So I'm have some sqlPlus processes that are being called through a java app, but I need to push up the original files prior to processing. Is there an easy method to ftp'ing up files to oracle through java or should I just write a bat file process and call that instead?

Give us more informations do you mean triggers - procedures or what?
You may write code as stored procedures or triggers in the oracle db and call them from java or use jdbc
triggers
tutorial.

In oracle I have stored procedures that take a file and load it into a table and then compares the new table vs a production table. The differences between the tables get pushed into the prod table. My java front-end app is currently calling the oracle stored procedures, but I need a quick and easy method to take the original files off a client machine and ftp them up to the oracle database.

What is the easiest method of ftp'ing up the content files to oracle? Is there an easy java or oracle method of ftp'ing?

It seems to me that you want a java method that
1. load each "row" from file
2.Call a stored procedure that return true (for example) if elements exist at db or false if do not and
3.If false load to prod. table the elements.
Maybe there are other ideas too.