Bridging a Python back-end and JavaScript front-end
Apache is a web server, flask is a web framework in python, websockets are a protocol, and cgi is something totally different, and none of them help you on the front end.
You could deploy a simple backend in flask or django or pylons or any other python web framework. I like django, but it may be a little heavy for your purpose, flask is a bit more lightweight.  You deploy them to a server with a web server installed and use something like apache to distribute.  
Then you need a front end and a way of delivering your front end.  Flask / Django are both fully capable of doing so in conjunction with a web server, or you could use a static file server like Amazon S3.  
On your front end, you need to load D3 and probably some kind of utility like jQuery to load and parse your data from the back end, then use D3 however you like to present it on screen.
I'm currently working on a project that involves parsing through a user-supplied file, doing computations with that data, and visualizing the results using graphing utilities. Right now, I'm stuck with using Python as the back-end because it has scientific libraries unavailable in JavaScript, but I want to move the entire tool to a web server, where I can do much slicker visualizations using D3.js.
The workflow would be something like: obtain the file contents from the browser, execute the Python script with the contents, return jsonified objects of computed values, and plot those objects using D3. I already have the back-end and front-end working by themselves, but want to know: How can I go about bridging the two? From what I've gathered, I need to do something along the lines of launching a server, sending AJAX requests to the server, and retrieving data from the server. But with the number of frameworks out there (Flask, cgi, apache, websockets, etc.), I'm not really sure where to start. This will likely only be a very simple web app with just a file submit page and a data visualization page. Any help is appreciated!