RQM indexing errors upgrading from CLM 3.0.1 to 4.0.6

Hello,

I have upgraded a CLM 3.0.1 environment to 4.0.6.  We are using Websphere 7.0 as the Application Server.

After upgrading, I am getting errors when performing searches in RQM. 

After pressing enter int he quick search box I get the following error.

I have tried re-indexing JTS, RQM and CCM, but that hasn't helped.

My RQM log on start-up displays the following errors:

2014-11-12 19:48:17,946 [  Start Level Event Dispatcher] ERROR com.ibm.team.server.monitoring.Activator            - CRJSS0021E Smarter Server Disabled! No Platform MBean Server 
2014-11-12 19:49:21,085 [              WebContainer : 2]  WARN com.ibm.rqm.appscan                                 - Login failed for user 'sa'.
2014-11-12 19:49:21,086 [              WebContainer : 2]  WARN com.ibm.rqm.appscan                                 - AppScan Tester Edition Integration is not configured properly.
2014-11-12 19:49:21,647 [              WebContainer : 2]  INFO pository.service.internal.ServerDescriptionService  - CRJAZ1778I This server is configured as an application.
2014-11-12 19:49:23,572 [              WebContainer : 2]  INFO .repository.service.internal.rdb.ConnectionFactory  - CRJAZ1365I The server is attempting to connect to the following database: "//localhost:1433;databaseName=qm;user=xxxxxxxx;password=xxxxxxxx"
2014-11-12 19:49:23,718 [              WebContainer : 2]  INFO .repository.service.internal.rdb.ConnectionFactory  - CRJAZ1364I The connection to the following database was successful:
 Db Product Name: Microsoft SQL Server
  Db Product Version: 10.00.4000
  Db URL: jdbc:sqlserver://localhost:1433;databaseName=qm;user=xxxxxxxx;password=xxxxxxxx
  Jdbc Driver Name: Microsoft SQL Server JDBC Driver 2.0
  Jdbc Driver Version: 2.0.1803.100
2014-11-12 19:49:27,011 [              WebContainer : 2]  INFO rvice.mapping.internal.ServerRenameProgressService  - CRJAZ2558I Setting the local server rename state to false and the openServerDescriptionServiceTemporarily state to false.
2014-11-12 19:49:29,557 [              WebContainer : 2]  INFO pository.service.internal.ServerDescriptionService  - CRJAZ1970I The application is configured with:
  Public URI: "https://xxx.xxx.xx/qm"
  Jazz Team Server location: "https://xxx.xxx.xx/jts/"
2014-11-12 19:49:31,332 [              WebContainer : 2]  WARN ice.internal.verticalRegistry.ComponentORMProvider  - The Helper reference at VariableMapEntry#value is marked not as a containment reference but it should be. All Helper references should be marked as containment. Please update your model so that the containment is correct.
2014-11-12 19:49:31,366 [              WebContainer : 2]  WARN ice.internal.verticalRegistry.ComponentORMProvider  - The Item reference at ManualExecutionScript#elements is marked as a containment reference but it should not be. All Item references should be marked as non-containment. Please update your model so that the containment is correct.
2014-11-12 19:49:31,873 [              WebContainer : 2]  WARN ice.internal.verticalRegistry.ComponentORMProvider  - The Helper reference at VariableMapEntry#value is marked not as a containment reference but it should be. All Helper references should be marked as containment. Please update your model so that the containment is correct.
2014-11-12 19:49:32,380 [              WebContainer : 2]  WARN ice.internal.verticalRegistry.ComponentORMProvider  - The Helper reference at DatapoolVariable#suggestedType is marked not as a containment reference but it should be. All Helper references should be marked as containment. Please update your model so that the containment is correct.
2014-11-12 19:49:34,478 [              WebContainer : 2]  INFO mapping.internal.GlobalServerRenameProgressService  - CRJAZ2523I Setting the global server rename state to false and the validation state to false.
2014-11-12 19:49:35,202 [              WebContainer : 2]  INFO team.fulltext.service.internal.FullTextServiceImpl  - CRJAZ8192I: Full-text Index Location: D:\IBM\JazzTeamServer4.0.6\server\conf\jts\indices\workitemindex\fulltext_index
2014-11-12 19:50:11,452 [qm: AsynchronousTaskRunner-1 @@ 19:49] ERROR y.migration.internal.textindex.TextIndexerRegistry  - CRJAZ1972E The "com.ibm.rational.test.lm.service.internal.query.LabManagementItemReIndexer" service failed to activate because a service that it depends on, "com.ibm.rational.test.lm.catalog.common.ISavedConfigurationRestService", failed to be activated.
com.ibm.team.repository.common.transport.TeamServiceRegistryException: CRJAZ1972E The "com.ibm.rational.test.lm.service.internal.query.LabManagementItemReIndexer" service failed to activate because a service that it depends on, "com.ibm.rational.test.lm.catalog.common.ISavedConfigurationRestService", failed to be activated.
 at com.ibm.team.repository.common.transport.internal.registry.AbstractActivationManagerOwner.buildServicesMap(AbstractActivationManagerOwner.java:368)
 at com.ibm.team.repository.common.transport.internal.registry.AbstractActivationManagerOwner.doActivate(AbstractActivationManagerOwner.java:733)
 at com.ibm.team.repository.common.transport.internal.registry.ExtensionServiceActivationManagerOwner.doActivate(ExtensionServiceActivationManagerOwner.java:92)
 at com.ibm.team.repository.common.transport.internal.registry.ExtensionServiceActivationManagerOwner.forceActivate(ExtensionServiceActivationManagerOwner.java:114)
 at com.ibm.team.repository.common.transport.registry.ExtensionServiceElementDescriptor.getImplementation(ExtensionServiceElementDescriptor.java:367)
 at com.ibm.team.repository.common.transport.registry.ExtensionServiceElementDescriptor.getImplementation(ExtensionServiceElementDescriptor.java:345)
 at com.ibm.team.repository.migration.internal.textindex.TextIndexerRegistry.getTextIndexer(TextIndexerRegistry.java:113)
 at com.ibm.team.repository.migration.internal.textindex.TextIndexerRegistry.getTextIndexers(TextIndexerRegistry.java:99)
 at com.ibm.team.repository.migration.internal.textindex.TextIndexerService.rebuildTextIndexes(TextIndexerService.java:25)
 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:48)
 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:37)
 at java.lang.reflect.Method.invoke(Method.java:600)
 at org.eclipse.soda.sat.core.internal.record.ExportProxyServiceRecord.invoke(ExportProxyServiceRecord.java:361)
 at org.eclipse.soda.sat.core.internal.record.ExportProxyServiceRecord.access$0(ExportProxyServiceRecord.java:347)
 at org.eclipse.soda.sat.core.internal.record.ExportProxyServiceRecord$ExportedServiceInvocationHandler.invoke(ExportProxyServiceRecord.java:56)
 at $Proxy137.rebuildTextIndexes(Unknown Source)
 at com.ibm.team.fulltext.service.internal.FulltextIndexingTask.runTask(FulltextIndexingTask.java:58)
 at com.ibm.team.repository.service.async.AbstractAutoScheduledTask.executeTask(AbstractAutoScheduledTask.java:92)
 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:48)
 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:37)
 at java.lang.reflect.Method.invoke(Method.java:600)
 at org.eclipse.soda.sat.core.internal.record.ExportProxyServiceRecord.invoke(ExportProxyServiceRecord.java:361)
 at org.eclipse.soda.sat.core.internal.record.ExportProxyServiceRecord.access$0(ExportProxyServiceRecord.java:347)
 at org.eclipse.soda.sat.core.internal.record.ExportProxyServiceRecord$ExportedServiceInvocationHandler.invoke(ExportProxyServiceRecord.java:56)
 at $Proxy417.executeTask(Unknown Source)
 at com.ibm.team.repository.service.internal.scheduler.AsynchronousTaskRunner.runTask(AsynchronousTaskRunner.java:158)
 at com.ibm.team.repository.service.internal.scheduler.AsynchronousTaskRunner.run(AsynchronousTaskRunner.java:119)
 at java.lang.Thread.run(Thread.java:736)
Caused by: com.ibm.team.repository.common.transport.TeamServiceRegistryException: CRJAZ2671E The "com.ibm.rational.test.lm.catalog.service.configuration.SavedConfigurationRestService" service failed to activate because a service that it depends on, "com.ibm.rqm.history.common.service.ITrsEventService", is not registered.
 at com.ibm.team.repository.common.transport.internal.registry.AbstractActivationManagerOwner.buildServicesMap(AbstractActivationManagerOwner.java:365)
 at com.ibm.team.repository.common.transport.internal.registry.AbstractActivationManagerOwner.doActivate(AbstractActivationManagerOwner.java:733)
 at com.ibm.team.repository.common.transport.internal.registry.ServiceProviderActivationManagerOwner.getService(ServiceProviderActivationManagerOwner.java:129)
 at com.ibm.team.repository.common.transport.internal.registry.OsgiServicesManager.getService(OsgiServicesManager.java:282)
 at com.ibm.team.repository.common.transport.internal.registry.OsgiServicesManager.getService(OsgiServicesManager.java:291)
 at com.ibm.team.repository.common.transport.internal.registry.AbstractActivationManagerOwner.buildServicesMap(AbstractActivationManagerOwner.java:357)
 ... 29 more
Caused by: com.ibm.team.repository.common.transport.ServiceNotRegisteredException: CRJAZ1115I The "com.ibm.rqm.history.common.service.ITrsEventService" service was not registered.
 at com.ibm.team.repository.common.transport.internal.registry.OsgiServicesManager.getClassForInterface(OsgiServicesManager.java:224)
 at com.ibm.team.repository.common.transport.internal.registry.OsgiServicesManager.getService(OsgiServicesManager.java:290)
 at com.ibm.team.repository.common.transport.internal.registry.AbstractActivationManagerOwner.buildServicesMap(AbstractActivationManagerOwner.java:357)
 ... 34 more
2014-11-12 19:50:11,467 [qm: AsynchronousTaskRunner-1 @@ 19:49] ERROR y.migration.internal.textindex.TextIndexerRegistry  - CRJAZ1972E The "com.ibm.team.workitem.service.internal.WorkItemReIndexer" service failed to activate because a service that it depends on, "com.ibm.team.workitem.service.internal.lucene.IWorkItemIndexingService", failed to be activated.
com.ibm.team.repository.common.transport.TeamServiceRegistryException: CRJAZ1972E The "com.ibm.team.workitem.service.internal.WorkItemReIndexer" service failed to activate because a service that it depends on, "com.ibm.team.workitem.service.internal.lucene.IWorkItemIndexingService", failed to be activated.
 at com.ibm.team.repository.common.transport.internal.registry.AbstractActivationManagerOwner.buildServicesMap(AbstractActivationManagerOwner.java:368)
 at com.ibm.team.repository.common.transport.internal.registry.AbstractActivationManagerOwner.doActivate(AbstractActivationManagerOwner.java:733)
 at com.ibm.team.repository.common.transport.internal.registry.ExtensionServiceActivationManagerOwner.doActivate(ExtensionServiceActivationManagerOwner.java:92)
 at com.ibm.team.repository.common.transport.internal.registry.ExtensionServiceActivationManagerOwner.forceActivate(ExtensionServiceActivationManagerOwner.java:114)
 at com.ibm.team.repository.common.transport.registry.ExtensionServiceElementDescriptor.getImplementation(ExtensionServiceElementDescriptor.java:367)
 at com.ibm.team.repository.common.transport.registry.ExtensionServiceElementDescriptor.getImplementation(ExtensionServiceElementDescriptor.java:345)
 at com.ibm.team.repository.migration.internal.textindex.TextIndexerRegistry.getTextIndexer(TextIndexerRegistry.java:113)
 at com.ibm.team.repository.migration.internal.textindex.TextIndexerRegistry.getTextIndexers(TextIndexerRegistry.java:99)
 at com.ibm.team.repository.migration.internal.textindex.TextIndexerService.rebuildTextIndexes(TextIndexerService.java:25)
 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:48)
 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:37)
 at java.lang.reflect.Method.invoke(Method.java:600)
 at org.eclipse.soda.sat.core.internal.record.ExportProxyServiceRecord.invoke(ExportProxyServiceRecord.java:361)
 at org.eclipse.soda.sat.core.internal.record.ExportProxyServiceRecord.access$0(ExportProxyServiceRecord.java:347)
 at org.eclipse.soda.sat.core.internal.record.ExportProxyServiceRecord$ExportedServiceInvocationHandler.invoke(ExportProxyServiceRecord.java:56)
 at $Proxy137.rebuildTextIndexes(Unknown Source)
 at com.ibm.team.fulltext.service.internal.FulltextIndexingTask.runTask(FulltextIndexingTask.java:58)
 at com.ibm.team.repository.service.async.AbstractAutoScheduledTask.executeTask(AbstractAutoScheduledTask.java:92)
 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:48)
 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:37)
 at java.lang.reflect.Method.invoke(Method.java:600)
 at org.eclipse.soda.sat.core.internal.record.ExportProxyServiceRecord.invoke(ExportProxyServiceRecord.java:361)
 at org.eclipse.soda.sat.core.internal.record.ExportProxyServiceRecord.access$0(ExportProxyServiceRecord.java:347)
 at org.eclipse.soda.sat.core.internal.record.ExportProxyServiceRecord$ExportedServiceInvocationHandler.invoke(ExportProxyServiceRecord.java:56)
 at $Proxy417.executeTask(Unknown Source)
 at com.ibm.team.repository.service.internal.scheduler.AsynchronousTaskRunner.runTask(AsynchronousTaskRunner.java:158)
 at com.ibm.team.repository.service.internal.scheduler.AsynchronousTaskRunner.run(AsynchronousTaskRunner.java:119)
 at java.lang.Thread.run(Thread.java:736)
Caused by: com.ibm.team.repository.common.transport.TeamServiceRegistryException: CRJAZ2671E The "com.ibm.team.workitem.service.internal.lucene.WorkItemIndexingService" service failed to activate because a service that it depends on, "com.ibm.team.workitem.service.IWorkItemServer", is not registered.
 at com.ibm.team.repository.common.transport.internal.registry.AbstractActivationManagerOwner.buildServicesMap(AbstractActivationManagerOwner.java:365)
 at com.ibm.team.repository.common.transport.internal.registry.AbstractActivationManagerOwner.doActivate(AbstractActivationManagerOwner.java:733)
 at com.ibm.team.repository.common.transport.internal.registry.ServiceProviderActivationManagerOwner.getService(ServiceProviderActivationManagerOwner.java:129)
 at com.ibm.team.repository.common.transport.internal.registry.OsgiServicesManager.getService(OsgiServicesManager.java:282)
 at com.ibm.team.repository.common.transport.internal.registry.OsgiServicesManager.getService(OsgiServicesManager.java:291)
 at com.ibm.team.repository.common.transport.internal.registry.AbstractActivationManagerOwner.buildServicesMap(AbstractActivationManagerOwner.java:357)
 ... 29 more
Caused by: com.ibm.team.repository.common.transport.ServiceNotRegisteredException: CRJAZ1115I The "com.ibm.team.workitem.service.IWorkItemServer" service was not registered.
 at com.ibm.team.repository.common.transport.internal.registry.OsgiServicesManager.getClassForInterface(OsgiServicesManager.java:224)
 at com.ibm.team.repository.common.transport.internal.registry.OsgiServicesManager.getService(OsgiServicesManager.java:290)
 at com.ibm.team.repository.common.transport.internal.registry.AbstractActivationManagerOwner.buildServicesMap(AbstractActivationManagerOwner.java:357)
 ... 34 more
2014-11-12 19:50:11,573 [qm: AsynchronousTaskRunner-1 @@ 19:49]  INFO tion.internal.stats.AbstractMigrationEventListener  - Pre-Rebuild index for Planning took 62 ms.

2014-11-12 19:50:11,573 [qm: AsynchronousTaskRunner-1 @@ 19:49]  INFO tion.internal.stats.AbstractMigrationEventListener  - Pre-Rebuild index for RQM Keyword took 0 ms.

2014-11-12 19:50:11,573 [qm: AsynchronousTaskRunner-1 @@ 19:49]  INFO tion.internal.stats.AbstractMigrationEventListener  - Pre-Rebuild index for RQM Datapool took 0 ms.

2014-11-12 19:50:11,573 [qm: AsynchronousTaskRunner-1 @@ 19:49]  INFO tion.internal.stats.AbstractMigrationEventListener  - Pre-Rebuild index for RQM Build Integration took 0 ms.

2014-11-12 19:50:11,573 [qm: AsynchronousTaskRunner-1 @@ 19:49]  INFO tion.internal.stats.AbstractMigrationEventListener  - Pre-Rebuild index for Execution took 0 ms.

2014-11-12 19:50:11,573 [qm: AsynchronousTaskRunner-1 @@ 19:49]  INFO tion.internal.stats.AbstractMigrationEventListener  - Pre-Rebuild index for RQM Requirement took 0 ms.

2014-11-12 19:50:11,573 [qm: AsynchronousTaskRunner-1 @@ 19:49]  INFO tion.internal.stats.AbstractMigrationEventListener  - Pre-Rebuild index for LM Sequencer took 0 ms.

2014-11-12 19:50:16,202 [              WebContainer : 2]  INFO com.ibm.team.repository.servlet.TeamServerServlet   - CRJAZ2076I Product Details:
  Quality Management - Core Libraries, Version 4.0.6 (I20140205_1831)
  Jazz Foundation - Core Libraries, Version 4.0.6 (RJF-I20140130-1407)

2014-11-12 19:54:26,036 [qm: AsynchronousTaskRunner-1 @@ 19:49]  INFO tion.internal.stats.AbstractMigrationEventListener  - Rebuilding indices for Planning took 254462 ms.

2014-11-12 19:54:26,101 [qm: AsynchronousTaskRunner-1 @@ 19:49]  INFO tion.internal.stats.AbstractMigrationEventListener  - Rebuilding indices for RQM Keyword took 64 ms.

2014-11-12 19:54:26,196 [qm: AsynchronousTaskRunner-1 @@ 19:49]  INFO tion.internal.stats.AbstractMigrationEventListener  - Rebuilding indices for RQM Datapool took 95 ms.

2014-11-12 19:54:26,368 [qm: AsynchronousTaskRunner-1 @@ 19:49]  INFO tion.internal.stats.AbstractMigrationEventListener  - Rebuilding indices for RQM Build Integration took 172 ms.

2014-11-12 19:54:36,068 [qm: AsynchronousTaskRunner-1 @@ 19:49]  INFO tion.internal.stats.AbstractMigrationEventListener  - Rebuilding indices for Execution took 9700 ms.

2014-11-12 19:54:36,073 [qm: AsynchronousTaskRunner-1 @@ 19:49]  INFO tion.internal.stats.AbstractMigrationEventListener  - Rebuilding indices for RQM Requirement took 5 ms.

2014-11-12 19:54:36,169 [qm: AsynchronousTaskRunner-1 @@ 19:49]  INFO tion.internal.stats.AbstractMigrationEventListener  - Rebuilding indices for LM Sequencer took 96 ms.

2014-11-12 19:58:41,217 [qm: AsynchronousTaskRunner-3 @@ 19:58]  WARN com.ibm.rqm.defects.service                         - ChangeRequestCollector:hadInitialized AQXIN2503W Blocking defects cannot be automatically synchronized between the Quality Management application and the Change and Configuration Management (CCM) application. The integration of the applications is incorrectly configured.

Any help with this is greatly appreciated.