Yes it's possible to call Stored Procedure. At least it works in my application with MS SQL Server and Glassfish 2.1
Here is example:
public void doMerge(int sourcePatientId, int destinationPatientId) {
Query query = getEntityManager().createNativeQuery("{call dbo.MergePatient(?,?)}");
query.setParameter(1, sourcePatientId);
query.setParameter(2, destinationPatientId);
getEntityManager().getTransaction().begin();
query.executeUpdate();
getEntityManager().getTransaction().commit();
}
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