caruby-tissue 1.2.2 → 1.2.3

data/lib/catissue/domain/container.rb

@@ -22,8 +22,8 @@ module CaTissue
     # located_at_position is cascaded but not fetched.
     add_dependent_attribute(:located_at_position, :unfetched)
 
-    # Like SCG, Container name is ignored and assigned by caTissue. Therefore, this
-    # attribute is marked auto-generated.
+    # caTissue alert - 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 ContainerType which constrains a Container in its roles as a Storable
@@ -53,9 +53,6 @@ module CaTissue
 
     # Lazy-initializes this Container's capacity to a copy of the {#storable_type} capacity.
     def capacity
-      # caTissue alert - this override is necessary because the +caTissue+ API does
-      # not make the reasonable assumption that the default Container capacity is the
-      # ContainerType capacity.
       getCapacity or copy_container_type_capacity
     end
 
@@ -151,9 +148,11 @@ module CaTissue
     # coordinate. The default coordinate is the first available slot within this Container.
     # The storable Storable position is updated to reflect the new location. Returns self.
     #
-    # Raises IndexError if this Container is full.
-    # Raises IndexError if the row and column are given but exceed the Container bounds.
-    def add(storable, coordinate=nil, attribute=nil)
+    # @param [Storable] storable the item to add
+    # @param [CaRuby::Coordinate, nil] coordinate the x-y coordinate to place the item
+    # @raise [IndexError] if this Container is full
+    # @raise [IndexError] if the row and column are given but exceed the Container bounds
+    def add(storable, coordinate=nil)
       validate_type(storable)
       loc = create_location(coordinate)
       pos = storable.position || storable.position_class.new
@@ -219,12 +218,17 @@ module CaTissue
 
     # Copies this Container's ContainerType capacity, if it exists, to the Container capacity.
     #
+    # caTissue alert - this method must be called by subclass initializers. The caTissue API
+    # does not make the reasonable assumption that the default Container capacity is the
+    # ContainerType capacity.
+    #
     # @return [Capacity, nil] the initialized capacity, if any
     def copy_container_type_capacity
       return unless container_type and container_type.capacity
-      self.capacity = container_type.capacity.copy(:rows, :columns)
+      self.capacity = cpc = container_type.capacity.copy(:rows, :columns)
+      logger.debug { "Initialized #{qp} capacity from #{container_type.qp} capacity #{cpc}." }
       update_full_flag
-      capacity
+      cpc
     end
     
     def update_full_flag

data/lib/catissue/domain/container_position.rb

@@ -17,5 +17,13 @@ module CaTissue
     set_attribute_inverse(:occupied_container, :located_at_position)
     
     qualify_attribute(:parent_container, :fetched)
+    
+    # @raise [ValidationError] if the parent is the same as the occupant 
+    def validate
+      super
+      if parent == occupant or (parent.identifier and parent.identifier == occupant.identifier) then
+         raise ValidationError.new("#{self} has a circular containment reference to subcontainer #{occupant}")
+      end
+    end
   end
 end

data/lib/catissue/domain/container_type.rb

@@ -8,9 +8,10 @@ module CaTissue
   # Each {ContainerType} subclass is required to implement the container_class method.
   #
   # caTissue alert - the ContainerType and Container class hierarchy is a confusing
-  # olio of entangled relationships. Conceptually, specimens are contained in boxes,
-  # vials and specimen arrays of various types. When specimens are frozen, these
-  # containers are placed on a rack in a freezer.
+  # olio of entangled relationships. The canonical use case is as follows:
+  # * A Specimen is contained in a box, vial or specimen array.
+  # * A vial or specimen array can also be placed in a box.
+  # * A frozen specimen container is placed on a rack in a freezer.
   #
   # This conceptual model is implemented in caTissue as follows:
   # * The specimen collection container type, e.g. +Citrate Vacutainer+, is captured
@@ -43,18 +44,24 @@ module CaTissue
   #   a specimen position in a box, whereas {CaTissue::SpecimenArrayContent} is functionally
   #   a specimen position in a specimen array.
   #
-  # The ContainerType/Container mish-mash is partially alleviated in caRuby as follows:
+  # The ContainerType/Container mish-mash is partially rationalized in caRuby as follows:
   # * {CaTissue::StorageType} and {CaTissue::StorageContainer} include the
   #   {CaTissue::StorageTypeHolder} module, which unifies treatment of contained
   #   types.
   # * Similarly, {CaTissue::AbstractPosition} and {CaTissue::SpecimenArrayContent} include
   #   the {CaTissue::Position} module, which unifies treatment of positions.
-  # * Contained child types are consolidated into {CaTissue::StorageTypeHolder#child_types}
+  # * Contained child types are consolidated into {CaTissue::StorageTypeHolder#child_types}.
   # * Similarly, {CaTissue::StorageContainer} child items are consolidated into
-  #   {CaTissue::StorageContainer#child_types}
+  #   {CaTissue::StorageContainer#child_types}.
   # * The various container and position classes are augmented with helper methods to
   #   add, move and find specimens and subcontainers. These methods hide the mind-numbing
   #   eccentricity of caTissue specimen storage interaction.
+  # The entire amalgamation is further simplifying by introducing the standard Ruby
+  # container add method {CaTissue::Container::<<}. The only call the caRuby client
+  # 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:
+  #   freezer.add box :at => 
   class ContainerType
     include Resource
 

data/lib/catissue/domain/participant.rb

@@ -34,24 +34,29 @@ module CaTissue
     # it appears as Female in the GUI even though it is null in the database.
     add_mandatory_attributes(:activity_status, :gender)
 
-    add_dependent_attribute(:collection_protocol_registrations, :logical)
+    # caTissue alert - Participant CPR cascade is simulated in the bizlogic.
+    # See the PMI comment below.
+    add_dependent_attribute(:collection_protocol_registrations)
 
     add_dependent_attribute(:races)
 
-    # PMI is not cascaded, but insert is done in the bizlogic.
+    # caTissue alert - 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.
     qualify_attribute(:social_security_number, :optional)
+    
+    # The clinicial annotation.
+    add_annotation('Clinical', :package => 'clinical_annotation', :service => 'CA')
 
-    qualify_attribute(:collection_protocol_registrations, :fetched)
-
-    qualify_attribute(:participant_medical_identifiers, :fetched)
-
-    def merge_attribute_value(attribute, oldval, newval)
-      # caTissue alert - remove the autogenerated blank PMI.
-      # TODO - file bug
-      # @see CaTissue::Database#query_safe
+    # caTissue alert - 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)
       if attribute == :participant_medical_identifiers and newval then
         CaTissue::Participant.remove_empty_medical_identifier(newval)
       end

data/lib/catissue/domain/site.rb

@@ -5,9 +5,6 @@ module CaTissue
   # The Site domain class.
   class Site
     include Resource
-    
-    # The default pre-defined caTissue site name.
-    DEF_SITE_NAME = 'In Transit'
 
     # caTissue alert - 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
@@ -29,5 +26,14 @@ module CaTissue
       LABORATORY = 'Laboratory'
       REPOSITORY = 'Repository'
     end
+    
+    def self.default_site
+      @@def_site ||= new(:name => DEF_SITE_NAME)
+    end
+    
+    private
+        
+    # The default pre-defined caTissue site name.
+    DEF_SITE_NAME = 'In Transit'
   end
 end

data/lib/catissue/domain/specimen.rb

@@ -12,7 +12,7 @@ module CaTissue
     include Validation, Storable, Resource
     
     # caTissue alert - Bug #64: Some domain collection properties not initialized.
-    # Initialize consent_tier_statuses if necessary. 
+    # Initialize consent_tier_statuses if necessary.
     #
     # @return [Java::JavaUtil::Set] the statuses
     def consent_tier_statuses
@@ -50,9 +50,18 @@ module CaTissue
     # A child Specimen is auto-generated from a SpecimenRequirement template if it
     # is part of a hierarchy built by SCG create. Unlike SpecimenRequirement,
     # Specimen children are cascaded.
-    add_dependent_attribute(:child_specimens, :autogenerated, :no_cascade_update_to_create)
+    qualify_attribute(:child_specimens, :autogenerated)
 
     # caTissue alert - Specimen consent_tier_statuses is cascaded but not fetched.
+    #
+    # caTissue alert - When a Specimen is auto-generated or created, a consent tier
+    # status is created for each registration consent. A created Specimen has a
+    # a well-formed status record. An auto-generated status record is malformed,
+    # missing the Specimen id reference. This differs from the auto-generated
+    # SCG status record, which is malformed in a different way which results in
+    # a severe display error, as described in Bug #156. The malformed Specimen
+    # status record results in displaying null field values in the Specimen Consent
+    # page, but otherwise no adverse effects.
     add_dependent_attribute(:consent_tier_statuses, :unfetched)
 
     # caTissue alert - Bug #163: ExternalIdentifer not fetched with Specimen in API.
@@ -87,10 +96,19 @@ module CaTissue
     # 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
-    # and reupdate the Specimen if the stored available_quantity differs from the save
-    # argument.
+    # 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)
 
+    # caTissue alert - 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 pathology annotation.
+    add_annotation('Pathology', :package => 'pathology_specimen', :service => 'pathologySpecimen')
+    
     # Specimen storage is constrained on the basis of the +specimen_class+.
     alias :storable_type :specimen_class
 
@@ -114,11 +132,17 @@ module CaTissue
     def collected?
       collection_status == 'Collected'
     end
-    
-    def merge_attribute_value(attribute, oldval, newval)
-      # caTissue alert - remove the autogenerated blank ExternalIdentifier.
-      # @see https://cabig-kc.nci.nih.gov/Biospecimen/forums/viewtopic.php?f=19&t=436&sid=ef98f502fc0ab242781b7759a0eaff36
-      # @see CaTissue::Database#query_safe
+
+    # 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)
+    def fetch_saved?
+      super and available_quantity_changed?
+    end    
+    # caTissue alert - remove the autogenerated blank ExternalIdentifier.
+    # cf. https://cabig-kc.nci.nih.gov/Biospecimen/forums/viewtopic.php?f=19&t=436&sid=ef98f502fc0ab242781b7759a0eaff36
+    def merge_attribute(attribute, newval, matches=nil)
       if attribute == :external_identifiers and newval then
         CaTissue::Specimen.remove_empty_external_identifier(newval)
       end
@@ -140,22 +164,21 @@ module CaTissue
     # Override default {CaRuby::Resource#merge_attributes} to ignore a source SpecimenRequirement parent_specimen.
     def merge_attributes(other, attributes=nil)
       case other
-      when SpecimenRequirement then
-        # merge with the default requirement merge attributes if necessary
-        attributes ||= MERGEABLE_RQMT_ATTRS
-        super(other, attributes)
-        # copy the requirement characteristics
-        sc = other.specimen_characteristics
-        self.specimen_characteristics ||= sc.copy(MERGEABLE_SPC_CHR_ATTRS) if sc
-      when Hash then
-        # the requirement template
-        rqmt = other[:specimen_requirement] || other[:requirement]
-        # merge the attribute => value hash
-        super
-        # merge the SpecimenRequirement after the hash
-        merge_attributes(rqmt) if rqmt
-      else
-        super
+        when SpecimenRequirement then
+          # merge with the default requirement merge attributes if necessary
+          attributes ||= MERGEABLE_RQMT_ATTRS
+          super(other, attributes)
+          # copy the requirement characteristics
+          sc = other.specimen_characteristics
+          self.specimen_characteristics ||= sc.copy(MERGEABLE_SPC_CHR_ATTRS) if sc
+        when Hashable then
+          # the requirement template
+          rqmt = other[:specimen_requirement] || other[:requirement]
+          # merge the attribute => value hash
+          super
+          # merge the SpecimenRequirement after the hash
+          merge_attributes(rqmt) if rqmt
+        else super
       end
       self
     end
@@ -200,6 +223,17 @@ module CaTissue
       end
     end
 
+    # Augments {AbstractSpecimen#minimal_match?} with an additional restriction that the other
+    # specimen is in pending state. This ensures that a specimen submitted for create matches
+    # 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?)
+    def minimal_match?(other)
+      super and other.collection_status == 'Pending'
+    end
+    
     # @return the SpecimenPosition class which this Specimen's Storable can occupy
     def position_class
       CaTissue::SpecimenPosition
@@ -334,7 +368,24 @@ module CaTissue
     MERGEABLE_RQMT_ATTRS = nondomain_java_attributes - primary_key_attributes
 
     MERGEABLE_SPC_CHR_ATTRS = SpecimenCharacteristics.nondomain_java_attributes - SpecimenCharacteristics.primary_key_attributes
-
+     
+    # @see #fetch_saved
+    def available_quantity_changed?
+      oldval = snapshot && snapshot[:available_quantity]
+      newval = available_quantity
+      if oldval and oldval != newval then
+        logger.debug { "Saved #{qp} must be fetched from the database to reflect the current database state, since the available quantity was changed from #{oldval} to #{newval}." }
+        true
+      else
+        false
+      end
+    end
+    
+    def format_saved_fetch_message(fetch, reason)
+      args = fetch ? [qp, 'must', reason] : [qp, 'does not need to', reason]
+      SAVED_FETCH_MSG % args
+    end
+    
     # Adds this Specimen's defaults, as follows:
     # * The default specimen_collection_group is the parent specimen_collection_group.
     # * Add default collection and received event parameters if this Specimen is collected.
@@ -353,7 +404,7 @@ module CaTissue
     # is set to false (0 database value) when the record is inserted.
     #
     # caTissue alert - a collected Specimen without a collection and received event parameters
-    # results in the dreaded 'Severe Error' server message. TODO - isolate and report.
+    # results in the dreaded 'Severe Error' caTissue server message. Create default SEPs if necessary.
     def add_defaults_local
       super
       self.specimen_collection_group ||= parent.specimen_collection_group if parent
@@ -373,7 +424,7 @@ module CaTissue
     # Adds the default collection and received event parameters if the collection status
     # is +Collected+.
     def add_default_event_parameters
-      if collection_status == 'Collected' and specimen_collection_group then
+      if collected? and specimen_collection_group then
         unless event_parameters.detect { |ep| CaTissue::CollectionEventParameters === ep } then
           CaTissue::CollectionEventParameters.new(:specimen => self, :user => specimen_collection_group.collector)
         end
@@ -428,18 +479,6 @@ module CaTissue
       CaTissue.domain_type_with_name(class_name) or raise ArgumentError.new("Specimen class #{class_name} is not recognized for specimen type parameter #{symbol}")
     end
 
-#    def default_specimen_characteristics
-#      return if specimen_collection_group.nil?
-#      rqmts = specimen_collection_group.requirements
-#      # match the requirement specimen type
-#      rqmt = specimen_collection_group.requirements.detect { |rqmt| specimen_type == rqmt.specimen_type }
-#      # fallback is match on requirement class and generic requirment specimen type
-#      rqmt ||= specimen_collection_group.requirements.detect do |rqmt|
-#        specimen_class === rqmt.specimen_class and rqmt.specimen_type.nil? or rqmt.specimen_type == 'Not Specified'
-#      end
-#      rqmt.specimen_characteristics.copy if rqmt
-#    end
-
     # Decrements this parent's available quantity by the given child's initial quantity, if the specimen types are the same and there
     # are the relevant quantities.
     def decrement_derived_quantity(child)

data/lib/catissue/domain/specimen_array.rb

@@ -9,7 +9,17 @@ module CaTissue
     
     # caTissue alert - the superclass Container occupied_positions does not apply to SpecimenArray.
     remove_attribute(:occupied_positions)
-    
+ 
+    # Initializes this instance's child storage types from the given type.
+    #
+    # @param [<StorageType>] the type to set
+    def specimen_array_type=(type)
+      setSpecimenArrayType(type)
+      unless type.nil? then
+        copy_container_type_capacity
+      end
+      type
+    end    
     add_attribute_aliases(:container_type => :specimen_array_type, :contents => :specimen_array_contents)
 
     set_attribute_type(:new_specimen_array_order_items, CaTissue::SpecimenArrayOrderItem)

data/lib/catissue/domain/specimen_collection_group.rb

@@ -39,19 +39,28 @@ module CaTissue
       setSurgicalPathologyNumber(value)
     end
 
-    add_attribute_aliases(:collection_event => :collection_protocol_event,
+    add_attribute_aliases(:site => :specimen_collection_site,
+      :collection_site => :specimen_collection_site,
+      :collection_event => :collection_protocol_event,
       :event_parameters => :specimen_event_parameters,
       :events => :specimen_event_parameters,
       :registration => :collection_protocol_registration)
 
+    # caTissue alert - Bug #116: specimen_collection_site is incorrectly attached in the caTissue class
+    # model to AbstractSpecimenCollectionGroup rather than SpecimenCollectionGroup. CollectionProtocolEvent
+    # is a subclass of AbstractSpecimenCollectionGroup but does not have a collection site. Therfore, the
+    # specimen_collection_site is ignored in the caRuby AbstractSpecimenCollectionGroup class declaration
+    # and declared as an aliased, mandatory, fetched attribute for the SpecimenCollectionGroup subclass only.
     add_mandatory_attributes(:specimen_event_parameters, :specimen_collection_site, :clinical_diagnosis, :collection_status)
+    
+    qualify_attribute(:specimen_collection_site, :fetched)
 
     set_secondary_key_attributes(:name)
 
     set_alternate_key_attributes(:surgical_pathology_number, :collection_protocol_registration)
 
-    # caTissue alert - An auto-generated SCG in turn auto-generates a ConsentTierStatus
-    # for each ConsentTierResponse defined in the SCG owner CPR.
+    # caTissue alert - An auto-generated or created SCG auto-generates a ConsentTierStatus for each
+    # ConsentTierResponse defined in the SCG owner CPR.
     #
     # caTissue alert - SCG consent_tier_statuses is cascaded but not fetched.
     add_dependent_attribute(:consent_tier_statuses, :autogenerated, :unfetched)
@@ -70,6 +79,12 @@ module CaTissue
 
     # SCG Specimens are auto-generated from SpecimenRequirement templates when the SCG is created.
     # The Specimens are not cascaded.
+    #
+    # caTissue alert - SCG specimens query result does not set the Specimen children and parent, even
+    # though they are guaranteed to be in the SCG specimens result set. The children and parent must be
+    # fetched separately, resulting in redundant copies of the same Specimen and additional fetches.
+    # caRuby partially rectifies this lapse by reconciling the SCG specimens parent-child relationships
+    # within the SCG scope.
     add_dependent_attribute(:specimens, :logical, :autogenerated)
 
     # The CPE-SCG association is bi-directional.
@@ -82,12 +97,14 @@ module CaTissue
     # SpecimenCollectionGroup update object references a CollectionProtocolRegistration with a Participant reference.
     # The CPR identifier should be sufficient for a SCG update, but caTissue bizlogic requires an extraneous
     # CPR -> Participant reference.
-    # TODO - file a bug and reference it here
     qualify_attribute(:collection_protocol_registration, :cascaded)
 
     # caTissue alert - Bug #65: Although SCG name uniquely identifies a SCG, the SCG name is auto-generated on create
     # and cannnot be set by the client. Therefore, name is marked as update_only.
     qualify_attribute(:name, :autogenerated, :update_only)
+    
+    # The SCG pathology annotation.
+    add_annotation('Pathology', :package => 'pathology_scg', :service => 'pathologySCG')
 
     # caTissue alert - Bug #64: Initialize the SCG consent_tier_statuses to an empty set.
     def initialize(params=nil)
@@ -223,6 +240,17 @@ module CaTissue
         super
       end
     end
+    
+    CONSENT_TIER_STATUS_ATTRS = [:consent_tier_statuses]
+    
+    def mandatory_attributes
+      attrs = super
+      if registration and not registration.consent_tier_responses.empty? then
+        attrs + CONSENT_TIER_STATUS_ATTRS
+      else
+        attrs
+      end
+    end
 
     def validate
       super
@@ -230,60 +258,58 @@ module CaTissue
       validate_event_parameters
     end
 
-    # Restricts the {CaRuby::Persistable#fetch_saved?} condition for a SCG as follows:
-    #
-    # If the SCG status was created or was updated from +Pending+ to +Collected+,
-    # then fetch the saved SCG. Otherwise, forego fetching the saved SCG.
+    # Relaxes the {CaRuby::Persistable#saved_fetch_attributes} condition for a SCG as follows:
+    # * If the SCG status was updated from +Pending+ to +Collected+, then fetch the saved SCG event parameters.
     # 
-    # @return (see CaRuby::Persistable#fetch_saved)
-    def fetch_saved?
-      super and status_changed_to_complete?
+    # @param (see CaRuby::Persistable#saved_fetch_attributes)
+    # @return (see CaRuby::Persistable#saved_fetch_attributes)
+    def saved_fetch_attributes(operation)
+      operation == :update && status_changed_to_complete? ? EVENT_PARAM_ATTRS : super
+    end
+    
+    # Relaxes the {CaRuby::Persistable#saved_fetch_attributes} condition for a SCG as follows:
+    # * If the SCG status was updated from +Pending+ to +Collected+, then fetch the saved SCG event parameters.
+    # 
+    # @param (see CaRuby::Persistable#saved_fetch_attributes)
+    # @return (see CaRuby::Persistable#saved_fetch_attributes)
+    def autogenerated?(operation)
+      operation == :update && status_changed_to_complete? ? EVENT_PARAM_ATTRS : super
     end
 
     private
-     
-    SAVED_FETCH_MSG = "Saved #{qp} %s be fetched from the database to reflect the current database state, since it was %s."
-
+    
+    EVENT_PARAM_ATTRS = [:specimen_event_parameters]
+    
     # @see #fetch_saved
     def status_changed_to_complete?
-      if identifier.nil? then
-        logger.debug { format_saved_fetch_message(true, "created") }
-        true
-      elsif collected? and (snapshot.nil? or snapshot[:collection_status] == 'Pending') then
-        logger.debug { format_saved_fetch_message(true, "updated to status Complete") }
+      if collected? and snapshot and snapshot[:collection_status] == 'Pending' then
+        logger.debug { "Saved #{qp} event parameters must be fetched from the database to reflect the current database state, since the status was changed from Pending to Complete." }
         true
       else
-        logger.debug { format_saved_fetch_message(false, "not updated from pending to complete") }
         false
       end
     end
-    
-    def format_saved_fetch_message(fetch, reason)
-      args = fetch ? [qp, 'must', reason] : [qp, 'does not need to', reason]
-      SAVED_FETCH_MSG % args
-    end
    
     def each_defaults_dependent
       # visit ReceivedEventParameters first
       rep = received_event_parameters
       yield rep if rep
       # add other dependent defaults
-      each_dependent { |dep| yield dep unless ReceivedEventParameters === dep }
+     each_dependent { |dep| yield dep unless ReceivedEventParameters === dep }
     end
 
     # Adds defaults as follows:
-    # * the default collection event is the first event in the protocol registered with this SCG.
-    # * the default collection status is 'Complete' if there is a received event, 'Pending' otherwise.
-    # * the default collection site is the CP site, if this SCG is {#received?} and there is only CP one,
-    #   otherwise the {CaTissue::Site::DEF_SITE_NAME} site.
-    # * the default conset tier status is 'Complete' if there is a received event, 'Pending' otherwise.
-    # * a default ReceivedEventParameters is added to this SCG if the collection status is
+    # * The default collection event is the first event in the protocol registered with this SCG.
+    # * The default collection status is 'Complete' if there is a received event, 'Pending' otherwise.
+    # * The default collection site is the CP site, if this SCG is {#received?} and there is only CP one,
+    #   otherwise the {CaTissue::Site.default_site}.
+    # * The default conset tier status is 'Complete' if there is a received event, 'Pending' otherwise.
+    # * A default ReceivedEventParameters is added to this SCG if the collection status is
     #   'Complete' and there is no other ReceivedEventParameters. The receiver is an arbitrary
     #   protocol coordinator.
     #
-    # Raises ValidationError if the default ReceivedEventParameters could not be created because
-    # there is no protocol or protocol coordinator.
-    #
+    # @raise [ValidationError] if the default ReceivedEventParameters could not be created because
+    #   there is no protocol or protocol coordinator
     # @see CollectionProtocol#first_event
     def add_defaults_local
       super
@@ -322,16 +348,22 @@ module CaTissue
       # ensure that there is a CT status for each consent tier
       registration.consent_tier_responses.each do |ctr|
         ct = ctr.consent_tier
+        # skip if there is a status for the response tier
         next if ctses.include?(ct)
-        cts = CaTissue::ConsentTierStatus.new(:consent_tier => ct).add_defaults
+        # make a new status
+        cts = CaTissue::ConsentTierStatus.new(:consent_tier => ct)
+        cts.add_defaults
         consent_tier_statuses << cts
         logger.debug { "Made default #{qp} #{cts.qp} for consent tier #{ct.qp}." }
       end
     end
 
     def default_site
-      cp = collection_event.protocol if collection_event
-      cp.default_site if cp
+      return if collection_event.nil?
+      cp = collection_event.protocol || return
+      site = cp.default_site || return
+      logger.debug { "Default #{qp} site is #{site}." }
+      site
     end
 
     # Returns the first event in the protocol registered with this SCG.
@@ -340,7 +372,9 @@ module CaTissue
       pcl = registration.protocol || return
       # if no protocol event, then add the default event
       pcl.add_defaults if pcl.events.empty?
-      pcl.first_event
+      ev = pcl.first_event || return
+      logger.debug { "Default #{qp} collection event is the registration protocol #{pcl.qp} first event #{ev.qp}." }
+      ev
     end
 
     def create_default_received_event_parameters
@@ -353,13 +387,17 @@ module CaTissue
         raise ValidationError.new("SCG with status Complete default CollectionEventParameters could not be created since there is no collection protocol coordinator: #{self}")
       end
       # make the REP
-      CaTissue::SpecimenEventParameters.create_parameters(:received, self, :user => rcvr)
+      ev = CaTissue::SpecimenEventParameters.create_parameters(:received, self, :user => rcvr)
+      logger.debug { "Made default #{qp} received event parameter #{ev.qp}." }
+      ev
     end
 
     def create_default_collection_event_parameters
       rep = received_event_parameters || return
       # make the CEP from the REP
-      CaTissue::SpecimenEventParameters.create_parameters(:collection, self, :user => rep.user, :timestamp => rep.timestamp)
+      ev = CaTissue::SpecimenEventParameters.create_parameters(:collection, self, :user => rep.user, :timestamp => rep.timestamp)
+      logger.debug { "Made default #{qp} collected event parameter #{ev.qp}." }
+      ev
     end
 
     # Verifies that each registration consent tier response has a corresponding SCG consent tier status.

data/lib/catissue/domain/specimen_event_parameters.rb

@@ -46,14 +46,11 @@ module CaTissue
       end
       event_params = klass.new(params)
       case scg_or_specimen
-      when SpecimenCollectionGroup then
-        event_params.specimen_collection_group = scg_or_specimen
-      when Specimen then
-        event_params.specimen = scg_or_specimen
-      when nil then
-        raise ArgumentError.new("Missing SpecimenEventParameters scg_or_specimen factory argument")
-      else
-        raise ArgumentError.new("Unsupported SpecimenEventParameters factory argument - expected SpecimenCollectionGroup or Specimen, found #{scg_or_specimen.class}")
+        when SpecimenCollectionGroup then event_params.specimen_collection_group = scg_or_specimen
+        when Specimen then event_params.specimen = scg_or_specimen
+        when nil then raise ArgumentError.new("Missing SpecimenEventParameters scg_or_specimen factory argument")
+        else
+          raise ArgumentError.new("Unsupported SpecimenEventParameters factory argument - expected SpecimenCollectionGroup or Specimen, found #{scg_or_specimen.class}")
       end
       event_params
     end

data/lib/catissue/domain/specimen_position.rb

@@ -1,5 +1,3 @@
-
-
 module CaTissue
   # import the Java class
   java_import('edu.wustl.catissuecore.domain.SpecimenPosition')

data/lib/catissue/domain/specimen_requirement.rb

@@ -34,7 +34,7 @@ module CaTissue
     # Unlike Specimen, a child SpecimenRequirement is not cascaded by caTissue.
     # It is not auto-generated, i.e. it is not created from a template when the
     # parent CPE is created.
-    add_dependent_attribute(:child_specimens, :logical)
+    qualify_attribute(:child_specimens, :logical)
     
     # Overrides {Resource#owner} to return the parent_specimen, if it exists, or the collection_protocol_event otherwise.
     def owner