caruby-tissue 1.2.2 → 1.2.3

data/lib/catissue/domain/storage_container.rb

@@ -17,24 +17,18 @@ module CaTissue
     def specimen_positions
       getSpecimenPositionCollection or (self.specimen_positions = Java::JavaUtil::LinkedHashSet.new)
     end
-
-    # Sets the storage type to the given value. Each empty holds collection is initialized
-    # from the corresponding StorageType holds collection.
-    def storage_type=(value)
-      if value and holds_storage_types and holds_storage_types.empty? then
-        holds_storage_types.merge!(value.holds_storage_types)
-      end
-      if value and holds_specimen_array_types and holds_specimen_array_types.empty? then
-        holds_specimen_array_types.merge!(value.holds_specimen_array_types)
-      end
-      if value and holds_specimen_classes and holds_specimen_classes.empty? then
-        holds_specimen_classes.merge!(value.holds_specimen_classes)
-      end
-      setStorageType(value)
-    end
-    
-    def located_at_position=(value)
-      setLocatedAtPosition(value)
+ 
+    # Copies the given container type child types to this container instance child types.
+    #
+    # caTissue alert - caTissue API does not initialize the container child types to
+    # the container type child types. This method copies the container type child types
+    # to this container instance before it is created.
+    #
+    # @param [<StorageType>] type the storage type to set
+    def storage_type=(type)
+      setStorageType(type)
+      copy_child_types(type) if type
+      type
     end
 
     add_attribute_aliases(:container_type => :storage_type)
@@ -42,7 +36,7 @@ module CaTissue
     # Aternative to the inherited secondary key +name+.
     set_alternate_key_attributes(:site, :barcode)
 
-    add_mandatory_attributes(:site, :storage_type)
+    add_mandatory_attributes(:storage_type)
 
     qualify_attribute(:collection_protocols, :fetched)
 
@@ -53,8 +47,9 @@ module CaTissue
     set_attribute_type(:holds_storage_types, CaTissue::StorageType)
 
     def initialize(params=nil)
+      # set params below to enable storage_type setter work-around
       super(params)
-      # JRuby alert - specimen_positions is sometimes unrecognized unless primed with respond_to? call
+      # JRuby alert - specimen_positions is not recognized unless primed with respond_to? call
       respond_to?(:specimen_positions)
       # work around caTissue Bug #64
       self.specimen_positions ||= Java::JavaUtil::LinkedHashSet.new
@@ -67,12 +62,18 @@ module CaTissue
 
     alias :add_local :add
 
-    # Moves the given Storable from its current Position, if any, to this Container at the optional
-    # coordinate. The default coordinate is the first available slot within this Container.
-    # The storable Storable position is updated to reflect the new location. Returns self.
+    # 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
+    # by the given coordinate, if given to this method.
     #
-    # If there is no coordinate and this container cannot hold the storable type, then the
-    # storable is added to a subcontainer which can hold the storable type.
+    #The default coordinate is the first available slot within this Container.
+    # If this container cannot hold the storable type, then the storable is added to a
+    # subcontainer which can hold the storable type.
+    #
+    # @example
+    #   rack << box #=> places the tissue box on the rack
+    #   freezer << box #=> places the tissue box on a rack in the freezer
+    #   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)
@@ -105,7 +106,7 @@ module CaTissue
       box
     end
 
-    # @return a new Container with the given name and type in this Container
+    # @return [Container] a new container with the given name and type, located in this container
     def create_subcontainer(name, type)
       logger.debug { "Creating #{qp} subcontainer of type #{type} with name #{name}..." }
       ctr = type.create_container(:name => name, :site => site)
@@ -115,6 +116,17 @@ module CaTissue
       ctr
     end
 
+    # Overrides {Container#can_hold_child?} to detect account for the potential instance-specific
+    # {StorageTypeHolder#child_types} override allowed by caTissue.
+    #
+    # @param [Storable] (see #add)
+    # @return [Boolean] whether this container is not full and can hold the given item's
+    #   {CaTissue::StorableType}
+    def can_hold_child?(storable)
+      st = storable.storable_type
+      not full? and child_types.any? { |ct| CaRuby::Resource.value_equal?(ct, st) }
+    end
+    
     protected
     
     # Returns the the content collection to which the storable is added, specimen_positions
@@ -127,14 +139,33 @@ module CaTissue
     #
     # @param @storable (see #add)
     # @return [StorageContainer, nil] self if added, nil otherwise
+    # @raise [ValidationError] if this container does not have a storage type, or if a circular
+    #   containment reference is detected
     def add_to_existing_container(storable)
+      if storage_type.nil? then raise ValidationError.new("Cannot add #{storable.qp} to #{qp} with missing storage type") end
       # the subcontainers in column, row sort order
       scs = subcontainers.sort { |sc1, sc2| sc1.position.location <=> sc2.position.location }
+      logger.debug { "Looking for a #{self} subcontainer from among #{scs.pp_s} to place #{storable.qp}..." } unless scs.empty?
       # the first subcontainer that can hold the storable is preferred
-      if scs.detect { |ctr| ctr.add_to_existing_container(storable) if StorageContainer === ctr } then
+      sc = scs.detect do |sc|
+        # Check for circular reference. This occurred as a result of the caTissue bug described
+        # in CaTissue::Database#query_object. The work-around circumvents the bug for now, but
+        # it doesn't hurt to check again.
+        if identifier and sc.identifier == identifier then
+          raise ValidationError.new("#{self} has a circular containment reference to subcontainer #{sc}")
+        end
+        # No circular reference; add to subcontainer if possible
+        sc.add_to_existing_container(storable) if StorageContainer === sc
+      end
+      if sc then
+        logger.debug { "#{self} subcontainer #{sc} stored #{storable.qp}." }
         self
       elsif can_hold_child?(storable) then
+        logger.debug { "#{self} can hold #{storable.qp}." }
         add_local(storable)
+      else
+        logger.debug { "Neither #{self} of type #{storage_type.name} nor its subcontainers can hold #{storable.qp}." }
+        nil
       end
     end
 
@@ -145,31 +176,38 @@ module CaTissue
     def add_to_new_subcontainer(storable)
       # the subcontainers in column, row sort order
       scs = subcontainers.sort { |sc1, sc2| sc1.position.location <=> sc2.position.location }
+      logger.debug { "Looking for a #{self} subcontainer #{scs} to place a new #{storable.qp} container..." } unless scs.empty?
       # the first subcontainer that can hold the new subcontainer is preferred
-      if scs.detect { |ctr| ctr.add_to_new_subcontainer(storable) if StorageContainer === ctr } then
+      sc = scs.detect { |sc| sc.add_to_new_subcontainer(storable) if StorageContainer === sc }
+      if sc then
+        logger.debug { "#{self} subcontainer #{sc} stored #{storable.qp}." }
         self
       elsif not full? then
+        logger.debug { "Creating #{self} of type #{storage_type} subcontainer to hold #{storable.qp}..." }
         create_subcontainer_for(storable)
       end
     end
 
-    # @param [Storable] (see #add)
-    # @return whether this StorageContainer is not full and can hold the given item's StorableType
-    def can_hold_child?(storable)
-      st = storable.storable_type
-      not full? and child_types.any? { |ct| CaRuby::Resource.value_equal?(ct, st) }
+    def child_types
+      holds_storage_types.union(holds_specimen_classes).union(holds_specimen_array_types)
     end
-
+    
     private
-
-    # Adds the follwing defaults:
-    # * the default child_types are this container's CaTissue::ContainerType child_types.
+    
+    # Copies the other child types into this container's child types.
+    #
+    # @param [StorageTypeHolder] other the source child type holder
+    # @see #storage_type=
+    def copy_child_types(other)
+      child_storage_types.merge!(other.child_storage_types)
+      child_specimen_array_types.merge!(other.child_specimen_array_types)
+      child_specimen_classes.merge!(other.child_specimen_classes)
+    end
+    
+    # Adds the following defaults:
     # * the default site is the parent container site, if any.
     def add_defaults_local
       super
-      if child_types.empty? and container_type and not container_type.child_types.empty? then
-        container_type.child_types.each { |type| add_child_type(type) }
-      end
       # Although this default is set by the caTissue app, it is good practice to do so here
       # for clarity.
       self.site ||= parent.site if parent
@@ -180,23 +218,46 @@ module CaTissue
       # the StorageType path to storable
       type_path = type_path_to(storable) || return
       # create a container for each type leading to storable and add it to the parent container
-      ctr = type_path.reverse.inject(storable) do |occ, type|
-        subctr = type.create_container
-        subctr.site = site
-        logger.debug { "Created #{qp} #{subctr.container_type.name} subcontainer #{subctr} to hold #{occ}." }
-        subctr << occ
+      sc = type_path.reverse.inject(storable) do |occ, type|
+        ctr = type.create_container
+        ctr.site = site
+        logger.debug { "Created #{qp} #{ctr.container_type.name} subcontainer #{ctr} to hold #{occ}." }
+        ctr << occ
       end
-      add_local(ctr)
+      logger.debug { "Adding #{qp} subcontainer #{sc.qp} with stored #{storable.qp}." }
+      add_local(sc)
     end
 
     # Returns a StorageType array from a child StorageType to a descendant StorageType which can
     # hold the given storable, or nil if no such path exists.
+    #
+    # @param [Storable] the domain object to store in this container
+    # @return [<StorageType>] the {StorageType}s leading from this container to the storable holder
     def type_path_to(storable)
       holds_storage_types.detect_value { |type| type.path_to(storable) }
     end
 
-    private
-
+    # Adds the given storage type to the set of types which can be held.
+    #
+    # @param type [StorageType] the type to add
+    def add_storage_type(type)
+      storage_types << type
+    end    
+    
+    # Adds the given speicmen array type to the set of types which can be held.
+    #
+    # @param type [SpecimenArrayType] the type to add
+    def add_specimen_array_type(type)
+      storage_types << type
+    end    
+    
+    # Adds the given specimen class to the set of types which can be held.
+    #
+    # @param type [String] the type to add
+    def add_specimen_class(type)
+      storage_types << type
+    end
+    
     def out_of_bounds(storable)
       raise IndexError.new("Container #{name} does not have an available position for #{storable}")
     end

data/lib/catissue/domain/storage_type.rb

@@ -41,7 +41,7 @@ module CaTissue
     # Returns a StorageType array from this StorageType to a descendant StorageType which can
     # hold the given storable, or nil if no such path exists.
     def path_to(storable)
-     return [self] if can_hold_child?(storable)
+      return [self] if can_hold_child?(storable)
       path = holds_storage_types.detect_value { |child| child.path_to(storable) }
       return path.unshift(self) if path
     end

data/lib/catissue/migration/migrator.rb

@@ -5,13 +5,6 @@ require 'catissue/database/controlled_values'
 require 'catissue/database/controlled_value_finder'
 
 module CaTissue
-  # Even though Migratable is included in CaRuby::Resource, the Migratable methods
-  # are not appended to a CaTissue Resource class since the class already includes
-  # CaRuby::Resource. In Ruby, A include B followed by B include C does not imply
-  # that A includes C. Therefore, notify CaTissue that its mixin has changed and each
-  # loaded class must reinclude the mixin.
-  CaTissue.mixin_changed
-  
   # Migrates a CSV extract to caTissue. See the {#initialize} documentation for usage options.
   #
   # See the Galena Cancer Center Tissue Bank Migration Example for further information
@@ -88,19 +81,18 @@ module CaTissue
     def clear(target)
       pcl = target_protocol(target) || return
       logger.debug { "Clearing #{pcl.qp} CPR and SCG references..." }
-      pcl.suspend_lazy_loader do
+      @database.lazy_loader.suspend do
         pcl.registrations.clear
-        pcl.events.each { |event| event.suspend_lazy_loader { event.specimen_collection_groups.clear } }
+        pcl.events.each { |event| event.specimen_collection_groups.clear }
       end
     end
     
     def target_protocol(target)
       case target
-      when CaTissue::SpecimenCollectionGroup then
-        cpe = target.collection_protocol_event
-        cpe.collection_protocol if cpe
-      when CaTissue::Specimen then
-        target_protocol(target.specimen_collection_group)
+        when CaTissue::SpecimenCollectionGroup then
+          cpe = target.collection_protocol_event
+          cpe.collection_protocol if cpe
+        when CaTissue::Specimen then target_protocol(target.specimen_collection_group)
       end
     end
   end

data/lib/catissue/resource.rb

@@ -1,12 +1,27 @@
 require 'caruby/resource'
+require 'caruby/domain/attribute_initializer'
 require 'caruby/domain/resource_module'
+require 'catissue/annotation/annotatable'
 
 module CaTissue
   extend CaRuby::ResourceModule
 
   # The module included by all CaTissue domain classes.
   module Resource
-    include CaRuby::Resource
+    include CaRuby::Resource, CaRuby::IdAlias, CaRuby::AttributeInitializer, Annotatable
+
+    # Adds the given domain class to the CaTissue domain module.
+    #
+    # @param [Class] klass the included class
+    def self.included(klass)
+      super
+      CaTissue.add_class(klass)
+      # defer loading AnnotatableClass to avoid pulling in Database, which in turn
+      # attempts to import java classes before the path is established. obscure
+      # detail, but don't know how to avoid it.
+      require 'catissue/annotation/annotatable_class'
+      klass.extend(AnnotatableClass)
+    end
     
     # Returns whether each of the given attribute values either equals the
     # respective other attribute value or one of the values is nil or 'Not Specified'.
@@ -21,7 +36,7 @@ module CaTissue
 
     # Returns the CaTissue::Database which stores this object.
     def database
-      @@database ||= Database.instance
+      CaTissue::Database.instance
     end
 
     protected
@@ -60,14 +75,9 @@ module CaTissue
     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.
+  # The include mix-in module.
   @mixin = Resource
 
   # The required Java package name.

data/lib/catissue/util/position.rb

@@ -1,9 +1,11 @@
 require 'catissue/util/location'
+require 'caruby/util/validation'
 
 module CaTissue
   # The Position mix-in encapsulates the location of an occupant in a holder.
   # Classes which include Position are required to implement the column, row, occupant
-  # and holder methods.
+  # and holder methods. The occupant must be a {Storable}. The holder must be
+  # a {Container}.
   module Position
     include Comparable
 
@@ -50,5 +52,13 @@ module CaTissue
     def to_a
       [column, row]
     end
+    
+    # @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}")
+      end
+    end
   end
 end

data/lib/catissue/util/storable.rb

@@ -12,19 +12,26 @@ module CaTissue
       position and position.container
     end
 
-    # Moves this Storable from its current Position, if any, to the given container at the optional
-    # Coordinate coordinate. Returns the new position.
+    # Moves this storable from its current {Position}, if any, to the location given by the argument.
     #
+    # @param [CaTissue::Container, CaTissue::Location, Hash] arg the target container, location, or options
+    # @option arg [CaTissue::Container] :in the target container
+    # @option arg [CaRuby::Coordinate, (Integer, Integer)] :at the target coordinates
+    # @return [Position] the new position 
     # @see Container#add
-    def move_to(container_or_location)
-      case container_or_location
-      when CaTissue::Container then
-        container_or_location.add(self)
-      when CaTissue::Location then
-        loc = container_or_location
-        loc.container.add(self, loc.coordinate)
-      else
-        raise ArgumentError.new("Target location is neither a Container nor a Location: #{container_or_location.class.qp}")
+    def move_to(arg)
+      case arg
+        when CaTissue::Container then arg.add(self)
+        when CaTissue::Location then
+          loc = arg
+          loc.container.add(self, loc.coordinate)
+        when Hash then
+          dest = arg[:in]
+          if at.nil? then raise ArgumentError.new("#{self} move_to container :in option not found") end
+          coord = arg[:at]
+          dest = CaTissue::Location.new(dest, coord) if coord
+          move_to(dest)
+        else raise ArgumentError.new("Target location is neither a Container nor a Location: #{arg.class.qp}")
       end
       position
     end

data/lib/catissue/util/storage_type_holder.rb

@@ -4,13 +4,28 @@ module CaTissue
   # The StorageTypeHolder mix-in adds common methods for the StorageType or StorageContainer child type accessors.
   module StorageTypeHolder
     include PartialOrder
+    
+    # @return [StorageType] the allowable child storage types
+    def child_storage_types
+      holds_storage_types
+    end
+    
+    # @return [String] the allowable child specimen classes
+    def child_specimen_classes
+      holds_specimen_classes
+    end
+    
+    # @return [StorageType] the allowable child specimen array types
+    def child_specimen_array_types
+      holds_specimen_array_types
+    end
 
     # Returns the {CaTissue::SpecimenArrayType}, {CaTissue::AbstractSpecimen#specimen_class} or {CaTissue::StorageType}
     # children which this StorageTypeHolder can hold.
     def child_types
-      @child_types ||= holds_storage_types.union(holds_specimen_classes).union(holds_specimen_array_types)
+      child_storage_types.union(child_specimen_classes).union(child_specimen_array_types)
     end
-
+    
     # Adds the given subtype to the list of subtypes which this StorageType can hold.
     #
     # @param [CaTissue::StorageType, CaTissue::SpecimenArrayType, String] the subcontainer type or
@@ -19,12 +34,35 @@ module CaTissue
     # @raise [ArgumentError] if the type to add is not a supported parameter
     def add_child_type(type)
       case type
-      when CaTissue::StorageType then holds_storage_types << type
-      when CaTissue::SpecimenArrayType then holds_specimen_array_types << type
-      when String then holds_specimen_classes << type
-      else raise ArgumentError.new("Storage type child not supported - #{type}")
+        when CaTissue::StorageType then add_storage_type(type)
+        when CaTissue::SpecimenArrayType then add_specimen_array_type(type)
+        when String then add_specimen_class(type)
+        else raise ArgumentError.new("Storage type child not supported - #{type}")
       end
       self
     end
+    
+    private
+    
+    # Adds the given storage type to the set of types which can be held.
+    #
+    # @param type [StorageType] the type to add
+    def add_storage_type(type)
+      child_storage_types << type
+    end
+    
+    # Adds the given speicmen array type to the set of types which can be held.
+    #
+    # @param type [SpecimenArrayType] the type to add
+    def add_specimen_array_type(type)
+      child_specimen_array_types << type
+    end    
+    
+    # Adds the given specimen class to the set of types which can be held.
+    #
+    # @param type [String] the type to add
+    def add_specimen_class(type)
+      child_specimen_classes << type
+    end
   end
 end

data/lib/catissue/version.rb

@@ -1,6 +1,6 @@
 module CaTissue
   # The version of this caRuby Tissue release.
-  VERSION = "1.2.2"
+  VERSION = "1.2.3"
   
   # The supported caTissue release versions.
   CATISSUE_VERSIONS = "1.1.2"

metadata

@@ -10,11 +10,11 @@ executables:
 - crtsmoke
 version: !ruby/object:Gem::Version 
   prerelease: false
-  version: 1.2.2
+  version: 1.2.3
   segments: 
   - 1
   - 2
-  - 2
+  - 3
 post_install_message: 
 date: 2010-11-30 08:00:00 +00:00
 files: 
@@ -22,10 +22,79 @@ files:
 - bin/crtexample
 - bin/crtextract
 - bin/crtmigrate
+- bin/crtseed
 - bin/crtsmoke
-- bin/migrate.rb
-- bin/seed
-- bin/seed.rb
+- conf/annotation/pathology_scg/AdditionalFinding.hbm.xml
+- conf/annotation/pathology_scg/BasePathologyAnnotation.hbm.xml
+- conf/annotation/pathology_scg/BreastMargin.hbm.xml
+- conf/annotation/pathology_scg/BreastMarginInvolved.hbm.xml
+- conf/annotation/pathology_scg/BreastMarginUninvolved.hbm.xml
+- conf/annotation/pathology_scg/CarcinomaInSituStatus.hbm.xml
+- conf/annotation/pathology_scg/CNSMargin.hbm.xml
+- conf/annotation/pathology_scg/CNSMarginLocation.hbm.xml
+- conf/annotation/pathology_scg/ColorectalLocalExcisionMarginUninvolved.hbm.xml
+- conf/annotation/pathology_scg/ColorectalResectedMarginUninvolved.hbm.xml
+- conf/annotation/pathology_scg/Cytogenetics.hbm.xml
+- conf/annotation/pathology_scg/DeepMelanomaMargin.hbm.xml
+- conf/annotation/pathology_scg/Details.hbm.xml
+- conf/annotation/pathology_scg/DirectExtensionOfTumor.hbm.xml
+- conf/annotation/pathology_scg/DistalMargin.hbm.xml
+- conf/annotation/pathology_scg/DistanceFromAnalVerge.hbm.xml
+- conf/annotation/pathology_scg/DistantMetastasis.hbm.xml
+- conf/annotation/pathology_scg/ExcionalBiopsyMarginUninvolved.hbm.xml
+- conf/annotation/pathology_scg/ExcisionalBiopsyColorectalDeepMargin.hbm.xml
+- conf/annotation/pathology_scg/ExcisionalBiopsyColorectalLateralOrMucosalMargin.hbm.xml
+- conf/annotation/pathology_scg/ExtraprostaticExtension.hbm.xml
+- conf/annotation/pathology_scg/ExtraprostaticExtensionTissueSites.hbm.xml
+- conf/annotation/pathology_scg/GleasonScore.hbm.xml
+- conf/annotation/pathology_scg/HistologicGrade.hbm.xml
+- conf/annotation/pathology_scg/HistologicType.hbm.xml
+- conf/annotation/pathology_scg/HistologicVariantType.hbm.xml
+- conf/annotation/pathology_scg/ImmunoPhenotyping.hbm.xml
+- conf/annotation/pathology_scg/Invasion.hbm.xml
+- conf/annotation/pathology_scg/KidneyMarginLocation.hbm.xml
+- conf/annotation/pathology_scg/KidneyNephrectomyMargin.hbm.xml
+- conf/annotation/pathology_scg/LateralMelanomaMargin.hbm.xml
+- conf/annotation/pathology_scg/LocalExcisionColorectalDeepMargin.hbm.xml
+- conf/annotation/pathology_scg/LocalExcisionColorectalLateralMargin.hbm.xml
+- conf/annotation/pathology_scg/LungResectionMargin.hbm.xml
+- conf/annotation/pathology_scg/LungResectionMarginsUninvolved.hbm.xml
+- conf/annotation/pathology_scg/MacroscopicExtentOfTumor.hbm.xml
+- conf/annotation/pathology_scg/MesentricMargin.hbm.xml
+- conf/annotation/pathology_scg/MetastasisTissueSite.hbm.xml
+- conf/annotation/pathology_scg/Microcalcification.hbm.xml
+- conf/annotation/pathology_scg/NottinghamHistologicScore.hbm.xml
+- conf/annotation/pathology_scg/OtherResectedOrgans.hbm.xml
+- conf/annotation/pathology_scg/PancreasMargin.hbm.xml
+- conf/annotation/pathology_scg/PancreasMarginInvolvedByInvasiveCarcinoma.hbm.xml
+- conf/annotation/pathology_scg/PancreasMarginUninvolvedByInvasiveCarcinoma.hbm.xml
+- conf/annotation/pathology_scg/PathologicalStaging.hbm.xml
+- conf/annotation/pathology_scg/PolypConfiguration.hbm.xml
+- conf/annotation/pathology_scg/PrimaryTumorStage.hbm.xml
+- conf/annotation/pathology_scg/ProstateMarginLocation.hbm.xml
+- conf/annotation/pathology_scg/ProximalMargin.hbm.xml
+- conf/annotation/pathology_scg/RadialMargin.hbm.xml
+- conf/annotation/pathology_scg/RadicalProstatectomyMargin.hbm.xml
+- conf/annotation/pathology_scg/RegionalLymphNode.hbm.xml
+- conf/annotation/pathology_scg/SatelliteNodule.hbm.xml
+- conf/annotation/pathology_scg/SpecimenCollectionGroup.hbm.xml
+- conf/annotation/pathology_scg/SpecimenIntegrity.hbm.xml
+- conf/annotation/pathology_scg/SpecimenSize.hbm.xml
+- conf/annotation/pathology_scg/TissueSide.hbm.xml
+- conf/annotation/pathology_scg/TumorSize.hbm.xml
+- conf/annotation/pathology_scg/TumorTissueSite.hbm.xml
+- conf/annotation/pathology_scg/UninvolvedMelanomaMargin.hbm.xml
+- conf/annotation/pathology_specimen/AdditionalFinding.hbm.xml
+- conf/annotation/pathology_specimen/AdditionalPathologicFinding.hbm.xml
+- conf/annotation/pathology_specimen/Details.hbm.xml
+- conf/annotation/pathology_specimen/GleasonScore.hbm.xml
+- conf/annotation/pathology_specimen/HistologicGrade.hbm.xml
+- conf/annotation/pathology_specimen/HistologicType.hbm.xml
+- conf/annotation/pathology_specimen/HistologicVariantType.hbm.xml
+- conf/annotation/pathology_specimen/Invasion.hbm.xml
+- conf/annotation/pathology_specimen/NottinghamHistologicScore.hbm.xml
+- conf/annotation/pathology_specimen/Specimen.hbm.xml
+- conf/annotation/pathology_specimen/SpecimenBaseSolidTissuePathologyAnnotation.hbm.xml
 - conf/extract/simple_fields.yaml
 - conf/migration/filter_fields.yaml
 - conf/migration/filter_migration.yaml
@@ -50,49 +119,35 @@ files:
 - examples/galena/data/minimal.csv
 - examples/galena/data/simple.csv
 - examples/galena/data/small.csv
-- examples/galena/doc/_index.html
-- examples/galena/doc/CaTissue.html
-- examples/galena/doc/class_list.html
-- examples/galena/doc/file.README.html
-- examples/galena/doc/file_list.html
-- examples/galena/doc/frames.html
-- examples/galena/doc/Galena.html
-- examples/galena/doc/index.html
-- examples/galena/doc/method_list.html
-- examples/galena/doc/top-level-namespace.html
-- examples/galena/doc/CaTissue/Participant.html
-- examples/galena/doc/CaTissue/SpecimenCollectionGroup.html
-- examples/galena/doc/CaTissue/StorageContainer.html
-- examples/galena/doc/CaTissue/TissueSpecimen.html
-- examples/galena/doc/css/common.css
-- examples/galena/doc/css/full_list.css
-- examples/galena/doc/css/style.css
-- examples/galena/doc/Galena/Seed.html
-- examples/galena/doc/Galena/Seed/Defaults.html
-- examples/galena/doc/js/app.js
-- examples/galena/doc/js/full_list.js
-- examples/galena/doc/js/jquery.js
+- examples/galena/lib/galena.rb
 - examples/galena/lib/galena/cli/seed.rb
 - examples/galena/lib/galena/migration/filter_shims.rb
 - examples/galena/lib/galena/migration/frozen_shims.rb
 - examples/galena/lib/galena/seed/defaults.rb
 - lib/catissue.rb
-- lib/galena.rb
-- lib/README.html
 - lib/catissue/database.rb
 - lib/catissue/resource.rb
 - lib/catissue/version.rb
+- lib/catissue/annotation/annotatable.rb
+- lib/catissue/annotation/annotatable_class.rb
+- lib/catissue/annotation/annotation.rb
+- lib/catissue/annotation/annotation_class.rb
+- lib/catissue/annotation/annotation_module.rb
+- lib/catissue/annotation/hibernate_mapping.rb
+- lib/catissue/annotation/proxy.rb
+- lib/catissue/annotation/proxy_class.rb
 - lib/catissue/cli/command.rb
 - lib/catissue/cli/example.rb
 - lib/catissue/cli/migrate.rb
 - lib/catissue/cli/smoke.rb
 - lib/catissue/database/controlled_value_finder.rb
 - lib/catissue/database/controlled_values.rb
-- lib/catissue/database/annotation/annotatable_service.rb
 - lib/catissue/database/annotation/annotation_service.rb
 - lib/catissue/database/annotation/annotator.rb
-- lib/catissue/database/annotation/entity_manager.rb
+- lib/catissue/database/annotation/entity_facade.rb
+- lib/catissue/database/annotation/id_generator.rb
 - lib/catissue/database/annotation/integration_service.rb
+- lib/catissue/database/annotation/reference_writer.rb
 - lib/catissue/domain/abstract_domain_object.rb
 - lib/catissue/domain/abstract_position.rb
 - lib/catissue/domain/abstract_specimen.rb
@@ -152,10 +207,6 @@ files:
 - lib/catissue/util/position.rb
 - lib/catissue/util/storable.rb
 - lib/catissue/util/storage_type_holder.rb
-- lib/galena/cli/seed.rb
-- lib/galena/migration/filter_shims.rb
-- lib/galena/migration/frozen_shims.rb
-- lib/galena/seed/defaults.rb
 - History.txt
 - LEGAL
 - LICENSE