Changes between Version 7 and Version 8 of DespoinaLog/2010/12/09

Timestamp:

2010-12-09T13:01:36+01:00 (14 years ago)

Author:

antonak

Comment:

--

DespoinaLog/2010/12/09

@@ +1 @@
+
 == Inconsistency with biobank table (pheno & gcc project) ==
-==  problem: ==
+== 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).
 
@@ -7 +8 @@
  * create new table biobank from pheno project as follows:
 
-  mysql> create  table biobank_new select Acronym, Category, Type, Size, !LastUpdate    , Description, id from biobank ;
+  mysql> create  table biobank_new select Acronym, Category, Type, Size, !LastUpdate     , Description, id from biobank ;
 
   (only fields that exist in biobank in gcc project)
@@ -28 +29 @@
 '''!ObservationElement''' ON (Biobank.id = !ObservationElement.id) LEFT JOIN
 
-  ''' Investigation'''  AS xref_Investigation  ON xref_Investigation.id = !ObservationElement .Investigation 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
@@ -38 +39 @@
 '''!OntologyTerm''' AS xref_Category  ON xref_Category.id = Biobank.Category WHERE !ObservationElement.!__Type = 'Biobank'
 
-== Approach 3) Fix the xls data file according to the consistencies between these entities.  ==
+== Approach 3) Fix the xls data file according to the consistencies between these entities. ==
+xls colums : 
+
+
+{{{
+Name    Type    Acronym category_term   topics_term     institutes_name contacts_lastName       size    materials_term  GWA data n =    GWA platform    GWA comments    description
+}}}