TODO:

 * sent email to pheno group about the conflict of the entities : Institute & contact
   * This problem will be solved if the bbmri model is merged in the pheno model.
 * update the ontocat jar in local & svn version (DONE)
   * commit to svn (DONE)
 * ontologies directory changed: this is included in the project , so update the configuration file.
 * update from svn . Eric has added the manuals inside the doc directory .
 * merge the pheno model with the contents of teh bbmri model.  delete the bbmri model and use only pheno model . (this is the solution to the 500 error -- or just add the module auth in the bbmri model . )
 * The problem with the D2RQ server is a compatibility of the .n3 file and the database . The database that is used has a different scheme (pheno database ) with the one that is described in the model file)  .
   * '''Model conflict problem that should be solved : '''
     * The pheno data model contains the auth module
     * The  bbmri does not contain the auth module .
     * the bbmri_generate does not run without the module inside . More specifically I receive an error :
       * java.io.!FileNotFoundException: /Users/despoina/Documents/molgenis4phenotypeWorkspace_helios_cocoa32/molgenis4phenotype_latest1/auth_db.xml (No such file or directory)
     * if the module is added the Exception in thread "main" java.lang.!IllegalArgumentException: elements already exists with name = 'MolgenisUserGroup' is shown.
 * SVN conflict :
   * When committing the whole project : a lot of files seems to need to be committed , especially from the metadata folder. But in the comparison with the previous version this problem does not seem to appear . The only differences are in the classpath , the project and the current changes file.
 * Sent an email to the [mailto:Beheer-raetonline@umcg.nl] about the online system file that admins the paycheck . *
 * Null exception in creation of (db) index. (DONE)
   * Some field was null
     * When retrieved from DB the table contact contains :
       * id,
       * !FirstName,
       * !MidInitials, !LastName,
       * '''Affiliation, ,<---- this is strange. Is not contained in the DB , where does it come from ?? '''
       * Address,
       * Phone, Email, Fax, tollFreePhone, labworker, xref_Affiliation.name AS Affiliation_name FROM Contact  LEFT JOIN Institute AS xref_Affiliation  ON xref_Affiliation.id....
   * Affiliation exists in model? but not in db ! update database .
     * database now empty
     * upload xls ..ok
     * rebuild index.
 * Search in the db index was not working for the field name 
   * name is not included in the model or the database, but data are here!
     * this creepy feature is because this column was created by the XLS IMPORT!

DONE:

 * added <entity name="Biobank" extends="Panel"> in pheno_db.xml
 * bbmri_db.xml is empty
 * bbmri.molgenis.properties: removed the auth_db.xml
 * molgenis.properties does not exist.
 * created Semantic search plugin example configuration file.
 * The Ontocat index is build correctly  :
   * search working.