== DONE : new configuration file in biobank search plugin ==
In order to add a configuration file and retrieve variables :

 * Properties configFile = new Properties();
 * configFile.load(new !FileInputStream(INDEX_CONFIGURATION));
 * String numberOfFields = configFile.getProperty(NUM_OF_FIELDS);
 * http://www.bartbusschots.ie/blog/?p=360

So all of the db field names need to be written in configuration file (LuceneIndexConfiguration.properties) as well as the number of them .

== TODO ; ==
== explanation contains various variable infor from lucene . ask if anything is useful 1.2512041 = (MATCH) product of: ==
 * 2.5024083 = (MATCH) sum of:
   * 2.5024083 = (MATCH) weight(!description:enter in 2980), product of:
     * 0.62739843 = queryWeight(!description:enter), product of:
       * 10.636126 = idf(docFreq=12, maxDocs=199003)
       * 0.0589875 = queryNorm
     * 3.988547 = (MATCH) fieldWeight(!description:enter in 2980), product of:
       * 1.0 = tf(termFreq(!description:enter)=1)
       * 10.636126 = idf(docFreq=12, maxDocs=199003)
       * 0.375 = fieldNorm(field=description, doc=2980)

 * 0.5 = coord(1/2)
 * the next things to todo , include    * removing all of the hardcoded staff (in the a configuration file) ,
   * debug, debug , debug (I have the sense we are getting some duplicates)
   * implement the option of leaving out the ontologies (- But please do add a configuration option that disables the feature in the plug-in constructor)
   * complete a manual (this is partly done) - ( And complete your 'search' plugin with a little manual that explains what you need to do to get it running)
 * TEST search strings :
   * simple search : Knaagdieren :
   * #results returned : 5
   * #entries in DB : 1
   * s'''o the multiple results returned''' come from search function or '''are  actually stored 5 times in index''' ?? check through lukeall:
     * === save as xml : search Knaagdieren : 5 times found in the index . --''' multiple results are actually stored 5 times in index''' ===\

== DONE : ==
 * BUG fixed : ==> two write.document in BuildIndex..()

Bug fixed : Multiple entries returned as same result.

== DEMO : (try in query expansion search ) ==
 * simple search : '''''Knaagdieren'''''
 * term contained among:  '''''wereld'''''
 * term contained in multiple entries
   * '''''Gering'''''
   * '''''stoffen'''''
 * term contained in multiple tables :
   * '''''gene (description, name)'''''
   * '''''House'''''
 * After data & gene tables added :
   * '''''lung disease ,'''''
   * '''''ATP'''''

== DONE : Added data & gene  table and model in molgenis4phenotype : ==
 1. mysql> create table data select * from biobank_search.data;
 1. * mysql> CREATE TABLE IF NOT EXISTS gene  SELECT * FROM biobank_search.gene;
 1. '''In pheno_db.xml :'''

 1. * <entity name="Gene">

 * <field name="id" type="autoid" />
 * <field name="!GeneName" unique="true" />
 * <field name="chromosomeLocation" />
 * <field name="geneDescription" type="text" />
 * </entity>
 * 
   * <entity name="data">
     * <field name="id" type="autoid" />
     * <field name="name" type="string" nillable="true" />
     * <field name="investigation" type="string" nillable="true" />
     * <field name="inv_name" type="string" nillable="true" />
     * <field name="description" type="text" nillable="true" />
     * <field name="ontologyReference" type="string" nillable="true"/>
     * <field name="ontologyReference_ontology_name" type="string" nillable="true" />
     * <field name="ontologyReference_term" type="string" nillable="true" />
     * <field name="unit" type="string" nillable="true" />
     * <field name="unit_ontology_name" type="string" nillable="true" />
     * <field name="unit_term" type="string" nillable="true" />
   * </entity>

 1. AnimalDBGenerate.java RUN
 1. AnimalDBUpdateDatabase.java RUN
 1. From Ui -> System tasks -> '''stem tasks'''Fill database

==  TODO :  ==
Merge  tables in pheno_db model . (new table data )