caruby-tissue 1.2.3 → 1.3.1

data/History.txt

@@ -10,3 +10,7 @@
 
 * Support Dynamic Extensions
 
+=== 1.3.1 / 2011-02-18
+
+* Full PCBIN DE support
+

data/lib/catissue/annotation/annotation_class.rb

@@ -1,4 +1,3 @@
-require 'xmlsimple'
 require 'catissue/annotation/annotation'
 require 'catissue/database/annotation/reference_writer'
 

data/lib/catissue/version.rb

@@ -1,6 +1,6 @@
 module CaTissue
   # The version of this caRuby Tissue release.
-  VERSION = "1.2.3"
+  VERSION = "1.3.1"
   
   # The supported caTissue release versions.
   CATISSUE_VERSIONS = "1.1.2"

metadata

@@ -10,11 +10,11 @@ executables:
 - crtsmoke
 version: !ruby/object:Gem::Version 
   prerelease: false
-  version: 1.2.3
+  version: 1.3.1
   segments: 
   - 1
-  - 2
   - 3
+  - 1
 post_install_message: 
 date: 2010-11-30 08:00:00 +00:00
 files: 
@@ -22,79 +22,7 @@ files:
 - bin/crtexample
 - bin/crtextract
 - bin/crtmigrate
-- bin/crtseed
 - bin/crtsmoke
-- conf/annotation/pathology_scg/AdditionalFinding.hbm.xml
-- conf/annotation/pathology_scg/BasePathologyAnnotation.hbm.xml
-- conf/annotation/pathology_scg/BreastMargin.hbm.xml
-- conf/annotation/pathology_scg/BreastMarginInvolved.hbm.xml
-- conf/annotation/pathology_scg/BreastMarginUninvolved.hbm.xml
-- conf/annotation/pathology_scg/CarcinomaInSituStatus.hbm.xml
-- conf/annotation/pathology_scg/CNSMargin.hbm.xml
-- conf/annotation/pathology_scg/CNSMarginLocation.hbm.xml
-- conf/annotation/pathology_scg/ColorectalLocalExcisionMarginUninvolved.hbm.xml
-- conf/annotation/pathology_scg/ColorectalResectedMarginUninvolved.hbm.xml
-- conf/annotation/pathology_scg/Cytogenetics.hbm.xml
-- conf/annotation/pathology_scg/DeepMelanomaMargin.hbm.xml
-- conf/annotation/pathology_scg/Details.hbm.xml
-- conf/annotation/pathology_scg/DirectExtensionOfTumor.hbm.xml
-- conf/annotation/pathology_scg/DistalMargin.hbm.xml
-- conf/annotation/pathology_scg/DistanceFromAnalVerge.hbm.xml
-- conf/annotation/pathology_scg/DistantMetastasis.hbm.xml
-- conf/annotation/pathology_scg/ExcionalBiopsyMarginUninvolved.hbm.xml
-- conf/annotation/pathology_scg/ExcisionalBiopsyColorectalDeepMargin.hbm.xml
-- conf/annotation/pathology_scg/ExcisionalBiopsyColorectalLateralOrMucosalMargin.hbm.xml
-- conf/annotation/pathology_scg/ExtraprostaticExtension.hbm.xml
-- conf/annotation/pathology_scg/ExtraprostaticExtensionTissueSites.hbm.xml
-- conf/annotation/pathology_scg/GleasonScore.hbm.xml
-- conf/annotation/pathology_scg/HistologicGrade.hbm.xml
-- conf/annotation/pathology_scg/HistologicType.hbm.xml
-- conf/annotation/pathology_scg/HistologicVariantType.hbm.xml
-- conf/annotation/pathology_scg/ImmunoPhenotyping.hbm.xml
-- conf/annotation/pathology_scg/Invasion.hbm.xml
-- conf/annotation/pathology_scg/KidneyMarginLocation.hbm.xml
-- conf/annotation/pathology_scg/KidneyNephrectomyMargin.hbm.xml
-- conf/annotation/pathology_scg/LateralMelanomaMargin.hbm.xml
-- conf/annotation/pathology_scg/LocalExcisionColorectalDeepMargin.hbm.xml
-- conf/annotation/pathology_scg/LocalExcisionColorectalLateralMargin.hbm.xml
-- conf/annotation/pathology_scg/LungResectionMargin.hbm.xml
-- conf/annotation/pathology_scg/LungResectionMarginsUninvolved.hbm.xml
-- conf/annotation/pathology_scg/MacroscopicExtentOfTumor.hbm.xml
-- conf/annotation/pathology_scg/MesentricMargin.hbm.xml
-- conf/annotation/pathology_scg/MetastasisTissueSite.hbm.xml
-- conf/annotation/pathology_scg/Microcalcification.hbm.xml
-- conf/annotation/pathology_scg/NottinghamHistologicScore.hbm.xml
-- conf/annotation/pathology_scg/OtherResectedOrgans.hbm.xml
-- conf/annotation/pathology_scg/PancreasMargin.hbm.xml
-- conf/annotation/pathology_scg/PancreasMarginInvolvedByInvasiveCarcinoma.hbm.xml
-- conf/annotation/pathology_scg/PancreasMarginUninvolvedByInvasiveCarcinoma.hbm.xml
-- conf/annotation/pathology_scg/PathologicalStaging.hbm.xml
-- conf/annotation/pathology_scg/PolypConfiguration.hbm.xml
-- conf/annotation/pathology_scg/PrimaryTumorStage.hbm.xml
-- conf/annotation/pathology_scg/ProstateMarginLocation.hbm.xml
-- conf/annotation/pathology_scg/ProximalMargin.hbm.xml
-- conf/annotation/pathology_scg/RadialMargin.hbm.xml
-- conf/annotation/pathology_scg/RadicalProstatectomyMargin.hbm.xml
-- conf/annotation/pathology_scg/RegionalLymphNode.hbm.xml
-- conf/annotation/pathology_scg/SatelliteNodule.hbm.xml
-- conf/annotation/pathology_scg/SpecimenCollectionGroup.hbm.xml
-- conf/annotation/pathology_scg/SpecimenIntegrity.hbm.xml
-- conf/annotation/pathology_scg/SpecimenSize.hbm.xml
-- conf/annotation/pathology_scg/TissueSide.hbm.xml
-- conf/annotation/pathology_scg/TumorSize.hbm.xml
-- conf/annotation/pathology_scg/TumorTissueSite.hbm.xml
-- conf/annotation/pathology_scg/UninvolvedMelanomaMargin.hbm.xml
-- conf/annotation/pathology_specimen/AdditionalFinding.hbm.xml
-- conf/annotation/pathology_specimen/AdditionalPathologicFinding.hbm.xml
-- conf/annotation/pathology_specimen/Details.hbm.xml
-- conf/annotation/pathology_specimen/GleasonScore.hbm.xml
-- conf/annotation/pathology_specimen/HistologicGrade.hbm.xml
-- conf/annotation/pathology_specimen/HistologicType.hbm.xml
-- conf/annotation/pathology_specimen/HistologicVariantType.hbm.xml
-- conf/annotation/pathology_specimen/Invasion.hbm.xml
-- conf/annotation/pathology_specimen/NottinghamHistologicScore.hbm.xml
-- conf/annotation/pathology_specimen/Specimen.hbm.xml
-- conf/annotation/pathology_specimen/SpecimenBaseSolidTissuePathologyAnnotation.hbm.xml
 - conf/extract/simple_fields.yaml
 - conf/migration/filter_fields.yaml
 - conf/migration/filter_migration.yaml
@@ -133,7 +61,6 @@ files:
 - lib/catissue/annotation/annotation.rb
 - lib/catissue/annotation/annotation_class.rb
 - lib/catissue/annotation/annotation_module.rb
-- lib/catissue/annotation/hibernate_mapping.rb
 - lib/catissue/annotation/proxy.rb
 - lib/catissue/annotation/proxy_class.rb
 - lib/catissue/cli/command.rb

data/bin/crtseed

@@ -1,26 +0,0 @@
-#!/usr/bin/env jruby
-#
-# seed: seeds the Galena example administrative objects in the database
-#
-
-# load the caRuby Tissue gem
-require 'rubygems'
-begin
-  gem 'caruby-tissue'
-rescue LoadError
-  # if the gem is not available, then try a local source
-  $:.unshift File.join(File.dirname(__FILE__), '..', '..', '..', 'lib')
-end
-
-# add the Galena lib to the path
-$:.unshift File.join(File.dirname(__FILE__), '..', 'lib')
-
-# the default log file
-DEF_LOG_FILE = 'log/migration.log'
-
-require 'catissue'
-require 'catissue/cli/command'
-
-require 'galena/seed/defaults'
-
-CaTissue::CLI::Command.new.start { Galena::Seed.defaults.ensure_exists }

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

@@ -1,19 +0,0 @@
-<?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

@@ -1,260 +0,0 @@
-<?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

@@ -1,21 +0,0 @@
-<?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

@@ -1,15 +0,0 @@
-<?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

@@ -1,14 +0,0 @@
-<?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

@@ -1,19 +0,0 @@
-<?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

@@ -1,14 +0,0 @@
-<?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

@@ -1,14 +0,0 @@
-<?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

@@ -1,15 +0,0 @@
-<?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

@@ -1,22 +0,0 @@
-<?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

@@ -1,15 +0,0 @@
-<?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

@@ -1,16 +0,0 @@
-<?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>
-