After much research, I learned that setting the database default to InnoDB is not good practice. A great number of reasons is given, such as InnoDB is expensive. In light of all the reasonings, I concluded that clearly if making InnoDB default was best practice then it's likely the database would come configured as such. So I kept looking for a different solution.
Anyway, the solution was this:
Go to glassfish and add the following properties to the JDBC connection pool in question.
Name: SessionVariables
Value: storage_engine=InnoDB.
This works for me like a charm.
If someone has a better solution, I would really love to hear it.