caruby-tissue 1.3.4 → 1.3.5

data/lib/catissue/domain/collection_protocol_registration.rb

@@ -2,7 +2,7 @@ require 'caruby/util/collection'
 
 module CaTissue
   # import the Java class
-  java_import('edu.wustl.catissuecore.domain.CollectionProtocolRegistration')
+  java_import Java::edu.wustl.catissuecore.domain.CollectionProtocolRegistration
 
   # The CollectionProtocolRegistration domain class.
   class CollectionProtocolRegistration

data/lib/catissue/domain/consent_tier_response.rb

@@ -1,6 +1,6 @@
 module CaTissue
   # import the Java class
-  java_import('edu.wustl.catissuecore.domain.ConsentTierResponse')
+  java_import Java::edu.wustl.catissuecore.domain.ConsentTierResponse
 
   class ConsentTierResponse
     include Resource

data/lib/catissue/domain/consent_tier_status.rb

@@ -1,6 +1,6 @@
 module CaTissue
   # import the Java class
-  java_import('edu.wustl.catissuecore.domain.ConsentTierStatus')
+  java_import Java::edu.wustl.catissuecore.domain.ConsentTierStatus
 
   class ConsentTierStatus
     include Resource

data/lib/catissue/domain/container.rb

@@ -4,7 +4,7 @@ require 'catissue/util/location'
 
 module CaTissue
   # import the Java class
-  java_import('edu.wustl.catissuecore.domain.Container')
+  java_import Java::edu.wustl.catissuecore.domain.Container
 
   # The +caTissue+ +Container+ domain class wrapper.
   # Each Container subclass is required to implement the {#container_type} method.

data/lib/catissue/domain/container_position.rb

@@ -1,6 +1,6 @@
 module CaTissue
   # import the Java class
-  java_import('edu.wustl.catissuecore.domain.ContainerPosition')
+  java_import Java::edu.wustl.catissuecore.domain.ContainerPosition
 
   class ContainerPosition
     include Resource
@@ -18,8 +18,10 @@ module CaTissue
     
     qualify_attribute(:parent_container, :fetched)
     
+    private
+    
     # @raise [ValidationError] if the parent is the same as the occupant 
-    def validate
+    def validate_local
       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}")

data/lib/catissue/domain/container_type.rb

@@ -2,7 +2,7 @@ require 'caruby/util/options'
 
 module CaTissue
   # import the Java class
-  java_import('edu.wustl.catissuecore.domain.ContainerType')
+  java_import Java::edu.wustl.catissuecore.domain.ContainerType
 
   # The caTissue ContainerType domain class wrapper.
   # Each {ContainerType} subclass is required to implement the container_class method.

data/lib/catissue/domain/department.rb

@@ -2,7 +2,7 @@
 
 module CaTissue
   # import the Java class
-  java_import('edu.wustl.catissuecore.domain.Department')
+  java_import Java::edu.wustl.catissuecore.domain.Department
 
   # The Department domain class.
   class Department

data/lib/catissue/domain/disposal_event_parameters.rb

@@ -1,6 +1,6 @@
 module CaTissue
   # import the Java class
-  java_import('edu.wustl.catissuecore.domain.DisposalEventParameters')
+  java_import Java::edu.wustl.catissuecore.domain.DisposalEventParameters
 
   class DisposalEventParameters
     include Resource

data/lib/catissue/domain/embedded_event_parameters.rb

@@ -1,6 +1,6 @@
 module CaTissue
   # import the Java class
-  java_import('edu.wustl.catissuecore.domain.EmbeddedEventParameters')
+  java_import Java::edu.wustl.catissuecore.domain.EmbeddedEventParameters
 
   class EmbeddedEventParameters
     include Resource

data/lib/catissue/domain/external_identifier.rb

@@ -2,7 +2,7 @@
 
 module CaTissue
   # import the Java class
-  java_import('edu.wustl.catissuecore.domain.ExternalIdentifier')
+  java_import Java::edu.wustl.catissuecore.domain.ExternalIdentifier
 
   # The ExternalIdentifier domain class.
   class ExternalIdentifier

data/lib/catissue/domain/frozen_event_parameters.rb

@@ -1,6 +1,6 @@
 module CaTissue
   # import the Java class
-  java_import('edu.wustl.catissuecore.domain.FrozenEventParameters')
+  java_import Java::edu.wustl.catissuecore.domain.FrozenEventParameters
 
   class FrozenEventParameters
     include Resource

data/lib/catissue/domain/institution.rb

@@ -2,7 +2,7 @@
 
 module CaTissue
   # import the Java class
-  java_import('edu.wustl.catissuecore.domain.Institution')
+  java_import Java::edu.wustl.catissuecore.domain.Institution
 
   # The Institution domain class.
   class Institution

data/lib/catissue/domain/new_specimen_array_order_item.rb

@@ -2,7 +2,7 @@ require 'catissue/resource'
 
 module CaTissue
   # import the Java class
-  java_import('edu.wustl.catissuecore.domain.NewSpecimenArrayOrderItem')
+  java_import Java::edu.wustl.catissuecore.domain.NewSpecimenArrayOrderItem
 
   # The NewSpecimenArrayOrderItem domain class.
   class NewSpecimenArrayOrderItem

data/lib/catissue/domain/order_details.rb

@@ -1,7 +1,7 @@
 
 
 module CaTissue
-  java_import('edu.wustl.catissuecore.domain.OrderDetails')
+  java_import Java::edu.wustl.catissuecore.domain.OrderDetails
 
   # The OrderDetails domain class.
   class OrderDetails

data/lib/catissue/domain/participant.rb

@@ -4,7 +4,7 @@ require 'catissue/util/person'
 
 module CaTissue
   # import the Java class
-  java_import('edu.wustl.catissuecore.domain.Participant')
+  java_import Java::edu.wustl.catissuecore.domain.Participant
 
   # The Participant domain class.
   class Participant
@@ -137,7 +137,7 @@ module CaTissue
       # Make a new default Race which references this Participant, if necessary. Setting the Race
       # participant to self automatically adds the Race to this Participant's races collection.
       # The Race name defaults to Unknown.
-      if races.empty? then CaTissue::Race.new(:participant => self).add_defaults end
+      if races.empty? then CaTissue::Race.new(:participant => self).add_defaults_recursive end
     end
   end
 end

data/lib/catissue/domain/participant_medical_identifier.rb

@@ -2,7 +2,7 @@
 
 module CaTissue
   # import the Java class
-  java_import('edu.wustl.catissuecore.domain.ParticipantMedicalIdentifier')
+  java_import Java::edu.wustl.catissuecore.domain.ParticipantMedicalIdentifier
 
 
   # The ParticipantMedicalIdentifier domain class.

data/lib/catissue/domain/password.rb

@@ -1,6 +1,6 @@
 module CaTissue
   # import the Java class
-  java_import('edu.wustl.catissuecore.domain.Password')
+  java_import Java::edu.wustl.catissuecore.domain.Password
 
   class Password
     include Resource

data/lib/catissue/domain/race.rb

@@ -1,6 +1,6 @@
 module CaTissue
   # import the Java class
-  java_import('edu.wustl.catissuecore.domain.Race')
+  java_import Java::edu.wustl.catissuecore.domain.Race
 
   class Race
     include Resource

data/lib/catissue/domain/received_event_parameters.rb

@@ -2,7 +2,7 @@ require 'catissue/domain/scg_event_parameters'
 
 module CaTissue
   # import the Java class
-  java_import('edu.wustl.catissuecore.domain.ReceivedEventParameters')
+  java_import Java::edu.wustl.catissuecore.domain.ReceivedEventParameters
 
   class ReceivedEventParameters
     include Resource, SCGEventParameters

data/lib/catissue/domain/site.rb

@@ -1,6 +1,6 @@
 module CaTissue
   # import the Java class
-  java_import('edu.wustl.catissuecore.domain.Site')
+  java_import Java::edu.wustl.catissuecore.domain.Site
 
   # The Site domain class.
   class Site

data/lib/catissue/domain/specimen.rb

@@ -5,7 +5,7 @@ require 'catissue/util/storable'
 
 module CaTissue
   # import the Java class
-  java_import('edu.wustl.catissuecore.domain.Specimen')
+  java_import Java::edu.wustl.catissuecore.domain.Specimen
 
   # The Specimen domain class.
   class Specimen
@@ -183,35 +183,6 @@ module CaTissue
       self
     end
 
-    # Raises a ValidationError when one the following conditions holds:
-    # * a top-level Specimen does not have a SGC
-    # * the available_quantity exceeds the initial_quantity
-    # * the availability flag is set and the available_quantity is zero
-    #
-    # caTissue alert - Bug #160: Missing Is Available? validation.
-    # Updating Specimen with the availablity flag set and available_quantity zero
-    # silently leaves the availablity flag unset.
-    def validate
-      super
-      if parent.nil? and specimen_collection_group.nil? then
-        raise 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}")
-      end
-      if available? and available_quantity.zero? then
-        raise 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")
-        end
-        unless event_parameters.detect { |ep| CaTissue::ReceivedEventParameters === ep } then
-          raise ValidationError.new("#{self} is missing ReceivedEventParameters")
-        end
-      end
-    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
     # one external identifier.
@@ -367,6 +338,37 @@ module CaTissue
 
     MERGEABLE_SPC_CHR_ATTRS = SpecimenCharacteristics.nondomain_java_attributes - SpecimenCharacteristics.primary_key_attributes
 
+    # Validates that the following conditions hold:
+    # * a top-level Specimen does not have a SGC
+    # * the available_quantity exceeds the initial_quantity
+    # * the availability flag is set and the available_quantity is zero
+    #
+    # caTissue alert - Bug #160: Missing Is Available? validation.
+    # Updating Specimen with the availablity flag set and available_quantity zero
+    # silently leaves the availablity flag unset.
+    #
+    #  @raise [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")
+      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}")
+      end
+      if available? and available_quantity.zero? then
+        raise 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")
+        end
+        unless event_parameters.detect { |ep| CaTissue::ReceivedEventParameters === ep } then
+          raise ValidationError.new("#{self} is missing ReceivedEventParameters")
+        end
+      end
+    end
+    
     # @param [Resource] other the object to match
     # @return [Boolean] whether this specimen matches the other specimen on at least one external identifier
     def external_identifier_match?(other)
@@ -405,9 +407,9 @@ module CaTissue
     #
     # caTissue alert - initial_quantity cannot be null (cf. Bug #160).
     #
-    # caTissue alert - the default available status must be left nil rather than set to false, since
-    # caTissue allows a nil available status on insert but not a false value, even though a nil status
-    # is set to false (0 database value) when the record is inserted.
+    # caTissue alert - the available status cannot be set to to false. The status must be set to nil
+    # instead. caTissue allows a nil available status on insert but not a false value, even though a
+    # nil status 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' caTissue server message. Create default SEPs if necessary.
@@ -417,14 +419,21 @@ module CaTissue
       add_default_event_parameters
       
       # The default available quantity is the initial quantity.
-      aq = available_quantity
-      if aq.nil? or aq.zero? then
-        self.available_quantity = is_available == false ? 0.0 : initial_quantity
-      end
+      self.available_quantity ||= is_available ? initial_quantity : 0
       
-      # The specimen is available by default if there is a positive available quantity.
-      # If is_available is set to false, then set it to nil to work around a caTissue bug.
-      self.is_available ||= available_quantity.zero? ? nil : true
+      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.
+        self.is_available = nil
+      end
+    end
+    
+    # The specimen is available by default if there is a positive available quantity.
+    #
+    # @return [Boolean, nil] +nil+ if the available quantity is zero, +true+ otherwise
+    def default_availablility
+      available_quantity.zero? ? nil : true
     end
     
     # Adds the default collection and received event parameters if the collection status

data/lib/catissue/domain/specimen_array.rb

@@ -2,7 +2,7 @@
 
 module CaTissue
   # import the Java class
-  java_import('edu.wustl.catissuecore.domain.SpecimenArray')
+  java_import Java::edu.wustl.catissuecore.domain.SpecimenArray
 
   class SpecimenArray
     include Resource

data/lib/catissue/domain/specimen_array_content.rb

@@ -2,7 +2,7 @@ require 'catissue/util/position'
 
 module CaTissue
   # import the Java class
-  java_import('edu.wustl.catissuecore.domain.SpecimenArrayContent')
+  java_import Java::edu.wustl.catissuecore.domain.SpecimenArrayContent
 
   # caTissue alert - #{CaTissue::SpecimenArrayContent} should be derived from
   # {CaTissue::AbstractPosition} but isn't (cf. {CaTissue::ContainerType}).

data/lib/catissue/domain/specimen_array_type.rb

@@ -1,6 +1,6 @@
 module CaTissue
   # import the Java class
-  java_import('edu.wustl.catissuecore.domain.SpecimenArrayType')
+  java_import Java::edu.wustl.catissuecore.domain.SpecimenArrayType
 
   class SpecimenArrayType
     include Resource

data/lib/catissue/domain/specimen_characteristics.rb

@@ -2,7 +2,7 @@
 
 module CaTissue
   # import the Java class
-  java_import('edu.wustl.catissuecore.domain.SpecimenCharacteristics')
+  java_import Java::edu.wustl.catissuecore.domain.SpecimenCharacteristics
 
   class SpecimenCharacteristics
     include Resource

data/lib/catissue/domain/specimen_collection_group.rb

@@ -2,7 +2,7 @@ require 'caruby/util/transitive_closure'
 
 module CaTissue
   # import the Java class
-  java_import('edu.wustl.catissuecore.domain.SpecimenCollectionGroup')
+  java_import Java::edu.wustl.catissuecore.domain.SpecimenCollectionGroup
 
   # The SpecimenCollectionGroup domain class.
   #
@@ -252,12 +252,6 @@ module CaTissue
       end
     end
 
-    def validate
-      super
-      validate_consent
-      validate_event_parameters
-    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.
     # 
@@ -279,6 +273,12 @@ module CaTissue
     private
     
     EVENT_PARAM_ATTRS = [:specimen_event_parameters]
+
+    def validate_local
+      super
+      validate_consent
+      validate_event_parameters
+    end
     
     # @see #fetch_saved
     def status_changed_to_complete?

data/lib/catissue/domain/specimen_event_parameters.rb

@@ -3,7 +3,7 @@ require 'caruby/util/inflector'
 
 module CaTissue
   # import the Java class
-  java_import('edu.wustl.catissuecore.domain.SpecimenEventParameters')
+  java_import Java::edu.wustl.catissuecore.domain.SpecimenEventParameters
 
   class SpecimenEventParameters
     include Resource
@@ -73,17 +73,17 @@ module CaTissue
       specimen_collection_group.collection_protocol if specimen_collection_group
     end
 
-    def validate
+    private
+
+    SUBCLASS_SUFFIX = 'EventParameters'
+
+    def validate_local
       super
       if subject.nil? then
         raise ValidationError.new("Both specimen_collection_group and specimen are missing in SpecimenEventParameters #{self}")
       end
     end
 
-    private
-
-    SUBCLASS_SUFFIX = 'EventParameters'
-
     # Sets each missing value to a default as follows:
     # * default user is the SCG receiver
     # * default timestamp is now

data/lib/catissue/domain/specimen_position.rb

@@ -1,6 +1,6 @@
 module CaTissue
   # import the Java class
-  java_import('edu.wustl.catissuecore.domain.SpecimenPosition')
+  java_import Java::edu.wustl.catissuecore.domain.SpecimenPosition
 
   class SpecimenPosition
     include Resource