Changes between Version 1 and Version 2 of DespoinaLog/2010/12/09


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Timestamp:
2010-12-09T10:56:43+01:00 (14 years ago)
Author:
antonak
Comment:

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  • DespoinaLog/2010/12/09

    v1 v2  
    11== Inconsistency with biobank table (pheno & gcc project) ==
    2 == problem:  ==
    3 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).
     2== problem: ==
     3The 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).
    44
    55== Solution ==
    6 create new table biobank from pheno project as follows: 
     6create new table biobank from pheno project as follows:
     7
     8mysql> create  table biobank_new select Acronym, Category, Type, Size, !LastUpdate, Description, id from biobank ; 
     9
     10(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 mysql5 -u root -p bbmri < biobank_new.mysql