I have some experience writing web applications in Java for class projects. My first project used Servlets and my second, the Stripes framework.
However, I feel that I am missing the greater picture of Java web development. I don't really understand the web.xml and context.xml files. I'm not sure what constitutes a Java EE application as opposed to a generic Java web application. I can't figure out how a bean is different from an ordinary Java class (POJO?) and how that differs from an Enterprise Java Bean (EJB). These are just the first few questions I could think of, but there are many more.
What is a good way to learn how Java web applications function from the top down rather than simply how to develop an application with a specific framework? (Is there a book for this sort of thing?) Ultimately, I would like to understand Java web applications well enough to write my own framework.
Update: To be clear, I am not interested in learning how to use specific frameworks (for instance, Spring or Java EE). I am looking for an explanation of the internals of a generic Java web application.
I recommend Head First Servlets and JSPs by Bates and Sierra. Some don't care for the whimsical style, but it is a solid intro to Java EE. EJB's aren't covered, but one book can't do everything.
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