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Is there any programming libraries available that will parse an HTML document, execute JavaScript and then allow me to navigate the DOM? This needs to be performed server side, not client side. Any language will do, but Java, PHP, or Ruby are preferred.
in java: http://lobobrowser.org/cobra/java-html-parser.jsp
this is a a Javascript-aware, CSS-aware HTML parser
the most important feature in relation to your question: It is Javascript-aware. DOM modifications that occur during parsing will be reflected in the resulting DOM.