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I am having problems evaluating a script.js file which is dependent of prototype.js. When i am trying to evaluate the script.js file through rhino script engine in java i got Script Exception like "TypeError: $H is not a function, it is java.lang.String.". How do I evaluate the files and how to include prototype.js and to define the prototype objects?

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You cannot evaluate prototype.js using Rhino only. prototype.js have many references to the HTML DOM which is not implemented in Rhino/Java. For example (from prototype.js): document.createTextNode('') The document global object is not defined in Rhino context and createTextNode is not defined too.

The solution is to remove all Objects/Functions from your copy of prototype.js that references the document, window or navigator objects. (assuming your js file does not use them)

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You could also get away with declaring some dummy objects for document, window, navigator and so on. This way you do not have to change prototype.js.
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have you evaluated them in the correct order? They need to be evaluated from the bottom up

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Take a look at env-js, which is a mock browser environment for Rhino. It's based on some work by John Resig to get JQuery working in Rhino. I wouldn't be surprised if Prototype worked as well.

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