So I have a lot of .js files that I have used to query MongoDB from the Command Line Interface before, but now I want to be able to run those same queries through Java (I am
This not possible in an efficient way in current JAVA driver. Have a look here : mongodb java driver - raw command?
If you need to executye your js files during buildtime, you can use maven-mongodb-plugin. This plugin uses db.eval()...
using Java IO to read your js files, filter the queries , execute the queries.