How do I fix 'CRJAZ0688I Unable to initialize service "repository item service"' error when verifying the db?

Unfortunately, the install doesn't work. The server will start, and the JTS admin interface will load, but the ccm component can't seem to communicate with the JTS component (no list of projects on the dropdown menu on the top left). At one stage, we had the Eclipse RTC client working with the /ccm web interface, but the web interface wouldn't load the details of a project (although it did let me configure the process for the project area). Now that's not working either. Also, the server can't be shutdown using the ./server-shutdown.sh script - it stops accepting HTTP connections but the java/tomcat process has to be killed from the command line.

The /jts admin diagnostics seemed like a good place to start looking for a fix, so I ran it. It reports 2 errors, one in the Application and Friends section:

Application: the root services resource at https://pthlin2:9443/ccm/rootservices for "/ccm" cannot be accessed:
java.net.SocketTimeoutException: Read timed out
Application: the discovery resource at https://pthlin2:9443/ccm/scr for "/ccm" cannot be accessed:
The returned HTTP status was 503
The response body was

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HTTP Status 503 - CRJAZ1173I Service "com.ibm.team.repository.service.internal.discovery.IServiceContributionResourceService" is not available.

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type Status report

message CRJAZ1173I Service "com.ibm.team.repository.service.internal.discovery.IServiceContributionResourceService" is not available.

description The requested service (CRJAZ1173I Service "com.ibm.team.repository.service.internal.discovery.IServiceContributionResourceService" is not available.) is not currently available.

(despite /ccm/ being listed in the Consumers JTS admin page), and one database diagnostic error directing me to look at the JTS logs (CRJAZ2069E An error occurred during the execution of this diagnostic with the error message "com.ibm.team.repository.common.TeamRepositoryException: CRJAZ0810I Failed to detect whether the "JT40L2_AUTH.JAUTH_TKN_STT_D_DX" index already exists.". See the server log for more details.). Looking at the logs, I see http://pastebin.com/raw.php?i=t79hLFM5 .

Sudhakar Frederick/Australia/IBM advised me to try the following:

• Clear the tomcat work directory at /opt/IBM/JazzTeamServer/server/tomcat/work (DONE)
• Change the indice locations in the teamserver.properties for jts & ccm to use absolute paths (DONE)
• Verify the db for JTS & CCM. JTS output is the following (after shutting down the server):

ckriege@pthlin2:/opt/IBM/JazzTeamServer/server> ./repotools-jts.sh -verify level=10
Repo Tools
Provisioning using "./conf/jts/provision_profiles".
  Jazz Foundation - Core Libraries, Version 4.0 (RJF-I20120531-1400)
CRJAZ1363I Loading the configuration from "file:conf/jts/teamserver.properties".
CRJAZ1779I This server is configured as a JTS.
CRJAZ1365I The server is attempting to connect to the following database: "//pthfmd1:5020/QXPFMD1DF11:user=xxxxxxxx;password=xxxxxxxx;"
CRJAZ1364I The connection to the following database was successful:
Db Product Name: DB2
  Db Product Version: DSN10015
  Db URL: jdbc:db2://pthfmd1:5020/QXPFMD1DF11:user=xxxxxxxx;password=xxxxxxxx;
  Jdbc Driver Name: IBM DB2 JDBC Universal Driver Architecture
  Jdbc Driver Version: 3.61.73
CRJAZ1971I The server is configured with:
  Public URI: "https://pthlin2:9443/jts"
CRJAZ1093I The following service class was not activated: "com.ibm.team.repository.service.internal.ContentService"
CRJAZ2105I Checking for a running server...
CRJAZ0688I Unable to initialize service "repository item service".
CRJAZ1161I Failed to get "com.ibm.team.reports.service.internal.ReportVerifier" implementation.
CRJAZ1161I Failed to get "com.ibm.team.process.internal.service.migration.ProcessMigrationVerifier" implementation.
CRJAZ1161I Failed to get "com.ibm.team.repository.service.internal.verifiers.RepositoryVerifier" implementation.
CRJAZ1161I Failed to get "com.ibm.team.dashboard.service.internal.migration.RepositoryVerifier" implementation.
Verifying the repository contents using verification level 10.
CRJAZ2222I Verification was successful.
		
		

Worth noting - the verify command was run from my user, which has rw permissions for the entire /opt/IBM/JazzTeamServer/ dir.