1 | <molgenis name="impuwise" label="LifeLines Molgenis/Wise integration - Proof of Concept">
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2 |
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3 | <module name="system">
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4 | <description> This package describes basic classes that are used as building
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5 | blocks for the model.</description>
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6 |
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7 | <entity name="DBObject" abstract="true">
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8 | <description>Essential abstract class containing the primary key</description>
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9 | <field name="object_id" type="hexa" unique="true" nillable="false"
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10 | description="Unique identifier (hexadecimal)" />
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11 | </entity>
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12 | <entity name="DataObject" implements="DBObject" abstract="false">
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13 | <description>The entity File provides the basic fields for file classes</description>
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14 | <field name="globalname" nillable="true" type="varchar" readonly="false"
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15 | description="The name used to store and retrieve file to and from Storage" />
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16 | <field name="filename" nillable="true" type="varchar" readonly="false" unique="true"
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17 | description="The name of the associated file " />
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18 | </entity>
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19 | </module>
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20 |
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21 | <module name="data">
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22 |
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23 | <entity name="ReferenceData" extends="DataObject" abstract="false">
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24 | <description>Reference data set in Plink/hapmap format (not Beagle format!)</description>
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25 | <field name="creationdate" type="datetime"/>
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26 | <field name="name" type="varchar" unique="true"/>
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27 | <field name="type" type="varchar" />
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28 | <field name="chromosome" type="varchar" /> <!-- ??? -->
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29 | </entity>
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30 |
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31 | <entity name="OriginalData" extends="DataObject">
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32 | <description>Original non-imputed data</description>
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33 | <field name="ingestdate" type="datetime"/>
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34 | <field name="name" type="varchar" unique="true"/>
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35 | <field name="version" type="varchar" />
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36 | <field name="genotypemethod" type="varchar" />
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37 | <field name="nrchromosomes" type="int" />
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38 | </entity>
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39 |
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40 | <entity name="SplittedOrigData" extends="DataObject">
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41 | <description>Splitted original non-imputed data</description>
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42 | <field name="creationdate" type="datetime"/>
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43 | <field name="name" type="varchar" unique="true"/>
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44 | <field name="OriginalData" type="xref" xref_entity="OriginalData"
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45 | xref_label="name" readonly="true" description="Original data source"/>
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46 | <field name="ReferenceData" type="xref" xref_entity="ReferenceData"
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47 | xref_label="name" readonly="true" description="Reference data set"/>
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48 | <field name="chromosome" type="int" />
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49 | <field name="batch" type="int" />
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50 | <field name="steps" type="mref" xref_entity="ExecutableStep"
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51 | xref_label="name" readonly="true" description="Executable steps"/>
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52 | </entity>
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53 |
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54 | <entity name="SplittedOrigDataParameters" implements="DBObject">
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55 | <description>Parameters for splitting data into batches</description>
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56 | <field name="batchsize" type="int" default="300"/>
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57 | </entity>
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58 |
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59 | <entity name="SplittedImputedData" extends="DataObject" abstract="false">
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60 | <description>Imputed splitted data</description>
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61 | <field name="creationdate" type="datetime"/>
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62 | <field name="name" type="varchar" unique="true"/>
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63 | <field name="SplittedOrigData" type="xref" xref_entity="SplittedOrigData"
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64 | xref_label="name" readonly="true" description="Original data source"/>
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65 | <field name="ReferenceData" type="xref" xref_entity="ReferenceData"
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66 | xref_label="name" readonly="true" description="Reference data set"/>
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67 | <field name="chromosome" type="varchar" />
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68 | <field name="batch" type="varchar" />
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69 | </entity>
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70 |
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71 | <entity name="ImputedBeagleData" extends="SplittedImputedData">
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72 | <description>Imputed data from Beagle (splitted)</description>
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73 | <field name="versionBeagle" type="varchar" />
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74 | <field name="paramsBeagle" type="xref" xref_entity="BeagleParameters"
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75 | readonly="true" description="Process Parameters for Beagle"/>
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76 | <field name="steps" type="mref" xref_entity="ExecutableStep"
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77 | xref_label="name" readonly="true" description="Executable steps"/>
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78 | </entity>
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79 | <entity name="ImputedImputeData" extends="SplittedImputedData">
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80 | <description>Imputed data from Impute (splitted)</description>
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81 | <field name="versionImpute" type="varchar" />
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82 | <field name="paramsImpute" type="xref" xref_entity="ImputeParameters"
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83 | readonly="true" description="Process Parameters for Impute"/>
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84 | <field name="steps" type="mref" xref_entity="ExecutableStep"
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85 | xref_label="name" readonly="true" description="Executable steps"/>
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86 | </entity>
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87 |
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88 | <entity name="ExecutableStep" extends="DataObject">
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89 | <description>Step to generate an executable script (this is a hack)</description>
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90 | <field name="name" type="varchar" />
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91 | <field name="version" type="varchar" />
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92 | <field name="ordernr" type="int"/>
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93 | <unique fields="name,version" />
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94 | </entity>
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95 |
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96 | <entity name="CombinedImputedData" extends="DataObject">
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97 | <description>Combined imputed data</description>
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98 | <field name="creationdate" type="datetime"/>
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99 | <field name="SplittedImputedData" type="xref" xref_entity="SplittedImputedData"
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100 | xref_label="name" readonly="true" description="Imputed splitted data"/>
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101 | <field name="name" type="varchar" />
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102 | <field name="version" type="varchar" />
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103 | <field name="steps" type="mref" xref_entity="ExecutableStep"
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104 | xref_label="name" readonly="true" description="Executable steps"/>
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105 | </entity>
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106 |
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107 | <entity name="BeagleParameters" implements="DBObject">
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108 | <description>Parameters for Beagle</description>
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109 | <field name="missing" type="decimal" default="0"/>
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110 | </entity>
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111 | <entity name="ImputeParameters" implements="DBObject">
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112 | <description>Parameters for Impute</description>
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113 | </entity>
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114 |
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115 | </module>
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116 |
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117 | </molgenis> |
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