I really don't want to write code to create the Lucene indexes nor the mysql tables in metadataindex, and ontologyindexrelation. Fortunately, it looks like their might be code to do so in indexingService.jar :
To create the tables in database metadataindex (start with MetadataIndexManager):
And finish with indexManagerLucene.class for Lucene Indexes:
To create ontologyindextable in ontologyindexrelation database:
Thanks to phpmyadmin for the database query and jd-gui (http://jd.benow.ca/) for the Java decompiler to view the code.