I'm not sure where you are in your configuration, but here's a tricky naming 
convention that finally allowed my 
crystal reports to work with JNDI.

The JNDI datasource that I've been using for some time with my web app is 
called cdhp.  It shouldn't matter, 
but it happens to be an MS SQL Server database.  Just for reference, here's the 
entry in mssql-ds.xml:
<datasources>
  |   <local-tx-datasource>
  |     <jndi-name>cdhp</jndi-name>
  |     <connection-url>
  |       
jdbc:microsoft:sqlserver://myServer:1433;DatabaseName=myDatabase;SelectMethod=Cursor
  |     </connection-url>
  |     
<driver-class>com.microsoft.jdbc.sqlserver.SQLServerDriver</driver-class>
  |     <user-name>myUser</user-name>
  |     <password>myPassword</password>
  |   </local-tx-datasource>
  | </datasources>
To match this JNDI datasource, I set up an ODBC datasource named java:/cdhp .  
This is the datasource I use 
in Crystal Designer to create the reports.

I still don't know exactly why this worked, but through trial & error, I 
finally stumbled upon it.  From reading the 
Crystal docs, it seemed like both the jndi name & ODBC name should be exactly 
the same.  But (as you probably 
found out) that just didn't work for me.

Hope this helps.
Sue.

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