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Hopefully I can provide some partial answers now, and work through more detailed example later. OEPE has support for running WLST scripts.
a.) Project Setup Example: Create Web Service Project: File>New>Other>Oracle>WebLogic>Web Services>Web Service Project. Enable the Oracle WebLogic Scripting Tools (WLST) Support Facet. You can also enable this facet by rt clicking the project and navigate to the project facets.
b.) Rt Click the new wlst source directory and you can create a new WLST script here. There are some templates to get you started or if you have an existing template you can put it here.
c.) You can perform Run-As operation on your wlst script and it will get run from OEPE.
See the Help Documentation on this feature for additional detail.
Using wlst for this is a good idea to start with. Outside of the wlst scripting, you will have to create and specify the weblogic-webservices.xml file containing <webservice-type>JAXRPC</webservice-type>. Additionally, a webservices.xml will exist describing jaxrpc-mapping. I havent tried this in awhile, and will make an attempt a little later in the week.
Here is a link that may serve as a reference: http://docs.oracle.com/cd/E23943_01/web.1111/e13760/toc.htm