This week's book giveaway is in the OO, Patterns, UML and Refactoring forum. We're giving away four copies of Refactoring for Software Design Smells: Managing Technical Debt and have Girish Suryanarayana, Ganesh Samarthyam & Tushar Sharma on-line! See this thread for details.
BufferedReader br = new BufferedReader(new FileReader(filename));
That looks like your problem right there. With only the file name, the FileReader will look in the "current" directory - something you have no control over in the servlet environment. You MUST provide a complete path.
When you tried this code you should have gotten an informative error message or had one show up in the logs.