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BPEL Mapper does add proper prefixes to generated XPath expressions, if the prefix for the namespace they are using is not declared in the BPEL document. Once you declare the prefix, it will be generated correctly. I'm attaching a sample project -- just do some mapping for the only Assign out there.
Created attachment 57883 [details] Sample project
Possibly related: issue 126037.
Assigning to Nikita for evaluation
Now the XPath model is responsible for generating prefixes. It's necessary to specify an ExNamespaceContext instead of simple NamespaceContext See the XPathModel.setNamespaceContext() interface for details
Verified with NetBeans IDE 6.1 RC1 (Build 200804100130).