JorisLog/2010/12/07: impuwise_db.xml

<molgenis name="impuwise" label="LifeLines Molgenis/Wise integration - Proof of Concept">

        <module name="system">
                <description> This package describes basic classes that are used as building
                        blocks for the model.</description>
                
                <entity name="DBObject" abstract="true">
                        <description>Essential abstract class containing the primary key</description>
                        <field name="object_id" type="hexa" unique="true" nillable="false"
                                description="Unique identifier (hexadecimal)" />
                </entity>
                <entity name="DataObject" implements="DBObject" abstract="false">
                        <description>The entity File provides the basic fields for file classes</description>
                        <field name="globalname" nillable="true" type="varchar" readonly="false"
                                description="The name used to store and retrieve file to and from Storage" />
                        <field name="filename" nillable="true" type="varchar" readonly="false" unique="true"
                                description="The name of the associated file " />
                </entity>
        </module>
        
        <module name="data">
                                
                <entity name="ReferenceData" extends="DataObject" abstract="false">
                        <description>Reference data set in Plink/hapmap format (not Beagle format!)</description>
                        <field name="creationdate" type="datetime"/>
                        <field name="name" type="varchar" unique="true"/>
                        <field name="type" type="varchar" />
                        <field name="chromosome" type="varchar" />      <!-- ??? -->
                </entity>
                
                <entity name="OriginalData" extends="DataObject">
                        <description>Original non-imputed data</description>
                        <field name="ingestdate" type="datetime"/>
                        <field name="name" type="varchar" unique="true"/>
                        <field name="version" type="varchar" />
                        <field name="genotypemethod" type="varchar" />
                        <field name="nrchromosomes" type="int" />
                </entity>
                
                <entity name="SplittedOrigData" extends="DataObject">
                        <description>Splitted original non-imputed data</description>
                        <field name="creationdate" type="datetime"/>
                        <field name="name" type="varchar" unique="true"/>
                        <field name="OriginalData" type="xref" xref_entity="OriginalData" 
                                xref_label="name" readonly="true" description="Original data source"/>
                        <field name="ReferenceData" type="xref" xref_entity="ReferenceData" 
                                xref_label="name" readonly="true" description="Reference data set"/>
                        <field name="chromosome" type="int" />
                        <field name="batch" type="int" />
                        <field name="steps" type="mref" xref_entity="ExecutableStep" 
                                xref_label="name" readonly="true" description="Executable steps"/>
                </entity>
                
                <entity name="SplittedOrigDataParameters" implements="DBObject">
                        <description>Parameters for splitting data into batches</description>
                        <field name="batchsize" type="int" default="300"/>
                </entity>
                
                <entity name="SplittedImputedData" extends="DataObject" abstract="false">
                        <description>Imputed splitted data</description>
                        <field name="creationdate" type="datetime"/>
                        <field name="name" type="varchar" unique="true"/>
                        <field name="SplittedOrigData" type="xref" xref_entity="SplittedOrigData" 
                                xref_label="name" readonly="true" description="Original data source"/>
                        <field name="ReferenceData" type="xref" xref_entity="ReferenceData" 
                                xref_label="name" readonly="true" description="Reference data set"/>
                        <field name="chromosome" type="varchar" />
                        <field name="batch" type="varchar" />
                </entity>
                                                
                <entity name="ImputedBeagleData" extends="SplittedImputedData">
                        <description>Imputed data from Beagle (splitted)</description>
                        <field name="versionBeagle" type="varchar" />
                        <field name="paramsBeagle" type="xref" xref_entity="BeagleParameters" 
                                readonly="true" description="Process Parameters for Beagle"/>
                        <field name="steps" type="mref" xref_entity="ExecutableStep" 
                                xref_label="name" readonly="true" description="Executable steps"/>
                </entity>
                <entity name="ImputedImputeData" extends="SplittedImputedData">
                        <description>Imputed data from Impute (splitted)</description>
                        <field name="versionImpute" type="varchar" />
                        <field name="paramsImpute" type="xref" xref_entity="ImputeParameters" 
                                readonly="true" description="Process Parameters for Impute"/>
                        <field name="steps" type="mref" xref_entity="ExecutableStep" 
                                xref_label="name" readonly="true" description="Executable steps"/>
                </entity>
                
                <entity name="ExecutableStep" extends="DataObject">
                        <description>Step to generate an executable script (this is a hack)</description>
                        <field name="name" type="varchar" />
                        <field name="version" type="varchar" />
                        <field name="ordernr" type="int"/>
                        <unique fields="name,version" />
                </entity>
                
                <entity name="CombinedImputedData" extends="DataObject">
                        <description>Combined imputed data</description>
                        <field name="creationdate" type="datetime"/>
                        <field name="SplittedImputedData" type="xref" xref_entity="SplittedImputedData" 
                                xref_label="name" readonly="true" description="Imputed splitted data"/>
                        <field name="name" type="varchar" />
                        <field name="version" type="varchar" />
                        <field name="steps" type="mref" xref_entity="ExecutableStep" 
                                xref_label="name" readonly="true" description="Executable steps"/>
                </entity>
        
                <entity name="BeagleParameters" implements="DBObject">
                        <description>Parameters for Beagle</description>
                        <field name="missing" type="decimal" default="0"/>
                </entity>
                <entity name="ImputeParameters" implements="DBObject">
                        <description>Parameters for Impute</description>
                </entity>
        
        </module>

</molgenis>