caruby-tissue 1.5.4 → 1.5.5

data/lib/catissue/database/controlled_values.rb

@@ -6,12 +6,11 @@ require 'caruby/util/visitor'
 require 'catissue/resource'
 require 'catissue/database'
 require 'catissue/util/controlled_value'
-require 'caruby/util/transitive_closure'
 require 'caruby/domain/properties'
 
 module CaTissue
   # This ControlledValues class loads caTissue permissible values from the database.
-  # Use of this class requires the +dbi+ gem. See +CaRuby::SQLExecutor.initialize+
+  # Use of this class requires the +dbi+ gem. See {CaRuby::SQLExecutor#initialize}
   # for a description of the database access properties.
   class ControlledValues
     include Singleton
@@ -31,7 +30,7 @@ module CaTissue
     # * :tissue_site
     # * :clinical_diagnosis
     #
-    # @param [String,Symbol] public_id_or_alias the caTissue public id or an alias defined above
+    #@param [String,Symbol] public_id_or_alias the caTissue public id or an alias defined above
     # @return [<ControlledValue>] instances for the given public_id_or_alias
     def for_public_id(public_id_or_alias)
       pid = ControlledValue.standard_public_id(public_id_or_alias)

data/lib/catissue/database.rb

@@ -7,20 +7,20 @@ require 'catissue/database/annotation/annotator'
 require 'catissue/util/collectible_event_parameters'
 
 module CaTissue
-  # A CaTissue: Database mediates access to the caTissue database.
-  # The superclass +CaRuby::Database+ functionality is preserved and not expanded, but this CaTissue
-  # Database implementation overrides several base class private methods to enable alternate
-  # caTissue-specific search strategies and work-arounds.
+  # Database mediates access to the caTissue application server.
+  # Superclass +CaRuby::Database+ functionality base class methods are overridden as necessary
+  # to enable caTissue-specific work-arounds and alternate search strategies.
+  # A CaTissue::Database mediates access to the caTissue database.
+  # The CaRuby::Database functionality is preserved and not expanded, but this CaTissue::Database overrides
+  # several base class private methods to enable alternate CaTissue-specific search strategies and work
+  # around caTissue and caCORE bugs.
   class Database < CaRuby::Database
     include Singleton
     
-    # @return [CaRuby::SQLExecutor] a utility SQL executor
-    attr_reader :executor
-    
-    # @return [{Symbol => Object}] the server access properties
-    attr_reader :access_properties
+    # return [CaRuby::SQLExecutor] a utility SQL executor
+    attr_reader :executor, :access_properties
 
-    # Creates a new Database with the +catissuecore+ service.
+    # Creates a new Database with the +catissuecore+ service and {CaTissue.access_properties}.
     def initialize
       @access_properties = CaTissue.access_properties
       super(SVC_NAME, @access_properties)
@@ -32,7 +32,7 @@ module CaTissue
       @annotator ||= Annotator.new(self)
     end
 
-    # If the given domain object is an {Annotation}, then this method returns the {Annotation::AnnotationService}
+    # If the given domain object is an {Annotation}, then this method returns the {AnnotationService}
     # for the object {AnnotationModule}, otherwise this method returns the standard {CaTissue::Database}
     # service.
     #
@@ -42,7 +42,7 @@ module CaTissue
       klass < Annotation ? klass.annotation_module.persistence_service : super
     end
     
-    # Augments +CaRuby::Database.ensure_exists+ to ensure that an {Annotation::Proxy} reference identifier
+    # Augments {CaRuby::Database#ensure_exists} to ensure that an {Annotation::Proxy} reference identifier
     # reflects the hook identifier.
     #
     # @param (see CaRuby::Database::Writer#ensure_exists)
@@ -55,14 +55,14 @@ module CaTissue
     
     private
 
-    # The application service name
+    # The application service name.
     SVC_NAME = 'catissuecore'
     
     UPD_EID_SQL = 'update catissue_external_identifier set name = ?, value = ?, specimen_id = ? where identifier = ?'
     
     UPD_CTR_SQL = 'update catissue_consent_tier_response set response = ? where identifier = ?'
 
-    # Overrides #+CaRuby::Database::Writer.recursive_save?+ to support the update work-around
+    # Overrides #{CaRuby::Database::Writer#recursive_save?} to support the update work-around
     # described in {#update_object}. A recursive SCG update is allowed if the nested
     # transaction sequence is:
     # * Update SCG
@@ -195,7 +195,7 @@ module CaTissue
       penultimate and penultimate.subject == obj
     end
       
-    # Augments +CaRuby::Database.save_with_template+ to work around the following caTissue anomalies:
+    # Augments {CaRuby::Database#save_with_template} to work around the following caTissue anomalies:
     #
     # @quirk caTissue Bug #149: API update TissueSpecimen position validation incorrect.
     #   The Specimen update argument must reference the old position, even though the position is not
@@ -206,21 +206,21 @@ module CaTissue
     #   position in the caTissue service update argument. A Specimen position is altered as a side-effect
     #   by creating a proxy save {CaTissue::TransferEventParameters}. The changed position is not reflected
     #   in the Specimen position, which must be refetched to reflect the database state. This fetch is
-    #   done automatically by +CaRuby::Database+ as part of the save proxy mechanism. The Specimen update
+    #   done automatically by {CaRuby::Database} as part of the save proxy mechanism. The Specimen update
     #   template must include a reference to the former position but not the changed position.
     #
-    #   However, the Specimen +CaRuby::Writer.update+ argument will include the changed position, not the
-    #   former position. The template built +CaRuby::Writer.update+ for submission to the caTissue app
+    #   However, the Specimen {CaRuby::Writer#update} argument will include the changed position, not the
+    #   former position. The template built {CaRuby::Writer#update} for submission to the caTissue app
     #   does not include a position reference, since the position has a save proxy which handles position
-    #   change as part of the +CaRuby::Writer+ update dependent propagation.
+    #   change as part of the {CaRuby::Writer} update dependent propagation.
     #
     #   Thus, updating a Specimen which includes a position change is performed as follows:
     #   * reconstitute the former position from the Position snapshot taken as part of the
-    #      +CaRuby::Persistable+ change tracker.
-    #   * add the former position to the template (which will now differ from the +CaRuby::Writer.update+
+    #      {CaRuby::Persistable} change tracker.
+    #   * add the former position to the template (which will now differ from the {CaRuby::Writer#update}
     #     argument).
     #   * submit the adjusted Specimen template to the caTissue app updateObject.
-    #   * +CaRuby::Writer.update+ will propagate the Specimen update to the changed position dependent,
+    #   * {CaRuby::Writer#update} will propagate the Specimen update to the changed position dependent,
     #     which in turn saves via the {CaTissue::TransferEventParameters} proxy.
     #   * The proxy save will in turn refetch the proxied Specimen position to obtain the identifier
     #     and merge this into the Specimen position.
@@ -294,7 +294,7 @@ module CaTissue
         logger.debug { "caTissue #{ctr} update work-around completed." }
     end
 
-    # Overrides +CaRuby::Database::Writer.save_changed_dependents+ to handle the following anomalies:
+    # Overrides {CaRuby::Database::Writer#save_changed_dependents} to handle the following anomalies:
     # * create Specimen disposal event last, as described in {#save_changed_specimen_dependents}
     #
     # @param (see CaRuby::Writer#save_dependents)
@@ -305,7 +305,7 @@ module CaTissue
       end   
     end
     
-    # Overrides +CaRuby::Database::Writer.save_changed_dependents+ on a Specimen to correct the
+    # Overrides {CaRuby::Database::Writer#save_changed_dependents} on a Specimen to correct the
     # following problem:
     #
     # @quirk caTissue DisposalEventParameters must be created after all other Specimen SEPs.
@@ -324,7 +324,7 @@ module CaTissue
     # for the subtle interaction required between these two work-arounds.
     #
     # @param [CaTissue::Specimen] the specimen whose dependents are to be saved
-    # @yield [dependent] calls the base +CaRuby::Writer.save_changed_dependents+ 
+    # @yield [dependent] calls the base {CaRuby::Writer#save_changed_dependents} 
     # @yieldparam [Resource] dependent the dependent to save
     def save_changed_specimen_dependents(specimen)
       dsp = specimen.specimen_events.detect { |ep| CaTissue::DisposalEventParameters === ep }
@@ -346,7 +346,7 @@ module CaTissue
       end
     end
     
-    # Overrides +CaRuby::Database.build_save_template+ to return obj itself if
+    # Overrides {CaRuby::Database#build_save_template} to return obj itself if
     # obj is an {Annotation}, since annotations do not employ a separate template.
     #
     # @param (see CaRuby::Database#build_save_template)
@@ -372,7 +372,7 @@ module CaTissue
       annotation
     end
 
-    # Overrides +CaRuby::Database::Writer.save_with_template+ to work around caTissue bugs.
+    # Overrides {CaRuby::Database::Writer#save_with_template} to work around caTissue bugs.
     # @quirk caTissue  Bug #63: a SpecimenCollectionGroup update requires the referenced CollectionProtocolRegistration
     #   with an identifier to hold extraneous CollectionProtocolRegistration content, including the CPR
     #   collection protocol and PPI.
@@ -482,7 +482,7 @@ module CaTissue
       template.send(wtr, pxy)
     end
 
-    # Augment +CaRuby::Database::Writer.create_object+ to work around caTissue bugs.
+    # Augment {CaRuby::Database::Writer#create_object} to work around caTissue bugs.
     # @quirk caTissue Bug #124: SCG SpecimenEventParameters save fails validation.
     #   Work-around is to create the SEP by updating the SCG.
     # @quirk If obj is a CaTissue::Specimen with the is_available flag set to false, then work around the bug
@@ -517,7 +517,7 @@ module CaTissue
       obj
     end
     
-    # Overrides +CaRuby::Database.create_from_template+ as follows:
+    # Overrides {CaRuby::Database#create_from_template} as follows:
     # * Surrogate {Annotation::Proxy} is "created" by setting the identifier to its hook owner.
     #   The create operation then creates referenced uncreated dependents.
     #
@@ -552,7 +552,7 @@ module CaTissue
     # to a non-zero value, create the Specimen and then update the created Specimen with
     # the original values.
     #
-    # If spc has a disposal event, then this work-around interacts with the {#save_dependents}
+    # If spc has a disposal event, then this work-around interacts with the {#save_changed_dependents}
     # work-around as follows:
     # * delete that event from the Specimen.
     # * Create the Specimen as described above.
@@ -599,7 +599,7 @@ module CaTissue
       specimen
     end
 
-    # Overrides +CaRuby::Database::Reader.fetch_object+ to circumvent {Annotation} fetch, since an annotation
+    # Overrides {CaRuby::Database::Reader#fetch_object} to circumvent {Annotation} fetch, since an annotation
     # does not have a key.
     def fetch_object(obj)
       super or fetch_alternative(obj)
@@ -611,8 +611,37 @@ module CaTissue
         when CaTissue::Participant then fetch_participant_alternative(obj)
       end
     end
+    
+    # @quirk JRuby fetching a CPR CP swizzles the CPR participant. This only occurs when the CP exists in
+    #   the database. The work-around is to reset the swizzled participant. However, merely capturing the
+    #   participant before the CP find is sufficient to prevent this bug. JRuby does not corrupt the CPR
+    #   participant if it is referenced by a local variable. The CPR is too complicated to reformulate as
+    #   this bug as an isolated non-caTissue test case.
+    def finder_parameter(obj, attribute)
+      if CaTissue::CollectionProtocolRegistration === obj and attribute == :collection_protocol then
+        # Simply assigning the pnt variable prevents the bug from occurring.
+        pnt = obj.participant
+      end
+      value = super
+      if value and pnt and pnt != obj.participant then
+        swzld = obj.participant
+        obj.participant = pnt
+        logger.debug { "Worked around #{obj} corruption by restoring the swizzled participant from #{swzld} to the original #{pnt}." }
+      end
+      value
+    end
+    
+    # Augments the +CaRuby::Writer+ exclusion filter to exclude annotations from the create template.
+    # Annotations are created following the owner create.
+    #
+    # @param obj (see #create_object)
+    # @param [Attribute] attr_md the candidate attribute metadata
+    # @return [Boolean] whether the attribute should not be included in the create template
+    def exclude_pending_create_attribute?(obj, attr_md)
+      attr_md.type < Annotation or super
+    end
       
-    # Override +CaRuby::Database.query_safe+ to work around the following +caTissue+ bugs:
+    # Override {CaRuby::Database#query_safe} to work around the following +caTissue+ bugs:
     # * @quirk caTissue Specimen auto-generates blank ExternalIdentifier.
     #     cf. https://cabig-kc.nci.nih.gov/Biospecimen/forums/viewtopic.php?f=19&t=436&sid=ef98f502fc0ab242781b7759a0eaff36
     # * @quirk caTissue Specimen auto-generates blank PMI. 
@@ -662,7 +691,7 @@ module CaTissue
       attr_md.declarer < Annotatable and attr_md.type < Annotation::Proxy
     end
     
-    # Queries on the given object attribute using the {Annotation::IntegationService}.
+    # Queries on the given object attribute using the {Annotation::IntegrationService}.
     #
     # @param [Annotatable] hook the annotated domain object
     # @param [Symbol] attribute the proxy attribute
@@ -679,7 +708,7 @@ module CaTissue
       proxies
     end    
     
-    # Queries on the given proxy using the {Annotation::IntegationService}.
+    # Queries on the given proxy using the {Annotation::IntegrationService}.
     #
     # @param [Annotation::Proxy] proxy the proxy object
     # @param hook (see #query_hook_proxies)
@@ -693,7 +722,7 @@ module CaTissue
       annotator.integrator.find(proxy)
     end
     
-    # @quirk caCORE Override +CaRuby::Database::Reader.invertible_query?+ to enable the Bug #147 work
+    # @quirk caCORE Override {CaRuby::Database::Reader#invertible_query?} to enable the Bug #147 work
     #   around in {#query_object}. Invertible queries are performed to work around Bug #79. However, this
     #   work-around induces Bug #147, so we disable the Bug #79 work-around here for the special case of
     #   a CPE in order to enable the Bug #147 work-around. And so it goes....

data/lib/catissue/domain/abstract_specimen.rb

@@ -5,25 +5,6 @@ require 'caruby/util/validation'
 module CaTissue
   resource_import Java::edu.wustl.catissuecore.domain.AbstractSpecimen
   
-    # @quirk caTissue initial_quantity must be set (cf. Bug #160).
-    #
-    # @quirk caTissue Specimen characteristics are auto-generated but SpecimenRequirement
-    #   characteristics are not. It is safe to set the :autogenerated flag for both
-    #   AbstractSpecimen subclasses. This results in an unnecessary SpecimenRequirement
-    #   create database query, but SpecimenRequirement create is rare and there is no harm.
-    #
-    # @quirk caTissue Specimen characteristics is cascaded but is not an exclusive dependent,
-    #   since it is shared by aliquots.
-    #
-    # @quirk caTissue Bug 166: API update Specimen ignores a SpecimenCharacteristics with a
-    #   different id. Guard against updating a Specimen with a SpecimenCharacteristics whose id
-    #   differs from the existing id.
-    #
-    # @quirk caTissue Unlike other dependents, AbstractSpecimen characteristics, events and child
-    #   specimens have cascade style 'all'. This implies that an AbstractSpecimen update does not
-    #   create a referenced dependent. AbstractSpecimen create cascades to create and AbstractSpecimen
-    #   update cascades to update, but AbstractSpecimen update does not cascade to create.
-    #   The :no_cascade_update_to_create flag is set to handle this feature of cascade style 'all'.
   class AbstractSpecimen
     # Sets the specimen type to the specified value. The value can be a permissible caTissue String value or
     # the shortcut symbols :fresh, :fixed and :frozen.
@@ -41,10 +22,28 @@ module CaTissue
      :event_parameters => :specimen_events,
      :characteristics => :specimen_characteristics)
 
+    # @quirk caTissue initial_quantity must be set (cf. Bug #160)
     add_attribute_defaults(:initial_quantity => 0.0, :pathological_status => 'Not Specified', :specimen_type => 'Not Specified')
 
     add_mandatory_attributes(:lineage, :pathological_status, :specimen_class, :specimen_type, :specimen_characteristics)
 
+    # @quirk caTissue Specimen characteristics are auto-generated but SpecimenRequirement
+    #   characteristics are not. It is safe to set the :autogenerated flag for both
+    #   AbstractSpecimen subclasses. This results in an unnecessary SpecimenRequirement
+    #   create database query, but SpecimenRequirement create is rare and there is no harm.
+    #
+    # @quirk caTissue Specimen characteristics is cascaded but is not an exclusive dependent,
+    #   since it is shared by aliquots.
+    #
+    # @quirk caTissue Bug 166: API update Specimen ignores a SpecimenCharacteristics with a
+    #   different id. Guard against updating a Specimen with a SpecimenCharacteristics whose id
+    #   differs from the existing id.
+    #
+    # @quirk caTissue Unlike other dependents, AbstractSpecimen characteristics, events and child
+    #   specimens have cascade style 'all'. This implies that an AbstractSpecimen update does not
+    #   create a referenced dependent. AbstractSpecimen create cascades to create and AbstractSpecimen
+    #   update cascades to update, but AbstractSpecimen update does not cascade to create.
+    #   The :no_cascade_update_to_create flag is set to handle this feature of cascade style 'all'.
     qualify_attribute(:specimen_characteristics, :cascaded, :fetched, :autogenerated, :no_cascade_update_to_create)
 
     # The :no_cascade_update_to_create flag is set since events has cascade style 'all'.
@@ -120,11 +119,11 @@ module CaTissue
       SpecimenClass::UNIT_HASH[self.specimen_class]
     end
 
-    # Derives a specimen from this specimen. The parameters are described in {Specimen.create_specimen},
-    # with one addition: a +:count+ option which specifies the number of specimens to derive.
+    # Derives a specimen from this specimen. The params are described in {Specimen#create_specimen},
+    # with one addition: an optional :count, the optional number of specimens to derive.
     #
-    # If the +:count+ option is greater than one and the +:specimen_class+,
-    # +:specimen_type+ and +:specimen_characteristics+ parameters are not set to values
+    # If the :count parameter is greater than one and the :specimen_class,
+    # :specimen_type and :specimen_characteristics parameters are not set to values
     # which differ from the respective values for this Specimen, then the specimen is
     # aliquoted, otherwise the derived specimens are created independently, e.g.:
     #   spc = Specimen.create_specimen(:specimen_class => :tissue, :specimen_type => :frozen)
@@ -147,7 +146,6 @@ module CaTissue
     # label and _n_ is this specimen's child count after including the new derived specimen,
     # e.g. 3090_3 for the third child in parent specimen with label 3090.
     #
-    # @param (see Specimen.create_specimen)
     # @return the new derived specimen if _count_ is one, otherwise an Array of _count_ derived specimens
     # @raise [ValidationError] if an aliquoted parent available quantity is not greater than zero
     #   or the derived specimen quantities exceed the parent available quantity
@@ -182,7 +180,7 @@ module CaTissue
     end
 
     # Returns whether this AbstractSpecimen is minimally consistent with the other specimen.
-    # This method augments the +CaRuby::Resource.minimal_match?+ with an additional restriction
+    # This method augments the {CaRuby::Resource#minimal_match?} with an additional restriction
     # that the other specimen is the same type as this specimen and
     # is a tolerant match on specimen class, specimen type and pathological status.
     # A _tolerant_ match condition holds if the other attribute value is equal to this
@@ -208,7 +206,7 @@ module CaTissue
     # @param [Integer] count the number of aliquots
     def set_aliquot_parameters(params, count); end
 
-    # Overrides +CaRuby::Resource.each_defaults_dependent+ to visit the {SpecimenCharacteristics}.
+    # Overrides {CaRuby::Resource#each_defaults_dependent} to visit the {CaTissue::SpecimenCharacteristics}.
     # The characteristics are not dependent since they can be shared among aliquots.
     # However, the defaults should be added to them. Do so here.
     #

data/lib/catissue/domain/abstract_specimen_collection_group.rb

@@ -8,7 +8,7 @@ module CaTissue
 
     add_mandatory_attributes(:activity_status)
 
-    # Overrides +CaRuby::Resource.each_dependent+ to exclude Specimens or SpecimenRequirements with a parent,
+    # Overrides {CaRuby::Resource#each_dependent} to exclude Specimens or SpecimenRequirements with a parent,
     # since parent is the immediate Specimen or SpecimenRequirement owner.
     #
     # @yield (see CaRuby::Resource#each_dependent)

data/lib/catissue/domain/capacity.rb

@@ -24,7 +24,7 @@ module CaTissue
 
     add_mandatory_attributes(:one_dimension_capacity, :two_dimension_capacity)
 
-    # @return [CaRuby::Coordinate] the read-only coordinate with this capacity's rows and columns
+    # Returns the read-only Coordinate with this Capacity's #rows and {#columns}.
     def bounds
       @bounds ||= Coordinate.new(columns, rows)
     end

data/lib/catissue/domain/collection_protocol.rb

@@ -1,6 +1,5 @@
 require 'date'
 require 'catissue/domain/hash_code'
-require 'catissue/util/collectible'
 
 module CaTissue
   # import the Java class
@@ -10,10 +9,6 @@ module CaTissue
   #
   # @quirk caTissue Augment the standard metadata storable reference attributes to work around caTissue Bug #150:
   #   Create CollectionProtocol in API ignores startDate.
-  # @quirk caTissue Augment the standard metadata storable reference attributes to work around caTissue Bug #150:
-  #   Create CollectionProtocol in API ignores startDate.
-  # @quirk caTissue Augment the standard metadata storable reference attributes to work around caTissue Bug #150:
-  #   Create CollectionProtocol in API ignores startDate.
   class CollectionProtocol
     include HashCode
     
@@ -35,16 +30,24 @@ module CaTissue
 
     add_dependent_attribute(:consent_tiers)
 
+    # @quirk caTissue Augment the standard metadata storable reference attributes to work around caTissue Bug #150:
+    #   Create CollectionProtocol in API ignores startDate.
     qualify_attribute(:start_date, :update_only)
 
+    # @quirk caTissue Augment the standard metadata storable reference attributes to work around caTissue Bug #150:
+    #   Create CollectionProtocol in API ignores startDate.
     set_attribute_type(:coordinators, CaTissue::User)
 
+    # @quirk caTissue Augment the standard metadata storable reference attributes to work around caTissue Bug #150:
+    #   Create CollectionProtocol in API ignores startDate.
     qualify_attribute(:coordinators, :fetched)
 
+    # @quirk caTissue Bug #64 - consent tiers collection property is not initialized to an empty set in the Java constructor.
+    #   Initialize it to a +LinkedHashSet+ in caRuby.
     def initialize
       super
+      # @quirk JRuby consent_tiers property method is not accessible until respond_to? is called.
       respond_to?(:consent_tiers)
-      # work around caTissue Bug #64 - consent tiers is nil rather than an empty set
       self.consent_tiers ||= Java::JavaUtil::LinkedHashSet.new
     end
 
@@ -80,7 +83,7 @@ module CaTissue
     # Adds specimens to this protocol. The following parameter options are supported:
     # * :participant - the Participant from whom the specimen is collected
     # * :biospecimens - the collected top-level underived specimens
-    # * additional SCG parameters as described in {Collectible#merge_attributes}.
+    # * additional SCG parameters as described in {SpecimenCollectionGroup#merge}.
     #
     # If the options does not include a +:collection_protocol_event+, then the SCG is assigned
     # to the first collection event in this protocol.
@@ -89,8 +92,8 @@ module CaTissue
     # if that can be uniquely determined.
     #
     # This add_specimens method adds the following parameter options before calling the
-    # {SpecimenCollectionGroup} constructor:
-    # * :registration => a new {CollectionProtocolRegistration} for this protocol
+    # {CaTissue::SpecimenCollectionGroup} constructor:
+    # * :registration => a new {CaTissue::CollectionProtocolRegistration} for this protocol
     #   and the specified participant
     #
     # @param [(<Specimen>, {Symbol => Object})] specimens_and_params the specimens to add followed

data/lib/catissue/domain/collection_protocol_event.rb

@@ -6,14 +6,15 @@ module CaTissue
   resource_import Java::edu.wustl.catissuecore.domain.CollectionProtocolEvent
 
   # The CollectionProtocolRegistration domain class.
-  #
-  # @quirk caTissue specimen_requirements is a cascaded dependent, but it is not fetched.
-  #   CollectionProtocol create cascades through each dependent CPE to each SpecimenRequirement.
   class CollectionProtocolEvent
     include HashCode
     
     # @quirk caTissue Bug #64: Some domain collection properties not initialized.
     #    Initialize specimen_collection_groups if necessary.
+    # @quirk caTissue The +specimen_collection_groups+ is unnecessary and expensive to maintain inverse integrity.
+    #    The SCG event attribute is required, but adding the SCG to the event SCG inverse attribute value requires
+    #    loading all of the SCGs. +specimen_collection_groups+ is not used in practice. The event SCGs can be
+    #    easily obtained by a query.
     #
     # @return [Java::JavaUtil::Set] the SCGs
     def specimen_collection_groups
@@ -36,24 +37,21 @@ module CaTissue
 
     add_mandatory_attributes(:collection_protocol, :clinical_diagnosis, :specimen_requirements)
 
+    # @quirk caTissue specimen_requirements is a cascaded dependent, but it is not fetched.
+    #   CollectionProtocol create cascades through each dependent CPE to each SpecimenRequirement.
     add_dependent_attribute(:specimen_requirements, :unfetched)
 
+    remove_attribute(:specimen_collection_groups)
+
     # The event point used for saving this CollectionProtocolEvent if none other is set.
     DEFAULT_EVENT_POINT = 1.0
 
-    def initialize
-      super
-      respond_to?(:specimen_collection_groups)
-      # work around caTissue Bug #64
-      self.specimen_collection_groups ||= Java::JavaUtil::LinkedHashSet.new
-    end
-
     # Removes associations to this registration
     def delete
       protocol.events.delete(self) if protocol
     end
 
-    # Overrides +CaRuby::Resource.references+ in the case of the _specimen_requirements_ attribute to select
+    # Overrides {CaRuby::Resource#references} in the case of the _specimen_requirements_ attribute to select
     # only top-level SpecimenRequirements not derived from another SpecimenRequirement.
     def direct_dependents(attribute)
       if attribute == :specimen_requirements then