caruby-tissue 1.5.4 → 1.5.5

data/lib/catissue/domain/collection_protocol_registration.rb

@@ -6,9 +6,6 @@ module CaTissue
   resource_import Java::edu.wustl.catissuecore.domain.CollectionProtocolRegistration
 
   # The CollectionProtocolRegistration domain class.
-  #
-  # @quirk caTissue Augment the standard CPR storable reference attributes to work around caTissue Bug #150:
-  #   Create CollectionProtocol in API ignores startDate.
   class CollectionProtocolRegistration
     # @quirk caTissue Bug #64: Some domain collection properties not initialized.
     #   Initialize consent_tier_responses if necessary. 
@@ -70,12 +67,15 @@ module CaTissue
     # must exist. This is checked in the special purpose {#validate_local} method.
     qualify_attribute(:protocol_participant_identifier, :optional)
 
+    # @quirk caTissue  Augment the standard metadata storable reference attributes to work around caTissue Bug #150:
+    #   Create CollectionProtocol in API ignores startDate.
     qualify_attribute(:registration_date, :update_only)
 
+    # @quirk caTissue Bug #64 - consent tier responses is is not initialized to an empty set
+    #    in the Java constructor. Initialize it to a +LinkedHashSet+ in caRuby.
     def initialize
       super
-      # following line works around an obscure problem whereby CPR init could not call consent_tier_responses below;
-      # TODO - verify that it is still necessary
+      # @quirk JRuby consent_tier_responses property method is not accessible until respond_to? is called.
       respond_to?(:consent_tier_responses)
       # work around caTissue Bug #64
       self.consent_tier_responses ||= Java::JavaUtil::LinkedHashSet.new

data/lib/catissue/domain/container.rb

@@ -9,10 +9,6 @@ module CaTissue
 
   # The +caTissue+ +Container+ domain class wrapper.
   # Each Container subclass is required to implement the {#container_type} method.
-  #
-  # @quirk caTissue container capacity was auto-generated in 1.1.2, but is not in 1.2.
-  # @quirk caTissue Like SCG, the Container save argument name value is ignored and assigned by caTissue
-  #   to a different value instead. Therefore, this attribute is marked auto-generated.
   class Container
     include Storable
 
@@ -22,11 +18,14 @@ module CaTissue
 
     add_attribute_defaults(:activity_status => 'Active', :full => false)
 
+    # @quirk caTissue container capacity was auto-generated in 1.1.2, but is not in 1.2.
     add_dependent_attribute(:capacity)
 
     # located_at_position is cascaded but not fetched.
     add_dependent_attribute(:located_at_position, :unfetched)
 
+    # @quirk caTissue Like SCG, the Container save argument name value is ignored and assigned by caTissue
+    #   to a different value instead. Therefore, this attribute is marked auto-generated.
     qualify_attribute(:name, :autogenerated)
 
     # Returns the meta-type which constrains this Container in its role as a {Storable}

data/lib/catissue/domain/container_type.rb

@@ -5,7 +5,7 @@ module CaTissue
   resource_import Java::edu.wustl.catissuecore.domain.ContainerType
 
   # The caTissue ContainerType domain class wrapper.
-  # Each subclass is required to implement the +container_class+ method.
+  # Each {ContainerType} subclass is required to implement the container_class method.
   #
   # @quirk caTissue the ContainerType and Container class hierarchy is a confusing
   #   olio of entangled relationships. The canonical use case is as follows:
@@ -61,10 +61,7 @@ module CaTissue
   #   needs to make to add a specimen box to a freezer is:
   #     freezer << box
   #   which places the box in the first available rack slot in the freezer, or:
-  #     box >> freezer
-  #
-  # @quirk caTissue although capacity is not marked cascaded in Hibernate, it is created when the
-  #   ContainerType is created.
+  #     box >> freezer 
   class ContainerType
     add_attribute_aliases(:column_label => :oneDimensionLabel, :row_label => :twoDimensionLabel)
 
@@ -74,9 +71,11 @@ module CaTissue
 
     add_mandatory_attributes(:activity_status, :capacity, :one_dimension_label, :two_dimension_label)
 
+    # @quirk caTissue although capacity is not marked cascaded in Hibernate, it is created when the
+    #   ContainerType is created.
     add_dependent_attribute(:capacity)
     
-    # Override default +CaRuby::Resource.merge_attributes+ to support the Capacity :rows and :columns
+    # Override default {CaRuby::Resource#merge_attributes} to support the Capacity :rows and :columns
     # pseudo-attributes.
     #
     # @quirk JRuby Subclasses do not pick up this class's Resource method overrides.
@@ -84,13 +83,13 @@ module CaTissue
     #   not pick up ContainerType Resource overrides. Work-around is that each ContainerType
     #   subclass must alias +merge_attributes+ to this method.
     #
-    # @param (see CaRuby::Resource#merge_attributes)
+    # @param (see #merge_attributes)
     def merge_attributes(other, attributes=nil)
       if Hash === other then
         # partition the other hash into the Capacity attributes and ContainerType attributes
-        cp_hash, ct_hash = other.partition { |key, value| key == :rows or key == :columns }
-        self.capacity ||= CaTissue::Capacity.new(cp_hash).add_defaults unless cp_hash.empty?
-        super(ct_hash, attributes)
+        cph, cth = other.split { |key, value| key == :rows or key == :columns }
+        self.capacity ||= CaTissue::Capacity.new(cph).add_defaults unless cph.empty?
+        super(cth, attributes)
       else
         super(other, attributes)
       end
@@ -134,8 +133,8 @@ module CaTissue
     private
     
     # Adds an empty capacity and default dimension labels, if necessary.
-    # The default {#one_dimension_label} is 'Column' if there is a non-zero dimension capacity, 'Unused' otherwise.
-    # The default {#two_dimension_label} is 'Row' if there is a non-zero dimension capacity, 'Unused' otherwise.
+    # The default +one_dimension_label+ is 'Column' if there is a non-zero dimension capacity, 'Unused' otherwise.
+    # The default +two_dimension_label+ is 'Row' if there is a non-zero dimension capacity, 'Unused' otherwise.
     #
     # @quirk JRuby See {#merge_container_type_attributes}. Work-around is that each ContainerType
     #   subclass must alias +add_defaults_local+ to this method.

data/lib/catissue/domain/disposal_event_parameters.rb

@@ -2,10 +2,10 @@ module CaTissue
   # import the Java class
   resource_import Java::edu.wustl.catissuecore.domain.DisposalEventParameters
 
-  # @quirk caTissue DisposalEventParameters activity status is transient.
   class DisposalEventParameters < CaTissue::SpecimenEventParameters
     add_attribute_defaults(:activity_status => 'Closed')
 
+    # @quirk caTissue DisposalEventParameters activity status is transient.
     qualify_attribute(:activity_status, :unfetched)
   end
 end

data/lib/catissue/domain/new_specimen_array_order_item.rb

@@ -6,23 +6,24 @@ module CaTissue
 
   # The NewSpecimenArrayOrderItem domain class.
   class NewSpecimenArrayOrderItem
-    # @quirk caTissue Bug #64: Some domain collection properties not initialized.
-    #   Initialize order_items if necessary. 
+    # @quirk caTissue Bug #64: order items collection property is not initialized to an empty set
+    #    in the Java constructor. Initialize it to a +LinkedHashSet+ in caRuby. 
     #
     # @return [Java::JavaUtil::Set] the items
     def order_items
       getOrderItemCollection or (self.order_items = Java::JavaUtil::LinkedHashSet.new)
     end
     
-    # @quirk caTissue Bug #64: Some domain collection properties not initialized.
-    #   Initialize distributions if necessary. 
+   # @quirk caTissue Bug #64: distributions collection property is not initialized to an empty set
+    #    in the Java constructor. Initialize it to a +LinkedHashSet+ in caRuby.
     def distributions
       getDistributionCollection or (self.distributions = Java::JavaUtil::LinkedHashSet.new)
     end
 
     def initialize
       super
-      # jRuby bug? - Java methods not acceesible until respond_to? called; TODO - reconfirm this
+      # @quirk JRuby order_items and distributions property methods are not accessible until
+      # respond_to? is called.
       respond_to?(:order_items)
       respond_to?(:distributions)
       # work around caTissue Bug #64

data/lib/catissue/domain/order_details.rb

@@ -13,9 +13,13 @@ module CaTissue
       getOrderItemCollection or (self.order_items = Java::JavaUtil::LinkedHashSet.new)
     end
     
+    # @quirk caTissue Bug #64 - consent tier responses is not initialized to an empty set
+    #    in the Java constructor. Initialize it to a +LinkedHashSet+ in caRuby.
     def initialize
       super
+      # @quirk JRuby order_items property method isnot accessible until respond_to? is called.
       respond_to?(:order_items)
+      # @quirk caTissue work around caTissue Bug #64
       self.order_items ||= Java::JavaUtil::LinkedHashSet.new
     end
   end

data/lib/catissue/domain/participant.rb

@@ -7,18 +7,6 @@ module CaTissue
   resource_import Java::edu.wustl.catissuecore.domain.Participant
 
   # The Participant domain class.
-  #
-  # @quirk caTissue clinical study is unsupported by 1.1.x caTissue, removed in 1.2.
-  # @quirk caTissue Bug #154: Participant gender is specified by caTissue as optional, but if it is not set then
-  #   it appears as Female in the GUI even though it is null in the database.
-  # @quirk caTissue Participant CPR cascade is simulated in the bizlogic.
-  #   See the PMI comment below.
-  # @quirk caTissue Participant PMI is fetched but not cascaded. However, the Participant bizlogic
-  #   simulates PMI cascade. The bizlogic doesn't document why this is done, but it appears that the
-  #   reason is to inject an empty PMI if necessary in order to work around a caTissue query bug
-  #   (see merge_attribute comment). At any rate, mark PMI as cascaded in the caRuby metadata
-  #   to reflect the bizlogic simulation. However, this designation should be revisited with each
-  #   release, since if the bizlogic hack is removed then caRuby Participant PMI save will break.
   class Participant
     include Person
 
@@ -26,27 +14,39 @@ module CaTissue
     # which is reflected in the saved Java property name subfields.
     add_attribute(:name, CaRuby::Person::Name)
 
-    remove_attribute(:clinical_study_registrations) if attribute_defined?(:clinical_study_registrations)
+    # @quirk caTissue clinical study is unsupported by 1.1.x caTissue, removed in 1.2.
+    if attribute_defined?(:clinical_study_registrations) then remove_attribute(:clinical_study_registrations) end
 
     add_attribute_aliases(:collection_registrations => :collection_protocol_registrations,
-    :registrations => :collection_protocol_registrations,
-    :medical_identifiers => :participant_medical_identifiers)
+      :registrations => :collection_protocol_registrations,
+      :medical_identifiers => :participant_medical_identifiers)
 
     set_secondary_key_attributes(:social_security_number)
 
     # Clarification on defaults:
     # * 'Unknown': value is unknown by anybody
     # * 'Unspecified': value is known by somebody, but the data was not communicated to the bank
-    # cf. https://cabig-kc.nci.nih.gov/Biospecimen/forums/viewtopic.php?f=16&t=672&p=2343&e=2343
+    #
+    # Cf. https://cabig-kc.nci.nih.gov/Biospecimen/forums/viewtopic.php?f=16&t=672&p=2343&e=2343
     add_attribute_defaults(:activity_status => 'Active', :ethnicity => 'Unknown', :gender => 'Unspecified',
       :sex_genotype => 'Unknown', :vital_status => 'Unknown')
 
+    # @quirk caTissue Bug #154: Participant gender is specified by caTissue as optional, but if it is not set then
+    #   it appears as Female in the GUI even though it is null in the database.
     add_mandatory_attributes(:activity_status, :gender)
 
+    # @quirk caTissue Participant CPR cascade is simulated in the bizlogic.
+    #   See the PMI comment below.
     add_dependent_attribute(:collection_protocol_registrations)
 
     add_dependent_attribute(:races)
 
+    # @quirk caTissue Participant PMI is fetched but not cascaded. However, the Participant bizlogic
+    #   simulates PMI cascade. The bizlogic doesn't document why this is done, but it appears that the
+    #   reason is to inject an empty PMI if necessary in order to work around a caTissue query bug
+    #   (see merge_attribute comment). At any rate, mark PMI as cascaded in the caRuby metadata
+    #   to reflect the bizlogic simulation. However, this designation should be revisited with each
+    #   release, since if the bizlogic hack is removed then caRuby Participant PMI save will break.
     add_dependent_attribute(:participant_medical_identifiers)
 
     # SSN is a key, if present, but is not required.
@@ -57,7 +57,7 @@ module CaTissue
     
     # The clinicial annotation.
     add_annotation('Clinical', :package => 'clinical_annotation', :service => 'CA')
-
+    
     # @quirk caTissue remove the autogenerated blank PMI.
     #   cf. https://cabig-kc.nci.nih.gov/Biospecimen/forums/viewtopic.php?f=19&t=436&sid=ef98f502fc0ab242781b7759a0eaff36
     def merge_attribute(attribute, newval, matches=nil)

data/lib/catissue/domain/participant_medical_identifier.rb

@@ -6,9 +6,6 @@ module CaTissue
 
 
   # The ParticipantMedicalIdentifier domain class.
-  #
-  # @quirk caTissue 1.2 PMI method signature is corrupted. Work-around is to explicitly set the attribute type.
-  #   Cf. https://cabig-kc.nci.nih.gov/Biospecimen/forums/viewtopic.php?f=19&t=984&sid=773ad8f0bbbfc6e9c9b45ec1bf43a6e9.
   class ParticipantMedicalIdentifier
     # Sets this ParticipantMedicalIdentifier's medical record number to the given value.
     # A Numeric value is converted to a String.
@@ -17,6 +14,8 @@ module CaTissue
       setMedicalRecordNumber(value)
     end
     
+    # @quirk caTissue 1.2 PMI method signature is corrupted. Work-around is to explicitly set the attribute type.
+    #   Cf. https://cabig-kc.nci.nih.gov/Biospecimen/forums/viewtopic.php?f=19&t=984&sid=773ad8f0bbbfc6e9c9b45ec1bf43a6e9.
     set_attribute_type(:site, CaTissue::Site)
 
     set_secondary_key_attributes(:site, :medical_record_number)

data/lib/catissue/domain/site.rb

@@ -3,18 +3,16 @@ module CaTissue
   resource_import Java::edu.wustl.catissuecore.domain.Site
 
   # The Site domain class.
-  #
-  # @quirk caTissue caTissue 1.2 Site has a facility_id Java property, but caTissue throws an
-  #   UnsupportedOperationException if they are called.
-  #
-  # @quirk caTissue the Site SCG collection is ignored, since it is not fetched with the Site,
-  #   the caCORE query builder doesn't support abstract types, and even if it worked it would
-  #   have limited value but high fetch cost. The work-around, which is also the more natural
-  #   mechanism, is to query on a concrete SCG subclass template which references the target Site.
   class Site
+    # @quirk caTissue the Site SCG collection is ignored, since it is not fetched with the Site,
+    #   the caCORE query builder doesn't support abstract types, and even if it worked it would
+    #   have limited value but high fetch cost. The work-around, which is also the more natural
+    #   mechanism, is to query on a concrete SCG subclass template which references the target Site.
     remove_attribute(:abstract_specimen_collection_groups)
 
-    remove_attribute(:facility_id) if attribute_defined?(:facility_id)
+    # @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
 
     set_secondary_key_attributes(:name)
 

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

@@ -1,6 +1,8 @@
 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)
@@ -11,9 +13,6 @@ module CaTissue
         const_set(:ProstateSpecimenGleasonScore, GleasonScore)
         logger.debug { "Aliased the caTissue 1.1 Specimen pathology annotation class GleasonScore class to the renamed 1.2 ProstateSpecimenGleasonScore." }
       end
-      # @quirk caTissue The 1.1 class GleasonScore is renamed to ProstateSpecimenGleasonScore in 1.2.
-      #   Alias the Ruby class constant for forward and backaward compatibility.
-      class ProstateSpecimenGleasonScore; end
     end
   end
 end

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

@@ -3,10 +3,11 @@ module CaTissue
     class Pathology
       begin
         resource_import Java::pathology_specimen.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.
+        const_set(:ProstatePathologyAnnotation, ProstateSpecimenPathologyAnnotation)
+        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

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

@@ -1,5 +1,10 @@
 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
@@ -11,13 +16,6 @@ module CaTissue
         const_set(:SpecimenAdditionalFinding, AdditionalFinding)
         logger.debug { "Aliased the caTissue 1.1 Specimen pathology annotation class AdditionalFinding class to the renamed 1.2 SpecimenAdditionalFinding." }
       end
-      
-      # @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 SpecimenAdditionalFinding; end
     end
   end
 end

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

@@ -4,6 +4,9 @@ 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)
@@ -15,21 +18,18 @@ module CaTissue
         logger.debug { "Aliased the caTissue 1.1 Specimen pathology annotation class BaseSolidTissuePathologyAnnotation class to the renamed 1.2 SpecimenBaseSolidTissuePathologyAnnotation." }
       end
       
-      # @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.
-      # @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.
-      # @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.
       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)
         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)
         set_attribute_inverse(:histologic_type, :specimen_base_solid_tissue_pathology_annotation)
       end

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

@@ -1,6 +1,8 @@
 module CaTissue
   class Specimen
     class 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)
@@ -11,10 +13,6 @@ module CaTissue
         const_set(:SpecimenDetails, Details)
         logger.debug { "Aliased the caTissue 1.1 Specimen pathology annotation class Details class to the renamed 1.2 SpecimenDetails." }
       end
-      
-      # @quirk caTissue The 1.1 class Details is renamed to SpecimenDetails in 1.2.
-      #   Alias the Ruby class constant for forward and backaward compatibility.
-      class SpecimenDetails; end
     end
   end
 end

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

@@ -1,6 +1,8 @@
 module CaTissue
   class Specimen
     class 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)
@@ -11,10 +13,6 @@ module CaTissue
         const_set(:SpecimenHistologicGrade, HistologicGrade)
         logger.debug { "Aliased the caTissue 1.1 Specimen pathology annotation class HistologicGrade class to the renamed 1.2 SpecimenHistologicGrade." }
       end
-
-      # @quirk caTissue The 1.1 class HistologicGrade is renamed to SpecimenHistologicGrade in 1.2.
-      #   Alias the Ruby class constant for forward and backaward compatibility.
-      class SpecimenHistologicGrade; end
     end
   end
 end

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

@@ -3,6 +3,8 @@ 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)
@@ -14,13 +16,11 @@ module CaTissue
         logger.debug { "Aliased the caTissue 1.1 Specimen pathology annotation class HistologicType class to the renamed 1.2 SpecimenHistologicType." }
       end
       
-      # @quirk caTissue The 1.1 class HistologicType is renamed to SpecimenHistologicType in 1.2.
-      #   Alias the Ruby class constant for forward and backaward compatibility.
-      # @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.
-      #   Work-around is to set these attribute features manually.
       class SpecimenHistologicType
+        # @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.
+        #   Work-around is to set these attribute features manually.
         set_attribute_type(:histologic_variant_type, CaTissue::Specimen::Pathology::SpecimenHistologicVariantType)
         set_attribute_inverse(:histologic_variant_type, :histologic_type)
       end