I have rebuilt my MySQL server system using a Pi version 2 and a new external hard drive. I did this one in a Linksys router case. These cases are really easy to work with and not hard to come by.
I skipped the USB hub on this build. There isn't enough room and I found an easier way. Power is spliced directly into a usb cable from a connector on the rear of the case. I found that this would not backfeed the Pi like I expected. (This does work on some of my older Pi systems.) To overcome this, I added a wire feeding 5V into GPIO pin #2.
The Raspberry Pi is mounted on the base of the case with the USB and network connectors facing the rear. The rear has to be trimmed a little for the connectors to be clearly accessible.
The hard drive is mounted onto the top of the case. The USB cable has to exit the case and to plug in the the Pi.
In the process of building this, I updated the instructions on how to run from an external hard drive.
This case mod makes a neat little case that stacks nicely. Here it is stacked with my cable modem and firewall. (The firewall is a Pi too!)