caruby-tissue 1.3.1 → 1.3.2

data/History.txt

@@ -14,3 +14,7 @@
 
 * Full PCBIN DE support
 
+=== 1.3.2 / 2011-02-25
+
+* Minor migration bug fixes
+

data/README.md

@@ -91,3 +91,9 @@ Common fields are as follows:
 * Box - Tissue storage container
 * X - the tissue box column
 * Y - the tissue box row
+
+Copyright
+---------
+
+caRuby © 2010, 2011 by [Oregon Health & Science University](http://www.ohsu.edu/xd/health/services/cancer/index.cfm).
+caRuby is licensed under the MIT license. Please see the LICENSE and LEGAL files for more information.

data/lib/catissue/annotation/annotation_class.rb

@@ -118,7 +118,7 @@ module CaTissue
     # Recurses the dependency hierarchy to this annotation class's dependents in a
     # breadth-first manner.
     #
-    # @param [<CaRuby::AttributeMetadata>] the visited attributes
+    # @param [<CaRuby::AttributeMetadata>] path the visited attributes
     def add_dependent_attribute_closure(path=[])
       return if path.include?(self)
       attrs = dependent_attributes(false)

data/lib/catissue/cli/migrate.rb

@@ -16,6 +16,7 @@ module CaTissue
         [:input, "-i", "input", "Source file to migrate"],
         [:target, "-t", "--target CLASS", "Migration target class"],
         [:mapping, "-m", "--mapping FILE", "The input field => caTissue attribute mapping file"],
+        [:defaults, "-d", "--defaults FILE", "The caTissue attribute => default value mapping file"],
         [:shims, "-s", "--shims FILE[,FILE...]", Array, "Migration customization shim files to load"],
         [:bad, "-b", "--bad FILE", "Write each invalid record to the given file and continue migration"],
         [:unique, "-u", "--unique", "Make the migrated objects unique for testing"],

data/lib/catissue/domain/container.rb

@@ -137,6 +137,7 @@ module CaTissue
 
     # @return the occupant at the given zero-based row and column, or nil if none
     def [](column, row)
+      return if column.nil? or row.nil?
       all_occupied_positions.detect_value do |pos|
         return if row < pos.row
         next unless row == pos.row
@@ -149,10 +150,10 @@ module CaTissue
     # The storable Storable position is updated to reflect the new location. Returns self.
     #
     # @param [Storable] storable the item to add
-    # @param [CaRuby::Coordinate, nil] coordinate the x-y coordinate to place the item
+    # @param [CaRuby::Coordinate, <Integer>] 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)
+    def add(storable, *coordinate)
       validate_type(storable)
       loc = create_location(coordinate)
       pos = storable.position || storable.position_class.new
@@ -185,18 +186,22 @@ module CaTissue
     # @param [Storable] the item to store
     # @raise [TypeError] if this container cannot hold the storable
     def validate_type(storable)
+      unless container_type then
+        raise TypeError.new("Container #{self} is missing a type")
+      end
       unless container_type.can_hold_child?(storable) then
-        raise TypeError.new("Container #{self} cannot hold an item of the #{storable} type")
+        raise TypeError.new("Container #{self} cannot hold an item of the #{storable} type #{storable.container_type}")
       end
     end
 
-    # @param [Coordinate] coordinate the optional location to create
+    # @param coordinate (see #add)
     # @return [Location] the created location
-    def create_location(coordinate=nil)
-      if coordinate then
-        Location.new(:in => self, :at => coordinate)
-      else
+    def create_location(coordinate)
+      if coordinate.empty? then
         first_available_location or raise IndexError.new("Container #{qp} does not have an available location")
+      else
+        if coordinate.size == 1 then coordinate = coordinate.first end
+        Location.new(:in => self, :at => coordinate)
       end
     end
 

data/lib/catissue/domain/specimen.rb

@@ -217,9 +217,7 @@ module CaTissue
     # one external identifier.
     def match_in_owner_scope(others)
       super or others.detect do |other|
-         external_identifiers.any? do |eid|
-           other.external_identifiers.detect { |oeid| eid.name == oeid.name and eid.value == oeid.value }
-         end
+        other.class == self.class and external_identifier_match?(other)
       end
     end
 
@@ -368,6 +366,14 @@ module CaTissue
     MERGEABLE_RQMT_ATTRS = nondomain_java_attributes - primary_key_attributes
 
     MERGEABLE_SPC_CHR_ATTRS = SpecimenCharacteristics.nondomain_java_attributes - SpecimenCharacteristics.primary_key_attributes
+
+    # @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)
+       external_identifiers.any? do |eid|
+         other.external_identifiers.detect { |oeid| eid.name == oeid.name and eid.value == oeid.value }
+      end
+    end
      
     # @see #fetch_saved
     def available_quantity_changed?

data/lib/catissue/domain/specimen_event_parameters.rb

@@ -93,15 +93,8 @@ module CaTissue
       self.user ||= default_user
     end
 
-    # Returns whether the given value is either nil, empty or equals other.
-    def missing_or_match?(attribute, other)
-      value = send(attr)
-      value.nil_or_empty? or value == other.send(attr)
-    end
-
     def default_user
-      scg = specimen_collection_group
-      scg ||= specimen.specimen_collection_group if specimen
+      scg = specimen_collection_group || (specimen.specimen_collection_group if specimen)
       scg.receiver if scg
     end
   end

data/lib/catissue/domain/specimen_requirement.rb

@@ -46,7 +46,7 @@ module CaTissue
     # in others with the same class, specimen type, pathological_status and characteristics.
     def match_in_owner_scope(others)
       others.detect do |other|
-        self.class === other and specimen_type == other.specimen_type and pathological_status == other.pathological_status and
+        self.class == other.class and specimen_type == other.specimen_type and pathological_status == other.pathological_status and
          characteristics and characteristics.match?(other.characteristics)
       end
     end

data/lib/catissue/domain/storage_container.rb

@@ -61,6 +61,7 @@ module CaTissue
     end
 
     alias :add_local :add
+    private :add_local
 
     # Adds the given storable to this container. If the storable has a current position, then
     # the storable is moved from that position to this container. The new position is given
@@ -76,12 +77,12 @@ module CaTissue
     #   freezer << specimen #=> places the specimen in the first available box in the freezer
     #
     # @param [Storable] the item to add
-    # @param [Coordinate] the storage location (default is first available location)
+    # @param [Coordinate, <Integer>] the storage location (default is first available location)
     # @return [StorageContainer] self
     # @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)
-      return add_local(storable, coordinate) if coordinate
+    def add(storable, *coordinate)
+      return add_local(storable, *coordinate) if coordinate
       add_to_existing_container(storable) or add_to_new_subcontainer(storable) or out_of_bounds(storable)
       self
     end

data/lib/catissue/domain/uniquify.rb

@@ -0,0 +1,82 @@
+require 'caruby/domain/uniquify'
+
+module CaTissue
+  class CollectionProtocol
+    include CaRuby::Resource::Unique
+    
+    # Makes this CP's short and long title unique.
+    def uniquify
+      super
+      self.title = short_title
+    end
+  end
+
+  class Container
+    include CaRuby::Resource::Unique
+    
+    # Makes this Container and all of its subcontainers unique.
+    def uniquify
+      super
+      subcontainers.each { |ctr| ctr.uniquify }
+    end
+  end
+
+  class ParticipantMedicalIdentifier
+    include CaRuby::Resource::Unique
+  end
+
+  class CollectionProtocolRegistration
+    include CaRuby::Resource::Unique
+    
+    # Makes this CPR's PPI unique.
+    def uniquify
+      oldval = protocol_participant_identifier || return
+      newval = uniquify_value(oldval)
+      self.protocol_participant_identifier = newval
+      logger.debug { "Reset #{qp} PPI from #{oldval} to unique value #{newval}." }
+    end
+  end
+
+  class SpecimenCollectionGroup
+    include CaRuby::Resource::Unique
+    
+    # Makes this SCG's SPN unique.
+    def uniquify
+      super
+      oldval = surgical_pathology_number || return
+      newval = uniquify_value(oldval)
+      self.surgical_pathology_number = newval
+      logger.debug { "Reset #{qp} SPN from #{oldval} to unique value #{newval}." }
+    end
+  end
+
+  class Specimen
+    include CaRuby::Resource::Unique
+  end
+
+  class ExternalIdentifier
+    include CaRuby::Resource::Unique
+    
+    # Makes this ExternalIdentifier's value unique.
+    def uniquify
+      oldval = value || return
+      newval = uniquify_value(oldval)
+      self.value = newval
+      logger.debug { "Reset #{qp} value from #{oldval} to unique value #{newval}." }
+    end
+  end
+
+  class User
+    include CaRuby::Resource::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/migration/migrator.rb

@@ -30,6 +30,8 @@ module CaTissue
     # @option opts [String] :target required target domain class
     # @option opts [String] :input required source file to migrate
     # @option opts [String] :shims optional array of shim files to load
+    # @option opts [String] :unique makes migrated objects unique object for testing
+    #   mix-in do not conflict with existing or future objects
     # @option opts [String] :bad write each invalid record to the given file and continue migration
     # @option opts [String] :offset zero-based starting source record number to process (default 0)
     def initialize(opts={})
@@ -40,12 +42,6 @@ module CaTissue
         # add config options but don't override the parameter options
         opts.merge!(conf, :deep) { |key, oldval, newval| oldval }
       end
-      
-      
-      # TODO - move opt parsing to CaTissue::CLI::Migrate and call that from test cases
-      # Migrate then calls this Migrator with parsed options
-      
-      
       # open the log file before building structure
       log_file = opts[:log]
       CaRuby::Log.instance.open(log_file, :debug => opts[:debug]) if log_file
@@ -60,12 +56,22 @@ module CaTissue
       # call the CaRuby::Migrator initializer with the augmented options
       super
 
-      # the options specific to this CaTissue::Migrator subclass
+      # The remaining options are specific to this CaTissue::Migrator subclass.
+
+      # If the unique option is set, then append the CaTissue-specific uniquifier shim.
+      if opts[:unique] then
+        # add the uniquify shim
+        @shims << UNIQUIFY_SHIM
+      end
+
+      # The tissue site CV look-up option.
       tissue_sites = opts[:tissue_sites]
       if tissue_sites then
         CaTissue::SpecimenCharacteristics.tissue_site_cv_finder = ControlledValueFinder.new(:tissue_site, tissue_sites)
         logger.info("Migrator enabled controlled value lookup.")
       end
+
+      # The clinical diagnosis CV look-up option.
       diagnoses = opts[:diagnoses]
       if diagnoses then
         CaTissue::SpecimenCollectionGroup.diagnosis_cv_finder = ControlledValueFinder.new(:clinical_diagnosis, diagnoses)
@@ -75,6 +81,8 @@ module CaTissue
 
     private
     
+    UNIQUIFY_SHIM = File.join(File.dirname(__FILE__), 'uniquify')
+    
     # Clears the migration protocol CPR and SCG references.
     # This action frees up memory for the next iteration, thereby ensuring that migration is an
     # O(1) rather than O(n) operation.

data/lib/catissue/migration/uniquify.rb

@@ -1,111 +1,2 @@
-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
+# This include file is a convenience CaTissue migrator shim which enables CaTissue class uniquification.
+require 'catissue/domain/uniquify'

data/lib/catissue/util/position.rb

@@ -47,6 +47,11 @@ module CaTissue
       self.row = @location.row
       self.column = @location.column
     end
+    
+    # @return whether either the column or the row is nil
+    def unspecified?
+      column.nil? or row.nil?
+    end
 
     # @return [(Integer, Integer)] this Position's zero-based ({#column}, {#row}) tuple.
     def to_a
@@ -56,8 +61,15 @@ module CaTissue
     # @raise [ValidationError] if the holder cannot hold the occupant type
     def validate
       super
-      unless holder.can_hold_child?(occupant) then
-        raise ValidationError.new("#{self} cannot be occupied by #{occupant}")
+      logger.debug { "Validating that #{holder} can hold #{occupant}..." }
+      curr_occ = holder[column, row]
+      if curr_occ.nil? then
+        unless holder.can_hold_child?(occupant) then
+          reason = holder.full? ? "it is full" : "the occupant type is not among the supported types #{holder.container_type.child_types.qp}"
+          raise ValidationError.new("#{holder} cannot hold #{occupant} since #{reason}")
+        end
+      elsif curr_occ != occupant
+        raise ValidationError.new("#{holder} cannot hold #{occupant} since the location #{[colum, row]} is already occupied by #{curr_occ}")
       end
     end
   end

data/lib/catissue/version.rb

@@ -1,6 +1,6 @@
 module CaTissue
   # The version of this caRuby Tissue release.
-  VERSION = "1.3.1"
+  VERSION = "1.3.2"
   
   # The supported caTissue release versions.
   CATISSUE_VERSIONS = "1.1.2"