contrapositive

MY QUESTION FOR BROOKS David Brooks on the NSA phone records story:

I think, basically, people think this is a legitimate way, if the NSA professionals want to do this, they're prepared to defer to the NSA professionals who seem to be doing it by the book within the NSA, which is a pretty good agency.

My question for Brooks: David, when you say that the NSA professionals, "seem to be doing it by the book"--which book are you talking about?

Or is "doing it by the book" just shorthand for "heeding the whims of the President"?