What is the best way to generate sql query using java from ETL mapping document

I am trying to automate ETL mapping validation using Java. I have to validate a number of interfaces each with one mapping document which has source and target mapping.

My approach was to read source and target tables and fields information, build the query and compare the both data sets.But this approach is becoming very complex when i have to join multiple tables with different combinations.

Is there any better approach to automate this validation, please suggest?