| | 1 | == DONE : new configuration file in biobank search plugin == |
| | 2 | In order to add a configuration file and retrieve variables : |
| | 3 | |
| | 4 | * Properties configFile = new Properties(); |
| | 5 | * configFile.load(new !FileInputStream(INDEX_CONFIGURATION)); |
| | 6 | * String numberOfFields = configFile.getProperty(NUM_OF_FIELDS); |
| | 7 | * http://www.bartbusschots.ie/blog/?p=360 |
| | 8 | |
| | 9 | So all of the db field names need to be written in configuration file (LuceneIndexConfiguration.properties) as well as the number of them . |
| | 10 | |
| | 11 | == TODO ; == |
| | 12 | == explanation contains various variable infor from lucene . ask if anything is useful 1.2512041 = (MATCH) product of: == |
| | 13 | * 2.5024083 = (MATCH) sum of: |
| | 14 | * 2.5024083 = (MATCH) weight(!description:enter in 2980), product of: |
| | 15 | * 0.62739843 = queryWeight(!description:enter), product of: |
| | 16 | * 10.636126 = idf(docFreq=12, maxDocs=199003) |
| | 17 | * 0.0589875 = queryNorm |
| | 18 | * 3.988547 = (MATCH) fieldWeight(!description:enter in 2980), product of: |
| | 19 | * 1.0 = tf(termFreq(!description:enter)=1) |
| | 20 | * 10.636126 = idf(docFreq=12, maxDocs=199003) |
| | 21 | * 0.375 = fieldNorm(field=description, doc=2980) |
| | 22 | |
| | 23 | * 0.5 = coord(1/2) |
| | 24 | * the next things to todo , include * removing all of the hardcoded staff (in the a configuration file) , |
| | 25 | * debug, debug , debug (I have the sense we are getting some duplicates) |
| | 26 | * implement the option of leaving out the ontologies (- But please do add a configuration option that disables the feature in the plug-in constructor) |
| | 27 | * 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) |
| | 28 | * TEST search strings : |
| | 29 | * simple search : Knaagdieren : |
| | 30 | * #results returned : 5 |
| | 31 | * #entries in DB : 1 |
| | 32 | * s'''o the multiple results returned''' come from search function or '''are actually stored 5 times in index''' ?? check through lukeall: |
| | 33 | * === save as xml : search Knaagdieren : 5 times found in the index . --''' multiple results are actually stored 5 times in index''' ===\ |
| | 34 | |
| | 35 | == DONE : == |
| | 36 | * BUG fixed : ==> two write.document in BuildIndex..() |
| | 37 | |
| | 38 | Bug fixed : Multiple entries returned as same result. |
| | 39 | |
| | 40 | == DEMO : (try in query expansion search ) == |
| | 41 | * simple search : '''''Knaagdieren''''' |
| | 42 | * term contained among: '''''wereld''''' |
| | 43 | * term contained in multiple entries |
| | 44 | * '''''Gering''''' |
| | 45 | * '''''stoffen''''' |
| | 46 | * term contained in multiple tables : |
| | 47 | * '''''gene (description, name)''''' |
| | 48 | * '''''House''''' |
| | 49 | * After data & gene tables added : |
| | 50 | * '''''lung disease ,''''' |
| | 51 | * '''''ATP''''' |
| | 52 | |
| | 53 | == DONE : Added data & gene table and model in molgenis4phenotype : == |
| | 54 | 1. mysql> create table data select * from biobank_search.data; |
| | 55 | 1. * mysql> CREATE TABLE IF NOT EXISTS gene SELECT * FROM biobank_search.gene; |
| | 56 | 1. '''In pheno_db.xml :''' |
| | 57 | |
| | 58 | 1. * <entity name="Gene"> |
| | 59 | |
| | 60 | * <field name="id" type="autoid" /> |
| | 61 | * <field name="!GeneName" unique="true" /> |
| | 62 | * <field name="chromosomeLocation" /> |
| | 63 | * <field name="geneDescription" type="text" /> |
| | 64 | * </entity> |
| | 65 | * |
| | 66 | * <entity name="data"> |
| | 67 | * <field name="id" type="autoid" /> |
| | 68 | * <field name="name" type="string" nillable="true" /> |
| | 69 | * <field name="investigation" type="string" nillable="true" /> |
| | 70 | * <field name="inv_name" type="string" nillable="true" /> |
| | 71 | * <field name="description" type="text" nillable="true" /> |
| | 72 | * <field name="ontologyReference" type="string" nillable="true"/> |
| | 73 | * <field name="ontologyReference_ontology_name" type="string" nillable="true" /> |
| | 74 | * <field name="ontologyReference_term" type="string" nillable="true" /> |
| | 75 | * <field name="unit" type="string" nillable="true" /> |
| | 76 | * <field name="unit_ontology_name" type="string" nillable="true" /> |
| | 77 | * <field name="unit_term" type="string" nillable="true" /> |
| | 78 | * </entity> |
| | 79 | |
| | 80 | 1. AnimalDBGenerate.java RUN |
| | 81 | 1. AnimalDBUpdateDatabase.java RUN |
| | 82 | 1. From Ui -> System tasks -> '''stem tasks'''Fill database |
| | 83 | |
| | 84 | == TODO : == |
| | 85 | Merge tables in pheno_db model . (new table data ) |
