* JENA/D2R sparql :
   * Set paths for jena/arq and add them in path in order to run sparql from command line (JENA)
   * Make d2rq server run :
     * Prequisites :
       * Java 1.4 or newer on the path OK
       * Supported DB (mysql)
       * Download a JDBC driver from your database vendor. Place the driver's JAR file into D2R Server's /lib directory. !jdbc:mysql://servername/database for MySQL) from the driver's documentation. Drivers for MySQL and PostgreSQL are already included with D2R Server.
   * Generate a mapping and an RDF file : DONE :
     * $ ./generate-mapping.bat -d com.mysql.jdbc.Driver -u molgenis -p molgenis [jdbc:!mysql://127.0.0.1/molgenis jdbc:mysql://127.0.0.1/molgenis] > molgenis.n3
     * * $ ./dump-rdf.bat -u molgenis -p molgenis  -d com.mysql.jdbc.Driver -j !jdbc:mysql://127.0.0.1/molgenis > molgenis.rdf
   * Start the server : $ ./d2r-server.bat mapping.n3 OK
     * http://localhost:2020/ (currently not working)
       * fix paths and start server again:
         * export D2R_ROOT="D:/..../d2r/d2r-server-0.7/"
         * export PATH=$PATH:$D2R_ROOT
     * * Potential problem cause : Alter the mapping file (molgenis.n3) in order to include SERVER configuration :

 * now on command line :
   * /cygdrive/d/despoina/d2r/d2r-server-0.7 $ ./d2r-server.bat molgenis.n3
     * ERROR : molgenis.n3: Line 4, column 5: Unresolved prefixed name: rdfs:label
     * * The !rdfs:label is the server name displayed throughout the HTML interface.(see here :http://www4.wiwiss.fu-berlin.de/bizer/d2r-server/#about)
 * '''alternative TODO 1''' : '''Running D2R Server as a service on Windows http://www4.wiwiss.fu-berlin.de/bizer/d2r-server/#about'''
 * alternative TODO 2''' : [http://www4.wiwiss.fu-berlin.de/bizer/d2r-server/#container Running D2R Server in an existing Servlet Container] '''
   * '''(TODO pre: for now in order to do this we have to correct the server config inside molgenis.n3) '''
 * Peregrine new version ...download? - the version installed in Peregrine_test3 is the latest! jar files are 0.3!
 * Added web content from  Ontocat Rest service into '''molgenis distro . (locally) '''. Runs ok , but how will retrieve return results from ontocat rest service since molgenis is running, not ontocat.
 * SVN commit : Added Jena & d2r into SVN --> http://www.molgenis.org/svn/molgenis_projects/Jena
 * SVN commit :Added Peregrine test 3 into SVN --> http://www.molgenis.org/svn/molgenis_projects/PeregrineTest3 *
 * Disease Book: @umcg : source code from Mark :
   * Disease book
   * Molgenis 3_3
   * Ontologiedatabasetest
     * First create database
     * run

Actions: (project in SVN: http://www.molgenis.org/svn/molgenis_projects/molgenis_rdf_test)

 * '''copy the d2rq libs into molgenis_distr/WEB-INF/lib ..'''
   * OK do we have also to include in proporties-> java EE module depenencies?
 * '''copy line 9-134 from d2r/webapp/WEB-INF/web.xml into molgenis_distr/WebContent/WEB-INF/web.xml -->'''
   * Ok in \desp\workspace\molgenis_distro\WebContent\WEB-INF\web.xml lines 71 - 196
     * (these are comments right? otherwise have to be removed! <!-- Configuration file for running the server in a servlet container.[[BR]]       Will be ignored if the server is started from the command line. -->
 * '''change line 128 that says /index.html to /rdf.html'''
   * ok     line 193 <url-pattern>/rdf.html</url-pattern>
 * '''copy a mapping file into molgenis_distro/WebContent/WEB-INF/  OK'''
   * run generate mapping (bat or sh)--> generate mapping for addressbook
   * $ ./generate-mapping.bat -d com.mysql.jdbc.Driver -u molgenis -p molgenis jdbc:!mysql://127.0.0.1/molgenis > molgenis.n3 OK
   * weirdly does not work for addressbook ...
   * [http://www4.wiwiss.fu-berlin.de/bizer/d2r-server/#configuration We have to alter the mapping file] ()..adding in the beginning:
     * 
{{{
@prefix : <#> .
@prefix ja: <http://jena.hpl.hp.com/2005/11/Assembler#> .
@prefix d2rq: <http://www.wiwiss.fu-berlin.de/suhl/bizer/D2RQ/0.1#> .

<> ja:imports d2rq: .

:myModel
  a d2rq:D2RQModel;
  d2rq:mappingFile <mapping-iswc.n3>;
  d2rq:resourceBaseURI <http://localhost:2020/>;
  .
}}}
     * 
{{{
@prefix d2rq Is this OUR installation of D2RQ?????  ALSO : 
}}}
     * 
{{{
  d2rq:resourceBaseURI <http://localhost:2020/>; this doesn't work . will this influence the servlet??
}}}
 * '''make sure the configFile in web.xml has same name as the file'''
 * '''Morris changes @ See commit messages http://www.molgenis.org/svn/molgenis_projects/molgenis_rdf_test); ended up hacking the D2RQ java class that loads the config file.'''