caruby-tissue 1.5.6 → 2.1.1

data/lib/catissue/domain/collection_protocol_event.rb

@@ -1,20 +1,14 @@
-require 'caruby/util/collection'
-require 'catissue/domain/hash_code'
+require 'jinx/helpers/collections'
 
-module CaTissue
-  # import the Java class
-  resource_import Java::edu.wustl.catissuecore.domain.CollectionProtocolEvent
+require 'catissue/helpers/hash_code'
 
-  # The CollectionProtocolRegistration domain class.
+module CaTissue
+  # The CollectionProtocolEvent domain class.
   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
@@ -41,6 +35,10 @@ module CaTissue
     #   CollectionProtocol create cascades through each dependent CPE to each SpecimenRequirement.
     add_dependent_attribute(:specimen_requirements, :unfetched)
 
+    # @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.
     remove_attribute(:specimen_collection_groups)
 
     # The event point used for saving this CollectionProtocolEvent if none other is set.
@@ -51,7 +49,7 @@ module CaTissue
       protocol.events.delete(self) if protocol
     end
 
-    # Overrides {CaRuby::Resource#references} in the case of the _specimen_requirements_ attribute to select
+    # Overrides +Jinx::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
@@ -70,7 +68,16 @@ module CaTissue
     end
 
     def default_label
-      "#{protocol.short_title.sub(' ', '_')}_#{event_point}" if protocol and protocol.short_title and event_point
+      pcl = protocol_label_component
+      if pcl and event_point then
+        "#{pcl}_#{event_point}"
+      end
+    end
+    
+    def protocol_label_component
+      return if protocol.nil?
+      pcl = protocol.short_title || protocol.title || return
+      pcl.sub(' ', '_')
     end
   end
 end

data/lib/catissue/domain/collection_protocol_registration.rb

@@ -1,10 +1,8 @@
-require 'caruby/util/collection'
-require 'caruby/util/validation'
+require 'jinx/helpers/collections'
 
-module CaTissue
-  # import the Java class
-  resource_import Java::edu.wustl.catissuecore.domain.CollectionProtocolRegistration
+require 'jinx/helpers/validation'
 
+module CaTissue
   # The CollectionProtocolRegistration domain class.
   class CollectionProtocolRegistration
     # @quirk caTissue Bug #64: Some domain collection properties not initialized.
@@ -36,9 +34,7 @@ module CaTissue
     add_attribute_aliases("consented?".to_sym => :is_consent_available, :protocol => :collection_protocol,
       :participant_identifier => :protocol_participant_identifier, :consent_responses => :consent_tier_responses)
 
-    set_secondary_key_attributes(:collection_protocol, :participant)
-
-    set_alternate_key_attributes(:collection_protocol, :protocol_participant_identifier)
+    set_secondary_key_attributes(:collection_protocol, :protocol_participant_identifier)
 
     add_attribute_defaults(:activity_status => 'Active')
 
@@ -67,7 +63,7 @@ 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:
+    # @quirk caTissue  Augment the standard metadata savable reference attributes to work around caTissue Bug #150:
     #   Create CollectionProtocol in API ignores startDate.
     qualify_attribute(:registration_date, :update_only)
 
@@ -89,7 +85,7 @@ module CaTissue
 
     # @return all specimens collected for this CollectionProtocolRegistration
     def specimens
-      Flattener.new(specimen_collection_groups.map { |group| group.specimens })
+      Jinx::Flattener.new(specimen_collection_groups.map { |scg| scg.specimens })
     end
 
     private
@@ -97,7 +93,7 @@ module CaTissue
     def validate_local
       super
       if participant.nil? and protocol_participant_identifier.nil? then
-        raise ValidationError.new("#{qp} requires a participant or a protocol participant identifier.")
+        raise Jinx::ValidationError.new("#{qp} requires a participant or a protocol participant identifier.")
       end
     end
     
@@ -107,7 +103,7 @@ module CaTissue
     def add_defaults_local
       super
       self.registration_date ||= Java.now
-      self.protocol_participant_identifier ||= Uniquifier.qualifier.to_s
+      self.protocol_participant_identifier ||= Jinx::Uniquifier.qualifier.to_s
     end
   end
 end

data/lib/catissue/domain/consent_tier_response.rb

@@ -1,13 +1,9 @@
 module CaTissue
-  # import the Java class
-  resource_import Java::edu.wustl.catissuecore.domain.ConsentTierResponse
-
   class ConsentTierResponse
     add_mandatory_attributes(:consent_tier, :response)
 
     add_attribute_defaults(:response => 'Not Specified')
     
     qualify_attribute(:consent_tier, :fetched)
-
   end
 end

data/lib/catissue/domain/consent_tier_status.rb

@@ -1,7 +1,4 @@
 module CaTissue
-  # import the Java class
-  resource_import Java::edu.wustl.catissuecore.domain.ConsentTierStatus
-
   class ConsentTierStatus
     add_mandatory_attributes(:consent_tier, :status)
 
@@ -23,7 +20,7 @@ module CaTissue
     def statement_match?(other)
       ct = consent_tier
       oct = other.consent_tier
-      (ct.nil? or oct.nil?) or (ct.identifier == oct.identifier or ct.statement == oct.statement)
+      ct.nil? or oct.nil? or ct.identifier == oct.identifier or ct.statement == oct.statement
     end
   end
 end

data/lib/catissue/domain/container.rb

@@ -1,12 +1,10 @@
-require 'caruby/util/validation'
-require 'caruby/util/coordinate'
-require 'catissue/util/storable'
-require 'catissue/util/location'
+require 'jinx/helpers/validation'
+require 'caruby/helpers/coordinate'
+require 'jinx/resource/reference_visitor'
+require 'catissue/helpers/storable'
+require 'catissue/helpers/location'
 
 module CaTissue
-  # import the Java class
-  resource_import Java::edu.wustl.catissuecore.domain.Container
-
   # The +caTissue+ +Container+ domain class wrapper.
   # Each Container subclass is required to implement the {#container_type} method.
   class Container
@@ -16,6 +14,8 @@ module CaTissue
 
     set_secondary_key_attributes(:name)
 
+    set_alternate_key_attributes(:barcode)
+
     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.
@@ -172,16 +172,16 @@ module CaTissue
     private
 
     # Subcontainer visitor.
-    SUBCTR_VISITOR = CaRuby::ReferenceVisitor.new { [:subcontainers] }
+    SUBCTR_VISITOR = Jinx::ReferenceVisitor.new { [:subcontainers] }
 
     # @param [Storable] the item to store
     # @raise [TypeError] if this container cannot hold the storable
     def validate_type(storable)
       unless container_type then
-        raise ValidationError.new("Container #{self} is missing a type")
+        raise Jinx::ValidationError.new("Container #{self} is missing a type")
       end
       unless container_type.can_hold_child?(storable) then
-        raise ValidationError.new("Container #{self} cannot hold an item of the #{storable} type #{storable.container_type}")
+        raise Jinx::ValidationError.new("Container #{self} cannot hold an item of the #{storable} type #{storable.container_type}")
       end
     end
 

data/lib/catissue/domain/container_position.rb

@@ -1,10 +1,7 @@
-require 'caruby/util/validation'
+require 'jinx/helpers/validation'
 
 module CaTissue
-  # import the Java class
-  resource_import Java::edu.wustl.catissuecore.domain.ContainerPosition
-
-  class ContainerPosition < CaTissue::AbstractPosition
+  class ContainerPosition
     add_mandatory_attributes(:parent_container)
 
     add_attribute_aliases(:parent => :parent_container, :holder => :parent_container, :occupant => :occupied_container)
@@ -20,11 +17,11 @@ module CaTissue
     
     private
     
-    # @raise [ValidationError] if the parent is the same as the occupant 
+    # @raise [Jinx::ValidationError] if the parent is the same as the occupant 
     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}")
+         raise Jinx::ValidationError.new("#{self} has a circular containment reference to subcontainer #{occupant}")
       end
     end
   end

data/lib/catissue/domain/container_type.rb

@@ -1,9 +1,6 @@
-require 'caruby/util/options'
+require 'jinx/helpers/options'
 
 module CaTissue
-  # import the Java class
-  resource_import Java::edu.wustl.catissuecore.domain.ContainerType
-
   # The caTissue ContainerType domain class wrapper.
   # Each {ContainerType} subclass is required to implement the container_class method.
   #
@@ -15,7 +12,7 @@ module CaTissue
   #
   #   This conceptual model is implemented in caTissue as follows:
   #   * The specimen collection container type, e.g. +Citrate Vacutainer+, is captured
-  #     as a {CaTissue::CollectionEventParameters#container} String. There is no separate
+  #     as a {CaTissue::CollectionEventParameters} +container+ String. There is no separate
   #     collection container instance or container type instance.
   #   * A tissue specimen storage box is captured as a {CaTissue::StorageContainer}
   #     instance constrained to a {CaTissue::StorageType} instance. Boxes with different
@@ -75,7 +72,7 @@ module CaTissue
     #   ContainerType is created.
     add_dependent_attribute(:capacity)
     
-    # Override default {CaRuby::Resource#merge_attributes} to support the Capacity :rows and :columns
+    # Override default +Jinx::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.
@@ -83,7 +80,7 @@ module CaTissue
     #   not pick up ContainerType Resource overrides. Work-around is that each ContainerType
     #   subclass must alias +merge_attributes+ to this method.
     #
-    # @param (see #merge_attributes)
+    # @param (see CaRuby::Mergeable#merge_attributes)
     def merge_attributes(other, attributes=nil)
       if Hash === other then
         # partition the other hash into the Capacity attributes and ContainerType attributes

data/lib/catissue/domain/department.rb

@@ -1,9 +1,6 @@
 
 
 module CaTissue
-  # import the Java class
-  resource_import Java::edu.wustl.catissuecore.domain.Department
-
   # The Department domain class.
   class Department
     set_secondary_key_attributes(:name)

data/lib/catissue/domain/disposal_event_parameters.rb

@@ -1,11 +1,11 @@
 module CaTissue
-  # import the Java class
-  resource_import Java::edu.wustl.catissuecore.domain.DisposalEventParameters
-
-  class DisposalEventParameters < CaTissue::SpecimenEventParameters
+  class DisposalEventParameters
     add_attribute_defaults(:activity_status => 'Closed')
 
     # @quirk caTissue DisposalEventParameters activity status is transient.
-    qualify_attribute(:activity_status, :unfetched)
+    #
+    # @quirk caTissue DisposalEventParameters activity status is not set in a create.
+    #   The work-around is to perform a subsequent update on the created event.
+    qualify_attribute(:activity_status, :unfetched, :update_only)
   end
 end

data/lib/catissue/domain/embedded_event_parameters.rb

@@ -1,8 +1,5 @@
 module CaTissue
-  # import the Java class
-  resource_import Java::edu.wustl.catissuecore.domain.EmbeddedEventParameters
-
-  class EmbeddedEventParameters < CaTissue::SpecimenEventParameters
+  class EmbeddedEventParameters
     add_attribute_aliases(:medium => :embedding_medium)
   end
 end

data/lib/catissue/domain/external_identifier.rb

@@ -1,18 +1,6 @@
-
-
 module CaTissue
-  # import the Java class
-  resource_import Java::edu.wustl.catissuecore.domain.ExternalIdentifier
-
   # The ExternalIdentifier domain class.
   class ExternalIdentifier
-    # Sets this ExternalIdentifier value to the given value.
-    # A Numeric value is converted to a String.
-    def value=(value)
-      value = value.to_s if value
-      setValue(value)
-    end
-
     add_mandatory_attributes(:value)
 
     set_secondary_key_attributes(:specimen, :name)

data/lib/catissue/domain/frozen_event_parameters.rb

@@ -1,8 +1,5 @@
 module CaTissue
-  # import the Java class
-  resource_import Java::edu.wustl.catissuecore.domain.FrozenEventParameters
-
-  class FrozenEventParameters < CaTissue::SpecimenEventParameters
+  class FrozenEventParameters
     add_attribute_aliases(:freeze_method => :frozen_event_parameters_method)
   end
 end

data/lib/catissue/domain/institution.rb

@@ -1,9 +1,6 @@
 
 
 module CaTissue
-  # import the Java class
-  resource_import Java::edu.wustl.catissuecore.domain.Institution
-
   # The Institution domain class.
   class Institution
     set_secondary_key_attributes(:name)

data/lib/catissue/domain/new_specimen_array_order_item.rb

@@ -1,9 +1,4 @@
-require 'catissue/resource'
-
 module CaTissue
-  # import the Java class
-  resource_import Java::edu.wustl.catissuecore.domain.NewSpecimenArrayOrderItem
-
   # The NewSpecimenArrayOrderItem domain class.
   class NewSpecimenArrayOrderItem
     # @quirk caTissue Bug #64: order items collection property is not initialized to an empty set

data/lib/catissue/domain/order_details.rb

@@ -1,8 +1,6 @@
 
 
 module CaTissue
-  resource_import Java::edu.wustl.catissuecore.domain.OrderDetails
-
   # The OrderDetails domain class.
   class OrderDetails
     # @quirk caTissue Bug #64: Some domain collection properties not initialized.

data/lib/catissue/domain/participant/clinical/chemotherapy.rb

@@ -1,9 +1,7 @@
 module CaTissue
   class Participant
-    class Clinical
+    module Clinical
       begin
-        resource_import Java::clinical_annotation.Chemotherapy
-      
         # @quirk caTissue The Chemotherapy DE class is not a primary entity with an entity id.
         #   ChemoRXAnnotation is used instead. The purpose of the caTissue Chemotherapy class is unknown,
         #   since it adds nothing to ChemoRXAnnotation.

data/lib/catissue/domain/participant/clinical/duration.rb

@@ -1,9 +1,7 @@
 module CaTissue
   class Participant
-    class Clinical
-      resource_import Java::clinical_annotation.Duration
-      
-      class Duration
+    module Clinical
+          class Duration
         add_attribute_aliases(:treatment => :treatment_annotation)
       end
     end

data/lib/catissue/domain/participant/clinical/radiation_therapy.rb

@@ -1,10 +1,8 @@
 module CaTissue
   class Participant
-    class Clinical
+    module Clinical
       begin
-        resource_import Java::clinical_annotation.RadiationTherapy
-        
-        # @quirk caTissue The RadiationTherapy DE class is not a primary entity with an entity id.
+              # @quirk caTissue The RadiationTherapy DE class is not a primary entity with an entity id.
         #   RadRXAnnotation is used instead. The purpose of the caTissue RadiationTherapy class is unknown,
         #   since it adds nothing to RadRXAnnotation.
         class RadiationTherapy

data/lib/catissue/domain/participant.rb

@@ -1,11 +1,7 @@
-require 'caruby/util/validation'
-require 'catissue/resource'
-require 'catissue/util/person'
+require 'jinx/helpers/validation'
+require 'catissue/helpers/person'
 
 module CaTissue
-  # import the Java class
-  resource_import Java::edu.wustl.catissuecore.domain.Participant
-
   # The Participant domain class.
   class Participant
     include Person
@@ -15,7 +11,7 @@ module CaTissue
     add_attribute(:name, CaRuby::Person::Name)
 
     # @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
+    if property_defined?(:clinical_study_registrations) then remove_attribute(:clinical_study_registrations) end
 
     add_attribute_aliases(:collection_registrations => :collection_protocol_registrations,
       :registrations => :collection_protocol_registrations,
@@ -44,25 +40,23 @@ module CaTissue
     # @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
+    #   (see merge_attribute comment). At any rate, PMI is marked 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.
+    #   In other words, fixing the caTissue bug will break this caRuby work-around.
     add_dependent_attribute(:participant_medical_identifiers)
 
     # SSN is a key, if present, but is not required.
     qualify_attribute(:social_security_number, :optional)
     
-    # The Participant proxy class.
-    self.annotation_proxy_class_name = 'ParticipantRecordEntry'
-    
     # 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
+    # Overrides +CaRuby::Mergable.merge_attribute+ to work around the caTissue
+    #  bugs described in {CaTissue::Participant.remove_phantom_medical_identifier}.
     def merge_attribute(attribute, newval, matches=nil)
       if attribute == :participant_medical_identifiers and newval then
-        CaTissue::Participant.remove_empty_medical_identifier(newval)
+        CaTissue::Participant.remove_phantom_medical_identifier(newval)
       end
       super
     end
@@ -88,7 +82,7 @@ module CaTissue
 
     # @return [<CTissue::Specimen>] all specimens collected from this participant
     def specimens
-      Flattener.new(registrations.specimens.map { |cpr| cpr.specimens })
+      Jinx::Flattener.new(registrations.map { |cpr| cpr.specimens })
     end
 
     # Returns this Participant's CollectionProtocolRegistration protocols.
@@ -118,16 +112,20 @@ module CaTissue
 
     protected
 
-    def self.remove_empty_medical_identifier(mids)
-      bogus = mids.detect { |mid| mid.medical_record_number.nil? }
-      if bogus then
-        logger.debug { "Work around caTissue bug by removing empty fetched #{bogus.participant.qp} #{bogus.qp}..." }
+    # @quirk caTissue auto-generates a phantom Participant PMI.
+    #   cf. https://cabig-kc.nci.nih.gov/Biospecimen/forums/viewtopic.php?f=19&t=436&sid=ef98f502fc0ab242781b7759a0eaff36
+    #
+    # @param [<CaTissue::ParticipantMedicalIdentifier>] pmis the PMIs to clean up
+    def self.remove_phantom_medical_identifier(pmis)
+      phantom = pmis.detect { |pmi| pmi.medical_record_number.nil? }
+      if phantom then
+        logger.debug { "Work around caTissue bug by removing the phantom fetched #{phantom.participant.qp} #{phantom.qp}..." }
         # dissociate the participant
-        bogus.participant = nil
-        # remove the bogus medical identifier
-        mids.delete(bogus)
+        phantom.participant = nil
+        # remove the phantom medical identifier
+        pmis.delete(phantom)
       end
-      mids
+      pmis
     end
 
     private
@@ -136,7 +134,7 @@ module CaTissue
     def alternate_key
       return if medical_identifiers.empty?
       pmi = medical_identifiers.first
-      pmi.key if pmi
+      pmi.secondary_key if pmi
     end
 
     # Adds a default Unknown Race, if necessary. Although Race is not strictly mandatory in the caTissue