wiki:bbmri_subtask3

Start d2r on molgenis n3 mapping on molgenis4phenotype :

  • In local installation d2r-server -p 2020 molgenis.n3
  • there are some problems about :
    • de.fuberlin.wiwiss.d2rq.D2RQException: Column @@digital_identity.digital_identity_id@@ not found in database (E0)
    • Exception in thread "main" java.lang.NullPointerException?
      • at de.fuberlin.wiwiss.d2rs.JettyLauncher .start(JettyLauncher.java:68 )
      • at d2r.server.startServer(server.java:86 )
      • at d2r.server.main(server.java:57 )
    • The problem above is a inconsistency of the model that lives in the directory where d2r server is run and the database schema.
      • Solved by steps:
        1. generate in molgenis .
        2. update database
        3. run
        4. copy generated .n3 file in d2r running directory

TODO :

  • Next steps : check which DB it makes use . This digital identity seems to be in a really old DB .(DONE)
  • after taking NULL EXCEPTION off the command line run of D2R..(DONE - see steps above)
  • check the SPARQL interface if is running om localhost/8080 http://localhost:2020/snorql/ (DONE check at http://localhost:2020/snorql/)

DONE :

23 d2rq:jdbcDSN "jdbc:mysql://127.0.0.1/addressbook "; this is actually used . So copy another molgenis n3 mapping from a valid database. The schemes seems to be incompatible .

Start d2r on molgenis n3 mapping on molgenisGCC project :

$$$ mv molgenis-rdf-mapping.n3 molgenis-rdf-mapping_gcc.n3

$$$ d2r-server molgenis-rdf-mapping_gcc.n3
  • Fix missing classes: (despoina)
    • * de.fuberlin.wiwiss.d2rq.D2RQException: Object for d2rq:refersToClassMap not found at d2rq:PropertyBridge map:Biobank_materials (E21) *
Last modified 13 years ago Last modified on 2010-12-07T14:01:51+01:00