caruby-tissue 1.5.6 → 2.1.1

data/lib/catissue/domain/specimen_array.rb

@@ -1,9 +1,6 @@
 
 
 module CaTissue
-  # import the Java class
-  resource_import Java::edu.wustl.catissuecore.domain.SpecimenArray
-
   class SpecimenArray
     # @quirk caTissue the superclass Container occupied_positions does not apply to SpecimenArray.
     remove_attribute(:occupied_positions)

data/lib/catissue/domain/specimen_array_content.rb

@@ -1,9 +1,6 @@
-require 'catissue/util/position'
+require 'catissue/helpers/position'
 
 module CaTissue
-  # import the Java class
-  resource_import Java::edu.wustl.catissuecore.domain.SpecimenArrayContent
-
   # @quirk caTissue #{CaTissue::SpecimenArrayContent} should be derived from
   #   {CaTissue::AbstractPosition} but isn't (cf. {CaTissue::ContainerType}).
   #   Partially rectify this by including the {Position} mix-in in common with

data/lib/catissue/domain/specimen_array_type.rb

@@ -1,8 +1,5 @@
 module CaTissue
-  # import the Java class
-  resource_import Java::edu.wustl.catissuecore.domain.SpecimenArrayType
-
-  class SpecimenArrayType < CaTissue::ContainerType
+  class SpecimenArrayType
     add_mandatory_attributes(:specimen_class, :specimen_types)
 
     # Returns SpecimenArray.

data/lib/catissue/domain/specimen_characteristics.rb

@@ -1,9 +1,6 @@
 
 
 module CaTissue
-  # import the Java class
-  resource_import Java::edu.wustl.catissuecore.domain.SpecimenCharacteristics
-
   class SpecimenCharacteristics
     add_attribute_defaults(:tissue_side => 'Not Specified', :tissue_site => 'Not Specified')
 

data/lib/catissue/domain/specimen_collection_group/pathology/base_pathology_annotation.rb

@@ -1,9 +1,7 @@
 module CaTissue
   class SpecimenCollectionGroup
-    class Pathology
-      resource_import Java::pathology_scg.BasePathologyAnnotation
-      
-      class BasePathologyAnnotation
+    module Pathology
+          class BasePathologyAnnotation
         # @quirk caTissue The BasePathologyAnnotation => HistologicType collection
         #   property is misnamed as histologicType rather than histologicTypeCollection. This misnaming
         #   prevents caRuby from inferring the attribute domain type and inverse. Work-around is to set

data/lib/catissue/domain/specimen_collection_group/pathology/base_solid_tissue_pathology_annotation.rb

@@ -1,9 +1,7 @@
 module CaTissue
   class SpecimenCollectionGroup
-    class Pathology
-      resource_import Java::pathology_scg.BaseSolidTissuePathologyAnnotation
-      
-      class BaseSolidTissuePathologyAnnotation
+    module Pathology
+          class BaseSolidTissuePathologyAnnotation
         # @quirk caTissue The BaseSolidTissuePathologyAnnotation => HistologicGrade collection
         #   property is misnamed as histologicGrade rather than histologicGradeCollection. This misnaming
         #   prevents caRuby from inferring the attribute domain type and inverse. Work-around is to set

data/lib/catissue/domain/specimen_collection_group.rb

@@ -1,16 +1,13 @@
-require 'caruby/util/transitive_closure'
-require 'caruby/util/validation'
-require 'catissue/util/collectible'
+require 'jinx/helpers/transitive_closure'
+require 'jinx/helpers/validation'
+require 'catissue/helpers/collectible'
 
 module CaTissue
-  # import the Java class
-  resource_import Java::edu.wustl.catissuecore.domain.SpecimenCollectionGroup
-
   # The SpecimenCollectionGroup domain class.
   #
   # _Note_: the SpecimenCollectionGroup name attribute is auto-generated on create in caTissue 1.1 API and should not
   # be set by API clients when creating a new SpecimenCollectionGroup in the database.
-  class SpecimenCollectionGroup < CaTissue::AbstractSpecimenCollectionGroup
+  class SpecimenCollectionGroup
     include Collectible
     
     # @quirk caTissue Bug #64: Some domain collection properties not initialized.
@@ -42,8 +39,8 @@ module CaTissue
     end
 
     add_attribute_aliases(:collection_event => :collection_protocol_event,
+      :event => :collection_protocol_event,
       :event_parameters => :specimen_event_parameters,
-      :events => :specimen_event_parameters,
       :registration => :collection_protocol_registration)
 
     # @quirk caTissue Bug #116: specimen_collection_site is incorrectly attached in the caTissue class
@@ -57,7 +54,7 @@ module CaTissue
 
     set_secondary_key_attributes(:name)
 
-    set_alternate_key_attributes(:surgical_pathology_number, :collection_protocol_registration)
+    set_alternate_key_attributes(:surgical_pathology_number, :specimen_collection_site)
 
     # @quirk caTissue An auto-generated or created SCG auto-generates a ConsentTierStatus for each
     #   ConsentTierResponse defined in the SCG owner CPR.
@@ -65,22 +62,21 @@ module CaTissue
     # @quirk caTissue SCG consent_tier_statuses is cascaded but not fetched.
     add_dependent_attribute(:consent_tier_statuses, :autogenerated, :unfetched)
 
-    # SCG event parameters are disjoint, since they are owned by either a SCG or a Specimen.
-    # An auto-generated SCG also auto-generates the Collection and Received SEPs.
-    # A SCG SEP is only created as a dependent when the SCG is created. A SCG SEP
-    # cannot be created for an existing SCG. By contrast, a Specimen SEP can only be
-    # created, not updated.
+    # @quirk caTissue SCG event parameters are disjoint, since they are owned by either a SCG
+    #   or a Specimen, but not both. An auto-generated SCG also auto-generates the Collection 
+    #   and Received SEPs. A SCG SEP is only created as a dependent when the SCG is created.
+    #   A SCG SEP cannot be created for an existing SCG. By contrast, a Specimen SEP can only
+    #   be created, not updated.
     #
-    # @quirk caTissue SpecimenCollectionGroup auto-generated update ignores the referenced
-    #   specimen_event_parameters and instead creates new parameters. This occurs only on the
-    #   first update, and an SEP cannot be added to an existing, updated SCG. Work-around is
-    #   to update the SCG template without the parameters, then update the parameters separately.
+    # @quirk caTissue Update of an auto-generated SpecimenCollectionGroup ignores the referenced
+    #   collection and received event parameters and instead creates new parameters. This occurs
+    #   only on the first update, and an SEP cannot be added to an existing, updated SCG.
+    #   Work-around is to update the SCG template without the parameters, merge the auto-generated
+    #   SEP into the referenced SEP, then save the SEPs separately.
     #
     # @quirk caTissue although SpecimenCollectionGroup auto-generated update ignores referenced
-    #   specimen_event_parameters, collection and received event parameters are mandatory for a
-    #   a created SCG. Set the +:autogenerated_on_update_only+ flag rather than the +:autogenerate+
-    #   to mark the attribute to handle this quirk.
-    add_dependent_attribute(:specimen_event_parameters, :autogenerated_on_update, :disjoint)
+    #   collection and received event parameters, these parameters are mandatory for the update.
+    add_dependent_attribute(:specimen_event_parameters, :disjoint, :fetch_saved)
 
     # SCG Specimens are auto-generated from SpecimenRequirement templates when the SCG is created.
     # The Specimens are not cascaded.
@@ -92,9 +88,6 @@ module CaTissue
     #   within the SCG scope.
     add_dependent_attribute(:specimens, :logical, :autogenerated)
 
-    # The CPE-SCG association is bi-directional.
-    set_attribute_inverse(:collection_protocol_event, :specimen_collection_groups)
-
     # CPE is fetched but not cascaded.
     qualify_attribute(:collection_protocol_event, :fetched)
 
@@ -108,12 +101,9 @@ module CaTissue
     # @quirk caTissue 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 proxy class.
-    self.annotation_proxy_class_name = 'SCGRecordEntry'
 
     # The SCG pathology annotation.
-    add_annotation('Pathology', :package => 'pathology_scg', :service => 'pathologySCG')
+    add_annotation('Pathology', :package => 'pathology_scg', :service => 'pathologySCG', :proxy_name => 'SCGRecordEntry')
 
     # @quirk caTissue Bug #64: Initialize the SCG consent_tier_statuses to an empty set.
     def initialize
@@ -123,7 +113,7 @@ module CaTissue
     end
 
      # @return [CollectionProtocol] the SCG CPE CP
-   def collection_protocol
+    def collection_protocol
       collection_protocol_event.collection_protocol if collection_protocol_event
     end
 
@@ -153,10 +143,10 @@ module CaTissue
     end
 
     # Merges the other object into this SpecimenCollectionGroup. This method augments
-    # {CaRuby::Resource#merge_attributes} as follows:
+    # +Jinx::Resource.merge_attributes+ as follows:
     # * Adds the transitive closure of each non-derived Specimen in other.
     #
-    # @param (see CaRuby::Resource#merge_attributes)
+    # @param (see Jinx::Resource#merge_attributes)
     # @option (see CaTissue::Collectible#merge_attributes)
     def merge_attributes(other, attributes=nil)
       if Hash === other then
@@ -185,7 +175,7 @@ module CaTissue
       super and event_point == other.event_point
     end
 
-    # Overrides {CaRuby::Resource#direct_dependents} in the case of the _specimens_ attribute to select
+    # Overrides +Jinx::Resource.direct_dependents+ in the case of the _specimens_ attribute to select
     # only top-level Specimens not derived from another Specimen.
     def direct_dependents(attribute)
       if attribute == :specimens then
@@ -198,28 +188,28 @@ module CaTissue
     CONSENT_TIER_STATUS_ATTRS = [:consent_tier_statuses]
     
     def mandatory_attributes
-      attrs = super
+      pas = super
       if registration and not registration.consent_tier_responses.empty? then
-        attrs + CONSENT_TIER_STATUS_ATTRS
+        pas + CONSENT_TIER_STATUS_ATTRS
       else
-        attrs
+        pas
       end
     end
 
-    # Relaxes the {CaRuby::Persistable#saved_fetch_attributes} condition for a SCG as follows:
+    # Relaxes the +CaRuby::Persistable.saved_attributes_to_fetch+ 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 saved_fetch_attributes(operation)
+    # @param (see CaRuby::Persistable#saved_attributes_to_fetch)
+    # @return (see CaRuby::Persistable#saved_attributes_to_fetch)
+    def saved_attributes_to_fetch(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:
+    # Relaxes the +CaRuby::Persistable.saved_attributes_to_fetch+ 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)
+    # @param (see CaRuby::Persistable#saved_attributes_to_fetch)
+    # @return (see CaRuby::Persistable#saved_attributes_to_fetch)
     def autogenerated?(operation)
       operation == :update && status_changed_to_complete? ? EVENT_PARAM_ATTRS : super
     end
@@ -233,8 +223,8 @@ module CaTissue
       validate_consent
       validate_event_parameters
     end
-    
-    # @see #fetch_saved
+        
+    # @see #autogenerated?
     def status_changed_to_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." }
@@ -254,7 +244,7 @@ module CaTissue
     #   'Complete' and there is no other ReceivedEventParameters. The receiver is an arbitrary
     #   protocol coordinator.
     #
-    # @raise [ValidationError] if the default ReceivedEventParameters could not be created because
+    # @raise [Jinx::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
@@ -317,7 +307,7 @@ module CaTissue
       pcl = registration.protocol || return
       # if no protocol event, then add the default event
       pcl.add_defaults if pcl.events.empty?
-      ev = pcl.first_event || return
+      ev = pcl.sorted_events.first || return
       logger.debug { "Default #{qp} collection event is the registration protocol #{pcl.qp} first event #{ev.qp}." }
       ev
     end
@@ -325,11 +315,11 @@ module CaTissue
     def create_default_received_event_parameters
       cp = collection_protocol
       if cp.nil? then
-        raise ValidationError.new("SCG with status Complete default CollectionEventParameters could not be created since there is no collection protocol: #{self}")
+        raise Jinx::ValidationError.new("SCG with status Complete default CollectionEventParameters could not be created since there is no collection protocol: #{self}")
       end
       rcvr = cp.coordinators.first
       if rcvr.nil? then
-        raise ValidationError.new("SCG with status Complete default CollectionEventParameters could not be created since there is no collection protocol coordinator: #{self}")
+        raise Jinx::ValidationError.new("SCG with status Complete default CollectionEventParameters could not be created since there is no collection protocol coordinator: #{self}")
       end
       # make the REP
       ev = CaTissue::SpecimenEventParameters.create_parameters(:received, self, :user => rcvr)
@@ -347,7 +337,7 @@ module CaTissue
       ev
     end
 
-    # @raise [ValidationError] if there is a registration consent tier response without a corresponding SCG consent tier status
+    # @raise [Jinx::ValidationError] if there is a registration consent tier response without a corresponding SCG consent tier status
     def validate_consent
       return unless registration
       # the default consent statuses
@@ -355,15 +345,15 @@ module CaTissue
       registration.consent_tier_responses.each do |ctr|
         ct = ctr.consent_tier
         unless ctses.include?(ct) then
-          raise ValidationError.new("#{self} is missing a ConsentTierStatus for consent statement #{ct.statement}")
+          raise Jinx::ValidationError.new("#{self} is missing a ConsentTierStatus for consent statement #{ct.statement}")
         end
       end
     end
 
-    # @raise [ValidationError] if the SCG has neither an identifier nor Received and Collection event parameters
+    # @raise [Jinx::ValidationError] if the SCG has neither an identifier nor Received and Collection event parameters
     def validate_event_parameters
       if identifier.nil? and event_parameters.empty? then
-        raise ValidationError.new("#{self} create is missing the required Received and Collection event parameters")
+        raise Jinx::ValidationError.new("#{self} create is missing the required Received and Collection event parameters")
       end
     end
   end

data/lib/catissue/domain/specimen_event_parameters.rb

@@ -1,11 +1,8 @@
-require 'caruby/util/validation'
-require 'caruby/util/inflector'
-require 'catissue/util/collectible'
+require 'jinx/helpers/validation'
+require 'jinx/helpers/inflector'
+require 'catissue/helpers/collectible'
 
 module CaTissue
-  # import the Java class
-  resource_import Java::edu.wustl.catissuecore.domain.SpecimenEventParameters
-
   class SpecimenEventParameters
     # date is a synonym for the more accurately titled timestamp attribute.
     add_attribute_aliases(:date => :timestamp)
@@ -15,14 +12,6 @@ module CaTissue
     # specimen is abstract but unfetched.
     qualify_attribute(:specimen, :unfetched)
 
-    private
-
-    def self.allocate
-      raise NotImplementedError.new("SpecimenEventParameters is abstract; use the create method to make a new instance")
-    end
-
-    public
-
     # Creates a SpecimenEventParameters of the specified subclass type. The type is a
     # SpecimenEventParameters subclass name without the +EventParameters+ suffix, e.g.
     # +Collection+. Lower-case, underscore symbols are supported and preferred, e.g. the
@@ -33,25 +22,29 @@ module CaTissue
     #
     # The optional params argument are attribute => value associations, e.g.
     #   SpecimenEventParameters.create_parameters(:collection, scg, :user => collector, :timestamp => DateTime.now)
+    #
+    # @param [String, Symbol] type the event type
+    # @param [SpecimenCollectionGroup, Specimen] scg_or_specimen the event owner
+    # @param [{Symbol => Object}, nil] params the attribute => value associations
     def self.create_parameters(type, scg_or_specimen, params=Hash::EMPTY_HASH)
       # make the class name by joining the camel-cased type prefix to the subclass suffix.
-      # classify converts a lower_case, underscore type to a valid class name, e.g. :check_in_check_out
-      # becomes CheckInCheckOut.
+      # classify converts a lower_case, underscore type to a valid class name,
+      # e.g. +:check_in_check_out+ becomes +CheckInCheckOut+.
       class_name = type.to_s.classify + SUBCLASS_SUFFIX
       begin
         klass = CaTissue.const_get(class_name.to_sym)
       rescue
         raise ArgumentError.new("Unsupported event parameters type: #{type}; #{class_name} must be a subtype of #{self}")
       end
-      event_params = klass.new(params)
+      ep = 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")
+        when CaTissue::SpecimenCollectionGroup then ep.specimen_collection_group = scg_or_specimen
+        when CaTissue::Specimen then ep.specimen = scg_or_specimen
+        when nil then raise ArgumentError.new("Missing SpecimenEventParameters SCG or Specimen owner argument")
         else
           raise ArgumentError.new("Unsupported SpecimenEventParameters factory argument - expected SpecimenCollectionGroup or Specimen, found #{scg_or_specimen.class}")
       end
-      event_params
+      ep
     end
 
     # @return [CaTissue::Collectible] specimen or SCG to which this event is attached
@@ -73,24 +66,20 @@ module CaTissue
       specimen_collection_group.collection_protocol if specimen_collection_group
     end
     
-    def saved_fetch_attributes(operation)
-      attrs = super
-      # TODO - KLUDGE!!!! simple_test migration test fails to set user ---- FIX!!!!
-      if identifier and not attrs.include?(:user) then
-        attrs + [:user]
-      else
-        attrs
-      end
-    end
-    
     private
 
+    # The class name suffix for all event parameter classes.
     SUBCLASS_SUFFIX = 'EventParameters'
 
+    def self.allocate
+      raise NotImplementedError.new("SpecimenEventParameters is abstract; use the create method to make a new instance")
+    end
+
+    # @raise [Jinx::ValidationError] if the subject is missing or there is both a SCG and a Specimen owner
     def validate_local
       super
       if subject.nil? then
-        raise ValidationError.new("Both specimen_collection_group and specimen are missing in SpecimenEventParameters #{self}")
+        raise Jinx::ValidationError.new("Both specimen_collection_group and specimen are missing in SpecimenEventParameters #{self}")
       end
     end
 
@@ -103,7 +92,10 @@ module CaTissue
       self.user ||= default_user
     end
 
+    # @return [CaTissue::User] the SCG receiver
     def default_user
+      user = specimen.receiver if specimen
+      return user if user
       scg = specimen_collection_group || (specimen.specimen_collection_group if specimen)
       scg.receiver if scg
     end

data/lib/catissue/domain/specimen_position.rb

@@ -1,8 +1,5 @@
 module CaTissue
-  # import the Java class
-  resource_import Java::edu.wustl.catissuecore.domain.SpecimenPosition
-
-  class SpecimenPosition < CaTissue::AbstractPosition
+  class SpecimenPosition
     add_mandatory_attributes(:storage_container)
 
     add_attribute_aliases(:holder => :storage_container, :container => :storage_container, :occupant => :specimen)
@@ -22,7 +19,13 @@ module CaTissue
     #   Creating a TransferEventParameters sets the SpecimenPosition as a side-effect. Therefore,
     #   SpecimenPosition save is accomplished by creating a proxy TransferEventParameters instead.
     def saver_proxy
-      xfr = CaTissue::TransferEventParameters.new(:specimen => specimen, :to => location)
+      # Look for a transfer event that matches the position.
+      xfr = specimen.event_parameters.detect do |sep|
+        CaTissue::TransferEventParameters === sep and sep.to == location
+      end
+      # Create a new transfer event, if necessary.
+      xfr ||= CaTissue::TransferEventParameters.new(:specimen => specimen, :to => location)
+      # If this position changed, then copy the original position to the transfer event from attributes.
       if snapshot and changed? then
         xfr.from_storage_container = snapshot[:storage_container]
         xfr.from_position_dimension_one = snapshot[:position_dimension_one]

data/lib/catissue/domain/specimen_protocol.rb

@@ -1,21 +1,18 @@
 require 'date'
 
 module CaTissue
-  # import the Java class
-  resource_import Java::edu.wustl.catissuecore.domain.SpecimenProtocol
-  
   # The SpecimenProtocol domain class.
   class SpecimenProtocol
     set_secondary_key_attributes(:title)
 
-    # @quirk caTissue Bug #155: enrollment is incorrectly defined in SpecimenProtocol rather
+    # @quirk caTissue Bug #155: Enrollment is incorrectly defined in SpecimenProtocol rather
     #   than CollectionProtocol. It is defaulted here until this defect is fixed.
     add_attribute_defaults(:activity_status => 'Active', :enrollment => 0)
 
     add_mandatory_attributes(:principal_investigator, :activity_status, :start_date, :short_title)
 
-    # @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 savable reference attributes to work around caTissue Bug #150:
+    #   Create CollectionProtocol in the caTissue API ignores +startDate+.
     qualify_attribute(:start_date, :update_only)
 
     private