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When you generate Session Beans for Entity Classes using the wizard, the wizard generates a public method getEntityManager(), in both the AbstractFacade superclass and in the concrete subclasses. This method should be protected, as noone outside of the EJB should use it. Another reason is that is breaks the New Web Service from EJB functionality, which generates delegates for all the public methods in the EJB.
Fixed in the web-main.
Integrated into 'main-golden', will be available in build *201002180200* on http://bits.netbeans.org/dev/nightly/ (upload may still be in progress) Changeset: http://hg.netbeans.org/main/rev/9f5aba2c5e1b User: Andrey Yamkovoy <kaktus@netbeans.org> Log: #180742 - Session Beans for Entity Classes should generate getEntityManager as protected