caruby-tissue 1.2.1

data/lib/catissue/migration/shims.rb

@@ -0,0 +1,108 @@
+require 'caruby/migration/migrator'
+
+module CaTissue
+  shims SpecimenCollectionGroup, CollectionProtocolRegistration, SpecimenCharacteristics,
+    SpecimenEventParameters, CollectionEventParameters, ReceivedEventParameters
+
+  class SpecimenCollectionGroup
+    @@diagnosis_cv_finder = nil
+
+    # Sets this SpecimenCollectionGroup diagnosis ControlledValueFinder.
+    def self.diagnosis_cv_finder=(finder)
+      @@diagnosis_cv_finder = finder
+    end
+
+    # Returns the diagnosis controlled value as follows:
+    # * If CV lookup is disabled, then this method returns value.
+    # * Otherwise, if the value is remapped via a configuration remap file,
+    #   then this method returns the remapped CV.
+    # * Otherwise, if the value is a valid CV, then this method returns value.
+    # * Otherwise, this method returns nil.
+    def self.diagnosis_controlled_value(value)
+      @@diagnosis_cv_finder.nil? ? value : @@diagnosis_cv_finder.controlled_value(value)
+    end
+
+    # Returns the {#diagnosis_controlled_value}.
+    def migrate_clinical_diagnosis(value, row)
+      SpecimenCollectionGroup.diagnosis_controlled_value(value)
+    end
+  end
+
+  class SpecimenCharacteristics
+    @@tissue_site_cv_finder = nil
+
+    # Sets this SpecimenCharacteristics tissue site ControlledValueFinder.
+    def self.tissue_site_cv_finder=(finder)
+      @@tissue_site_cv_finder = finder
+    end
+
+    # Returns the tissue site controlled value as follows:
+    # * If CV lookup is disabled, then this method returns value.
+    # * Otherwise, if the value is remapped via a configuration remap file,
+    #   then this method returns the remapped CV.
+    # * Otherwise, if the value is a valid CV, then this method returns value.
+    # * Otherwise, this method returns nil.
+    #
+    # @return the caTissue tissue site permissible value
+    def self.tissue_site_controlled_value(value)
+      @@tissue_site_cv_finder.nil? ? value : @@tissue_site_cv_finder.controlled_value(value)
+    end
+
+    # Returns the {#tissue_site_controlled_value}.
+    def migrate_tissue_site(value, row)
+      standard_cv_tissue_site(value) or variant_cv_tissue_site(value)
+    end
+
+    private
+
+    # Returns the {#tissue_site_controlled_value}.
+    #
+    # @return the caTissue tissue site permissible value
+    def standard_cv_tissue_site(value)
+      SpecimenCharacteristics.tissue_site_controlled_value(value)
+    end
+
+    # Returns the {#tissue_site_controlled_value} which adds the 'NOS' suffix to a value
+    # without one or removes 'NOS' from a value with the suffix.
+    #
+    # @return the caTissue tissue site permissible value
+    def variant_cv_tissue_site(value)
+      # try an NOS suffix variation
+      variation = value =~ /, NOS$/ ? value[0...-', NOS'.length] : value + ', NOS'
+      cv = SpecimenCharacteristics.tissue_site_controlled_value(variation)
+      logger.warn("Migrator substituted tissue site #{cv} for #{value}.") if cv
+      cv
+    end
+  end
+
+  class SpecimenEventParameters
+    # Returns nil by default, since only SCGEventParameters have a SCG owner.
+    # {SCGEventParameters#migrate_specimen_collection_group} overrides this method.
+    #
+    # @return nil
+    def migrate_specimen_collection_group(scg, row)
+      nil
+    end
+  end
+
+  module SCGEventParameters
+    #@param [SpecimenCollectionGroup] scg the migrated owner SCG
+    # @return [SpecimenCollectionGroup] scg
+    # @see SpecimenEventParameters#migrate_specimen_collection_group
+    def migrate_specimen_collection_group(scg, row)
+      # unset the specimen parent if necessary
+      self.specimen = nil if specimen and scg
+      scg
+    end
+    
+    # Returns the given Specimen spc unless this SCGEventParameters already has a SCG owner.
+    # A SCGEventParameters is preferentially set to a migrated SCG rather than a migrated
+    # Specimen.
+    #
+    #@param [Specimen] spc the migrated owner specimen
+    # @return [Specimen, nil] spc unless there is already a SCG owner
+    def migrate_specimen(spc, row)
+      spc unless specimen_collection_group
+    end
+  end
+end

data/lib/catissue/migration/uniquify.rb

@@ -0,0 +1,111 @@
+require 'caruby/migration/uniquify'
+
+module CaTissue
+  shims CollectionProtocol, Site, User, Container, ExternalIdentifier, ParticipantMedicalIdentifier,
+    CollectionProtocolRegistration, SpecimenCollectionGroup, Specimen
+
+  class CollectionProtocol
+    include CaRuby::Migratable::Unique
+    
+    # Makes this CP's title unique.
+    def uniquify
+      self.title = self.short_title = uniquify_value(short_title)
+    end
+  end
+  
+  class Site
+    include CaRuby::Migratable::Unique
+    
+    # Makes this Site's name unique.
+    def uniquify
+      self.name = uniquify_value(name)
+    end
+  end
+
+  class CollectionProtocolRegistration
+    include CaRuby::Migratable::Unique
+    
+    # Makes this CPR's PPI unique.
+    def uniquify
+      self.protocol_participant_identifier = uniquify_value(protocol_participant_identifier)
+    end
+  end
+
+  class Container
+    include CaRuby::Migratable::Unique
+    
+    # Makes this Container's name unique.
+    def uniquify
+      self.name = uniquify_value(name)
+    end
+  end
+
+  class ContainerType
+    include CaRuby::Migratable::Unique
+    
+    # Makes this ContainerType's name unique.
+    def uniquify
+      self.name = uniquify_value(name)
+    end
+  end
+
+  class StorageType
+    include CaRuby::Migratable::Unique
+    
+    # Makes this StorageType and the ContainerTypes which it holds unique.
+    def uniquify
+      super
+      child_types.each { |ct| ct.uniquify if ContainerType === ct }
+    end
+  end
+
+  class SpecimenCollectionGroup
+    include CaRuby::Migratable::Unique
+    
+    # Makes this SCG's SPN unique.
+    def uniquify
+      self.surgical_pathology_number = uniquify_value(surgical_pathology_number)
+    end
+  end
+
+  class Specimen
+    include CaRuby::Migratable::Unique
+    
+    # Makes this Specimen's label unique.
+    def uniquify
+      self.label = uniquify_value(label.uniquify) if label
+    end
+  end
+
+  class ExternalIdentifier
+    include CaRuby::Migratable::Unique
+    
+    # Makes this ExternalIdentifier's value unique.
+    def uniquify
+      self.value = uniquify_value(value)
+    end
+  end
+
+  class ParticipantMedicalIdentifier
+    include CaRuby::Migratable::Unique
+    
+    # Makes this PMI's MRN unique.
+    def uniquify
+      self.medical_record_number = uniquify_value(medical_record_number)
+    end
+  end
+
+  class User
+    include CaRuby::Migratable::Unique
+    
+    # Makes this User's login id and email address unique.
+    # The result is in the form _name___suffix_+@test.com+
+    # where:
+    # * _name_ is the name prefix portion of the original email address
+    # * _suffix_ is a unique number
+    def uniquify
+      email = email_address ||= self.login_name || return
+      self.login_name = self.email_address = uniquify_value(email[/[^@]+/]) + '@test.com'
+    end
+  end
+end

data/lib/catissue/resource.rb

@@ -0,0 +1,84 @@
+require 'caruby/resource'
+require 'caruby/domain/resource_module'
+
+module CaTissue
+  extend CaRuby::ResourceModule
+
+  # The module included by all CaTissue domain classes.
+  module Resource
+    include CaRuby::Resource
+    
+    # @param [Resource] other the domain object to compare
+    # @param [<Symbol>] attributes the  attributes to compare
+    # @return [Boolean} whether each of the given attribute values either equals the
+    #   respective other attribute value or one of the values is nil or 'Not Specified'
+    def tolerant_match?(other, attributes)
+      attributes.all? { |attr| Resource.tolerant_value_match?(send(attr), other.send(attr)) }
+    end
+
+    # Returns the CaTissue::Database which stores this object.
+    def database
+      @@database ||= Database.instance
+    end
+
+    protected
+
+    # Returns the required attributes which are nil for this domain object.
+    # Overrides the CaRuby::Resource method to handle the following bug:
+    #
+    # caTissue alert - Bug #67:  AbstractSpecimen.setActivityStatus
+    # is a no-op. The Specimen activityStatus property is incorrectly pulled
+    # up to AbstractSpecimen. AbstractSpecimen.activityStatus is marked as
+    # mandatory, since it is required for Specimen. However, it is not
+    # mandatory, and in fact can't be set, for SpecimenRequirement.
+    # Work-around is to add special code to exclude activityStatus from
+    # the caRuby SpecimenRequirement missing mandatory attributes validation
+    # check.
+    def missing_mandatory_attributes
+      invalid = super
+      # Special case: AbstractSpecimen.setActivityStatus is a no-op.
+      if invalid.include?(:activity_status) and CaTissue::SpecimenRequirement === self then
+        invalid.delete(:activity_status)
+      end
+      invalid
+    end
+
+    private
+    
+    # The unspecified value.
+    UNSPECIFIED = 'Not Specified'
+    
+    # @return whether the given value equals the other value or one of the values is nil or 'Not Specified'
+    def self.tolerant_value_match?(value, other)
+      value == other or unpsecified_value?(value) or unpsecified_value?(other)
+    end
+    
+    # @return whether the given value equals nil or {Resource.UNSPECIFIED}
+    def self.unpsecified_value?(value)
+      value.nil? or value == UNSPECIFIED
+    end
+
+    # Adds the given domain class to the CaTissue CaRuby::ResourceModule.
+    def self.included(klass)
+      CaTissue.add_class(klass)
+    end
+  end
+
+  # The required include mix-in module.
+  @mixin = Resource
+
+  # The required Java package name.
+  @java_package = 'edu.wustl.catissuecore.domain'
+
+  # Load the domain class definitions.
+  dir = File.join(File.dirname(__FILE__), 'domain')
+  load_dir(dir)
+end
+
+module JavaLogger
+  # caTissue alert - the caTissue logger must be initialized before caTissue objects are created.
+  # The logger at issue is the caTissue client logger, not the caTissue server logger nor
+  # the caRuby logger. The caTissue logger facade class is edu.wustl.common.util.logger.Logger,
+  # which is wrapped in Ruby as EduWustlCommonUtilLogger::Logger. TODO - isolate and report.
+  Java::EduWustlCommonUtilLogger::Logger.configure("")
+end

data/lib/catissue/util/controlled_value.rb

@@ -0,0 +1,29 @@
+require 'caruby/util/controlled_value'
+
+module CaTissue
+  class ControlledValue < CaRuby::ControlledValue
+
+    PUBLIC_ID_ALIAS_MAP = {:tissue_site => 'Tissue_Site_PID', :clinical_diagnosis => 'Clinical_Diagnosis_PID'}
+
+    # Returns the standard public id string for the given public_id_or_alias.
+    def self.standard_public_id(public_id_or_alias)
+      PUBLIC_ID_ALIAS_MAP[public_id_or_alias.to_sym] or public_id_or_alias.to_s
+    end
+
+    attr_accessor :identifier, :public_id
+
+    attr_reader :identifier
+
+    def parent_identifier
+      parent.identifier if parent
+    end
+
+    def public_id=(public_id_or_alias)
+      @public_id = self.class.standard_public_id(public_id_or_alias)
+    end
+
+    def to_s
+      "#{value}"
+    end
+  end
+end

data/lib/catissue/util/location.rb

@@ -0,0 +1,116 @@
+require 'caruby/util/coordinate'
+require 'caruby/util/validation'
+
+module CaTissue
+  # A Location is a non-Resource utility class which represents a Container row and column.
+  #
+  # Location does not capture the occupant; therefore, changing a location coordinate value alone does not
+  # change the storage assignment of an occupant.
+  class Location
+    include Comparable
+
+    attr_accessor :container, :coordinate
+
+    define_attribute_alias(:holder, :container)
+
+    # @param [{Symbol => Object}] params the location fields
+    # @option [Integer] params :in the container holding this location
+    # @option [Coordinate, (Integer, Integer)] params :at the location coordinate, expressed as either
+    #    a Coordinate or a (column, row) array
+    # @return the new Location
+    def initialize(params=nil)
+      Options.validate(params, INIT_OPTS)
+      @container = Options.get(:in, params)
+      coord = Options.get(:at, params, Coordinate.new)
+      # turn an :at Array value into a Coordinate
+      if Array === coord and not Coordinate === coord then
+        coord = Coordinate.new(*coord) 
+      end
+      validate_coordinate(coord)
+      @coordinate = coord
+    end
+
+    # @return this location's zero-based first dimension value
+    def column
+      @coordinate.x
+    end
+
+    # Sets this location's column to the given zero-based value.
+    def column=(value)
+      @coordinate.x = value
+    end
+
+    # @return this location's zero-based second dimension value
+    def row
+      @coordinate.y
+    end
+
+    # Sets this location's row to the given zero-based value.
+    def row=(value)
+      @coordinate.y = value
+    end
+
+    # @return [Boolean] whether other is a Location and has the same content as this Location
+    def ==(other)
+      super rescue false
+    end
+
+    # @param [Location] other the position to compare
+    # @return (see Coordinate#<=>)
+    # @raise [ArgumentError] if other is not an Location
+    def <=>(other)
+      raise ArgumentError.new("Can't compare #{qp} to #{other.qp}") unless @container and Location === other
+      unless container == other.container then
+        raise ArgumentError.new("Can't compare #{qp} in container #{container} to #{other.qp} in container #{other.container}")
+      end
+      @coordinate <=> other.coordinate
+    end
+
+    # @return [Location, nil] a new Location at the next slot in this Location's {#container},
+    #   or nil if there are no more locations
+    def succ
+      self.class.new(:in => container, :at => @coordinate).succ! rescue nil
+    end
+
+    # Sets this Location to the next slot in this Location's {#container}.
+    #
+    # @raise [IndexError] if the next slot exceeds the container capacity
+    # @return self
+    def succ!
+      raise IndexError.new("Location #{qp} container not set") unless @container
+      raise IndexError.new("Location #{qp} coordinate not set") unless @coordinate
+      c = column.succ % @container.capacity.columns
+      r = c.zero? ? row.succ : row
+      unless r < container.capacity.rows then
+        raise IndexError.new("Location #{[c, r].qp} exceeds #{@container} container capacity #{container.capacity.bounds}")
+      end
+      @coordinate.x = c
+      @coordinate.y = r
+      self
+    end
+
+    def to_s
+      ctr_s = @container.print_class_and_id if @container
+      coord_s = @coordinate.to_s if @coordinate
+      content_s = "{#{ctr_s}#{coord_s}}" if ctr_s or coord_s
+      "#{print_class_and_id}{#{content_s}"
+    end
+
+    alias :inspect :to_s
+
+    alias :qp :to_s
+
+    private
+    
+    INIT_OPTS = [:in, :at].to_set
+    
+    # @param [CaRuby::Coordinate] coord the coordinate to validate
+    # @raise [IndexError] if the coordinate exceeds the container bounds
+    def validate_coordinate(coord)
+      bnds = @container && @container.bounds
+      if bnds and coord >= bnds then
+        raise IndexError.new("Location #{coord} exceeds container #{@container} dimensions #{bnds}")
+      end
+    end
+  end
+end