I need to do a migration from Oracle to MySQL. The problem is that I have tables in several oracle schemas and my applications are coded like this:

SELECT * FROM SCHEMA1.TABLEA join SCHEMA2.TABLEB

How should I handle the migration? Should I create a mysql database for each of my oracle schema? How does this effect the java code?

Thanks.

This is one posibility... If you want you can just find and replace the schema... But this is a small problem... If you have dates on you select you'll have to convert them. You might have some problem converting numbers as well (unless all your numbers transfered into a single type in mysql).
Good luck

Should I create a mysql database for each of my oracle schema? - This is first option.

The second option is change your data model but i think you want not this.