Symptoms

Attempting to upgrade JIRA using the installer causes NullPointerException, the follow screen is shown instead of the login screen:

Also, the following appears in the atlassian-jira.log:

2013-03-04 16:45:07,255 localhost-startStop-1 WARN      [core.entity.transaction.JNDIFactory] [ConnectionFactory.getConnection] Failed to find DataSource named java:comp/env/jdbc/JiraDS in JNDI server with name default. Trying normal database.
javax.naming.NameNotFoundException: Name [jdbc/JiraDS] is not bound in this Context. Unable to find [jdbc].
... 
2013-03-04 16:45:07,259 localhost-startStop-1 ERROR      [ofbiz.core.entity.ConnectionFactory] ******* ERROR: No database connection found for helperName "defaultDS"
2013-03-04 16:45:07,260 localhost-startStop-1 ERROR      [atlassian.jira.startup.LauncherContextListener] Unable to start JIRA.
com.atlassian.jira.exception.DataAccessException: Unable to get a database connection for the OfBiz default data source.
...
2013-03-04 16:45:27,389 http-bio-8090-exec-2 ERROR      [500ErrorPage.jsp] Exception caught in 500 page java.lang.NullPointerException
com.atlassian.util.concurrent.LazyReference$InitializationException: java.lang.NullPointerException

Diagnosis

The dbconfig.xml file, which is located into JIRA Home Directory, contains a JNDI location:

<jira-database-config>
  <name>defaultDS</name>
  <delegator-name>default</delegator-name>
  <database-type>mysql</database-type>
  <jndi-datasource>
    <jndi-name>java:comp/env/jdbc/JiraDS</jndi-name>
  </jndi-datasource>
</jira-database-config>

Cause

The database resource was located within the server.xml file, which is not copied over during the upgrade.  

Workaround

There are two possible workarounds to this issue:

Reconfigure the dbconfig.xml file and stop using JNDI Location:

1. Shutdown JIRA
2. Navigate to JIRA Home Directory
3. Delete or move the current dbconfig.xml file to another folder
4. Navigate to $JIRA_install_dir/bin and execute JIRA configuration tool
5. Configure your database connection again
6. Restart JIRA

Or re-add the JNDI Location:

1. Shutdown JIRA

2. Check the server.xml file, which is located in $JIRA_install_dir/conf, from a backup prior to the upgrade attempt

3. Copy the JNDI Location that includes the database connection parameters, as in this example:

   <Resource auth="Container" driverClassName="com.mysql.jdbc.Driver" maxActive="20" name="jdbc/JiraDS" password="jira" type="javax.sql.DataSource" url="jdbc:mysql://localhost:3306/jira0?useUnicode=true&amp;characterEncoding=UTF8" username="jira" validationQuery="select 1"/>
   

   Do not copy the server.xml file into your new installation. Copy just the JNDI resource definition.

4. Paste the JNDI Location in the same location (inside the <Context/> node) in the server.xml file after the upgrade

5. Restart JIRA