I have done it with Resin. I think it is the same with Tomcat.

You need to initialise your DataObjects in the init method of your servlet :

  JDO jdo = new JDO();
  jdo.setConfiguration(...);
  jdo.setDatabaseName(...),

The you then can put it correctly  in your JNDI NameSpace :

  InitialContext ic = new InitialContex();
  Context jdoCtx = ic.createSubContext("java:comp/env/jdo");
  jdoCtx.bind("myDb", jdo);


After that, you just have to lookup on "java:/comp/env/jdo/myDb" to get your
DataObjects ready to use.

Additionnal informations :

   your database.xml and mapping.xml files must be in your classpath (under
   WEB-INF/classes) so that you can get them by getClass().getResource() as
   explained in  the servlet example,
   I think it is better to run a test query just after initialising the JDO
   configuration so as to check it and to throw a ServletException in the init
   method in case of pb.

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