouter.java:56)
... 7 filtered
at com.atlassian.jira.plugin.mobile.web.filter.MobileAppRequestFilter.doFilter(MobileAppRequestFilter.java:59)
... 4 filtered
at com.atlassian.jira.plugin.mobile.login.MobileLoginSuccessFilter.doFilter(MobileLoginSuccessFilter.java:54)
... 3 filtered
at com.atlassian.diagnostics.internal.platform.monitor.http.HttpRequestMonitoringFilter.doFilter(HttpRequestMonitoringFilter.java:55)
... 8 filtered
at com.atlassian.web.servlet.plugin.request.RedirectInterceptingFilter.doFilter(RedirectInterceptingFilter.java:21)
... 62 filtered
at com.atlassian.jira.security.JiraSecurityFilter.lambda$doFilter$0(JiraSecurityFilter.java:66)
... 1 filtered
at com.atlassian.jira.security.JiraSecurityFilter.doFilter(JiraSecurityFilter.java:64)
... 39 filtered
at com.atlassian.jira.servermetrics.CorrelationIdPopulatorFilter.doFilter(CorrelationIdPopulatorFilter.java:30)
... 5 filtered
at com.atlassian.servicedesk.internal.web.CustomerContextSettingFilter.lambda$invokeFilterChain$0(CustomerContextSettingFilter.java:215)
at com.atlassian.servicedesk.internal.api.util.context.ReentrantThreadLocalBasedCodeContext.rteInvoke(ReentrantThreadLocalBasedCodeContext.java:136)
at com.atlassian.servicedesk.internal.api.util.context.ReentrantThreadLocalBasedCodeContext.runOutOfContext(ReentrantThreadLocalBasedCodeContext.java:89)
at com.atlassian.servicedesk.internal.utils.context.CustomerContextServiceImpl.runOutOfCustomerContext(CustomerContextServiceImpl.java:47)
at com.atlassian.servicedesk.internal.web.CustomerContextSettingFilter.outOfCustomerContext(CustomerContextSettingFilter.java:206)
at com.atlassian.servicedesk.internal.web.CustomerContextSettingFilter.doFilterImpl(CustomerContextSettingFilter.java:134)
at com.atlassian.servicedesk.internal.web.CustomerContextSettingFilter.doFilter(CustomerContextSettingFilter.java:123)
... 9 filtered
at com.atlassian.jwt.internal.servlet.JwtAuthFilter.doFilter(JwtAuthFilter.java:37)
... 3 filtered
at com.atlassian.web.servlet.plugin.request.RedirectInterceptingFilter.doFilter(RedirectInterceptingFilter.java:21)
... 4 filtered
at com.atlassian.web.servlet.plugin.LocationCleanerFilter.doFilter(LocationCleanerFilter.java:36)
... 29 filtered
at com.atlassian.jira.servermetrics.MetricsCollectorFilter.doFilter(MetricsCollectorFilter.java:25)
... 25 filtered
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.base/java.lang.Thread.run(Thread.java:834)

Andreas Karner

The last two plugins we updated days before this happened was: Scriptrunner and Stagil Navigation.

But when I deactivate them, there is no change, still getting the same errors.

The message above I can confirm, we saw this one as well in our logs.

none_ms3ui7

I tried the same with scriptrunner but it didn't solve the issue. However, I noticed the same bug occurs when I have other linked issues which I want to delete. The only workaround is to convert the subtask into tasks (which also gives a error message but does the job) and then delete it.

andrea colombo_3zfqj1

We have the same problems also in deleting links.

Any suggestion?

none_ms3ui7

Yes, I have the same with links, not only with subtasks.

A workaround (not a pretty one) that worked for me is to add an automation rule when an issue is moved to another project where it first removes all links and then immediately deletes it.

Then I search for the issues and make a bulk move to a temporary project.

Not a pretty solution but gets the job done:) however for the subtask it doesn't work.

I hope this helps

andrea colombo_3zfqj1

We solved our problem.

One of the installed App (Email This Issue Server) was the reason.

Disabling the APP new issues can be deleted.

However, for the old issues created before disable the APP, the following SQL should be executed:

update issue_version set DELETED = 'N' where DELETED ='Y' and ISSUE_ID in (Select ID from jiraissue);

In case you have not installed the App Email This Issue Server, what I'm suggesting is:

- enter in Safe Mode (this option allows to disable all the installed App)

- try to reproduce the error (please create new Issues for that)

- if (with all Apps disable) problem is solved , exit from Safe Mode, and enable 1 App per time until you discover the App creating the problem.

Cheers

none_ms3ui7

@andrea colombo thanks a lot this indeed fixed the issue. I tried the safe mode before but it didn't work without the SQL update

Now I reverted back to an old version of "Email this Issue Server" and wait for a fix.

andrea colombo_3zfqj1

We solved our issue

We discovered (entering in safe mode) that the app Email This Issue Server has a bug. Disabling the App, we are now able to delete issues and link.

However, in order to delete the older issues, we executed the following DB script:

update issue_version set DELETED = 'N' where DELETED ='Y' and ISSUE_ID in
(Select ID from jiraissue);

Rudy Tixhon

Hello @andrea colombo do you know which is the latest version of JETI which do not have the bug?

none_ms3ui7

@Rudy Tixhon for me 8.1.0 works fine

Tibor Hegyi [META-INF]

Hi everyone, we deeply apologize for this trouble, the fix for this issue is being released over the next days.

We will provide a description of the solution to fix issue versions in the db.

Tibor

Patrick Chen

I had the same issue. I confirmed the issue was with Email this Issue 8.1.1

After upgrading to Email this Issue 8.1.2 that was released on 12/21, the bug does not occur anymore.

However, on the Issues with Subtasks where I already tried to delete it, I will attempt the manual DB fix.

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