caruby-tissue 1.5.6 → 2.1.1

data/lib/catissue/domain/participant_medical_identifier.rb

@@ -1,10 +1,6 @@
 
 
 module CaTissue
-  # import the Java class
-  resource_import Java::edu.wustl.catissuecore.domain.ParticipantMedicalIdentifier
-
-
   # The ParticipantMedicalIdentifier domain class.
   class ParticipantMedicalIdentifier
     # Sets this ParticipantMedicalIdentifier's medical record number to the given value.

data/lib/catissue/domain/password.rb

@@ -1,9 +1,5 @@
 module CaTissue
-  # import the Java class
-  resource_import Java::edu.wustl.catissuecore.domain.Password
-
   class Password
     qualify_attribute(:update_date, :unsaved)
-
   end
 end

data/lib/catissue/domain/race.rb

@@ -1,7 +1,4 @@
 module CaTissue
-  # import the Java class
-  resource_import Java::edu.wustl.catissuecore.domain.Race
-
   class Race
     add_attribute_aliases(:name => :race_name)
     

data/lib/catissue/domain/received_event_parameters.rb

@@ -1,10 +1,7 @@
-require 'catissue/util/collectible_event_parameters'
+require 'catissue/helpers/collectible_event_parameters'
 
 module CaTissue
-  # import the Java class
-  resource_import Java::edu.wustl.catissuecore.domain.ReceivedEventParameters
-
-  class ReceivedEventParameters < CaTissue::SpecimenEventParameters
+  class ReceivedEventParameters
     include CollectibleEventParameters
 
     add_attribute_aliases(:receiver => :user)
@@ -14,7 +11,7 @@ module CaTissue
     add_mandatory_attributes(:received_quality)
     
     # An auto-generated REP must fetch the user.
-    qualify_attribute(:user, :saved_fetch)
+    qualify_attribute(:user, :fetch_saved)
 
     private
 

data/lib/catissue/domain/site.rb

@@ -1,7 +1,4 @@
 module CaTissue
-  # import the Java class
-  resource_import Java::edu.wustl.catissuecore.domain.Site
-
   # The Site domain class.
   class Site
     # @quirk caTissue the Site SCG collection is ignored, since it is not fetched with the Site,
@@ -12,7 +9,7 @@ module CaTissue
 
     # @quirk caTissue caTissue 1.2 Site has a facility_id Java property, but caTissue throws an
     #   UnsupportedOperationException if they are called.
-    if attribute_defined?(:facility_id) then remove_attribute(:facility_id) end
+    if property_defined?(:facility_id) then remove_attribute(:facility_id) end
 
     set_secondary_key_attributes(:name)
 

data/lib/catissue/domain/specimen/pathology/additional_finding.rb

@@ -0,0 +1,12 @@
+module CaTissue
+  class Specimen
+    # @quirk caTissue The 1.1.2 class AdditionalFinding is renamed to SpecimenAdditionalFinding in 1.2.
+    # Alias the AdditionalFinding Ruby class constant to SpecimenAdditionalFinding for forward compatibility.
+    module Pathology
+      class AdditionalFinding
+        Pathology.const_set(:SpecimenAdditionalFinding, self)
+        logger.debug { "Aliased the caTissue 1.1.2 Specimen pathology annotation class AdditionalFinding class to the renamed 1.2 SpecimenAdditionalFinding." }
+      end
+    end
+  end
+end

data/lib/catissue/domain/specimen/pathology/details.rb

@@ -0,0 +1,12 @@
+module CaTissue
+  class Specimen
+    module Pathology
+      # @quirk caTissue The 1.1 class Details is renamed to SpecimenDetails in 1.2.
+      #   Alias the Details Ruby class to SpecimenDetails for forward compatibility.
+      class Details
+        Pathology.const_set(:SpecimenDetails, self)
+        logger.debug { "Aliased the Specimen pathology annotation class Details to SpecimenDetails." }
+      end
+    end
+  end
+end

data/lib/catissue/domain/specimen/pathology/gleason_score.rb

@@ -0,0 +1,12 @@
+module CaTissue
+  class Specimen
+    module Pathology
+      # @quirk caTissue The 1.1 class GleasonScore is renamed to ProstateSpecimenGleasonScore in 1.2.
+      #   Alias the GleasonScore Ruby class constant to ProstateSpecimenGleasonScore forward compatibility.
+      class GleasonScore
+        Pathology.const_set(:ProstateSpecimenGleasonScore, self)
+        logger.debug { "Aliased the caTissue 1.1 Specimen pathology annotation class GleasonScore class to the renamed 1.2 ProstateSpecimenGleasonScore." }
+      end
+    end
+  end
+end

data/lib/catissue/domain/specimen/pathology/histologic_grade.rb

@@ -0,0 +1,12 @@
+module CaTissue
+  class Specimen
+    module Pathology
+      # @quirk caTissue The 1.1.2 class HistologicGrade is renamed to SpecimenHistologicGrade in 1.2.
+      #   Alias the HistologicGrade Ruby class to SpecimenHistologicGrade for forward compatibility.
+      class HistologicGrade
+        Pathology.const_set(:SpecimenHistologicGrade, self)
+        logger.debug { "Aliased the caTissue 1.1 Specimen pathology annotation class HistologicGrade class to the renamed 1.2 SpecimenHistologicGrade." }
+      end
+    end
+  end
+end

data/lib/catissue/domain/specimen/pathology/histologic_type.rb

@@ -0,0 +1,19 @@
+module CaTissue
+  class Specimen
+    module Pathology
+      # @quirk caTissue The 1.1.2 class HistologicType is renamed to SpecimenHistologicType in 1.2.
+      #   Alias the HistologicType Ruby class to SpecimenHistologicType for forward compatibility.
+      class HistologicType
+        Pathology.const_set(:SpecimenHistologicType, self)
+        logger.debug { "Aliased the caTissue 1.1 Specimen pathology annotation class HistologicType class to the renamed 1.2 SpecimenHistologicType." }
+
+        # @quirk caTissue The HistologicType => HistologicVariantType collection
+        #   property is misnamed as histologicVariantType rather than histologicVariantTypeCollection.
+        #   This misnaming prevents caRuby from inferring the attribute domain type and inverse.
+        #   Work-around is to set these attribute features manually.
+        set_attribute_type(:histologic_variant_type, CaTissue::Specimen::Pathology::HistologicVariantType)
+        set_attribute_inverse(:histologic_variant_type, :histologic_type)
+      end
+    end
+  end
+end

data/lib/catissue/domain/specimen/pathology/histologic_variant_type.rb

@@ -0,0 +1,12 @@
+module CaTissue
+  class Specimen
+    module Pathology
+      # @quirk caTissue The 1.1.2 class HistologicVariantType is renamed to SpecimenHistologicVariantType in 1.2.
+      #   Alias the HistologicVariantType Ruby class to SpecimenHistologicVariantType for forward compatibility.
+      class HistologicVariantType
+        Pathology.const_set(:SpecimenHistologicVariantType, self)
+        logger.debug { "Aliased the caTissue 1.1 Specimen pathology annotation class HistologicVariantType class to the renamed 1.2 SpecimenHistologicVariantType." }
+      end
+    end
+  end
+end

data/lib/catissue/domain/specimen/pathology/invasion.rb

@@ -0,0 +1,12 @@
+module CaTissue
+  class Specimen
+    module Pathology
+      # @quirk caTissue The 1.1.2 class Invasion is renamed to SpecimenInvasion in 1.2.
+      #   Alias the Invasion Ruby class to SpecimenInvasion for forward compatibility.
+      class Invasion
+        Pathology.const_set(:SpecimenInvasion, self)
+        logger.debug { "Aliased the caTissue 1.1 Specimen pathology annotation class Invasion class to the renamed 1.2 SpecimenInvasion." }
+      end
+    end
+  end
+end

data/lib/catissue/domain/specimen/pathology/prostate_specimen_gleason_score.rb

@@ -1,17 +1,11 @@
 module CaTissue
   class Specimen
-    class Pathology
-      # @quirk caTissue The 1.1 class GleasonScore is renamed to ProstateSpecimenGleasonScore in 1.2.
-      #   Alias the Ruby class constant for forward and backaward compatibility.
-      begin
-        resource_import Java::pathology_specimen.ProstateSpecimenGleasonScore
-        const_set(:GleasonScore, ProstateSpecimenGleasonScore)
+    module Pathology
+      # @quirk caTissue The 1.1.2 class GleasonScore is renamed to ProstateSpecimenGleasonScore in 1.2.
+      #   Alias the ProstateSpecimenGleasonScore Ruby class to GleasonScore for backward compatibility.
+      class ProstateSpecimenGleasonScore
+        Pathology.const_set(:GleasonScore, self)
         logger.debug { "Aliased the Specimen pathology annotation class ProstateSpecimenGleasonScore to GleasonScore." }
-      rescue NameError
-        logger.debug { "SpecimenGleasonScore pathology annotation class not found; attempting to import the caTissue 1.1 GleasonScore variant..." }
-        resource_import Java::pathology_specimen.GleasonScore
-        const_set(:ProstateSpecimenGleasonScore, GleasonScore)
-        logger.debug { "Aliased the caTissue 1.1 Specimen pathology annotation class GleasonScore class to the renamed 1.2 ProstateSpecimenGleasonScore." }
       end
     end
   end

data/lib/catissue/domain/specimen/pathology/prostate_specimen_pathology_annotation.rb

@@ -1,18 +1,18 @@
 module CaTissue
   class Specimen
-    class Pathology
-      begin
-        resource_import Java::pathology_specimen.ProstateSpecimenPathologyAnnotation
-        const_set(:ProstatePathologyAnnotation, ProstateSpecimenPathologyAnnotation)
+    module Pathology
+      class ProstateSpecimenPathologyAnnotation
+        # @quirk caTissue the 'Specimen' in the ProstateSpecimenPathologyAnnotation class name is redundant
+        # and inconsisent. Alias to ProstatePathologyAnnotation.
+        Pathology.const_set(:ProstatePathologyAnnotation, self)
         logger.debug { "Aliased the Specimen pathology annotation class ProstateSpecimenPathologyAnnotation to ProstatePathologyAnnotation." }
-        class ProstateSpecimenPathologyAnnotation
-          # @quirk caTissue the Specimen prostate annotation 1.1 method gleasonScore is renamed to
-          #   prostateSpecimenGleasonScore in 1.2. Alias the JRuby wrapper method for backward compatibility.
-          if attribute_defined?(:prostate_specimen_gleason_score) then
-            add_attribute_aliases(:gleason_score => :prostate_specimen_gleason_score)
-          else
-            add_attribute_aliases(:prostate_specimen_gleason_score => :gleason_score)
-          end
+        
+        # @quirk caTissue the Specimen prostate annotation 1.1.2 method gleasonScore is renamed to
+        #   prostateSpecimenGleasonScore in 1.2. Alias the JRuby wrapper method for backward compatibility.
+        if property_defined?(:prostate_specimen_gleason_score) then
+          add_attribute_aliases(:gleason_score => :prostate_specimen_gleason_score)
+        else
+          add_attribute_aliases(:prostate_specimen_gleason_score => :gleason_score)
         end
       end
     end

data/lib/catissue/domain/specimen/pathology/specimen_additional_finding.rb

@@ -1,20 +1,11 @@
 module CaTissue
   class Specimen
-    # @quirk caTissue The 1.1 class AdditionalFinding is renamed to SpecimenAdditionalFinding in 1.2.
-    # Alias the Ruby class constant for forward and backaward compatibility.
-    #
-    # @quirk caTissue the Specimen additional finding annotation 1.1 method 'details' is renamed to
-    #   'specimenDetails' in 1.2.
-    class Pathology
-      begin
-        resource_import Java::pathology_specimen.SpecimenAdditionalFinding
-        const_set(:AdditionalFinding, SpecimenAdditionalFinding)
+    # @quirk caTissue The 1.1.2 class AdditionalFinding is renamed to SpecimenAdditionalFinding in 1.2.
+    # Alias the SpecimenAdditionalFinding Ruby class to AdditionalFinding for backward compatibility.
+    module Pathology
+      class SpecimenAdditionalFinding
+        Pathology.const_set(:AdditionalFinding, self)
         logger.debug { "Aliased the Specimen pathology annotation class SpecimenAdditionalFinding to AdditionalFinding." }
-      rescue NameError
-        logger.debug { "SpecimenAdditionalFinding pathology annotation class not found; attempting to import the caTissue 1.1 AdditionalFinding variant..." }
-        resource_import Java::pathology_specimen.AdditionalFinding
-        const_set(:SpecimenAdditionalFinding, AdditionalFinding)
-        logger.debug { "Aliased the caTissue 1.1 Specimen pathology annotation class AdditionalFinding class to the renamed 1.2 SpecimenAdditionalFinding." }
       end
     end
   end

data/lib/catissue/domain/specimen/pathology/specimen_base_solid_tissue_pathology_annotation.rb

@@ -1,36 +1,21 @@
-require File.join(File.dirname(__FILE__), 'specimen_histologic_grade')
-require File.join(File.dirname(__FILE__), 'specimen_histologic_type')
-
 module CaTissue
   class Specimen
-    class Pathology
-      # @quirk caTissue The 1.1 specimen pathology annotation class BaseSolidTissuePathologyAnnotation
-      #   is renamed to SpecimenBaseSolidTissuePathologyAnnotation in 1.2.
-      #   Alias the Ruby class constant for forward and backaward compatibility.
-      begin
-        resource_import Java::pathology_specimen.SpecimenBaseSolidTissuePathologyAnnotation
-        const_set(:BaseSolidTissuePathologyAnnotation, SpecimenBaseSolidTissuePathologyAnnotation)
-        logger.debug { "Aliased the Specimen pathology annotation class SpecimenBaseSolidTissuePathologyAnnotation to BaseSolidTissuePathologyAnnotation." }
-      rescue NameError
-        logger.debug { "SpecimenBaseSolidTissuePathologyAnnotation pathology annotation class not found; attempting to import the caTissue 1.1 BaseSolidTissuePathologyAnnotation variant..." }
-        resource_import Java::pathology_specimen.BaseSolidTissuePathologyAnnotation
-        const_set(:SpecimenBaseSolidTissuePathologyAnnotation, BaseSolidTissuePathologyAnnotation)
-        logger.debug { "Aliased the caTissue 1.1 Specimen pathology annotation class BaseSolidTissuePathologyAnnotation class to the renamed 1.2 SpecimenBaseSolidTissuePathologyAnnotation." }
-      end
-      
+    module Pathology
       class SpecimenBaseSolidTissuePathologyAnnotation
         # @quirk caTissue The SpecimenBaseSolidTissuePathologyAnnotation => SpecimenHistologicGrade collection
         #   property is misnamed as histologicGrade rather than histologicGradeCollection. This misnaming
         #   prevents caRuby from inferring the attribute domain type and inverse. Work-around is to set
         #   these attribute features manually.
-        set_attribute_type(:histologic_grade, CaTissue::Specimen::Pathology::SpecimenHistologicGrade)
+        klass = Pathology::SpecimenHistologicGrade rescue Pathology::HistologicGrade
+        set_attribute_type(:histologic_grade, klass)
         set_attribute_inverse(:histologic_grade, :specimen_base_solid_tissue_pathology_annotation)
-        
+
         # @quirk caTissue The SpecimenBaseSolidTissuePathologyAnnotation => SpecimenHistologicType collection
         #   property is misnamed as histologicType rather than histologicTypeCollection. This misnaming
         #   prevents caRuby from inferring the attribute domain type and inverse. Work-around is to set
         #   these attribute features manually.
-        set_attribute_type(:histologic_type, CaTissue::Specimen::Pathology::SpecimenHistologicType)
+        klass = Pathology::SpecimenHistologicType rescue Pathology::HistologicType
+        set_attribute_type(:histologic_type, klass)
         set_attribute_inverse(:histologic_type, :specimen_base_solid_tissue_pathology_annotation)
       end
     end

data/lib/catissue/domain/specimen/pathology/specimen_details.rb

@@ -1,17 +1,11 @@
 module CaTissue
   class Specimen
-    class Pathology
+    module Pathology
       # @quirk caTissue The 1.1 class Details is renamed to SpecimenDetails in 1.2.
-      #   Alias the Ruby class constant for forward and backaward compatibility.
-      begin
-        resource_import Java::pathology_specimen.SpecimenDetails
-        const_set(:Details, SpecimenDetails)
+      #   Alias the SpecimenDetails Ruby class to Details for backward compatibility.
+      class SpecimenDetails
+        Pathology.const_set(:Details, self)
         logger.debug { "Aliased the Specimen pathology annotation class SpecimenDetails to Details." }
-      rescue NameError
-        logger.debug { "SpecimenDetails pathology annotation class not found; attempting to import the caTissue 1.1 Details variant..." }
-        resource_import Java::pathology_specimen.Details
-        const_set(:SpecimenDetails, Details)
-        logger.debug { "Aliased the caTissue 1.1 Specimen pathology annotation class Details class to the renamed 1.2 SpecimenDetails." }
       end
     end
   end

data/lib/catissue/domain/specimen/pathology/specimen_histologic_grade.rb

@@ -1,17 +1,11 @@
 module CaTissue
   class Specimen
-    class Pathology
+    module Pathology
       # @quirk caTissue The 1.1 class HistologicGrade is renamed to SpecimenHistologicGrade in 1.2.
-      #   Alias the Ruby class constant for forward and backaward compatibility.
-      begin
-        resource_import Java::pathology_specimen.SpecimenHistologicGrade
-        const_set(:HistologicGrade, SpecimenHistologicGrade)
+      #   Alias the SpecimenHistologicGrade Ruby class constant to HistologicGrade backward compatibility.
+      class SpecimenHistologicGrade
+        Pathology.const_set(:HistologicGrade, self)
         logger.debug { "Aliased the Specimen pathology annotation class SpecimenHistologicGrade to HistologicGrade." }
-      rescue NameError
-        logger.debug { "SpecimenHistologicGrade pathology annotation class not found; attempting to import the caTissue 1.1 HistologicGrade variant..." }
-        resource_import Java::pathology_specimen.HistologicGrade
-        const_set(:SpecimenHistologicGrade, HistologicGrade)
-        logger.debug { "Aliased the caTissue 1.1 Specimen pathology annotation class HistologicGrade class to the renamed 1.2 SpecimenHistologicGrade." }
       end
     end
   end

data/lib/catissue/domain/specimen/pathology/specimen_histologic_type.rb

@@ -2,21 +2,13 @@ require File.join(File.dirname(__FILE__), 'specimen_histologic_variant_type')
 
 module CaTissue
   class Specimen
-    class Pathology
-      # @quirk caTissue The 1.1 class HistologicType is renamed to SpecimenHistologicType in 1.2.
-      #   Alias the Ruby class constant for forward and backaward compatibility.
-      begin
-        resource_import Java::pathology_specimen.SpecimenHistologicType
-        const_set(:HistologicType, SpecimenHistologicType)
-        logger.debug { "Aliased the Specimen pathology annotation class SpecimenHistologicType to HistologicType." }
-      rescue NameError
-        logger.debug { "SpecimenHistologicType pathology annotation class not found; attempting to import the caTissue 1.1 HistologicType variant..." }
-        resource_import Java::pathology_specimen.HistologicType
-        const_set(:SpecimenHistologicType, HistologicType)
-        logger.debug { "Aliased the caTissue 1.1 Specimen pathology annotation class HistologicType class to the renamed 1.2 SpecimenHistologicType." }
-      end
-      
+    module Pathology
+      # @quirk caTissue The 1.1.2 class HistologicType is renamed to SpecimenHistologicType in 1.2.
+      #   Alias the SpecimenHistologicType Ruby class to HistologicType for backward compatibility.
       class SpecimenHistologicType
+        Pathology.const_set(:HistologicType, self)
+        logger.debug { "Aliased the Specimen pathology annotation class SpecimenHistologicType to HistologicType." }
+
         # @quirk caTissue The SpecimenHistologicType => SpecimenHistologicVariantType collection
         #   property is misnamed as histologicVariantType rather than histologicVariantTypeCollection.
         #   This misnaming prevents caRuby from inferring the attribute domain type and inverse.

data/lib/catissue/domain/specimen/pathology/specimen_histologic_variant_type.rb

@@ -1,17 +1,11 @@
 module CaTissue
   class Specimen
-    class Pathology
-      # @quirk caTissue The 1.1 class HistologicVariantType is renamed to SpecimenHistologicVariantType in 1.2.
-      #   Alias the Ruby class constant for forward and backaward compatibility.
-      begin
-        resource_import Java::pathology_specimen.SpecimenHistologicVariantType
-        const_set(:HistologicVariantType, SpecimenHistologicVariantType)
+    module Pathology
+      # @quirk caTissue The 1.1.2 class HistologicVariantType is renamed to SpecimenHistologicVariantType in 1.2.
+      #   Alias the SpecimenHistologicVariantType Ruby class to HistologicVariantType for backward compatibility.
+      class SpecimenHistologicVariantType
+        Pathology.const_set(:HistologicVariantType, self)
         logger.debug { "Aliased the Specimen pathology annotation class SpecimenHistologicVariantType to HistologicVariantType." }
-      rescue NameError
-        logger.debug { "SpecimenHistologicVariantType pathology annotation class not found; attempting to import the caTissue 1.1 HistologicVariantType variant..." }
-        resource_import Java::pathology_specimen.HistologicVariantType
-        const_set(:SpecimenHistologicVariantType, HistologicVariantType)
-        logger.debug { "Aliased the caTissue 1.1 Specimen pathology annotation class HistologicVariantType class to the renamed 1.2 SpecimenHistologicVariantType." }
       end
     end
   end

data/lib/catissue/domain/specimen/pathology/specimen_invasion.rb

@@ -1,17 +1,11 @@
 module CaTissue
   class Specimen
-    class Pathology
-      # @quirk caTissue The 1.1 class Invasion is renamed to SpecimenInvasion in 1.2.
-      #   Alias the Ruby class constant for forward and backaward compatibility.
-      begin
-        resource_import Java::pathology_specimen.SpecimenInvasion
-        const_set(:Invasion, SpecimenInvasion)
+    module Pathology
+      # @quirk caTissue The 1.1.2 class Invasion is renamed to SpecimenInvasion in 1.2.
+      #   Alias the SpecimenInvasion Ruby class constant to Invasion for backward compatibility.
+      class SpecimenInvasion
+        Pathology.const_set(:Invasion, self)
         logger.debug { "Aliased the Specimen pathology annotation class SpecimenInvasion to Invasion." }
-      rescue NameError
-        logger.debug { "SpecimenInvasion pathology annotation class not found; attempting to import the caTissue 1.1 Invasion variant..." }
-        resource_import Java::pathology_specimen.Invasion
-        const_set(:SpecimenInvasion, Invasion)
-        logger.debug { "Aliased the caTissue 1.1 Specimen pathology annotation class Invasion class to the renamed 1.2 SpecimenInvasion." }
       end
     end
   end

data/lib/catissue/domain/specimen.rb

@@ -1,16 +1,14 @@
-require 'caruby/util/inflector'
-require 'caruby/util/uniquifier'
-require 'caruby/util/validation'
-require 'catissue/util/storable'
-require 'catissue/util/collectible'
+require 'jinx/helpers/hashable'
+require 'jinx/helpers/inflector'
+require 'jinx/helpers/uniquifier'
+require 'jinx/helpers/validation'
+require 'catissue/helpers/storable'
+require 'catissue/helpers/collectible'
 
 module CaTissue
-  # import the Java class
-  resource_import Java::edu.wustl.catissuecore.domain.Specimen
-
   # The Specimen domain class.
-  class Specimen < CaTissue::AbstractSpecimen
-    include Storable, Collectible
+  class Specimen
+    include Collectible, Storable
     
     # @quirk caTissue Bug #64: Some domain collection properties not initialized.
     #   Initialize consent_tier_statuses if necessary.
@@ -33,9 +31,8 @@ module CaTissue
     add_mandatory_attributes(:initial_quantity, :available_quantity)
 
     set_secondary_key_attributes(:label)
-
-    # The Specimen-SpecimenRequirement association is bi-directional.
-    set_attribute_inverse(:specimen_requirement, :specimens)
+    
+    set_alternate_key_attributes(:barcode)
 
     # Specimen children are constrained to Specimen.
     set_attribute_type(:child_specimens, Specimen)
@@ -72,17 +69,21 @@ module CaTissue
     #   TransferEventParameters proxy instead. SpecimenPosition work-around is to
     #   designate a save proxy.
     add_dependent_attribute(:specimen_position)
+    
+    # @quirk caTissue Even though the Specimen SCG is not fetched and cannot be changed,
+    # Specimen update requires that the Specimen reference an SCG.
+    qualify_attribute(:specimen_collection_group, :include_in_save_template)
 
-    # Although label is the key, it is auto-generated if not provided in the create.
+    # Although label is the secondary key, it is auto-generated if not provided in the create.
     qualify_attribute(:label, :optional)
+    
+    # Although barcode is the alternate key, it is auto-generated if not provided in the create.
+    qualify_attribute(:barcode, :optional)
 
-    # A default available flag is set on the server.
-    qualify_attribute(:is_available, :volatile)
-
-    # A default available quantity is set on the server.
-    qualify_attribute(:available_quantity, :volatile)
+    # The Specimen-SpecimenRequirement association is bi-directional.
+    set_attribute_inverse(:specimen_requirement, :specimens)
     
-    # A default created_on is set on the server.
+    # @quirk caTissue The Specimen save argument created_on flag is ignored and set by caTissue instead.
     qualify_attribute(:created_on, :volatile)
 
     # Oddly, the seldom-used biohazards are fetched along with Specimen.
@@ -92,26 +93,43 @@ module CaTissue
     # or create Specimen argument and is set on the server. Mark the attribute as unsaved.
     qualify_attribute(:parent_changed, :unsaved)
 
-    # @quirk caTissue Bug #159: Update pending Specimen ignores availableQuantity.
-    #   available_quantity is not reflected in the caCORE create or update result.
-    #   This is true even though the caTissue GUI supports available_quantity update.
-    #   Work-around is to set the :autogenerated flag, which will refetch a saved Specimen
-    #   if there is a change to the available_quantity value and will reupdate the Specimen
-    #   if the fetched available_quantity differs from the save argument value.
-    qualify_attribute(:available_quantity, :autogenerated)
+    # @quirk caTissue Bug #159: caTissue update of a pending Specimen ignores the available
+    #   quantity in the update argument. The available quantity is not accurately reflected
+    #   in the caCORE create or update result. This is true even though the caTissue GUI
+    #   supports available_ uantity update. The caRuby work-around is to set the
+    #   +:autogenerated+ flag, which will refetch a saved Specimen if there is a change
+    #   to the available quantity value and will reupdate the Specimen if the fetched
+    #   available quantity differs from the save argument value.
+    #
+    # @quirk caTissue caTissue sporadically updates the available quantity when the
+    #   initial quantity is changed as follows:
+    #
+    #   * Precondition: Available Quantity is less than the Initial Quantity
+    #     Action: User sets Available Quantity to the Initial Quantity
+    #     Result: Available Quantity is unchanged
+    #
+    #   * Action: User increases Initial Quantity
+    #     Result: Available Quantity is incremented by the same amount
+    #
+    #   * Action: User decreases Initial Quantity
+    #     Result: Available Quantity is unchanged
+    #
+    #   The caRuby work-around is to mark available quantity as +volatile+, implying that
+    #   all bets are off as to how a saved available quantity is reflected in the database.
+    qualify_attribute(:available_quantity, :autogenerated, :volatile)
 
     # @quirk caTissue An auto-generated Specimen auto-generates the collection and received events.
     #   Therefore, CPR create must match the complete auto-generated SCG-Specimen-Event hierarchy.
     #   However, SpecimenRequirement events are not auto-generated. Therefore, the AbstractSpecimen
     #   events behavior must be specialized for Specimen but not SpecimenRequirement.
-    qualify_attribute(:specimen_events, :autogenerated)
-    
-    # The Specimen proxy class.
-    self.annotation_proxy_class_name = 'SpecimenRecordEntry'
+    qualify_attribute(:specimen_event_parameters, :autogenerated, :fetch_saved)
     
     # The Specimen pathology annotation.
     add_annotation('Pathology', :package => 'pathology_specimen', :service => 'pathologySpecimen')
     
+    # The preferred owner attribute evaluation order is the parent specimen, then the SCG.
+    order_owner_attributes(:parent_specimen, :specimen_collection_group)
+    
     # Specimen storage is constrained on the basis of the +specimen_class+.
     alias :storable_type :specimen_class
 
@@ -120,11 +138,6 @@ module CaTissue
       # work around caTissue Bug #64
       self.consent_tier_statuses ||= Java::JavaUtil::LinkedHashSet.new
     end
-
-    # Overrides {Resource#owner} to return the parent_specimen, if it exists, or the specimen_collection_group otherwise.
-    def owner
-      parent_specimen or specimen_collection_group
-    end
     
     # @return [Boolean] whether this Specimen collection status is +Pending+
     def pending?
@@ -136,7 +149,7 @@ module CaTissue
       collection_status == 'Collected'
     end
 
-    # Relaxes the {CaRuby::Persistable#fetch_saved?} condition for a Specimen as follows:
+    # Relaxes the +CaRuby::Persistable.fetch_saved?+ condition for a Specimen as follows:
     # * If the Specimen available_quantity was updated, then fetch the saved Specimen.
     # 
     # @return (see CaRuby::Persistable#fetch_saved)
@@ -154,11 +167,11 @@ module CaTissue
       CaTissue::CheckInCheckOutEventParameter.new(:specimen => self, :storage_status => Status.CHECKED_IN)
     end
     
-    # @quirk caTissue remove the autogenerated blank ExternalIdentifier.
-    # cf. https://cabig-kc.nci.nih.gov/Biospecimen/forums/viewtopic.php?f=19&t=436&sid=ef98f502fc0ab242781b7759a0eaff36
+    # Overrides +CaRuby::Mergable.merge_attribute+ to work around the caTissue
+    #  bugs described in {CaTissue::Specimen.remove_phantom_external_identifier}.
     def merge_attribute(attribute, newval, matches=nil)
       if attribute == :external_identifiers and newval then
-        CaTissue::Specimen.remove_empty_external_identifier(newval)
+        CaTissue::Specimen.remove_phantom_external_identifier(newval)
       end
       super
     end
@@ -175,7 +188,7 @@ module CaTissue
 #      update
 #    end
 
-    # Override default {CaRuby::Resource#merge_attributes} to ignore a source SpecimenRequirement parent_specimen.
+    # Override default +Jinx::Resource.merge_attributes+ to ignore a source SpecimenRequirement parent_specimen.
     def merge_attributes(other, attributes=nil)
       case other
         when SpecimenRequirement then
@@ -185,7 +198,7 @@ module CaTissue
           # copy the requirement characteristics
           sc = other.specimen_characteristics
           self.specimen_characteristics ||= sc.copy(MERGEABLE_SPC_CHR_ATTRS) if sc
-        when Hashable then
+        when Jinx::Hashable then
           # the requirement template
           rqmt = other[:specimen_requirement] || other[:requirement]
           # merge the attribute => value hash
@@ -198,7 +211,7 @@ module CaTissue
     end
 
     # Returns the Specimen in others which matches this Specimen in the scope of an owner SCG.
-    # This method relaxes {CaRuby::Resource#match_in_owner_scope} to include a match on at least
+    # This method relaxes +Jinx::Resource.match_in_owner_scope+ to include a match on at least
     # one external identifier.
     def match_in_owner_scope(others)
       super or others.detect do |other|
@@ -211,8 +224,8 @@ module CaTissue
     # its auto-generated counterpart but a new specimen can be created even if it matches an
     # existing specimen on the features described in {AbstractSpecimen#minimal_match?}. 
     # 
-    # @param (see CaRuby::Resource#minimal_match?)
-    # @return (see CaRuby::Resource#minimal_match?)
+    # @param (see Jinx::Resource#minimal_match?)
+    # @return (see Jinx::Resource#minimal_match?)
     def minimal_match?(other)
       super and other.collection_status == 'Pending'
     end
@@ -231,17 +244,17 @@ module CaTissue
     #
     # The default class is inferred from the _class_ parameter, if given, or inherited
     # from this parent specimen otherwise. The inferred class is the camel-case parameter value
-    # with +Specimen+ appended, e.g. :tissue => +TissueSpecimen+. This class name is resolved to
+    # with +Specimen+ appended, e.g. +:tissue+ => +TissueSpecimen+. This class name is resolved to
     # a class in the CaTissue module context.
     #
-    # The supported :type parameter value includes the permissible caTissue specimen type String
-    # values as well as the shortcut tissue type symbols :fresh, :fixed and :frozen.
+    # The supported +:type+ parameter value includes the permissible caTissue specimen type String
+    # values as well as the shortcut tissue type symbols :fresh, :fixed and +:frozen+.
     #
     # If a SpecimenRequirement parameter is provided, then that SpecimenRequirement's attribute
     # values are merged into the new Specimen after the other parameters are merged. Thus, params
     # takes precedence over the SpecimenRequirement.
     #
-    # If the :count parameter is set to a number greater than one, then the specimen is aliquoted
+    # If the +:count+ parameter is set to a number greater than one, then the specimen is aliquoted
     # into the specified number of samples.
     #
     # This method is a convenience method to create either a Specimen or CaTissue::SpecimenRequirement.
@@ -306,18 +319,18 @@ module CaTissue
     # Otherwise an exception is thrown.
     #
     # @param [CaTissue::ConsentTier, nil] optional consent tier of the SCG CaTissue::ConsentTierStatus to withdraw
-    # @raise [ValidationError] if an unambiguous SCG CaTissue::ConsentTierStatus to withdraw could not be determined
+    # @raise [Jinx::ValidationError] if an unambiguous SCG CaTissue::ConsentTierStatus to withdraw could not be determined
     def withdraw_consent(consent_tier=nil)
       statuses = specimen_collection_group.consent_tier_statuses
       status = if consent_tier then
         statuses.detect { |cts| cts.consent_tier.identifier == consent_tier.identifier } or
-        raise ValidationError.new("SCG #{specimen_collection_group} consent status not found for consent '#{consent_tier.statement}'")
+        raise Jinx::ValidationError.new("SCG #{specimen_collection_group} consent status not found for consent '#{consent_tier.statement}'")
       elsif specimen_collection_group.consent_tier_statuses.size == 1 then
         statuses.first
       elsif specimen_collection_group.consent_tier_statuses.size == 0 then
-        raise ValidationError.new("Specimen #{self} SCG does not have a consent tier status")
+        raise Jinx::ValidationError.new("Specimen #{self} SCG does not have a consent tier status")
       else
-        raise ValidationError.new("Specimen #{self} SCG consent tier is ambiguous:#{consent_tier_statuses.select { |cts| "\n  #{cts.statement}" }.to_series('or')}")
+        raise Jinx::ValidationError.new("Specimen #{self} SCG consent tier is ambiguous:#{consent_tier_statuses.select { |cts| "\n  #{cts.statement}" }.to_series('or')}")
       end
       ct = status.consent_tier
       cts = consent_tier_statuses.detect { |item| item.consent_tier == ct }
@@ -325,7 +338,12 @@ module CaTissue
       cts.status = 'Withdrawn'
     end
     
-    # Permanently dispose of this specimen with status 'Closed'.
+    # @return [Boolean] whether this specimen includes a {CaTissue::DisposalEventParameters}
+    def disposed?
+      specimen_event_parameters.any? { |ep| CaTissue::DisposalEventParameters === ep }
+    end
+    
+    # Permanently dispose of this specimen.
     #
     # @param [String, nil] reason the optional disposal reason
     # @return [CaTissue::DisposalEventParameters] the disposal event
@@ -335,14 +353,18 @@ module CaTissue
     
     protected
 
-    def self.remove_empty_external_identifier(eids)
-      bogus = eids.detect { |eid| eid.name.nil? }
-      if bogus then
-        logger.debug { "Work around caTissue bug by removing empty fetched #{bogus.specimen.qp} #{bogus.qp} from #{eids.qp}..." }
+    # @quirk caTissue Specimen auto-generates a phantom ExternalIdentifier.
+    #   cf. https://cabig-kc.nci.nih.gov/Biospecimen/forums/viewtopic.php?f=19&t=436&sid=ef98f502fc0ab242781b7759a0eaff36
+    #
+    # @param [<CaTissue::ExternalIdentifier>] eids the ExternalIndentifiers to clean up
+    def self.remove_phantom_external_identifier(eids)
+      phantom = eids.detect { |eid| eid.name.nil? }
+      if phantom then
+        logger.debug { "Work around caTissue bug by removing the phantom fetched #{phantom.specimen.qp} #{phantom.qp} from #{eids.qp}..." }
         # dissociate the specimen
-        bogus.specimen = nil
-        # remove the bogus eid
-        eids.delete(bogus)
+        phantom.specimen = nil
+        # remove the phantom eid
+        eids.delete(phantom)
       end
       eids
     end
@@ -362,24 +384,24 @@ module CaTissue
     # Updating Specimen with the availablity flag set and available_quantity zero
     # silently leaves the availablity flag unset.
     #
-    #  @raise [ValidationError] if the validation fails
+    #  @raise [Jinx::ValidationError] if the validation fails
     def validate_local
       super
       if parent.nil? and specimen_collection_group.nil? then
-        raise ValidationError.new("Top-level specimen #{self} is missing specimen collection group")
+        raise Jinx::ValidationError.new("Top-level specimen #{self} is missing specimen collection group")
       end
       if available_quantity and initial_quantity and available_quantity > initial_quantity then
-        raise ValidationError.new("#{self} available quantity #{available_quantity} cannot exceed initial quantity #{initial_quantity}")
+        raise Jinx::ValidationError.new("#{self} available quantity #{available_quantity} cannot exceed initial quantity #{initial_quantity}")
       end
       if available? and available_quantity.zero? then
-        raise ValidationError.new("#{self} availablility flag cannot be set when the avaialble quantity is zero")
+        raise Jinx::ValidationError.new("#{self} availablility flag cannot be set when the avaialble quantity is zero")
       end
       if collected? then
         unless event_parameters.detect { |ep| CaTissue::CollectionEventParameters === ep } then
-          raise ValidationError.new("#{self} is missing CollectionEventParameters")
+          raise Jinx::ValidationError.new("#{self} is missing CollectionEventParameters")
         end
         unless event_parameters.detect { |ep| CaTissue::ReceivedEventParameters === ep } then
-          raise ValidationError.new("#{self} is missing ReceivedEventParameters")
+          raise Jinx::ValidationError.new("#{self} is missing ReceivedEventParameters")
         end
       end
     end
@@ -439,7 +461,8 @@ module CaTissue
       if is_available.nil? then
         self.is_available = default_availablility
       elsif is_available == false then
-        # Reset is_available value from false to nil to work around caTissue bug but described in method doc.
+        # Reset is_available value from false to nil to work around caTissue bug but described in
+        # the method rubydoc above.
         self.is_available = nil
       end
     end
@@ -464,34 +487,48 @@ module CaTissue
     
     # @return [CaTissue::ReceivedEventParameters] the default REP
     def create_default_received_event_parameters
-      user = specimen_collection_group.receiver || default_scg_coordinator || return
+      rep = parent.received_event_parameters if parent
+      user = rep.user if rep
+      user ||= scg_receiver || return
       rep = CaTissue::ReceivedEventParameters.new(:specimen => self, :user => user)
       logger.debug { "Created default #{qp} received event #{rep.qp}." }
       rep
     end
     
+    # The default CEP user is, by order of preference:
+    # * this specimen's parent specimen collector
+    # * this specimen's SCG collector
+    # * the receiver
+    # 
     # @param [CaTissue::ReceivedEventParameters] the required REP
     # @return [CaTissue::CollectionEventParameters] the default CEP
     def create_default_collection_event_parameters(rep)
-      user = scg_collector || rep.user || return
+      cep = parent.collection_event_parameters if parent
+      user = cep.user if cep
+      user ||= scg_collector || rep.user || return
       cep = CaTissue::CollectionEventParameters.new(:specimen => self, :user => user)
       logger.debug { "Created default #{qp} collection event #{cep.qp}." }
       cep
     end
     
+    # @return [CaTissue::User, nil] the SCG receiver, if any
+    def scg_receiver
+      scg = specimen_collection_group || return
+      scg.receiver or default_scg_coordinator(scg)
+    end
+    
     # @return [CaTissue::User, nil] the SCG collector, if any
     def scg_collector
       specimen_collection_group.collector if specimen_collection_group
     end
     
     # @return [CaTissue::User, nil] the first SCG protocol coordinator
-    def default_scg_coordinator
-      scg = specimen_collection_group || return
+    def default_scg_coordinator(scg)
       cp = scg.collection_protocol || return
       cp.coordinators.first
     end
 
-    # Sets the :specimen_class parameter to a permissible caTissue value.
+    # Sets the +:specimen_class+ parameter to a permissible caTissue value.
     def self.standardize_class_parameter(params)
       opt = params[:specimen_class]
       if opt.nil? then
@@ -545,15 +582,15 @@ module CaTissue
     def decrement_derived_quantity(child)
       return unless specimen_type == child.specimen_type and child.initial_quantity
       if available_quantity.nil? then
-        raise ValidationError.new("Derived specimen has an initial quantity #{child.initial_quantity} but the parent is missing an available quantity")
+        raise Jinx::ValidationError.new("Derived specimen has an initial quantity #{child.initial_quantity} but the parent is missing an available quantity")
       elsif (available_quantity - child.initial_quantity).abs < 0.00000001 then
         # rounding error
         self.available_quantity = 0.0
       elsif child.initial_quantity <= available_quantity then
         self.available_quantity -= child.initial_quantity
       else
-        raise ValidationError.new("Derived specimen initial quantity #{child.initial_quantity} exceeds parent available quantity #{available_quantity}")
+        raise Jinx::ValidationError.new("Derived specimen initial quantity #{child.initial_quantity} exceeds parent available quantity #{available_quantity}")
       end
     end
   end
-end
+end