I recently had the pleasure of reading through the book Java EE and HTML5 Enterprise Application Development by John Brock, Arun Gupta and Geertjan Wielenga.
First, a comment on file formats. I use Linux at home. I had the most trouble trying to get setup to actually read the book. The format used is only compatible with Adobe Digital Editions, which only works on Mac and Windows. I ended up getting a VM to do the reading on. Little bit of a pain if you're like me and use a tablet for a decent amount of reading.
The book takes the approach of wanting to build HTML5 applications, leveraging the Java server side as an API type server, with both REST APIs and WebSockets in use, and a front end based on Knockout and low level jQuery to process API calls. The backend is using your stereotypical Java EE stack of JPA, EJB and JAX-RS, plus WebSocket support. The way used in this book serves as an entry point for someone new to a lot of the technology and how to use them; it doesn't focus on changes over time in these specs or some of the new features. It's a bottom up approach for being able to expose your database over an API.
Probably the most confusing part of the book, and it may be because of different authors, is the crossing of example types. In the JPA and JAX-RS chapters, we use a book and author example. In the WebSocket chapter the authors use a board and tic tac toe example. I believe the consistent use of a fluid example is the best thing to do in a technical book. A good example of that is Continuous Enterprise Development by Andrew Lee Rubinger and Aslak Knutsen.
The chapter on application security is probably the best of the book, in my opinion. It goes through what you need to do not just server side but also client side to secure your web applications. For those new to this programming paradigm, it's some good information on some of the key differences versus traditional server side rendered web applications (JSF, Struts, etc).
The content of the book is brought about in an introductory manner. If you're new to these technologies, it's a good read to get up to speed on how they work. The JPA spec has only changed a little bit in 2.0 and 2.1, so if you're already familiar with how things worked previously, it's not a huge change. JAX-RS is a newer spec, in its 2.0 release already and shows how declarative it can be. Hidden in the REST chapter you'll find some interesting pieces on CDI, Transactions and Bean Validation. These other technologies really help build the bridge across all of the technology.