caruby-tissue 1.2.2 → 1.2.3

data/conf/annotation/pathology_scg/RadicalProstatectomyMargin.hbm.xml

@@ -0,0 +1,20 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE hibernate-mapping PUBLIC "-//Hibernate/Hibernate Mapping DTD 3.0//EN" "http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd">
+
+<hibernate-mapping package="pathology_scg">
+  <class name="RadicalProstatectomyMargin" table="DE_E_1680" lazy="true" polymorphism="explicit">
+    <cache usage="read-write" />
+    <id name="id" type="java.lang.Long" column="IDENTIFIER">
+      <generator class="assigned" />
+    </id>
+    <property name="FocalityOfInvolvedMargin" type="java.lang.String" column="DE_AT_1683" />
+    <property name="MarginStatus" type="java.lang.String" column="DE_AT_1684" />
+    <set name="ProstateMarginLocation" lazy="true" inverse="true">
+      <cache usage="read-write" />
+      <key column="DE_E_1680_1682_IDENTIFIER" />
+      <one-to-many class="pathology_scg.ProstateMarginLocation" />
+    </set>
+    <many-to-one name="radicalProstatectomyPathologyAnnotation" class="pathology_scg.RadicalProstatectomyPathologyAnnotation" column="DE_E_1676_1679_IDENTIFIER" unique="true" lazy="proxy" />
+  </class>
+</hibernate-mapping>
+

data/conf/annotation/pathology_scg/RegionalLymphNode.hbm.xml

@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE hibernate-mapping PUBLIC "-//Hibernate/Hibernate Mapping DTD 3.0//EN" "http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd">
+
+<hibernate-mapping package="pathology_scg">
+  <class name="RegionalLymphNode" table="DE_E_1489" lazy="true" polymorphism="explicit">
+    <cache usage="read-write" />
+    <id name="id" type="java.lang.Long" column="IDENTIFIER">
+      <generator class="assigned" />
+    </id>
+    <property name="MattedNodes" type="java.lang.String" column="DE_AT_1491" />
+    <property name="NumberPositiveMicroscopically" type="java.lang.Long" column="DE_AT_1492" />
+    <property name="NumberPositiveMacroscopically" type="java.lang.Long" column="DE_AT_1493" />
+    <property name="NumberInvolved" type="java.lang.Long" column="DE_AT_1494" />
+    <property name="NumberExamined" type="java.lang.Long" column="DE_AT_1495" />
+    <property name="LymphNodeStage" type="java.lang.String" column="DE_AT_1496" />
+    <many-to-one name="pathologicStaging" class="pathology_scg.PathologicalStaging" column="DE_E_1484_1488_IDENTIFIER" unique="true" lazy="proxy" />
+  </class>
+</hibernate-mapping>
+

data/conf/annotation/pathology_scg/SatelliteNodule.hbm.xml

@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE hibernate-mapping PUBLIC "-//Hibernate/Hibernate Mapping DTD 3.0//EN" "http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd">
+
+<hibernate-mapping package="pathology_scg">
+  <class name="SatelliteNodule" table="DE_E_1605" lazy="true" polymorphism="explicit">
+    <cache usage="read-write" />
+    <id name="id" type="java.lang.Long" column="IDENTIFIER">
+      <generator class="assigned" />
+    </id>
+    <property name="Site" type="java.lang.String" column="DE_AT_1607" />
+    <many-to-one name="MelanomaPathologyAnnotation" class="pathology_scg.MelanomaPathologyAnnotation" column="DE_E_1735_1746_IDENTIFIER" lazy="proxy" />
+  </class>
+</hibernate-mapping>
+

data/conf/annotation/pathology_scg/SpecimenCollectionGroup.hbm.xml

@@ -0,0 +1,87 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE hibernate-mapping PUBLIC "-//Hibernate/Hibernate Mapping DTD 3.0//EN" "http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd">
+
+<hibernate-mapping package="pathology_scg">
+  <class name="SpecimenCollectionGroup" table="CATISSUE_SPECIMEN_COLL_GROUP" lazy="true" polymorphism="explicit">
+    <cache usage="read-write" />
+    <id name="id" type="java.lang.Long" column="IDENTIFIER">
+      <generator class="assigned" />
+    </id>
+    <set name="ExcisionalBiopsyBasedColorectalPathologyAnnotationCollection" lazy="true" inverse="true">
+      <cache usage="read-write" />
+      <key column="DYEXTN_AS_379_1631" />
+      <one-to-many class="pathology_scg.ExcisionalBiopsyBasedColorectalPathologyAnnotation" />
+    </set>
+    <set name="LungResectionBasedPathologyAnnotationCollection" lazy="true" inverse="true">
+      <cache usage="read-write" />
+      <key column="DYEXTN_AS_379_1518" />
+      <one-to-many class="pathology_scg.LungResectionBasedPathologyAnnotation" />
+    </set>
+    <set name="KidneyBiopsyBasedPathologyAnnotationCollection" lazy="true" inverse="true">
+      <cache usage="read-write" />
+      <key column="DYEXTN_AS_379_1539" />
+      <one-to-many class="pathology_scg.KidneyBiopsyBasedPathologyAnnotation" />
+    </set>
+    <set name="LocalExcisionBasedColorectalPathologyAnnotationCollection" lazy="true" inverse="true">
+      <cache usage="read-write" />
+      <key column="DYEXTN_AS_379_1788" />
+      <one-to-many class="pathology_scg.LocalExcisionBasedColorectalPathologyAnnotation" />
+    </set>
+    <set name="LungBiopsyPathologyAnnotationCollection" lazy="true" inverse="true">
+      <cache usage="read-write" />
+      <key column="DYEXTN_AS_379_1559" />
+      <one-to-many class="pathology_scg.LungBiopsyPathologyAnnotation" />
+    </set>
+    <set name="RetropubicEnucleationPathologyAnnotationCollection" lazy="true" inverse="true">
+      <cache usage="read-write" />
+      <key column="DYEXTN_AS_379_1794" />
+      <one-to-many class="pathology_scg.RetropubicEnucleationPathologyAnnotation" />
+    </set>
+    <set name="BreastPathologyAnnotationCollection" lazy="true" inverse="true">
+      <cache usage="read-write" />
+      <key column="DYEXTN_AS_379_1754" />
+      <one-to-many class="pathology_scg.BreastPathologyAnnotation" />
+    </set>
+    <set name="MelanomaPathologyAnnotationCollection" lazy="true" inverse="true">
+      <cache usage="read-write" />
+      <key column="DYEXTN_AS_379_1735" />
+      <one-to-many class="pathology_scg.MelanomaPathologyAnnotation" />
+    </set>
+    <set name="ResectionBasedColorectalPathologyAnnotationCollection" lazy="true" inverse="true">
+      <cache usage="read-write" />
+      <key column="DYEXTN_AS_379_1715" />
+      <one-to-many class="pathology_scg.ResectionBasedColorectalPathologyAnnotation" />
+    </set>
+    <set name="NeedleBiopsyProstatePathologyAnnotationCollection" lazy="true" inverse="true">
+      <cache usage="read-write" />
+      <key column="DYEXTN_AS_379_1652" />
+      <one-to-many class="pathology_scg.NeedleBiopsyProstatePathologyAnnotation" />
+    </set>
+    <set name="RadicalProstatectomyPathologyAnnotationCollection" lazy="true" inverse="true">
+      <cache usage="read-write" />
+      <key column="DYEXTN_AS_379_1676" />
+      <one-to-many class="pathology_scg.RadicalProstatectomyPathologyAnnotation" />
+    </set>
+    <set name="TransurethralProstaticResectionPathologyAnnotationCollection" lazy="true" inverse="true">
+      <cache usage="read-write" />
+      <key column="DYEXTN_AS_379_1625" />
+      <one-to-many class="pathology_scg.TransurethralProstaticResectionPathologyAnnotation" />
+    </set>
+    <set name="KidneyNephrectomyBasedPathologyAnnotationCollection" lazy="true" inverse="true">
+      <cache usage="read-write" />
+      <key column="DYEXTN_AS_379_1797" />
+      <one-to-many class="pathology_scg.KidneyNephrectomyBasedPathologyAnnotation" />
+    </set>
+    <set name="CNSPathologyAnnotationCollection" lazy="true" inverse="true">
+      <cache usage="read-write" />
+      <key column="DYEXTN_AS_379_1773" />
+      <one-to-many class="pathology_scg.CNSPathologyAnnotation" />
+    </set>
+    <set name="PancreasPathologyAnnotationCollection" lazy="true" inverse="true">
+      <cache usage="read-write" />
+      <key column="DYEXTN_AS_379_1705" />
+      <one-to-many class="pathology_scg.PancreasPathologyAnnotation" />
+    </set>
+  </class>
+</hibernate-mapping>
+

data/conf/annotation/pathology_scg/SpecimenIntegrity.hbm.xml

@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE hibernate-mapping PUBLIC "-//Hibernate/Hibernate Mapping DTD 3.0//EN" "http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd">
+
+<hibernate-mapping package="pathology_scg">
+  <class name="SpecimenIntegrity" table="DE_E_1541" lazy="true" polymorphism="explicit">
+    <cache usage="read-write" />
+    <id name="id" type="java.lang.Long" column="IDENTIFIER">
+      <generator class="assigned" />
+    </id>
+    <property name="NumberOfPieces" type="java.lang.Long" column="DE_AT_1543" />
+    <property name="Type" type="java.lang.String" column="DE_AT_1544" />
+    <many-to-one name="LocalExcisionBasedColorectalPathologyAnnotation" class="pathology_scg.LocalExcisionBasedColorectalPathologyAnnotation" column="DE_E_1788_1790_IDENTIFIER" unique="true" lazy="proxy" />
+  </class>
+</hibernate-mapping>
+

data/conf/annotation/pathology_scg/SpecimenSize.hbm.xml

@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE hibernate-mapping PUBLIC "-//Hibernate/Hibernate Mapping DTD 3.0//EN" "http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd">
+
+<hibernate-mapping package="pathology_scg">
+  <class name="SpecimenSize" table="DE_E_1828" lazy="true" polymorphism="explicit">
+    <cache usage="read-write" />
+    <id name="id" type="java.lang.Long" column="IDENTIFIER">
+      <generator class="assigned" />
+    </id>
+    <property name="CannotBeDetermined" type="java.lang.Boolean" column="DE_AT_1830" />
+    <property name="AdditionalDimensionTwo" type="java.lang.Double" column="DE_AT_1831" />
+    <property name="AdditionalDimensionOne" type="java.lang.Double" column="DE_AT_1832" />
+    <property name="GreatestDimension" type="java.lang.Double" column="DE_AT_1833" />
+    <many-to-one name="CNSPathologyAnnotation" class="pathology_scg.CNSPathologyAnnotation" column="DE_E_1773_1827_IDENTIFIER" unique="true" lazy="proxy" />
+  </class>
+</hibernate-mapping>
+

data/conf/annotation/pathology_scg/TissueSide.hbm.xml

@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE hibernate-mapping PUBLIC "-//Hibernate/Hibernate Mapping DTD 3.0//EN" "http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd">
+
+<hibernate-mapping package="pathology_scg">
+  <class name="TissueSide" table="DE_E_1513" lazy="true" polymorphism="explicit">
+    <cache usage="read-write" />
+    <id name="id" type="java.lang.Long" column="IDENTIFIER">
+      <generator class="assigned" />
+    </id>
+    <property name="Side" type="java.lang.String" column="DE_AT_1515" />
+    <many-to-one name="TumorTissueSite" class="pathology_scg.TumorTissueSite" column="DE_E_1508_1510_IDENTIFIER" lazy="proxy" />
+  </class>
+</hibernate-mapping>
+

data/conf/annotation/pathology_scg/TumorSize.hbm.xml

@@ -0,0 +1,29 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE hibernate-mapping PUBLIC "-//Hibernate/Hibernate Mapping DTD 3.0//EN" "http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd">
+
+<hibernate-mapping package="pathology_scg">
+  <class name="TumorSize" table="DE_E_1473" lazy="true" polymorphism="explicit">
+    <cache usage="read-write" />
+    <id name="id" type="java.lang.Long" column="IDENTIFIER">
+      <generator class="assigned" />
+    </id>
+    <property name="GreatestDimension" type="java.lang.Double" column="DE_AT_1475" />
+    <property name="AdditionalDimensionTwo" type="java.lang.Double" column="DE_AT_1476" />
+    <property name="AdditionalDimensionOne" type="java.lang.Double" column="DE_AT_1477" />
+    <property name="CannotBeDetermined" type="java.lang.Boolean" column="DE_AT_1478" />
+    <many-to-one name="baseSolidTissuePathologyAnnotation" class="pathology_scg.BaseSolidTissuePathologyAnnotation" column="DE_E_1461_1466_IDENTIFIER" unique="true" lazy="proxy" />
+    <joined-subclass name="pathology_scg.SizeOfInvasiveCarcinoma" table="DE_E_1836" lazy="true">
+      <key column="IDENTIFIER" />
+      <many-to-one name="BreastPathologyAnnotation" class="pathology_scg.BreastPathologyAnnotation" column="DE_E_1754_1835_IDENTIFIER" unique="true" lazy="proxy" />
+    </joined-subclass>
+    <joined-subclass name="pathology_scg.SizeOfSpecimen" table="DE_E_1838" lazy="true">
+      <key column="IDENTIFIER" />
+      <many-to-one name="BreastPathologyAnnotation" class="pathology_scg.BreastPathologyAnnotation" column="DE_E_1754_1834_IDENTIFIER" unique="true" lazy="proxy" />
+    </joined-subclass>
+    <joined-subclass name="pathology_scg.PolypSize" table="DE_E_1841" lazy="true">
+      <key column="IDENTIFIER" />
+      <many-to-one name="ColorectalPathologyAnnotation" class="pathology_scg.ColorectalPathologyAnnotation" column="DE_E_1593_1840_IDENTIFIER" unique="true" lazy="proxy" />
+    </joined-subclass>
+  </class>
+</hibernate-mapping>
+

data/conf/annotation/pathology_scg/TumorTissueSite.hbm.xml

@@ -0,0 +1,20 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE hibernate-mapping PUBLIC "-//Hibernate/Hibernate Mapping DTD 3.0//EN" "http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd">
+
+<hibernate-mapping package="pathology_scg">
+  <class name="TumorTissueSite" table="DE_E_1508" lazy="true" polymorphism="explicit">
+    <cache usage="read-write" />
+    <id name="id" type="java.lang.Long" column="IDENTIFIER">
+      <generator class="assigned" />
+    </id>
+    <property name="OtherSite" type="java.lang.String" column="DE_AT_1511" />
+    <property name="Site" type="java.lang.String" column="DE_AT_1512" />
+    <set name="TissueSide" lazy="true" inverse="true">
+      <cache usage="read-write" />
+      <key column="DE_E_1508_1510_IDENTIFIER" />
+      <one-to-many class="pathology_scg.TissueSide" />
+    </set>
+    <many-to-one name="baseSolidTissuePathologyAnnotation" class="pathology_scg.BaseSolidTissuePathologyAnnotation" column="DE_E_1461_1463_IDENTIFIER" lazy="proxy" />
+  </class>
+</hibernate-mapping>
+

data/conf/annotation/pathology_scg/UninvolvedMelanomaMargin.hbm.xml

@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE hibernate-mapping PUBLIC "-//Hibernate/Hibernate Mapping DTD 3.0//EN" "http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd">
+
+<hibernate-mapping package="pathology_scg">
+  <class name="UninvolvedMelanomaMargin" table="DE_E_1556" lazy="true" polymorphism="explicit">
+    <cache usage="read-write" />
+    <id name="id" type="java.lang.Long" column="IDENTIFIER">
+      <generator class="assigned" />
+    </id>
+    <property name="closestDistanceToTumor" type="java.lang.Double" column="DE_AT_1558" />
+    <many-to-one name="DeepMelanomaMargin" class="pathology_scg.DeepMelanomaMargin" column="DE_E_1600_1602_IDENTIFIER" unique="true" lazy="proxy" />
+    <many-to-one name="LateralMelanomaMargin" class="pathology_scg.LateralMelanomaMargin" column="DE_E_1749_1751_IDENTIFIER" unique="true" lazy="proxy" />
+  </class>
+</hibernate-mapping>
+

data/conf/annotation/pathology_specimen/AdditionalFinding.hbm.xml

@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE hibernate-mapping PUBLIC "-//Hibernate/Hibernate Mapping DTD 3.0//EN" "http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd">
+
+<hibernate-mapping package="pathology_specimen">
+  <class name="AdditionalFinding" table="DE_E_1400" lazy="true" polymorphism="explicit">
+    <cache usage="read-write" />
+    <id name="id" type="java.lang.Long" column="IDENTIFIER">
+      <generator class="assigned" />
+    </id>
+    <property name="PathologicFinding" type="java.lang.String" column="DE_AT_1403" />
+    <many-to-one name="SpecimenBaseSolidTissuePathologyAnnotation" class="pathology_specimen.SpecimenBaseSolidTissuePathologyAnnotation" column="DE_E_1325_1399_IDENTIFIER" lazy="proxy" />
+    <set name="Details" lazy="true" inverse="true">
+      <cache usage="read-write" />
+      <key column="DE_E_1400_1402_IDENTIFIER" />
+      <one-to-many class="pathology_specimen.Details" />
+    </set>
+  </class>
+</hibernate-mapping>
+

data/conf/annotation/pathology_specimen/AdditionalPathologicFinding.hbm.xml

@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE hibernate-mapping PUBLIC "-//Hibernate/Hibernate Mapping DTD 3.0//EN" "http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd">
+
+<hibernate-mapping package="pathology_specimen">
+  <class name="AdditionalPathologicFinding" table="DE_E_1318" lazy="true" polymorphism="explicit">
+    <cache usage="read-write" />
+    <id name="id" type="java.lang.Long" column="IDENTIFIER">
+      <generator class="assigned" />
+    </id>
+    <property name="pathologicFinding" type="java.lang.String" column="DE_AT_1321" />
+    <set name="detailsCollection" lazy="true" inverse="true">
+      <cache usage="read-write" />
+      <key column="DE_E_1318_1320_IDENTIFIER" />
+      <one-to-many class="pathology_specimen.Details" />
+    </set>
+  </class>
+</hibernate-mapping>
+

data/conf/annotation/pathology_specimen/Details.hbm.xml

@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE hibernate-mapping PUBLIC "-//Hibernate/Hibernate Mapping DTD 3.0//EN" "http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd">
+
+<hibernate-mapping package="pathology_specimen">
+  <class name="Details" table="DE_E_1322" lazy="true" polymorphism="explicit">
+    <cache usage="read-write" />
+    <id name="id" type="java.lang.Long" column="IDENTIFIER">
+      <generator class="assigned" />
+    </id>
+    <property name="detail" type="java.lang.String" column="DE_AT_1324" />
+    <many-to-one name="additionalPathologicFinding" class="pathology_specimen.AdditionalPathologicFinding" column="DE_E_1318_1320_IDENTIFIER" lazy="proxy" />
+    <many-to-one name="AdditionalFinding" class="pathology_specimen.AdditionalFinding" column="DE_E_1400_1402_IDENTIFIER" lazy="proxy" />
+  </class>
+</hibernate-mapping>
+

data/conf/annotation/pathology_specimen/GleasonScore.hbm.xml

@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE hibernate-mapping PUBLIC "-//Hibernate/Hibernate Mapping DTD 3.0//EN" "http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd">
+
+<hibernate-mapping package="pathology_specimen">
+  <class name="GleasonScore" table="DE_E_1381" lazy="true" polymorphism="explicit">
+    <cache usage="read-write" />
+    <id name="id" type="java.lang.Long" column="IDENTIFIER">
+      <generator class="assigned" />
+    </id>
+    <property name="tertiaryPatternScore" type="java.lang.Integer" column="DE_AT_1383" />
+    <property name="secondaryPatternScore" type="java.lang.Integer" column="DE_AT_1384" />
+    <property name="primaryPatternScore" type="java.lang.Integer" column="DE_AT_1385" />
+  
+  </class>
+</hibernate-mapping>
+

data/conf/annotation/pathology_specimen/HistologicGrade.hbm.xml

@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE hibernate-mapping PUBLIC "-//Hibernate/Hibernate Mapping DTD 3.0//EN" "http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd">
+
+<hibernate-mapping package="pathology_specimen">
+  <class name="HistologicGrade" table="DE_E_1344" lazy="true" polymorphism="explicit">
+    <cache usage="read-write" />
+    <id name="id" type="java.lang.Long" column="IDENTIFIER">
+      <generator class="assigned" />
+    </id>
+    <property name="Grade" type="java.lang.String" column="DE_AT_1346" />
+    <property name="OtherGradingSystemName" type="java.lang.String" column="DE_AT_1347" />
+    <property name="GradingSystemName" type="java.lang.String" column="DE_AT_1348" />
+    <many-to-one name="specimenBaseSolidTissuePathologyAnnotation" class="pathology_specimen.SpecimenBaseSolidTissuePathologyAnnotation" column="DE_E_1325_1328_IDENTIFIER" lazy="proxy" />
+  </class>
+</hibernate-mapping>
+

data/conf/annotation/pathology_specimen/HistologicType.hbm.xml

@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE hibernate-mapping PUBLIC "-//Hibernate/Hibernate Mapping DTD 3.0//EN" "http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd">
+
+<hibernate-mapping package="pathology_specimen">
+  <class name="HistologicType" table="DE_E_1332" lazy="true" polymorphism="explicit">
+    <cache usage="read-write" />
+    <id name="id" type="java.lang.Long" column="IDENTIFIER">
+      <generator class="assigned" />
+    </id>
+    <property name="Type" type="java.lang.String" column="DE_AT_1335" />
+    <set name="HistologicVariantType" lazy="true" inverse="true">
+      <cache usage="read-write" />
+      <key column="DE_E_1332_1334_IDENTIFIER" />
+      <one-to-many class="pathology_specimen.HistologicVariantType" />
+    </set>
+    <many-to-one name="SpecimenBaseSolidTissuePathologyAnnotation" class="pathology_specimen.SpecimenBaseSolidTissuePathologyAnnotation" column="DE_E_1325_1330_IDENTIFIER" lazy="proxy" />
+  </class>
+</hibernate-mapping>
+

data/conf/annotation/pathology_specimen/HistologicVariantType.hbm.xml

@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE hibernate-mapping PUBLIC "-//Hibernate/Hibernate Mapping DTD 3.0//EN" "http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd">
+
+<hibernate-mapping package="pathology_specimen">
+  <class name="HistologicVariantType" table="DE_E_1336" lazy="true" polymorphism="explicit">
+    <cache usage="read-write" />
+    <id name="id" type="java.lang.Long" column="IDENTIFIER">
+      <generator class="assigned" />
+    </id>
+    <property name="OtherHistologicType" type="java.lang.String" column="DE_AT_1338" />
+    <many-to-one name="HistologicType" class="pathology_specimen.HistologicType" column="DE_E_1332_1334_IDENTIFIER" lazy="proxy" />
+  </class>
+</hibernate-mapping>
+

data/conf/annotation/pathology_specimen/Invasion.hbm.xml

@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE hibernate-mapping PUBLIC "-//Hibernate/Hibernate Mapping DTD 3.0//EN" "http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd">
+
+<hibernate-mapping package="pathology_specimen">
+  <class name="Invasion" table="DE_E_1339" lazy="true" polymorphism="explicit">
+    <cache usage="read-write" />
+    <id name="id" type="java.lang.Long" column="IDENTIFIER">
+      <generator class="assigned" />
+    </id>
+    <property name="PerineuralInvasion" type="java.lang.String" column="DE_AT_1341" />
+    <property name="VenousInvasion" type="java.lang.String" column="DE_AT_1342" />
+    <property name="LymphaticInvasion" type="java.lang.String" column="DE_AT_1343" />
+    <many-to-one name="specimenBaseSolidTissuePathologyAnnotation" class="pathology_specimen.SpecimenBaseSolidTissuePathologyAnnotation" column="DE_E_1325_1329_IDENTIFIER" unique="true" lazy="proxy" />
+  </class>
+</hibernate-mapping>
+

data/conf/annotation/pathology_specimen/NottinghamHistologicScore.hbm.xml

@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE hibernate-mapping PUBLIC "-//Hibernate/Hibernate Mapping DTD 3.0//EN" "http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd">
+
+<hibernate-mapping package="pathology_specimen">
+  <class name="NottinghamHistologicScore" table="DE_E_1369" lazy="true" polymorphism="explicit">
+    <cache usage="read-write" />
+    <id name="id" type="java.lang.Long" column="IDENTIFIER">
+      <generator class="assigned" />
+    </id>
+    <property name="totalNottinghamScore" type="java.lang.Integer" column="DE_AT_1371" />
+    <property name="mitoticCountScore" type="java.lang.Integer" column="DE_AT_1372" />
+    <property name="nuclearPleomorphismScore" type="java.lang.Integer" column="DE_AT_1373" />
+    <property name="tubuleFormationScore" type="java.lang.Integer" column="DE_AT_1374" />
+   
+  </class>
+</hibernate-mapping>
+

data/conf/annotation/pathology_specimen/Specimen.hbm.xml

@@ -0,0 +1,52 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE hibernate-mapping PUBLIC "-//Hibernate/Hibernate Mapping DTD 3.0//EN" "http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd">
+
+<hibernate-mapping package="pathology_specimen">
+  <class name="Specimen" table="CATISSUE_SPECIMEN" lazy="true" polymorphism="explicit">
+    <cache usage="read-write" />
+    <id name="id" type="java.lang.Long" column="IDENTIFIER">
+      <generator class="assigned" />
+    </id>
+    <set name="ProstateSpecimenPathologyAnnotationCollection" lazy="true" inverse="true">
+      <cache usage="read-write" />
+      <key column="DYEXTN_AS_4_1377" />
+      <one-to-many class="pathology_specimen.ProstateSpecimenPathologyAnnotation" />
+    </set>
+    <set name="MelanomaSpecimenPathologyAnnotationCollection" lazy="true" inverse="true">
+      <cache usage="read-write" />
+      <key column="DYEXTN_AS_4_1349" />
+      <one-to-many class="pathology_specimen.MelanomaSpecimenPathologyAnnotation" />
+    </set>
+    <set name="KidneySpecimenPathologyAnnotationCollection" lazy="true" inverse="true">
+      <cache usage="read-write" />
+      <key column="DYEXTN_AS_4_1357" />
+      <one-to-many class="pathology_specimen.KidneySpecimenPathologyAnnotation" />
+    </set>
+    <set name="LungSpecimenPathologyAnnotationCollection" lazy="true" inverse="true">
+      <cache usage="read-write" />
+      <key column="DYEXTN_AS_4_1386" />
+      <one-to-many class="pathology_specimen.LungSpecimenPathologyAnnotation" />
+    </set>
+    <set name="PancreasSpecimenPathologyAnnotationCollection" lazy="true" inverse="true">
+      <cache usage="read-write" />
+      <key column="DYEXTN_AS_4_1375" />
+      <one-to-many class="pathology_specimen.PancreasSpecimenPathologyAnnotation" />
+    </set>
+    <set name="CNSSpecimenPathologyAnnotationCollection" lazy="true" inverse="true">
+      <cache usage="read-write" />
+      <key column="DYEXTN_AS_4_1363" />
+      <one-to-many class="pathology_specimen.CNSSpecimenPathologyAnnotation" />
+    </set>
+    <set name="BreastSpecimenPathologyAnnotationCollection" lazy="true" inverse="true">
+      <cache usage="read-write" />
+      <key column="DYEXTN_AS_4_1365" />
+      <one-to-many class="pathology_specimen.BreastSpecimenPathologyAnnotation" />
+    </set>
+    <set name="ColorectalSpecimenPathologyAnnotationCollection" lazy="true" inverse="true">
+      <cache usage="read-write" />
+      <key column="DYEXTN_AS_4_1359" />
+      <one-to-many class="pathology_specimen.ColorectalSpecimenPathologyAnnotation" />
+    </set>
+  </class>
+</hibernate-mapping>
+

data/conf/annotation/pathology_specimen/SpecimenBaseSolidTissuePathologyAnnotation.hbm.xml

@@ -0,0 +1,73 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE hibernate-mapping PUBLIC "-//Hibernate/Hibernate Mapping DTD 3.0//EN" "http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd">
+
+<hibernate-mapping package="pathology_specimen">
+  <class name="SpecimenBaseSolidTissuePathologyAnnotation" table="DE_E_1325" lazy="true" polymorphism="explicit">
+    <cache usage="read-write" />
+    <id name="id" type="java.lang.Long" column="IDENTIFIER">
+      <generator class="assigned" />
+    </id>
+    <property name="Comments" type="java.lang.String" column="DE_AT_1331" />
+    <set name="AdditionalFinding" lazy="true" inverse="true">
+      <cache usage="read-write" />
+      <key column="DE_E_1325_1399_IDENTIFIER" />
+      <one-to-many class="pathology_specimen.AdditionalFinding" />
+    </set>
+    <set name="HistologicType" lazy="true" inverse="true">
+      <cache usage="read-write" />
+      <key column="DE_E_1325_1330_IDENTIFIER" />
+      <one-to-many class="pathology_specimen.HistologicType" />
+    </set>
+    <one-to-one name="invasion" class="pathology_specimen.Invasion" property-ref="specimenBaseSolidTissuePathologyAnnotation" />
+    <set name="histologicGrade" lazy="true" inverse="true">
+      <cache usage="read-write" />
+      <key column="DE_E_1325_1328_IDENTIFIER" />
+      <one-to-many class="pathology_specimen.HistologicGrade" />
+    </set>
+    <joined-subclass name="pathology_specimen.BreastSpecimenPathologyAnnotation" table="DE_E_1365" lazy="true">
+      <key column="IDENTIFIER" />
+      <property name="MitoticCountIfOtherGradingSystemUsed" type="java.lang.Long" column="DE_AT_1368" />
+      <many-to-one name="Specimen" class="pathology_specimen.Specimen" column="DYEXTN_AS_4_1365" lazy="proxy" />
+      <one-to-one name="nottinghamHistologicScore" class="pathology_specimen.NottinghamHistologicScore" />
+    </joined-subclass>
+    <joined-subclass name="pathology_specimen.CNSSpecimenPathologyAnnotation" table="DE_E_1363" lazy="true">
+      <key column="IDENTIFIER" />
+      <many-to-one name="Specimen" class="pathology_specimen.Specimen" column="DYEXTN_AS_4_1363" lazy="proxy" />
+    </joined-subclass>
+    <joined-subclass name="pathology_specimen.ColorectalSpecimenPathologyAnnotation" table="DE_E_1359" lazy="true">
+      <key column="IDENTIFIER" />
+      <property name="IntratumoralPeritumoralLymphocyticResponse" type="java.lang.String" column="DE_AT_1361" />
+      <property name="TumorBorderConfiguration" type="java.lang.String" column="DE_AT_1362" />
+      <many-to-one name="Specimen" class="pathology_specimen.Specimen" column="DYEXTN_AS_4_1359" lazy="proxy" />
+    </joined-subclass>
+    <joined-subclass name="pathology_specimen.KidneySpecimenPathologyAnnotation" table="DE_E_1357" lazy="true">
+      <key column="IDENTIFIER" />
+      <many-to-one name="Specimen" class="pathology_specimen.Specimen" column="DYEXTN_AS_4_1357" lazy="proxy" />
+    </joined-subclass>
+    <joined-subclass name="pathology_specimen.MelanomaSpecimenPathologyAnnotation" table="DE_E_1349" lazy="true">
+      <key column="IDENTIFIER" />
+      <property name="MitoticIndex" type="java.lang.String" column="DE_AT_1351" />
+      <property name="TumorRegression" type="java.lang.String" column="DE_AT_1352" />
+      <property name="TumorInfiltratingLymphocytes" type="java.lang.String" column="DE_AT_1353" />
+      <property name="DepthOfInvasionCannotBeDetermined" type="java.lang.Boolean" column="DE_AT_1354" />
+      <property name="DepthOfInvasion" type="java.lang.Double" column="DE_AT_1355" />
+      <property name="Ulceration" type="java.lang.String" column="DE_AT_1356" />
+      <many-to-one name="Specimen" class="pathology_specimen.Specimen" column="DYEXTN_AS_4_1349" lazy="proxy" />
+    </joined-subclass>
+    <joined-subclass name="pathology_specimen.PancreasSpecimenPathologyAnnotation" table="DE_E_1375" lazy="true">
+      <key column="IDENTIFIER" />
+      <many-to-one name="Specimen" class="pathology_specimen.Specimen" column="DYEXTN_AS_4_1375" lazy="proxy" />
+    </joined-subclass>
+    <joined-subclass name="pathology_specimen.ProstateSpecimenPathologyAnnotation" table="DE_E_1377" lazy="true">
+      <key column="IDENTIFIER" />
+      <property name="ProportionOrPercentOfProstaticTissueInvolvedByTumor" type="java.lang.Double" column="DE_AT_1380" />
+      <many-to-one name="Specimen" class="pathology_specimen.Specimen" column="DYEXTN_AS_4_1377" lazy="proxy" />
+      <one-to-one name="gleasonScore" class="pathology_specimen.GleasonScore" />
+    </joined-subclass>
+    <joined-subclass name="pathology_specimen.LungSpecimenPathologyAnnotation" table="DE_E_1386" lazy="true">
+      <key column="IDENTIFIER" />
+      <many-to-one name="Specimen" class="pathology_specimen.Specimen" column="DYEXTN_AS_4_1386" lazy="proxy" />
+    </joined-subclass>
+  </class>
+</hibernate-mapping>
+

data/examples/galena/lib/galena/cli/seed.rb

@@ -1,26 +1,5 @@
 #!/usr/bin/env jruby
 #
-# == Synopsis
-#
-# catissue-seed-galena.rb: seeds the Galena example administrative objects in the database
-#
-# == Usage
-#
-# catissue-seed-galena.rb [options] file
-#
-# --help, -h:
-# print this help message and exit
-#
-# --log file, -l file:
-# log file (default ./log/migration.log)
-#
-# --debug, -d:
-# print debug messages to log (optional)
-#
-# == License
-#
-# This program is licensed under the terms of the +LEGAL+ file in
-# the source distribution.
 
 # load the required gems
 require 'rubygems'

data/examples/galena/lib/galena/migration/frozen_shims.rb

@@ -14,26 +14,27 @@ module CaTissue
       self.specimen_type = 'Frozen Tissue'
     end
   end
-
+  
   class StorageContainer
     # Creates the migrated box in the database, if necessary.
     #
     # @param (see CaRuby::Migratable#migrate)
     def migrate(row, migrated)
       super
-      find or create_box
+      find or create_galena_box
     end
     
     private
-    
+
     # Creates a new box of type {Galena::Seed::Defaults#box_type} in a freezer of type
     # {Galena::Seed::Defaults#freezer_type}.
     # 
     # @return [StorageContainer] the new box
-    def create_box
+    def create_galena_box
       defs = Galena::Seed.defaults
       self.storage_type = defs.box_type
-      # A freezer with a spot for the box
+      site = defs.tissue_bank
+      # A freezer with a slot for the box.
       frz = defs.freezer_type.find_available(site, :create)
       if frz.nil? then raise CaRuby::MigrationError.new("Freezer not available to place #{self}") end
       # Add this box to the first open slot in the first unfilled rack in the freezer.