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I need to implement a rule engine either in java or in ruby (a independent project) which i have to integrate in a Java EE web-application so should I implement this in java because it will be easy to integrate or should I go with ruby on rails.
If you are trying to integrate it into a Java EE web-application then I’d definitely suggest going with a Java-based option. You want to minimise the proliferation of different application stacks as much as you can, and integration across different stacks is always painful.
I think you will also find that the Java libraries in this area (rules engines / workflow) are more mature. I’d suggest looking at Drools: It is open source and well-proven.
Alternatively, if you really want to use Ruby but still want to integrate with Java / use Java libraries like Drools then JRuby might be a good choice.