I recently had to migrate from MySQL to JavaDB for a project that our team is working on. I found a Java library written by Apache called DdlUtils that made this pretty easy. It provides an API that lets you do the following:
The tools that we ended up with weren't completely automated, but they worked pretty well. Even if your application is not in Java, it shouldn't be too difficult to whip up a few small tools to do a one-time migration. I think I was able to pull of our migration with less than 150 lines of code.