caruby-tissue 1.2.2 → 1.2.3

data/History.txt

@@ -6,3 +6,7 @@
 
 * Enable Galena example
 
+=== 1.2.3 / 2011-02-18
+
+* Support Dynamic Extensions
+

data/bin/crtdump

@@ -16,16 +16,24 @@ end
 DEF_LOG_FILE = 'log/catissue.log'
 
 require 'catissue/cli/command'
+      
+SPECS = [
+  [:class, "class", "The class of the object"],
+  [:id, "id", "The database identifier of the object"]
+]
 
+# Broken. TODO - fix.
 # run the command
-CaTissue::Command.new(:class, :id).execute do |opts, class_name, id|
+CaTissue::CLI::Command.new(SPECS).start do |opts|
+  class_name = opts[:class]
+  identifier = opts[:id].to_i
   # the search template
-  obj = CaTissue.const_get(class_name).new(:identifier=>id.to_i)
+  obj = CaTissue.const_get(class_name).new(:identifier=>identifier)
   unless obj.find then
     print("#{class_name} with identifier #{id} not found") and exit(-1)
   end
   # fetch the references
   obj.references
   # print the object graph
-  puts obj.dump
+  puts obj.database.lazy_loader.suspend { obj.dump }
 end

data/conf/annotation/pathology_scg/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_scg">
+  <class name="AdditionalFinding" table="DE_E_1454" 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_1457" />
+    <set name="Details" lazy="true" inverse="true">
+      <cache usage="read-write" />
+      <key column="DE_E_1454_1456_IDENTIFIER" />
+      <one-to-many class="pathology_scg.Details" />
+    </set>
+    <many-to-one name="BasePathologyAnnotation" class="pathology_scg.BasePathologyAnnotation" column="DE_E_1440_1442_IDENTIFIER" lazy="proxy" />
+  </class>
+</hibernate-mapping>
+

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

@@ -0,0 +1,260 @@
+<?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="BasePathologyAnnotation" table="DE_E_1440" lazy="true" polymorphism="explicit">
+    <cache usage="read-write" />
+    <id name="id" type="java.lang.Long" column="IDENTIFIER">
+      <generator class="assigned" />
+    </id>
+    <property name="Comment" type="java.lang.String" column="DE_AT_1444" />
+    <property name="OtherSpecimenProcedure" type="java.lang.String" column="DE_AT_1445" />
+    <property name="SpecimenProcedure" type="java.lang.String" column="DE_AT_1446" />
+    <set name="HistologicType" lazy="true" inverse="true">
+      <cache usage="read-write" />
+      <key column="DE_E_1440_1443_IDENTIFIER" />
+      <one-to-many class="pathology_scg.HistologicType" />
+    </set>
+    <set name="AdditionalFinding" lazy="true" inverse="true">
+      <cache usage="read-write" />
+      <key column="DE_E_1440_1442_IDENTIFIER" />
+      <one-to-many class="pathology_scg.AdditionalFinding" />
+    </set>
+    <joined-subclass name="pathology_scg.BaseHaematologyPathologyAnnotation" table="DE_E_1577" lazy="true">
+      <key column="IDENTIFIER" />
+      <property name="AdequacyOfSpecimen" type="java.lang.String" column="DE_AT_1581" />
+      <property name="OtherBiopsyOrAspirateSite" type="java.lang.String" column="DE_AT_1582" />
+      <property name="BiopsyOrAspirateSite" type="java.lang.String" column="DE_AT_1583" />
+      <one-to-one name="Cytogenetics" class="pathology_scg.Cytogenetics" property-ref="BaseHaematologyPathologyAnnotation" />
+      <one-to-one name="immunoPhenotyping" class="pathology_scg.ImmunoPhenotyping" property-ref="baseHaematologyPathologyAnnotation" />
+    </joined-subclass>
+    <joined-subclass name="pathology_scg.BaseSolidTissuePathologyAnnotation" table="DE_E_1461" lazy="true">
+      <key column="IDENTIFIER" />
+      <one-to-one name="invasion" class="pathology_scg.Invasion" property-ref="baseSolidTissuePathologyAnnotation" />
+      <one-to-one name="tumorSize" class="pathology_scg.TumorSize" property-ref="baseSolidTissuePathologyAnnotation" />
+      <set name="tumorTissueSite" lazy="true" inverse="true">
+        <cache usage="read-write" />
+        <key column="DE_E_1461_1463_IDENTIFIER" />
+        <one-to-many class="pathology_scg.TumorTissueSite" />
+      </set>
+      <set name="HistologicGrade" lazy="true" inverse="true">
+        <cache usage="read-write" />
+        <key column="DE_E_1461_1465_IDENTIFIER" />
+        <one-to-many class="pathology_scg.HistologicGrade" />
+      </set>
+      <one-to-one name="pathologicStaging" class="pathology_scg.PathologicalStaging" property-ref="baseSolidTissuePathologyAnnotation" />
+      <joined-subclass name="pathology_scg.ColorectalPathologyAnnotation" table="DE_E_1593" lazy="true">
+        <key column="IDENTIFIER" />
+        <property name="IntratumoralPeritumoralLymphocyticResponse" type="java.lang.String" column="DE_AT_1596" />
+        <property name="TumorBorderConfiguration" type="java.lang.String" column="DE_AT_1597" />
+        <property name="OtherTumorConfiguration" type="java.lang.String" column="DE_AT_1598" />
+        <property name="TumorConfiguration" type="java.lang.String" column="DE_AT_1599" />
+        <one-to-one name="PolypSize" class="pathology_scg.PolypSize" property-ref="ColorectalPathologyAnnotation" />
+        <joined-subclass name="pathology_scg.ExcisionalBiopsyBasedColorectalPathologyAnnotation" table="DE_E_1631" lazy="true">
+          <key column="IDENTIFIER" />
+          <property name="TypeOfPolypInWhichInvasiveCarcinomaArose" type="java.lang.String" column="DE_AT_1638" />
+          <property name="ExtentOfInvasion" type="java.lang.String" column="DE_AT_1639" />
+          <set name="lateralOrMucosalMarginCollection" lazy="true" inverse="true">
+            <cache usage="read-write" />
+            <key column="DE_E_1631_1634_IDENTIFIER" />
+            <one-to-many class="pathology_scg.ExcisionalBiopsyColorectalLateralOrMucosalMargin" />
+          </set>
+          <one-to-one name="PolypConfiguration" class="pathology_scg.PolypConfiguration" property-ref="ExcisionalBiopsyBasedColorectalPathologyAnnotation" />
+          <set name="deepMarginCollection" lazy="true" inverse="true">
+            <cache usage="read-write" />
+            <key column="DE_E_1631_1633_IDENTIFIER" />
+            <one-to-many class="pathology_scg.ExcisionalBiopsyColorectalDeepMargin" />
+          </set>
+          <one-to-one name="DistanceOfInvasiveCarcinoma" class="pathology_scg.DistanceOfInvasiveCarcinoma" property-ref="ExcisionalBiopsyBasedColorectalPathologyAnnotation" />
+          <one-to-one name="DistanceOfAdenoma" class="pathology_scg.DistanceOfAdenoma" property-ref="ExcisionalBiopsyBasedColorectalPathologyAnnotation" />
+          <many-to-one name="SpecimenCollectionGroup" class="pathology_scg.SpecimenCollectionGroup" column="DYEXTN_AS_379_1631" lazy="proxy" />
+        </joined-subclass>
+        <joined-subclass name="pathology_scg.ResectionBasedColorectalPathologyAnnotation" table="DE_E_1715" lazy="true">
+          <key column="IDENTIFIER" />
+          <property name="IntactnessOfMesorectum" type="java.lang.String" column="DE_AT_1721" />
+          <property name="specimenLength" type="java.lang.Double" column="DE_AT_1722" />
+          <set name="distalMarginCollection" lazy="true" inverse="true">
+            <cache usage="read-write" />
+            <key column="DE_E_1715_1719_IDENTIFIER" />
+            <one-to-many class="pathology_scg.DistalMargin" />
+          </set>
+          <set name="ResectionColorectalMesentricMargin" lazy="true" inverse="true">
+            <cache usage="read-write" />
+            <key column="DE_E_1715_1718_IDENTIFIER" />
+            <one-to-many class="pathology_scg.MesentricMargin" />
+          </set>
+          <set name="ResectionColorectalRadialMargin" lazy="true" inverse="true">
+            <cache usage="read-write" />
+            <key column="DE_E_1715_1717_IDENTIFIER" />
+            <one-to-many class="pathology_scg.RadialMargin" />
+          </set>
+          <many-to-one name="SpecimenCollectionGroup" class="pathology_scg.SpecimenCollectionGroup" column="DYEXTN_AS_379_1715" lazy="proxy" />
+          <set name="proximalMarginCollection" lazy="true" inverse="true">
+            <cache usage="read-write" />
+            <key column="DE_E_1715_1720_IDENTIFIER" />
+            <one-to-many class="pathology_scg.ProximalMargin" />
+          </set>
+        </joined-subclass>
+        <joined-subclass name="pathology_scg.LocalExcisionBasedColorectalPathologyAnnotation" table="DE_E_1788" lazy="true">
+          <key column="IDENTIFIER" />
+          <set name="localExcisionColorectalLateralMargin" lazy="true" inverse="true">
+            <cache usage="read-write" />
+            <key column="DE_E_1788_1793_IDENTIFIER" />
+            <one-to-many class="pathology_scg.LocalExcisionColorectalLateralMargin" />
+          </set>
+          <set name="localExcisionColorectalDeepMargin" lazy="true" inverse="true">
+            <cache usage="read-write" />
+            <key column="DE_E_1788_1791_IDENTIFIER" />
+            <one-to-many class="pathology_scg.LocalExcisionColorectalDeepMargin" />
+          </set>
+          <one-to-one name="SpecimenIntegrity" class="pathology_scg.SpecimenIntegrity" property-ref="LocalExcisionBasedColorectalPathologyAnnotation" />
+          <many-to-one name="SpecimenCollectionGroup" class="pathology_scg.SpecimenCollectionGroup" column="DYEXTN_AS_379_1788" lazy="proxy" />
+          <one-to-one name="distanceOfTumor" class="pathology_scg.DistanceFromAnalVerge" property-ref="localExcisionBasedColorectalPathologyAnnotation" />
+        </joined-subclass>
+      </joined-subclass>
+      <joined-subclass name="pathology_scg.ProstatePathologyAnnotation" table="DE_E_1545" lazy="true">
+        <key column="IDENTIFIER" />
+        <property name="PeriprostaticFatInvasion" type="java.lang.String" column="DE_AT_1548" />
+        <property name="SeminalVesicleInvasion" type="java.lang.String" column="DE_AT_1549" />
+        <property name="ProportionOrPercentOfProstaticTissueInvolvedByTumor" type="java.lang.Double" column="DE_AT_1550" />
+        <one-to-one name="GleasonScore" class="pathology_scg.GleasonScore" property-ref="ProstatePathologyAnnotation" />
+        <joined-subclass name="pathology_scg.NeedleBiopsyProstatePathologyAnnotation" table="DE_E_1652" lazy="true">
+          <key column="IDENTIFIER" />
+          <property name="TotalNumberOfCores" type="java.lang.Long" column="DE_AT_1654" />
+          <property name="NumberOfPositiveCores" type="java.lang.Long" column="DE_AT_1655" />
+          <property name="OtherQuantitiation" type="java.lang.String" column="DE_AT_1656" />
+          <property name="CoreLengthInMillimeter" type="java.lang.Double" column="DE_AT_1657" />
+          <property name="TotalLinearCarcinomaInMillimeter" type="java.lang.Double" column="DE_AT_1658" />
+          <many-to-one name="SpecimenCollectionGroup" class="pathology_scg.SpecimenCollectionGroup" column="DYEXTN_AS_379_1652" lazy="proxy" />
+        </joined-subclass>
+        <joined-subclass name="pathology_scg.TransurethralProstaticResectionPathologyAnnotation" table="DE_E_1625" lazy="true">
+          <key column="IDENTIFIER" />
+          <property name="TotalNumberOfChips" type="java.lang.Long" column="DE_AT_1627" />
+          <property name="NumberOfPositiveChips" type="java.lang.Long" column="DE_AT_1628" />
+          <property name="IsTumorIncidentalHistologicFindingAbove5Percent" type="java.lang.Boolean" column="DE_AT_1629" />
+          <property name="SpecimenWeight" type="java.lang.Double" column="DE_AT_1630" />
+          <many-to-one name="SpecimenCollectionGroup" class="pathology_scg.SpecimenCollectionGroup" column="DYEXTN_AS_379_1625" lazy="proxy" />
+        </joined-subclass>
+        <joined-subclass name="pathology_scg.RadicalProstatectomyPathologyAnnotation" table="DE_E_1676" lazy="true">
+          <key column="IDENTIFIER" />
+          <one-to-one name="ExtraprostaticExtension" class="pathology_scg.ExtraprostaticExtension" property-ref="RadicalProstatectomyPathologyAnnotation" />
+          <many-to-one name="SpecimenCollectionGroup" class="pathology_scg.SpecimenCollectionGroup" column="DYEXTN_AS_379_1676" lazy="proxy" />
+          <one-to-one name="radicalProstatectomyMargin" class="pathology_scg.RadicalProstatectomyMargin" property-ref="radicalProstatectomyPathologyAnnotation" />
+        </joined-subclass>
+        <joined-subclass name="pathology_scg.RetropubicEnucleationPathologyAnnotation" table="DE_E_1794" lazy="true">
+          <key column="IDENTIFIER" />
+          <property name="SpecimenWeight" type="java.lang.Double" column="DE_AT_1796" />
+          <many-to-one name="SpecimenCollectionGroup" class="pathology_scg.SpecimenCollectionGroup" column="DYEXTN_AS_379_1794" lazy="proxy" />
+        </joined-subclass>
+      </joined-subclass>
+      <joined-subclass name="pathology_scg.LungPathologyAnnotation" table="DE_E_1516" lazy="true">
+        <key column="IDENTIFIER" />
+        <joined-subclass name="pathology_scg.LungBiopsyPathologyAnnotation" table="DE_E_1559" lazy="true">
+          <key column="IDENTIFIER" />
+          <property name="VisceralPleuraInvasion" type="java.lang.String" column="DE_AT_1561" />
+          <many-to-one name="SpecimenCollectionGroup" class="pathology_scg.SpecimenCollectionGroup" column="DYEXTN_AS_379_1559" lazy="proxy" />
+        </joined-subclass>
+        <joined-subclass name="pathology_scg.LungResectionBasedPathologyAnnotation" table="DE_E_1518" lazy="true">
+          <key column="IDENTIFIER" />
+          <property name="ArterialInvasion" type="java.lang.String" column="DE_AT_1522" />
+          <property name="OtherTumorExtensions" type="java.lang.String" column="DE_AT_1523" />
+          <set name="DirectExtensionOfTumor" lazy="true" inverse="true">
+            <cache usage="read-write" />
+            <key column="DE_E_1518_1521_IDENTIFIER" />
+            <one-to-many class="pathology_scg.DirectExtensionOfTumor" />
+          </set>
+          <many-to-one name="SpecimenCollectionGroup" class="pathology_scg.SpecimenCollectionGroup" column="DYEXTN_AS_379_1518" lazy="proxy" />
+          <set name="LungResectionMargin" lazy="true" inverse="true">
+            <cache usage="read-write" />
+            <key column="DE_E_1518_1520_IDENTIFIER" />
+            <one-to-many class="pathology_scg.LungResectionMargin" />
+          </set>
+        </joined-subclass>
+      </joined-subclass>
+      <joined-subclass name="pathology_scg.KidneyPathologyAnnotation" table="DE_E_1536" lazy="true">
+        <key column="IDENTIFIER" />
+        <property name="PercentOfSarcomatoidElement" type="java.lang.Double" column="DE_AT_1538" />
+        <joined-subclass name="pathology_scg.KidneyBiopsyBasedPathologyAnnotation" table="DE_E_1539" lazy="true">
+          <key column="IDENTIFIER" />
+          <many-to-one name="SpecimenCollectionGroup" class="pathology_scg.SpecimenCollectionGroup" column="DYEXTN_AS_379_1539" lazy="proxy" />
+        </joined-subclass>
+        <joined-subclass name="pathology_scg.KidneyNephrectomyBasedPathologyAnnotation" table="DE_E_1797" lazy="true">
+          <key column="IDENTIFIER" />
+          <property name="AdrenalGlandStage" type="java.lang.String" column="DE_AT_1801" />
+          <property name="Focality" type="java.lang.String" column="DE_AT_1802" />
+          <one-to-one name="KidneyNephrectomyMargin" class="pathology_scg.KidneyNephrectomyMargin" property-ref="KidneyNephrectomyBasedPathologyAnnotation" />
+          <set name="MacroscopicExtentOfTumor" lazy="true" inverse="true">
+            <cache usage="read-write" />
+            <key column="DE_E_1797_1800_IDENTIFIER" />
+            <one-to-many class="pathology_scg.MacroscopicExtentOfTumor" />
+          </set>
+          <many-to-one name="SpecimenCollectionGroup" class="pathology_scg.SpecimenCollectionGroup" column="DYEXTN_AS_379_1797" lazy="proxy" />
+        </joined-subclass>
+      </joined-subclass>
+      <joined-subclass name="pathology_scg.PancreasPathologyAnnotation" table="DE_E_1705" lazy="true">
+        <key column="IDENTIFIER" />
+        <one-to-one name="pancreaseMargin" class="pathology_scg.PancreasMargin" property-ref="pancreasePathologyAnnotation" />
+        <set name="otherResectedOrgans" lazy="true" inverse="true">
+          <cache usage="read-write" />
+          <key column="DE_E_1705_1708_IDENTIFIER" />
+          <one-to-many class="pathology_scg.OtherResectedOrgans" />
+        </set>
+        <many-to-one name="SpecimenCollectionGroup" class="pathology_scg.SpecimenCollectionGroup" column="DYEXTN_AS_379_1705" lazy="proxy" />
+      </joined-subclass>
+      <joined-subclass name="pathology_scg.MelanomaPathologyAnnotation" table="DE_E_1735" lazy="true">
+        <key column="IDENTIFIER" />
+        <property name="SatelliteNoduleStatus" type="java.lang.String" column="DE_AT_1744" />
+        <property name="MitoticIndex" type="java.lang.String" column="DE_AT_1743" />
+        <property name="TumorRegression" type="java.lang.String" column="DE_AT_1742" />
+        <property name="TumorInfiltratingLymphocytes" type="java.lang.String" column="DE_AT_1741" />
+        <property name="DepthOfInvasionCannotBeDetermined" type="java.lang.Boolean" column="DE_AT_1740" />
+        <property name="DepthOfInvasion" type="java.lang.Double" column="DE_AT_1739" />
+        <property name="Ulceration" type="java.lang.String" column="DE_AT_1738" />
+        <property name="Pigmentation" type="java.lang.String" column="DE_AT_1737" />
+        <property name="MacroscopicTumor" type="java.lang.String" column="DE_AT_1736" />
+        <set name="lateralMarginCollection" lazy="true" inverse="true">
+          <cache usage="read-write" />
+          <key column="DE_E_1735_1745_IDENTIFIER" />
+          <one-to-many class="pathology_scg.LateralMelanomaMargin" />
+        </set>
+        <set name="SatelliteNodule" lazy="true" inverse="true">
+          <cache usage="read-write" />
+          <key column="DE_E_1735_1746_IDENTIFIER" />
+          <one-to-many class="pathology_scg.SatelliteNodule" />
+        </set>
+        <many-to-one name="SpecimenCollectionGroup" class="pathology_scg.SpecimenCollectionGroup" column="DYEXTN_AS_379_1735" lazy="proxy" />
+        <set name="deepMarginCollection" lazy="true" inverse="true">
+          <cache usage="read-write" />
+          <key column="DE_E_1735_1747_IDENTIFIER" />
+          <one-to-many class="pathology_scg.DeepMelanomaMargin" />
+        </set>
+      </joined-subclass>
+      <joined-subclass name="pathology_scg.BreastPathologyAnnotation" table="DE_E_1754" lazy="true">
+        <key column="IDENTIFIER" />
+        <property name="mitoticCountIfOtherGradingSystemUsed" type="java.lang.Integer" column="DE_AT_1760" />
+        <property name="LymphNodeSampling" type="java.lang.String" column="DE_AT_1761" />
+        <set name="Microcalcification" lazy="true" inverse="true">
+          <cache usage="read-write" />
+          <key column="DE_E_1754_1756_IDENTIFIER" />
+          <one-to-many class="pathology_scg.Microcalcification" />
+        </set>
+        <one-to-one name="SizeOfInvasiveCarcinoma" class="pathology_scg.SizeOfInvasiveCarcinoma" property-ref="BreastPathologyAnnotation" />
+        <set name="breastMarginCollection" lazy="true" inverse="true">
+          <cache usage="read-write" />
+          <key column="DE_E_1754_1758_IDENTIFIER" />
+          <one-to-many class="pathology_scg.BreastMargin" />
+        </set>
+        <one-to-one name="NottinghamHistologicScore" class="pathology_scg.NottinghamHistologicScore" property-ref="BreastPathologyAnnotation" />
+        <one-to-one name="SizeOfSpecimen" class="pathology_scg.SizeOfSpecimen" property-ref="BreastPathologyAnnotation" />
+        <many-to-one name="SpecimenCollectionGroup" class="pathology_scg.SpecimenCollectionGroup" column="DYEXTN_AS_379_1754" lazy="proxy" />
+      </joined-subclass>
+      <joined-subclass name="pathology_scg.CNSPathologyAnnotation" table="DE_E_1773" lazy="true">
+        <key column="IDENTIFIER" />
+        <one-to-one name="cnsMargin" class="pathology_scg.CNSMargin" property-ref="cnsPathologyAnnotation" />
+        <one-to-one name="SpecimenSize" class="pathology_scg.SpecimenSize" property-ref="CNSPathologyAnnotation" />
+        <many-to-one name="SpecimenCollectionGroup" class="pathology_scg.SpecimenCollectionGroup" column="DYEXTN_AS_379_1773" lazy="proxy" />
+      </joined-subclass>
+    </joined-subclass>
+  </class>
+</hibernate-mapping>
+

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

@@ -0,0 +1,21 @@
+<?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="BreastMargin" table="DE_E_1667" lazy="true" polymorphism="explicit">
+    <cache usage="read-write" />
+    <id name="id" type="java.lang.Long" column="IDENTIFIER">
+      <generator class="assigned" />
+    </id>
+    <property name="MarginLocation" type="java.lang.String" column="DE_AT_1671" />
+    <property name="MarginStatus" type="java.lang.String" column="DE_AT_1672" />
+    <many-to-one name="breastPathologyAnnotation" class="pathology_scg.BreastPathologyAnnotation" column="DE_E_1754_1758_IDENTIFIER" lazy="proxy" />
+    <one-to-one name="BreastMarginUninvolved" class="pathology_scg.BreastMarginUninvolved" property-ref="BreastMargin" />
+    <set name="involvedMarginCollection" lazy="true" inverse="true">
+      <cache usage="read-write" />
+      <key column="DE_E_1667_1670_IDENTIFIER" />
+      <one-to-many class="pathology_scg.BreastMarginInvolved" />
+    </set>
+  </class>
+</hibernate-mapping>
+

data/conf/annotation/pathology_scg/BreastMarginInvolved.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="BreastMarginInvolved" table="DE_E_1659" lazy="true" polymorphism="explicit">
+    <cache usage="read-write" />
+    <id name="id" type="java.lang.Long" column="IDENTIFIER">
+      <generator class="assigned" />
+    </id>
+    <property name="OtherExtentOfInvolvement" type="java.lang.String" column="DE_AT_1661" />
+    <property name="ExtentOfInvolvement" type="java.lang.String" column="DE_AT_1662" />
+    <many-to-one name="breastMargin" class="pathology_scg.BreastMargin" column="DE_E_1667_1670_IDENTIFIER" lazy="proxy" />
+  </class>
+</hibernate-mapping>
+

data/conf/annotation/pathology_scg/BreastMarginUninvolved.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="BreastMarginUninvolved" table="DE_E_1673" 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_1675" />
+    <many-to-one name="BreastMargin" class="pathology_scg.BreastMargin" column="DE_E_1667_1669_IDENTIFIER" unique="true" lazy="proxy" />
+  </class>
+</hibernate-mapping>
+

data/conf/annotation/pathology_scg/CNSMargin.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="CNSMargin" table="DE_E_1777" lazy="true" polymorphism="explicit">
+    <cache usage="read-write" />
+    <id name="id" type="java.lang.Long" column="IDENTIFIER">
+      <generator class="assigned" />
+    </id>
+    <property name="MarginStatus" type="java.lang.String" column="DE_AT_1780" />
+    <set name="CNSMarginLocation" lazy="true" inverse="true">
+      <cache usage="read-write" />
+      <key column="DE_E_1777_1779_IDENTIFIER" />
+      <one-to-many class="pathology_scg.CNSMarginLocation" />
+    </set>
+    <many-to-one name="cnsPathologyAnnotation" class="pathology_scg.CNSPathologyAnnotation" column="DE_E_1773_1776_IDENTIFIER" unique="true" lazy="proxy" />
+  </class>
+</hibernate-mapping>
+

data/conf/annotation/pathology_scg/CNSMarginLocation.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="CNSMarginLocation" table="DE_E_1781" lazy="true" polymorphism="explicit">
+    <cache usage="read-write" />
+    <id name="id" type="java.lang.Long" column="IDENTIFIER">
+      <generator class="assigned" />
+    </id>
+    <property name="MarginLocation" type="java.lang.String" column="DE_AT_1783" />
+    <many-to-one name="CNSMargin" class="pathology_scg.CNSMargin" column="DE_E_1777_1779_IDENTIFIER" lazy="proxy" />
+  </class>
+</hibernate-mapping>
+

data/conf/annotation/pathology_scg/CarcinomaInSituStatus.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="CarcinomaInSituStatus" table="DE_E_1437" lazy="true" polymorphism="explicit">
+    <cache usage="read-write" />
+    <id name="id" type="java.lang.Long" column="IDENTIFIER">
+      <generator class="assigned" />
+    </id>
+    <property name="Status" type="java.lang.String" column="DE_AT_1439" />
+    <many-to-one name="PancreasMarginUninvolvedByInvasiveCarcinoma" class="pathology_scg.PancreasMarginUninvolvedByInvasiveCarcinoma" column="DE_E_1620_1622_IDENTIFIER" lazy="proxy" />
+  </class>
+</hibernate-mapping>
+

data/conf/annotation/pathology_scg/ColorectalLocalExcisionMarginUninvolved.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="ColorectalLocalExcisionMarginUninvolved" table="DE_E_1770" 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_1772" />
+    <many-to-one name="LocalExcisionColorectalDeepMargin" class="pathology_scg.LocalExcisionColorectalDeepMargin" column="DE_E_1784_1786_IDENTIFIER" unique="true" lazy="proxy" />
+    <many-to-one name="LocalExcisionColorectalLateralMargin" class="pathology_scg.LocalExcisionColorectalLateralMargin" column="DE_E_1765_1767_IDENTIFIER" lazy="proxy" />
+  </class>
+</hibernate-mapping>
+

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

@@ -0,0 +1,22 @@
+<?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="ColorectalResectedMarginUninvolved" table="DE_E_1697" lazy="true" polymorphism="explicit">
+    <cache usage="read-write" />
+    <id name="id" type="java.lang.Long" column="IDENTIFIER">
+      <generator class="assigned" />
+    </id>
+    <property name="marginLocation" type="java.lang.String" column="DE_AT_1699" />
+    <property name="closestDistanceToTumor" type="java.lang.Double" column="DE_AT_1700" />
+    <many-to-one name="resectionColorectalProximalMargin" class="pathology_scg.ProximalMargin" column="DE_E_1723_1725_IDENTIFIER" unique="true" lazy="proxy" />
+    <set name="resectionColorectalRadialMargin" lazy="true" inverse="true">
+      <cache usage="read-write" />
+      <key column="DE_E_1697_1733_IDENTIFIER" />
+      <one-to-many class="pathology_scg.RadialMargin" />
+    </set>
+    <many-to-one name="resectionColorectalMesentricMargin" class="pathology_scg.MesentricMargin" column="DE_E_1693_1695_IDENTIFIER" unique="true" lazy="proxy" />
+    <many-to-one name="resectionColorectalDistalMargin" class="pathology_scg.DistalMargin" column="DE_E_1727_1729_IDENTIFIER" unique="true" lazy="proxy" />
+  </class>
+</hibernate-mapping>
+

data/conf/annotation/pathology_scg/Cytogenetics.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="Cytogenetics" table="DE_E_1589" lazy="true" polymorphism="explicit">
+    <cache usage="read-write" />
+    <id name="id" type="java.lang.Long" column="IDENTIFIER">
+      <generator class="assigned" />
+    </id>
+    <property name="Result" type="java.lang.String" column="DE_AT_1591" />
+    <property name="Status" type="java.lang.String" column="DE_AT_1592" />
+    <many-to-one name="BaseHaematologyPathologyAnnotation" class="pathology_scg.BaseHaematologyPathologyAnnotation" column="DE_E_1577_1579_IDENTIFIER" unique="true" lazy="proxy" />
+  </class>
+</hibernate-mapping>
+

data/conf/annotation/pathology_scg/DeepMelanomaMargin.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_scg">
+  <class name="DeepMelanomaMargin" table="DE_E_1600" lazy="true" polymorphism="explicit">
+    <cache usage="read-write" />
+    <id name="id" type="java.lang.Long" column="IDENTIFIER">
+      <generator class="assigned" />
+    </id>
+    <property name="MarginLocation" type="java.lang.String" column="DE_AT_1603" />
+    <property name="MarginStatus" type="java.lang.String" column="DE_AT_1604" />
+    <one-to-one name="UninvolvedMelanomaMargin" class="pathology_scg.UninvolvedMelanomaMargin" property-ref="DeepMelanomaMargin" />
+    <many-to-one name="melanomaPathologyAnnotation" class="pathology_scg.MelanomaPathologyAnnotation" column="DE_E_1735_1747_IDENTIFIER" lazy="proxy" />
+  </class>
+</hibernate-mapping>
+

data/conf/annotation/pathology_scg/Details.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="Details" table="DE_E_1458" 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_1460" />
+    <many-to-one name="AdditionalFinding" class="pathology_scg.AdditionalFinding" column="DE_E_1454_1456_IDENTIFIER" lazy="proxy" />
+  </class>
+</hibernate-mapping>
+

data/conf/annotation/pathology_scg/DirectExtensionOfTumor.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="DirectExtensionOfTumor" table="DE_E_1524" lazy="true" polymorphism="explicit">
+    <cache usage="read-write" />
+    <id name="id" type="java.lang.Long" column="IDENTIFIER">
+      <generator class="assigned" />
+    </id>
+    <property name="ExtensionOfTumor" type="java.lang.String" column="DE_AT_1526" />
+    <many-to-one name="LungResectionBasedPathologyAnnotation" class="pathology_scg.LungResectionBasedPathologyAnnotation" column="DE_E_1518_1521_IDENTIFIER" lazy="proxy" />
+  </class>
+</hibernate-mapping>
+

data/conf/annotation/pathology_scg/DistalMargin.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="DistalMargin" table="DE_E_1727" lazy="true" polymorphism="explicit">
+    <cache usage="read-write" />
+    <id name="id" type="java.lang.Long" column="IDENTIFIER">
+      <generator class="assigned" />
+    </id>
+    <property name="MarginStatus" type="java.lang.String" column="DE_AT_1730" />
+    <one-to-one name="uninvolvedMargin" class="pathology_scg.ColorectalResectedMarginUninvolved" property-ref="resectionColorectalDistalMargin" />
+    <many-to-one name="resectionBasedColorectalPathologyAnnotation" class="pathology_scg.ResectionBasedColorectalPathologyAnnotation" column="DE_E_1715_1719_IDENTIFIER" lazy="proxy" />
+  </class>
+</hibernate-mapping>
+

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

@@ -0,0 +1,23 @@
+<?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="DistanceFromAnalVerge" table="DE_E_1640" lazy="true" polymorphism="explicit">
+    <cache usage="read-write" />
+    <id name="id" type="java.lang.Long" column="IDENTIFIER">
+      <generator class="assigned" />
+    </id>
+    <property name="LengthInCentimeters" type="java.lang.Long" column="DE_AT_1642" />
+    <property name="DistanceKnown" type="java.lang.Boolean" column="DE_AT_1643" />
+    <many-to-one name="localExcisionBasedColorectalPathologyAnnotation" class="pathology_scg.LocalExcisionBasedColorectalPathologyAnnotation" column="DE_E_1788_1792_IDENTIFIER" unique="true" lazy="proxy" />
+    <joined-subclass name="pathology_scg.DistanceOfAdenoma" table="DE_E_1845" lazy="true">
+      <key column="IDENTIFIER" />
+      <many-to-one name="ExcisionalBiopsyBasedColorectalPathologyAnnotation" class="pathology_scg.ExcisionalBiopsyBasedColorectalPathologyAnnotation" column="DE_E_1631_1844_IDENTIFIER" unique="true" lazy="proxy" />
+    </joined-subclass>
+    <joined-subclass name="pathology_scg.DistanceOfInvasiveCarcinoma" table="DE_E_1847" lazy="true">
+      <key column="IDENTIFIER" />
+      <many-to-one name="ExcisionalBiopsyBasedColorectalPathologyAnnotation" class="pathology_scg.ExcisionalBiopsyBasedColorectalPathologyAnnotation" column="DE_E_1631_1843_IDENTIFIER" unique="true" lazy="proxy" />
+    </joined-subclass>
+  </class>
+</hibernate-mapping>
+

data/conf/annotation/pathology_scg/DistantMetastasis.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="DistantMetastasis" table="DE_E_1497" lazy="true" polymorphism="explicit">
+    <cache usage="read-write" />
+    <id name="id" type="java.lang.Long" column="IDENTIFIER">
+      <generator class="assigned" />
+    </id>
+    <property name="MetastasisStage" type="java.lang.String" column="DE_AT_1500" />
+    <set name="MetastasisTissueSite" lazy="true" inverse="true">
+      <cache usage="read-write" />
+      <key column="DE_E_1497_1499_IDENTIFIER" />
+      <one-to-many class="pathology_scg.MetastasisTissueSite" />
+    </set>
+    <many-to-one name="pathologicStaging" class="pathology_scg.PathologicalStaging" column="DE_E_1484_1487_IDENTIFIER" unique="true" lazy="proxy" />
+  </class>
+</hibernate-mapping>
+