caruby-tissue 1.2.3 → 1.3.1

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

@@ -1,73 +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_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/lib/catissue/annotation/hibernate_mapping.rb

@@ -1,46 +0,0 @@
-require 'xmlsimple'
-require 'caruby/util/inflector'
-require 'catissue/annotation/annotation'
-
-module CaTissue
-  module Annotation
-    # Annotation class Hibernate mapping encapsulation.
-    #
-    # caTissue alert - caTissue doesn't appear to use Hibernate for DEs. The mappings are incorrect
-    # and should not be used.
-    class HibernateMapping
-      
-      attr_accessor :table
-      
-      def initialize(klass)
-        hbm = hibernate_mapping(klass)
-        @table = hbm['table']
-        @attr_col_hash = {}
-        hbm['property'].each do |name, md|
-          @attr_col_hash[name.underscore.to_sym] = md['column']
-        end
-      end
-      
-      def column(attribute)
-        @attr_col_hash[attribute]
-      end
-    
-      private
-      
-      HBM_DIR = File.join(File.dirname(__FILE__), '..', '..', '..', 'conf', 'annotation')
-      
-      HBM_OPTS = { 'KeyAttr' => 'name' }
-      
-      def hibernate_mapping(klass)
-        file = hibernate_mapping_file(klass)
-        conf = XmlSimple.xml_in(file, HBM_OPTS)
-        conf['class'][klass.name.demodulize]
-      end
-      
-      def hibernate_mapping_file(klass)
-        dir = klass.java_class.name[/\w+/]
-        File.join(HBM_DIR, dir, "#{klass.name.demodulize}.hbm.xml")
-      end  
-    end
-  end
-end