• 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 : ​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.
      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 ...
  • ​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.