== Inconsistency with biobank table (pheno & gcc project) ==
== problem: ==
The bbmri.xml describes the table as follows :[[BR]]<entity name="Biobank" extends="Panel">[[BR]]                       <description>Describes one biobank cohort</description>[[BR]]                       <field name="Acronym" nillable="true" description="Acronym for this[[BR]]biobank" />[[BR]]                       <field name="Institutes" nillable="true" type="mref"[[BR]]xref_entity="Institute" mref_name="!BiobankInstitute"[[BR]]description="Institute that are custodian of this biobank" />[[BR]]                       <field name="Publications" type="mref" xref_entity="Publication"[[BR]]description="Publications for this biobank" />[[BR]]                       <field name="Category" type="xref" xref_entity="!OntologyTerm" />[[BR]]                       <field name="Type" type="enum" enum_options="[core,support,other]" />[[BR]]                       <field name="Contacts" type="mref" xref_entity="Contact"[[BR]]                               mref_name="!BiobankContact" description="Contact for this biobank" />[[BR]]                       <field name="Topics" type="mref" xref_entity="!OntologyTerm" />[[BR]]                       <field name="Materials" type="mref" xref_entity="!OntologyTerm" />[[BR]]                       <field name="Size" nillable="true" />[[BR]]                       <field name="!LastUpdate" type="date" auto="true" />[[BR]]                       <field name="Description" type="text" nillable="true" />[[BR]]               </entity>[[BR]][[BR]]Similarly the BBMRIupdateDatabase tries to create these fields. But[[BR]]the created table in DB is missing the fields:[[BR]][[BR]]Institutes  (mref), Publications(mref), Contacts (mref), Topics[[BR]](mref), Materials (mref).[[BR]][[BR]]Is this how was supposed to work? Because it causes a problem in mysql[[BR]]input from the previous scheme (in pheno).

== Solution ==
 * create new table biobank from pheno project as follows:

  mysql> create  table biobank_new select Acronym, Category, Type, Size, !LastUpdate   , Description, id from biobank ;

  (only fields that exist in biobank in gcc project)

 * Dump and insert new table in gcc project.
   * $ mysqldump5 -u root -p bbmri_old biobank_new > biobank_new.mysql
 * Edit  biobank_new.mysql and replace biobank_new (table) with biobank
 * 
   * mysql5 -u root -p bbmri < biobank_new.mysql

== select query retrieving records in molgenis form ==
=== We need data inside INNER/LEFT JOIN tables ===
select count(*) as num_rows  FROM Biobank  INNER JOIN

'''Panel''' ON (Biobank.id = Panel.id) INNER JOIN

'''!ObservationTarget''' ON (Biobank.id = !ObservationTarget.id) INNER JOIN

'''!ObservationElement''' ON (Biobank.id = !ObservationElement.id) LEFT JOIN

 '''Investigation''' AS xref_Investigation  ON xref_Investigation.id = !ObservationElement.Investigation LEFT JOIN 

'''!OntologyTerm''' AS xref_ontologyReference  ON xref_ontologyReference.id = !ObservationElement.ontologyReference LEFT JOIN 

'''!OntologyTerm''' AS xref_Species  ON xref_Species.id = Panel.Species LEFT JOIN 

'''!OntologyTerm''' AS xref_PanelType  ON xref_PanelType.id = Panel.!PanelType LEFT JOIN 

'''!OntologyTerm''' AS xref_Category  ON xref_Category.id = Biobank.Category WHERE !ObservationElement.!__Type = 'Biobank'