Should work.. just make sure you only have one EntityManager instance per 
request. I use a command pattern so I have one place where I can handle the 
transaction (create transaction before command handler executes and commit 
afterwards). But command pattern as well as DTO's leads to lots of classes 
for a simple server request...don't know if I would choose it again 
(command, command result, command handler, JPA entity, DTO class, possibly 
DAO class). Also JPA's query language (JPQL) does not support everything 
that native SQL supports so you have to keep that in mind (but sure you can 
also execute native SQL queries with JPA if there is no other possibility).

Currently I am looking into myBatis (http://www.mybatis.org/) for a new 
projects. It uses native SQL and has some nice code generator support. Maybe 
you should take a look at it, as you already have native SQL for a given 
database.

-- J.

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