Create a createLuceneIndex.sh file that works:

./indexListInformation/indexkmiweb07-mysql

index_properties.xml:

<?xml version="1.0" encoding="UTF-8"?>
<CONFIGURATION>
<INDEX>
<INDEX_DIRECTORY>indexkmiweb07mysql/index_dir/</INDEX_DIRECTORY>
<SPELL_INDEX_DIRECTORY>indexkmiweb07mysql/spell_index_dir/</SPELL_INDEX_DIRECTORY>
<METADATA_INDEX_DB>jdbc:mysql://localhost:3306/metadataindex</METADATA_INDEX_DB>
<METADATA_INDEX_DB_LOGIN>root</METADATA_INDEX_DB_LOGIN>
<METADATA_INDEX_DB_PASSWORD />
<METADATA_INDEX_TABLE>indexkmiweb07mysql</METADATA_INDEX_TABLE>
</INDEX></CONFIGURATION>

service_properties.xml

<?xml version="1.0" encoding="UTF-8"?>^M
<CONFIGURATION>^M
<PLUGIN_MANAGER>/Applications/apache-tomcat-5.5.23/webapps/powerAqua/WEB-INF/aquaplugins</PLUGIN_MANAGER>
^M
<REPOSITORY>
        <SERVER>http://kmi-web03.open.ac.uk:8080/sesame</SERVER>
        <PROXY>wwwcache.open.ac.uk</PROXY>
        <PORT>80</PORT>
        <LOGIN></LOGIN>
        <PASSWORD></PASSWORD>
        <PLUGIN_TYPE>sesame</PLUGIN_TYPE>
        <REPOSITORY_NAME>upm_lia</REPOSITORY_NAME>
        <TYPE>RDF</TYPE>
</REPOSITORY>
<REPOSITORY>
        <SERVER>http://kmi-web03.open.ac.uk:8080/sesame</SERVER>
        <PROXY>wwwcache.open.ac.uk</PROXY>
        <PORT>80</PORT>
        <LOGIN></LOGIN>
        <PASSWORD></PASSWORD>
        <PLUGIN_TYPE>sesame</PLUGIN_TYPE>
        <REPOSITORY_NAME>semanticconferences</REPOSITORY_NAME>
        <TYPE>RDF</TYPE>
</REPOSITORY>^M
</CONFIGURATION>^M

./indexListInformation/indexkmiweb07-linkeddata

index_properties.xml

<?xml version="1.0" encoding="UTF-8"?>
<CONFIGURATION>
<INDEX>
<INDEX_DIRECTORY>indexkmiweb07linkedata/index_dir/</INDEX_DIRECTORY>
<SPELL_INDEX_DIRECTORY>indexkmiweb07linkedata/spell_index_dir/</SPELL_INDEX_DIRECTORY>
<METADATA_INDEX_DB>jdbc:mysql://localhost:3306/metadataindex</METADATA_INDEX_DB>
<METADATA_INDEX_DB_LOGIN>root</METADATA_INDEX_DB_LOGIN>
<METADATA_INDEX_DB_PASSWORD />
<METADATA_INDEX_TABLE>indexkmiweb07linkedata</METADATA_INDEX_TABLE>
</INDEX></CONFIGURATION>


service_properties.xml

<?xml version="1.0" encoding="UTF-8"?>^M
<CONFIGURATION>^M
<PLUGIN_MANAGER>/Applications/apache-tomcat-5.5.23/webapps/powerAqua/WEB-INF/aquaplugins</PLUGIN_MANAGER> ^M
<REPOSITORY>^M
        <SERVER>http://kmi-web03.open.ac.uk:8080/sesame</SERVER>^M
        <PROXY>wwwcache.open.ac.uk</PROXY>^M
        <PORT>80</PORT>^M
        <LOGIN></LOGIN>^M
        <PASSWORD></PASSWORD>^M
        <PLUGIN_TYPE>sesame</PLUGIN_TYPE>^M
        <REPOSITORY_NAME>travel_destinations</REPOSITORY_NAME>^M
        <TYPE>OWL</TYPE>^M
</REPOSITORY>
<REPOSITORY>^M
        <SERVER>http://kmi-web03.open.ac.uk:8080/sesame</SERVER>^M
        <PROXY>wwwcache.open.ac.uk</PROXY>^M
        <PORT>80</PORT>^M
        <LOGIN></LOGIN>^M
        <PASSWORD></PASSWORD>^M
        <PLUGIN_TYPE>sesame</PLUGIN_TYPE>^M
        <REPOSITORY_NAME>mid_level_ontology</REPOSITORY_NAME>^M
        <TYPE>OWL</TYPE>^M
</REPOSITORY>^M
<REPOSITORY>^M
        <SERVER>http://kmi-web03.open.ac.uk:8080/sesame</SERVER>^M
        <PROXY>wwwcache.open.ac.uk</PROXY>^M
        <PORT>80</PORT>^M
        <LOGIN></LOGIN>^M
        <PASSWORD></PASSWORD>^M
        <PLUGIN_TYPE>sesame</PLUGIN_TYPE>^M
        <REPOSITORY_NAME>census</REPOSITORY_NAME>^M
        <TYPE>RDF</TYPE>^M
</REPOSITORY>^M
</CONFIGURATION>

Delete databases created from PowerAqua backup:

This is how they were created?
http://stackoverflow.com/questions/17666249/how-to-import-an-sql-file-using-the-command-line-in-mysql

mysql -u username -p database_name < file.sql

This is how they are dropped?
DROP DATABASE

https://www.cyberciti.biz/faq/how-do-i-empty-mysql-database/

mysql -u root -p (at the CLI) DROP DATABASE metadataindex;  (Can't drop database 'metadataindex'; database doesn't exist) DROP DATABASE ontologyindexrelation; (Query OK, 1 row affected (0.07 sec))