Problems while upgrading crowd to 3.1 from 2.8

[Chris Feamster]

So I hope someone can help. I don't know how well this can be troubleshooted without logs, but logs don't belong in the public domain so.... :-\

I'm trying to upgrade from 2.8.8 to 3.1.1. I have a XML backup. I proceed to the step of inputting the path to the back up. After about 45s the page is reloaded with an empty error box... Additionally the follow exception is recorded after some data migrations..

2017-12-07 02:52:36,654 http-nio-8095-exec-6 INFO [atlassian.crowd.migration.XmlMigrator] Using com.atlassian.crowd.migration.GrantedPermissionMapper to import.
2017-12-07 02:52:36,676 http-nio-8095-exec-6 ERROR [console.action.setup.Import] Error importing XML data
java.util.NoSuchElementException
 at java.util.ArrayList$Itr.next(ArrayList.java:862)
 at com.google.common.collect.Iterators.getOnlyElement(Iterators.java:302)
 at com.google.common.collect.Iterables.getOnlyElement(Iterables.java:289)
 at com.atlassian.crowd.manager.application.InternalApplicationHelperImpl.findCrowdConsoleApplication(InternalApplicationHelperImpl.java:29)
 at com.atlassian.crowd.migration.GrantedPermissionMapper.importXml(GrantedPermissionMapper.java:75)
 at com.atlassian.crowd.migration.XmlMigrator.importXml(XmlMigrator.java:40)
 at com.atlassian.crowd.migration.XmlMigrationManagerImpl.importXml(XmlMigrationManagerImpl.java:179)
 at com.atlassian.crowd.console.action.setup.Import.update(Import.java:61)
 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
 at java.lang.reflect.Method.invoke(Method.java:498)
 at ognl.OgnlRuntime.invokeMethod(OgnlRuntime.java:899)
 at ognl.OgnlRuntime.callAppropriateMethod(OgnlRuntime.java:1544)
 at ognl.ObjectMethodAccessor.callMethod(ObjectMethodAccessor.java:68)
 at com.opensymphony.xwork2.ognl.accessor.XWorkMethodAccessor.callMethodWithDebugInfo(XWorkMethodAccessor.java:96)
 at com.opensymphony.xwork2.ognl.accessor.XWorkMethodAccessor.callMethod(XWorkMethodAccessor.java:88)
 at ognl.OgnlRuntime.callMethod(OgnlRuntime.java:1620)
 at ognl.ASTMethod.getValueBody(ASTMethod.java:91)
 at ognl.SimpleNode.evaluateGetValueBody(SimpleNode.java:212)
 at ognl.SimpleNode.getValue(SimpleNode.java:258)
 at ognl.Ognl.getValue(Ognl.java:470)
 at ognl.Ognl.getValue(Ognl.java:434)
 at com.opensymphony.xwork2.ognl.OgnlUtil$3.execute(OgnlUtil.java:371)
 at com.opensymphony.xwork2.ognl.OgnlUtil.compileAndExecuteMethod(OgnlUtil.java:423)
 at com.opensymphony.xwork2.ognl.OgnlUtil.callMethod(OgnlUtil.java:369)
 at com.opensymphony.xwork2.DefaultActionInvocation.invokeAction(DefaultActionInvocation.java:436)
 at com.opensymphony.xwork2.DefaultActionInvocation.invokeActionOnly(DefaultActionInvocation.java:291)
 at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:252)
 at org.apache.struts2.interceptor.ServletConfigInterceptor.intercept(ServletConfigInterceptor.java:171)
 at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:247)
 at org.apache.struts2.interceptor.ServletConfigInterceptor.intercept(ServletConfigInterceptor.java:171)
 at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:247)
 at com.opensymphony.xwork2.interceptor.ParametersInterceptor.doIntercept(ParametersInterceptor.java:134)
 at com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(MethodFilterInterceptor.java:98)
 at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:247)
 at com.opensymphony.xwork2.interceptor.StaticParametersInterceptor.intercept(StaticParametersInterceptor.java:199)
 at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:247)
 at com.opensymphony.xwork2.interceptor.ModelDrivenInterceptor.intercept(ModelDrivenInterceptor.java:99)
 at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:247)
 at com.opensymphony.xwork2.interceptor.ChainingInterceptor.intercept(ChainingInterceptor.java:157)
 at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:247)
 at com.atlassian.crowd.xwork.interceptors.TransactionalInvocation.invokeAndHandleExceptions(TransactionalInvocation.java:60)
 at com.atlassian.crowd.xwork.interceptors.TransactionalInvocation.invokeInTransaction(TransactionalInvocation.java:50)
 at com.atlassian.crowd.xwork.interceptors.XWorkTransactionInterceptor.intercept(XWorkTransactionInterceptor.java:50)
 at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:247)
 at com.atlassian.crowd.console.interceptor.SetupCheckInterceptor.intercept(SetupCheckInterceptor.java:24)
 at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:247)
 at com.atlassian.crowd.xwork.interceptors.SecurityHeadersInterceptor.intercept(SecurityHeadersInterceptor.java:42)
 at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:247)
 at org.apache.struts2.factory.StrutsActionProxy.execute(StrutsActionProxy.java:53)
 at org.apache.struts2.dispatcher.Dispatcher.serviceAction(Dispatcher.java:577)
 at org.apache.struts2.dispatcher.ExecuteOperations.executeAction(ExecuteOperations.java:81)
 at org.apache.struts2.dispatcher.filter.StrutsExecuteFilter.doFilter(StrutsExecuteFilter.java:88)
 at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
 at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
 at com.opensymphony.sitemesh.webapp.SiteMeshFilter.obtainContent(SiteMeshFilter.java:125)
 at com.opensymphony.sitemesh.webapp.SiteMeshFilter.doFilter(SiteMeshFilter.java:76)
 at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
 at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:39)
 at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:70)
 at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:58)
 at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
 at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
 at com.atlassian.crowd.console.filter.CrowdDelegatingFilterProxy.doFilter(CrowdDelegatingFilterProxy.java:38)
 at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
 at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
 at org.apache.struts2.dispatcher.filter.StrutsPrepareFilter.doFilter(StrutsPrepareFilter.java:94)
 at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
 at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:39)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:58)
 at com.atlassian.oauth.serviceprovider.internal.servlet.OAuthFilter.doFilter(OAuthFilter.java:67)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:64)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:37)
 at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:70)
 at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:58)
 at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
 at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
 at com.atlassian.crowd.console.filter.CrowdDelegatingFilterProxy.doFilter(CrowdDelegatingFilterProxy.java:38)
 at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
 at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
 at com.atlassian.johnson.filters.AbstractJohnsonFilter.doFilter(AbstractJohnsonFilter.java:67)
 at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
 at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
 at org.springframework.orm.hibernate5.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:151)
 at com.atlassian.crowd.console.filter.CrowdOpenSessionInViewFilter.doFilterInternal(CrowdOpenSessionInViewFilter.java:23)
 at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
 at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
 at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
 at com.atlassian.crowd.plugin.web.filter.RequestCacheThreadLocalFilter.doFilter(RequestCacheThreadLocalFilter.java:27)
 at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
 at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:39)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:58)
 at com.atlassian.analytics.client.filter.DefaultAnalyticsFilter.doFilter(DefaultAnalyticsFilter.java:38)
 at com.atlassian.analytics.client.filter.AbstractHttpFilter.doFilter(AbstractHttpFilter.java:39)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:64)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:37)
 at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:70)
 at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:58)
 at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
 at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
 at com.atlassian.crowd.security.BlockOpenSocialRequestFilter.doFilter(BlockOpenSocialRequestFilter.java:39)
 at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
 at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
 at com.atlassian.crowd.console.filter.CrowdCachingFilter.doFilter(CrowdCachingFilter.java:25)
 at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
 at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
 at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:197)
 at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
 at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
 at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
 at com.atlassian.crowd.console.filter.CrowdDelegatingFilterProxy.doFilter(CrowdDelegatingFilterProxy.java:38)
 at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
 at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
 at com.atlassian.crowd.plugin.web.filter.HttpRequestLoggingFilter.doFilter(HttpRequestLoggingFilter.java:30)
 at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
 at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
 at com.atlassian.crowd.plugin.web.filter.HttpContextFilter.doFilter(HttpContextFilter.java:30)
 at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
 at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
 at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:198)
 at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:96)
 at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:140)
 at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:80)
 at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:87)
 at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:342)
 at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:799)
 at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66)
 at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:868)
 at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1457)
 at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)
 at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
 at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
 at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
 at java.lang.Thread.run(Thread.java:748)
2017-12-07 02:52:53,631 http-nio-8095-exec-11 INFO [atlassian.johnson.filters.JohnsonFilter] The application is not yet setup. Redirecting request from '/console/login.action' to '
/console/setup/selectsetupstep.action'
2017-12-07 02:52:53,680 http-nio-8095-exec-10 INFO [console.action.setup.SelectSetupStep] Current setup step is /console/setup/setupimport.action

 This exception appears generic to me.

Why would a backup that worked just moments ago fail during this upgrade. Are there manual data/model steps that need to be executed?

Any and all suggestions welcome.

Thank you.

[lpater · Accepted solution]

For reference, the issue turned out to be caused by not setting the MySQL transaction isolation level to READ-COMMITTED, as documented here. 

I've raised CWD-5007 to track the issue. The interim solution is to set the transaction isolation level appropriately.

[Rob Cascella]

What is the workaround for this in cases where one cannot configure the MySQL transaction isolation level, for example in Amazon RDS?

[AnnWorley]

Chris, you should get an email from our support portal shortly. We created a support request in your name so you could use the file sharing functionality to provide logs and a backup, etc. for Lukasz to examine.

[lpater]

Hi Chris,

It seems that the backup you're trying to restore doesn't contain an application of type CROWD, which is expected by the import process.

This generally shouldn't be the case, but might potentially might be caused by some manual changes in the database in the past, or some unexpected migration path in the past.

Please double-check your backup xml, to check if the Crowd application is there, and has the type CROWD. It should look like this:

...
 <application>
 <id>1234</id>
 <name>crowd</name>
...
 <active>true</active>
 <type>CROWD</type>
...

If the crowd application has a different type, please try changing it back to <type>CROWD</type> (for example <type>GENERIC_APPLICATION</type>, and trying to reimport the backup again.

Hope this helps, let us know if you run into any other issues.

[Chris Feamster]

@lpater Thanks for the lead!

Unfortunately that didn't go anywhere:

 <applications>
  <application>
   <id>2</id>
   <name>crowd</name>
   <createdDate>Fri Jan 03 02:44:41 +0000 2014</createdDate>
   <updatedDate>Sun May 10 05:26:34 +0000 2015</updatedDate>
   <active>true</active>
   <type>CROWD</type>

If not that, then what?

[Marcin Kempa]

Hi @Chris Feamster,

You mentioned that the 'backup worked just a moments ago', does that mean that you tested it on some previous Crowd version or was it just generated a moments ago on your 2.8.8 instance?

Do you see some other errors in the log file that preceded the one you've already mentioned, especially something like:

[ERROR] Could not add <name of application>

Could you also try to use this backup on the 2.8.8 Crowd version in your test environment and share with us the results?

Thanks,

Marcin Kempa

[Chris Feamster]

Hi @Marcin Kempa,

I meant that it was just generated moments ago. Indeed, technically this is a DR scenario. I restored a week-old backup to 3.1. It failed. I restored that back up to 2.8.8. It succeeded. I made a new backup yesterday to upgrade to 3.1.1, It failed (the cause of this ticket).

So actually this day old backup is the result of a successful restore of a previous week old backup. So right now it seems as if it is 3.1.1 specifically that is incompatible with the data from my installation.

Thoughts?

(I'd be great if there was a secure way to send you a sql dump... )

[Chris Feamster]

For the record, no, I do not see that message in the logs...

Prev 27 Lines

2017-12-07 02:52:35,421 http-nio-8095-exec-6 INFO [atlassian.crowd.migration.XmlMigrator] Using com.atlassian.crowd.migration.CrowdPropertiesMapper to import.
2017-12-07 02:52:35,423 http-nio-8095-exec-6 INFO [atlassian.crowd.util.PropertyUtils] Updating properties resource: file:/***REDACTED***/Crowd/crowd.properties adding property: session.lastvalidation|session.lastvalidation
2017-12-07 02:52:35,425 http-nio-8095-exec-6 INFO [atlassian.crowd.util.PropertyUtils] Updating properties resource: file:/***REDACTED***/Crowd/crowd.properties adding property: application.password|***REDACTED***
2017-12-07 02:52:35,428 http-nio-8095-exec-6 INFO [atlassian.crowd.util.PropertyUtils] Updating properties resource: file:/***REDACTED***/Crowd/crowd.properties adding property: session.isauthenticated|session.isauthenticated
2017-12-07 02:52:35,430 http-nio-8095-exec-6 INFO [atlassian.crowd.util.PropertyUtils] Updating properties resource: file:/***REDACTED***/Crowd/crowd.properties adding property: application.name|crowd
2017-12-07 02:52:35,432 http-nio-8095-exec-6 INFO [atlassian.crowd.util.PropertyUtils] Updating properties resource: file:/***REDACTED***/Crowd/crowd.properties adding property: session.validationinterval|0
2017-12-07 02:52:35,435 http-nio-8095-exec-6 INFO [atlassian.crowd.util.PropertyUtils] Updating properties resource: file:/***REDACTED***/Crowd/crowd.properties adding property: crowd.server.url|***REDACTED***
2017-12-07 02:52:35,438 http-nio-8095-exec-6 INFO [atlassian.crowd.util.PropertyUtils] Updating properties resource: file:/***REDACTED***/Crowd/crowd.properties adding property: session.tokenkey|session.tokenkey
2017-12-07 02:52:35,443 http-nio-8095-exec-6 INFO [atlassian.crowd.util.PropertyUtils] Updating properties resource: file:/***REDACTED***/Crowd/crowd.properties adding property: application.login.url|***REDACTED***
2017-12-07 02:52:35,446 http-nio-8095-exec-6 INFO [atlassian.crowd.migration.XmlMigrator] Using com.atlassian.crowd.migration.DirectoryMapper to import.
2017-12-07 02:52:35,557 http-nio-8095-exec-6 INFO [atlassian.crowd.migration.XmlMigrator] Using com.atlassian.crowd.migration.UserMapper to import.
2017-12-07 02:52:35,582 http-nio-8095-exec-6 INFO [atlassian.crowd.migration.UserMapper] About to replicate 23 users
2017-12-07 02:52:35,817 http-nio-8095-exec-6 INFO [atlassian.crowd.migration.UserMapper] User replication complete
2017-12-07 02:52:35,818 http-nio-8095-exec-6 INFO [atlassian.crowd.migration.UserMapper] About to replicate 111 user attributes
2017-12-07 02:52:35,950 http-nio-8095-exec-6 INFO [atlassian.crowd.migration.UserMapper] User attribute replication complete
2017-12-07 02:52:35,952 http-nio-8095-exec-6 INFO [atlassian.crowd.migration.XmlMigrator] Using com.atlassian.crowd.migration.GroupMapper to import.
2017-12-07 02:52:35,963 http-nio-8095-exec-6 INFO [atlassian.crowd.migration.GroupMapper] About to replicate 13 groups
2017-12-07 02:52:36,008 http-nio-8095-exec-6 INFO [atlassian.crowd.migration.GroupMapper] Group replication complete
2017-12-07 02:52:36,010 http-nio-8095-exec-6 INFO [atlassian.crowd.migration.GroupMapper] About to replicate 0 group attributes
2017-12-07 02:52:36,012 http-nio-8095-exec-6 INFO [atlassian.crowd.migration.GroupMapper] Group attribute replication complete
2017-12-07 02:52:36,013 http-nio-8095-exec-6 INFO [atlassian.crowd.migration.XmlMigrator] Using com.atlassian.crowd.migration.MembershipMapper to import.
2017-12-07 02:52:36,157 http-nio-8095-exec-6 INFO [atlassian.crowd.migration.MembershipMapper] About to replicate 60 memberships
2017-12-07 02:52:36,242 http-nio-8095-exec-6 INFO [atlassian.crowd.migration.MembershipMapper] Membership replication complete
2017-12-07 02:52:36,243 http-nio-8095-exec-6 INFO [atlassian.crowd.migration.XmlMigrator] Using com.atlassian.crowd.migration.ApplicationMapper to import.
2017-12-07 02:52:36,641 http-nio-8095-exec-6 INFO [atlassian.crowd.migration.XmlMigrator] Using com.atlassian.crowd.migration.AliasMapper to import.
2017-12-07 02:52:36,643 http-nio-8095-exec-6 INFO [atlassian.crowd.migration.XmlMigrator] Using com.atlassian.crowd.migration.PropertyMapper to import.
2017-12-07 02:52:36,645 http-nio-8095-exec-6 INFO [atlassian.crowd.migration.PropertyMapper] Using identity decoder to read properties 

[lpater]

It seems that for some reason the Crowd application is not created when restoring the backup, even though the data for it seems to be contained in the backup, and the module responsible for restoring it is run.

Could you let us know what database are you using, and did you customize the database configuration in Crowd in any way? After the failed backup could you connect to the database using an SQL query tool, and see whether the Crowd application is present in the cwd_application table?

Having a look at your backup file would be a useful way to diagnose further. If you can raise a support ticket you can securely attach files there. If you can't do that, reach out to me via email (lpater@atlassian.com), and I'll set up an alternate way for you to upload it.