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
  • so 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;
2. * mysql> CREATE TABLE IF NOT EXISTS gene SELECT * FROM biobank_search.gene;
3. 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
2. AnimalDBUpdateDatabase.java RUN
3. From Ui -> System tasks -> stem tasksFill database

TODO :

Merge tables in pheno_db model . (new table data )