| | 1 | * JENA/D2R sparql : |
| | 2 | * Set paths for jena/arq and add them in path in order to run sparql from command line (JENA) |
| | 3 | * Make d2rq server run : |
| | 4 | * Prequisites : |
| | 5 | * Java 1.4 or newer on the path OK |
| | 6 | * Supported DB (mysql) |
| | 7 | * 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. |
| | 8 | * Generate a mapping and an RDF file : DONE : |
| | 9 | * $ ./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 |
| | 10 | * * $ ./dump-rdf.bat -u molgenis -p molgenis -d com.mysql.jdbc.Driver -j !jdbc:mysql://127.0.0.1/molgenis > molgenis.rdf |
| | 11 | * Start the server : $ ./d2r-server.bat mapping.n3 OK |
| | 12 | * http://localhost:2020/ (currently not working) |
| | 13 | * fix paths and start server again: |
| | 14 | * export D2R_ROOT="D:/..../d2r/d2r-server-0.7/" |
| | 15 | * export PATH=$PATH:$D2R_ROOT |
| | 16 | * * Potential problem cause : Alter the mapping file (molgenis.n3) in order to include SERVER configuration : |
| | 17 | |
| | 18 | * now on command line : |
| | 19 | * /cygdrive/d/despoina/d2r/d2r-server-0.7 $ ./d2r-server.bat molgenis.n3 |
| | 20 | * ERROR : molgenis.n3: Line 4, column 5: Unresolved prefixed name: rdfs:label |
| | 21 | * * The !rdfs:label is the server name displayed throughout the HTML interface.(see here :http://www4.wiwiss.fu-berlin.de/bizer/d2r-server/#about) |
| | 22 | * '''alternative TODO 1''' : '''Running D2R Server as a service on Windows http://www4.wiwiss.fu-berlin.de/bizer/d2r-server/#about''' |
| | 23 | * alternative TODO 2''' : [http://www4.wiwiss.fu-berlin.de/bizer/d2r-server/#container Running D2R Server in an existing Servlet Container] ''' |
| | 24 | * '''(TODO pre: for now in order to do this we have to correct the server config inside molgenis.n3) ''' |
| | 25 | * Peregrine new version ...download? - the version installed in Peregrine_test3 is the latest! jar files are 0.3! |
| | 26 | * 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. |
| | 27 | * SVN commit : Added Jena & d2r into SVN --> http://www.molgenis.org/svn/molgenis_projects/Jena |
| | 28 | * SVN commit :Added Peregrine test 3 into SVN --> http://www.molgenis.org/svn/molgenis_projects/PeregrineTest3 * |
| | 29 | * Disease Book: @umcg : source code from Mark : |
| | 30 | * Disease book |
| | 31 | * Molgenis 3_3 |
| | 32 | * Ontologiedatabasetest |
| | 33 | * First create database |
| | 34 | * run |
| | 35 | |
| | 36 | Actions: (project in SVN: http://www.molgenis.org/svn/molgenis_projects/molgenis_rdf_test) |
| | 37 | |
| | 38 | * '''copy the d2rq libs into molgenis_distr/WEB-INF/lib ..''' |
| | 39 | * OK do we have also to include in proporties-> java EE module depenencies? |
| | 40 | * '''copy line 9-134 from d2r/webapp/WEB-INF/web.xml into molgenis_distr/WebContent/WEB-INF/web.xml -->''' |
| | 41 | * Ok in \desp\workspace\molgenis_distro\WebContent\WEB-INF\web.xml lines 71 - 196 |
| | 42 | * (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. --> |
| | 43 | * '''change line 128 that says /index.html to /rdf.html''' |
| | 44 | * ok line 193 <url-pattern>/rdf.html</url-pattern> |
| | 45 | * '''copy a mapping file into molgenis_distro/WebContent/WEB-INF/ OK''' |
| | 46 | * run generate mapping (bat or sh)--> generate mapping for addressbook |
| | 47 | * $ ./generate-mapping.bat -d com.mysql.jdbc.Driver -u molgenis -p molgenis jdbc:!mysql://127.0.0.1/molgenis > molgenis.n3 OK |
| | 48 | * weirdly does not work for addressbook ... |
| | 49 | * [http://www4.wiwiss.fu-berlin.de/bizer/d2r-server/#configuration We have to alter the mapping file] ()..adding in the beginning: |
| | 50 | * |
| | 51 | {{{ |
| | 52 | @prefix : <#> . |
| | 53 | @prefix ja: <http://jena.hpl.hp.com/2005/11/Assembler#> . |
| | 54 | @prefix d2rq: <http://www.wiwiss.fu-berlin.de/suhl/bizer/D2RQ/0.1#> . |
| | 55 | |
| | 56 | <> ja:imports d2rq: . |
| | 57 | |
| | 58 | :myModel |
| | 59 | a d2rq:D2RQModel; |
| | 60 | d2rq:mappingFile <mapping-iswc.n3>; |
| | 61 | d2rq:resourceBaseURI <http://localhost:2020/>; |
| | 62 | . |
| | 63 | }}} |
| | 64 | * |
| | 65 | {{{ |
| | 66 | @prefix d2rq Is this OUR installation of D2RQ????? ALSO : |
| | 67 | }}} |
| | 68 | * |
| | 69 | {{{ |
| | 70 | d2rq:resourceBaseURI <http://localhost:2020/>; this doesn't work . will this influence the servlet?? |
| | 71 | }}} |
| | 72 | * '''make sure the configFile in web.xml has same name as the file''' |
| | 73 | * '''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.''' |
