caruby-core 1.4.9 → 1.5.1

data/lib/caruby/util/pretty_print.rb

@@ -7,14 +7,15 @@ require 'caruby/util/collection'
 require 'caruby/util/inflector'
 
 class PrettyPrint
-  # Fixes the standard prettyprint gem SingleLine to add an output accessor and an optional output argument to {#initialize}.
+  # The standard +prettyprint+ gem SingleLine is adjusted to add an output accessor and an optional output argument to {#initialize}.
   class SingleLine
+    # @return [String] the print target
     attr_reader :output
 
     alias :base__initialize :initialize
     private :base__initialize
 
-    # Allow output to be optional, defaulting to ''
+    # Overrides the standard SingleLine initializer to supply an output parameter default.
     def initialize(output='', maxwidth=nil, newline=nil)
       base__initialize(output, maxwidth, newline)
     end
@@ -29,13 +30,14 @@ class PrintWrapper < Proc
     @args = args
   end
 
-  # Sets the arguments to wrap with this wrapper's print block and returns self.
+  # @param args this wrapper's print block parameters
+  # @return [PrintWrapper] self
   def wrap(*args)
     @args = args
     self
   end
 
-  # Calls this PrintWrapper's print procedure on its arguments.
+  # Calls this PrintWrapper's print procedure on the arguments set in the initializer.
   def to_s
     @args.empty? ? 'nil' : call(*@args)
   end
@@ -44,7 +46,7 @@ class PrintWrapper < Proc
 end
 
 class Object
-  # Prints this object's class demodulized name and object id.
+  # @return [String] this object's class demodulized name and object id
   def print_class_and_id
     "#{self.class.qp}@#{object_id}"
   end
@@ -52,11 +54,14 @@ class Object
   # qp, an abbreviation for quick-print, calls {#print_class_and_id} in this base implementation.
   alias :qp :print_class_and_id
 
-  # Formats this object as a String with PrettyPrint.
-  # If the :single_line option is set, then the output is printed to a single line.
-  def pp_s(options=nil)
+  # Formats this object with the standard {PrettyPrint}.
+  #
+  # @param [Hash, Symbol, nil] opts the print options
+  # @option opts [Boolean] :single_line print the output on a single line
+  # @return [String] the formatted print result
+  def pp_s(opts=nil)
     s = StringIO.new
-    if Options.get(:single_line, options) then
+    if Options.get(:single_line, opts) then
       PP.singleline_pp(self, s)
     else
       PP.pp(self, s)
@@ -67,58 +72,70 @@ class Object
 end
 
 class Numeric
-  # qp, an abbreviation for quick-print, is an alias for {#to_s} in this primitive class.
+  # Alias #{Object#qp} to {#to_s} in this primitive class.
   alias :qp :to_s
 end
 
 class String
-  # qp, an abbreviation for quick-print, is an alias for {#to_s} in this primitive class.
+  # Alias #{Object#qp} to {#to_s} in this primitive class.
   alias :qp :to_s
 end
 
 class TrueClass
-  # qp, an abbreviation for quick-print, is an alias for {#to_s} in this primitive class.
+  # Alias #{Object#qp} to {#to_s} in this primitive class.
   alias :qp :to_s
 end
 
 class FalseClass
-  # qp, an abbreviation for quick-print, is an alias for {#to_s} in this primitive class.
+  # Alias #{Object#qp} to {#to_s} in this primitive class.
   alias :qp :to_s
 end
 
 class NilClass
-  # qp, an abbreviation for quick-print, is an alias for {#inspect} in this NilClass.
+  # Alias #{Object#qp} to {#to_s} in this primitive class.
   alias :qp :inspect
 end
 
 class Symbol
-  # qp, an abbreviation for quick-print, is an alias for {#inspect} in this Symbol class.
+  # Alias #{Object#qp} to {#to_s} in this primitive class.
   alias :qp :inspect
 end
 
 class Module
-  # qp, an abbreviation for quick-print, prints this module's name unqualified by a parent module prefix.
+  # @return [String ] the demodulized name
   def qp
     name[/\w+$/]
   end
 end
 
 module Enumerable
-  # qp, short for quick-print, prints a collection Enumerable with a filter that calls qp on each item.
-  # Non-collection Enumerables delegate to the superclass method.
-  def qp
-    wrap { |item| item.qp }.pp_s
-  end
-
-  # If the transformer block is given to this method, then the transformer block to each
+  # Prints this Enumerable with a filter that calls qp on each item.
+  # Non-collection Enumerable classes override this method to delegate to {Object#qp}.
+  #
+  # Unlike {Object#qp}, this implementation accepts the {Object#pp_s} options.
+  # The options are used to format this Enumerable, but are not propagated to the
+  # enumerated items.
+  #
+  # @param (see Object#pp_s)
+  # @return [String] the formatted result
+  def qp(opts=nil)
+    wrap { |item| item.qp }.pp_s(opts)
+  end
+
+  # If a transformer block is given to this method, then the block is applied to each
   # enumerated item before pretty-printing the result.
-  def pp_s(options=nil, &transformer)
+  #
+  # @param (see Object#pp_s)
+  # @yield [item] transforms the item to print
+  # @yieldparam item the item to print
+  # @return (see Oblect#pp_s)
+  def pp_s(opts=nil)
     # delegate to Object if no block
-    return super(options) unless block_given?
+    return super unless block_given?
     # make a print wrapper
     wrapper = PrintWrapper.new { |item| yield item }
     # print using the wrapper on each item
-    wrap { |item| wrapper.wrap(item) }.pp_s(options)
+    wrap { |item| wrapper.wrap(item) }.pp_s(opts)
   end
 
   # Pretty-prints the content within brackets, as is done by the Array pretty printer.
@@ -138,6 +155,8 @@ end
 
 module Hashable
   # qp, short for quick-print, prints this Hashable with a filter that calls qp on each key and value.
+  #
+  # @return [String] the quick-print result
   def qp
     qph = {}
     each { |k, v| qph[k.qp] = v.qp }
@@ -161,6 +180,7 @@ class String
 end
 
 class DateTime
+  # @return [String] the formatted +strftime+
   def pretty_print(q)
     q.text(strftime)
   end

data/lib/caruby/util/topological_sync_enumerator.rb

@@ -3,16 +3,22 @@ require 'caruby/util/collection'
 class TopologicalSyncEnumerator
   include Enumerable
 
-  def initialize(targets, sources, symbol, &matcher)
+  # @param targets the objects to synch to
+  # @param sources the objects to synch from
+  # @param [Symbol] method the topological order reference method
+  # @yield (see #each)
+  def initialize(targets, sources, method, &matcher)
     @tgts = targets
     @srcs = sources
-    @mthd = symbol
+    @mthd = method
     @matcher = matcher || lambda { |tgt, srcs| srcs.first }
   end
 
   # Calls the given block on each matching target and source.
-  # Returns the matching target => source hash.
-  def each # :yields: target, source
+  #
+  # @yield [target, source] the objects to synchronize
+  # @return [Hash] the matching target => source hash
+  def each
     # the parent hashes for targets and sources
     pt = @tgts.to_compact_hash { |tgt| tgt.send(@mthd) }
     ps = @srcs.to_compact_hash { |src| src.send(@mthd) }

data/lib/caruby/util/transitive_closure.rb

@@ -34,9 +34,9 @@ module Enumerable
   # Returns the transitive closure over all items in this Enumerable.
   #
   # @see Object#transitive_closure
-  def transitive_closure(method=nil, &navigator)
+  def transitive_closure(method=nil)
     # delegate to Object if there is a method argument
-    return super(method, &navigator) if method
+    return super(method) if method
     # this Enumerable's children are this Enumerable's contents
     closure = super() { |node| node.equal?(self) ? self : yield(node) }
     # remove this collection from the closure

data/lib/caruby/util/visitor.rb

@@ -139,7 +139,7 @@ module CaRuby
   
     # @return [Enumerable] iterator over each visited node
     def to_enum(node)
-      # JRuby alert - could use Generator instead, but that results in dire behavior on any error
+      # JRuby could use Generator instead, but that results in dire behavior on any error
       # by crashing with an elided Java lineage trace.
       VisitorEnumerator.new(self, node)
     end

data/lib/caruby/version.rb

@@ -1,3 +1,3 @@
 module CaRuby
-  VERSION = "1.4.9"
+  VERSION = "1.5.1"
 end

data/test/lib/caruby/database/persistable_test.rb

@@ -85,7 +85,7 @@ class PersistableTest < Test::Unit::TestCase
 
   def duplicate_with_id(obj)
     return obj.map { |item| duplicate_with_id(item) } if Enumerable === obj
-    copy = obj.copy(obj.class.nondomain_attributes)
+    copy = obj.copy
     copy.identifier ||= @@counter += 1
     copy
   end

data/test/lib/caruby/domain/domain_test.rb

@@ -15,38 +15,24 @@ class DomainTest < Test::Unit::TestCase
     super
     @crd = ClinicalTrials::User.new(:login => 'study.coordinator@test.org')
     address = ClinicalTrials::Address.new(:street => '555 Elm St', :city => 'Burlington', :state => 'VT', :zip_code => '55555')
-    @pnt = ClinicalTrials::Participant.new(:name => 'Test Participant', :address => address)
-    @study = ClinicalTrials::Study.new(:name => 'Test Study', :coordinator => @crd, :enrollment => [@pnt])
+    @sbj = ClinicalTrials::Subject.new(:name => 'Test Subject', :address => address)
+    @study = ClinicalTrials::Study.new(:name => 'Test Study', :coordinator => @crd, :enrollment => [@sbj])
     @evt = ClinicalTrials::StudyEvent.new(:study => @study, :calendar_event_point => 1.0)
   end
 
   def test_alias
     assert(ClinicalTrials::Study.method_defined?(:events), "Study alias not recognized: events")
-    assert_equal(@pnt.address.zip_code, @pnt.address.postal_code, 'zip_code not aliased to postal_code')
-    assert_equal(:zip_code, @pnt.address.class.standard_attribute(:postal_code), 'postal_code does not map to a standard attribute symbol')
+    assert_equal(@sbj.address.zip_code, @sbj.address.postal_code, 'zip_code not aliased to postal_code')
+    assert_equal(:zip_code, @sbj.address.class.standard_attribute(:postal_code), 'postal_code does not map to a standard attribute symbol')
   end
 
   def test_redefine
-    @pnt.address.zip_code = 55555
-    assert_equal('55555', @pnt.address.zip_code, "Address zip_code not redefined to support a numeric value")
+    @sbj.address.zip_code = 55555
+    assert_equal('55555', @sbj.address.zip_code, "Address zip_code not redefined to support a numeric value")
   end
 
   def test_merge_attributes
-    assert_same(@study.enrollment.first, @pnt, "Merge incorrect")
-  end
-
-  def test_merge_unambiguous_dependent_collection_attribute
-    @study.enrollment.clear
-    assert_same(@study.enrollment, @study.merge_attribute(:enrollment, [@pnt]), "Merge collection attribute result incorrect")
-    assert_not_nil(@study.enrollment.first, "Merge collection attribute didn't add source item")
-    assert_same(@study.enrollment.first, @pnt, "Merge collection attribute incorrect")
-  end
-
-  def test_merge_ambiguous_dependent_collection_attribute
-    @study.enrollment.clear
-    assert_same(@study.enrollment, @study.merge_attribute(:enrollment, [@pnt]), "Merge collection attribute result incorrect")
-    assert_not_nil(@study.enrollment.first, "Merge collection attribute didn't add source item")
-    assert_same(@study.enrollment.first, @pnt, "Merge collection attribute incorrect")
+    assert_same(@study.enrollment.first, @sbj, "Merge incorrect")
   end
 
   def test_owner_inverse_setter
@@ -72,9 +58,9 @@ class DomainTest < Test::Unit::TestCase
 
   # Tests whether add_defaults method propagates to dependents.
   def test_participant_defaults
-    assert_nil(@pnt.address.country, 'Participant address country is already set')
-    @pnt.add_defaults
-    assert_equal('US', @pnt.address.country, 'Participant address country is not set to default')
+    assert_nil(@sbj.address.country, 'Subject address country is already set')
+    @sbj.add_defaults
+    assert_equal('US', @sbj.address.country, 'Subject address country is not set to default')
   end
 
   def test_dependents
@@ -91,9 +77,9 @@ class DomainTest < Test::Unit::TestCase
     assert_equal([@study, 1.0], @evt.key, "Event key incorrect")
   end
 
-#  def test_address_key
-#    assert_nil(@pnt.address.key, "Address key incorrect")
-#  end
+  def test_address_key
+    assert_nil(@sbj.address.key, "Address key incorrect")
+  end
 
   def test_set_collection_attribute
     consent = ClinicalTrials::Consent.new(:statement => 'Test Statement 1')
@@ -115,7 +101,7 @@ class DomainTest < Test::Unit::TestCase
   def test_visit_path
     visited = []
     @study.visit_path([:enrollment, :address]) { |ref| visited << ref }
-    assert_equal([@study, @pnt, @pnt.address], visited, "Path visitor incorrect")
+    assert_equal([@study, @sbj, @sbj.address], visited, "Path visitor incorrect")
   end
 
   def test_visit_dependents

data/test/lib/caruby/domain/inversible_test.rb

@@ -5,7 +5,7 @@ require "test/unit"
 
 class InversibleTest < Test::Unit::TestCase
   module Domain
-    extend CaRuby::ResourceModule
+    extend CaRuby::Domain
   end
   
   module Resource

data/test/lib/caruby/import/java_test.rb

@@ -20,6 +20,11 @@ class JavaTest < Test::Unit::TestCase
     end
   end
   
+  def test_zero_date
+    jdt = Java::JavaUtil::Date.new(0)
+    verify_java_to_ruby_date_conversion(jdt)
+  end
+  
   def flip_DST(cal)
     isdt = cal.timeZone.inDaylightTime(cal.time)
     11.times do

data/test/lib/caruby/migration/test_case.rb

@@ -44,7 +44,6 @@ module CaRuby
     # @return [CaTissue::Migrator]
     # @yield [opts] the optional Migrator factory
     def create_migrator(fixture, opts={}, &factory)
-      opts[:quiet] = true
       opts[:input] ||= File.join(@fixtures, fixture.to_s + '.csv')
       block_given? ? yield(opts) : CaRuby::Migrator.new(opts)
     end

data/test/lib/caruby/test_case.rb

@@ -113,8 +113,7 @@ module CaRuby
     
     def verify_dependency(dependent)
       return if dependent.class.owner_attribute.nil?
-      # kludge for annotation proxy nonsense (cf. Annotation#owner)
-      ownr = Annotation === dependent ? (dependent.hook or dependent.owner) : dependent.owner
+      ownr = dependent.owner
       assert_not_nil(ownr, "Owner missing for dependent: #{dependent}")
       attribute = ownr.class.dependent_attribute(dependent.class)
       assert_not_nil(attribute, "Dependent attribute missing for #{dependent} owner #{ownr}")
@@ -129,7 +128,7 @@ module CaRuby
     # Verifies that the given dependent has an identifier and that the given owner dependent attribute value
     # contains the dependent.
     #
-    # JRuby alert - Set include? incorrectly returns false in the OHSU PSR samples_test test_save_grade
+    # JRuby Set include? incorrectly returns false in the OHSU PSR samples_test test_save_grade
     # call to this method. Work around by using Set detect rather than include?.
     def verify_saved_dependent_collection_member(dependent, owner, attribute)
       deps = owner.send(attribute)
@@ -168,12 +167,12 @@ module CaRuby
     # Verifies that the given expected domain object has the same content as actual,
     # and that the dependents match.
     #
-    # caTissue alert - caTissue mutilates an unspecified specimen type available quantity, e.g.
-    # changing a Specimen with specimen type 'Not Specified' from available quantity 1, initial
-    # quantity 1 to available quantity 0, initial quantity 3 results in available quantity 2
-    # in database. The update is necessary when creating the Specimen with available quantity 0,
-    # initial quantity 3 to work around a different caTissue bug. Thus, the bug work-around
-    # is broken by a different caTissue bug.
+    # @quirk caTissue caTissue mutilates an unspecified specimen type available quantity, e.g.
+    #   changing a Specimen with specimen type 'Not Specified' from available quantity 1, initial
+    #   quantity 1 to available quantity 0, initial quantity 3 results in available quantity 2
+    #   in database. The update is necessary when creating the Specimen with available quantity 0,
+    #   initial quantity 3 to work around a different caTissue bug. Thus, the bug work-around
+    #   is broken by a different caTissue bug.
     #
     # @param [Resource] expected the saved value
     # @param [Resource] actual the fetched value
@@ -201,7 +200,7 @@ module CaRuby
       verify_dependents_match(expected, actual)
     end
     
-    # @param [AttributeMetadata] attr_md the saved attribute to check
+    # @param [Attribute] attr_md the saved attribute to check
     # @return whether the attribute is fetched, creatable and not volatile
     def verify_saved_attribute?(attr_md)
       attr_md.fetched? and attr_md.creatable? and not attr_md.volatile?

data/test/lib/caruby/util/collection_test.rb

@@ -127,6 +127,12 @@ class CollectionTest < Test::Unit::TestCase
     b << 5
     assert_equal([1, 2, 3, 3, 4, 5], ab.to_a, "Addition does not reflect change to second enumerable")
   end
+  
+  def test_partial_sort
+    sorted = [Array, Object, Numeric, Enumerable, Set].partial_sort
+    assert(sorted.index(Array) < sorted.index(Enumerable), "Partial sort order incorrect")
+    assert(sorted.index(Set) < sorted.index(Enumerable), "Partial sort order incorrect")
+  end
 
   def test_hash_union
     a = {:a => 1, :b => 2}
@@ -173,11 +179,11 @@ class CollectionTest < Test::Unit::TestCase
   end
 
   def test_hash_enum_keys
-    assert_equal([1, 2], { 1 => :a, 2 => :b }.enum_keys.sort)
-  end
-
-  def test_hash_partition
-    assert_equal([{:a => 1}, { :b => 2}], { :a => 1, :b => 2 }.partition { |key, value| value < 2 }, "Hash partition incorrect")
+    hash = { 1 => :a, 2 => :b }
+    ek = hash.enum_keys
+    assert_equal([1, 2], ek.sort, "Hash key enumerator incorrect")
+    hash[3] = :c
+    assert_equal([1, 2, 3], ek.sort, "Hash key enumerator does not reflect hash change")
   end
 
   def test_hash_enum_keys_with_value
@@ -188,6 +194,18 @@ class CollectionTest < Test::Unit::TestCase
     assert_equal([:b, :c], {:a => 1, :b => 2, :c => 3}.enum_keys_with_value { |value| value > 1 }.to_a, "Hash filtered value block keys incorrect")
   end
 
+  def test_hash_enum_values
+    hash = { :a => 1, :b => 2 }
+    ev = hash.enum_values
+    assert_equal([1, 2], ev.sort, "Hash value enumerator incorrect")
+    hash[:c] = 3
+    assert_equal([1, 2, 3], ev.sort, "Hash value enumerator does not reflect hash change")
+  end
+
+  def test_hash_partition
+    assert_equal([{:a => 1}, { :b => 2}], { :a => 1, :b => 2 }.partition { |key, value| value < 2 }, "Hash partition incorrect")
+  end
+
   def test_hash_flatten
     assert_equal([:a, :b, :c, :d, :e, :f, :g], {:a => {:b => :c}, :d => :e, :f => [:g]}.flatten, "Hash flatten incorrect")
   end

data/test/lib/caruby/util/module_test.rb

@@ -5,25 +5,21 @@ require 'caruby/util/module'
 
 module Outer
   module Middle
-    module InnerModule; end
-    class InnerClass; end
+    class C; end
   end
 end
 
 class ModuleTest < Test::Unit::TestCase
-  def test_top_level_module_with_name
-    assert_equal(Array, Module.module_with_name(nil, 'Array'), "Top level module incorrect")
-  end
-
-  def test_module_with_unqualified_name
+  def test_module_with_name
     assert_equal(Outer::Middle, Outer.module_with_name('Middle'), "Unqualified module incorrect")
+    assert_nil(Outer.module_with_name('Zed'), "Missing module incorrectly resolves to non-nil value")
+    assert_equal(Outer::Middle::C, Outer.module_with_name('Middle::C'), "Qualified module incorrect")
+    assert_equal(Outer, Kernel.module_with_name('Outer'), "Top-level module incorrect")
   end
-
-  def test_module_with_qualified_name
-    assert_equal(Outer::Middle::InnerModule, Outer.module_with_name('Middle::InnerModule'), "Qualified module incorrect")
-  end
-
-  def test_class_with_name
-    assert_equal(Outer::Middle::InnerClass, Outer.module_with_name('Middle::InnerClass'), "Inner class incorrect")
+  
+  def test_parent_module
+    assert_equal(Outer, Outer::Middle.parent_module, "Middle parent module incorrect")
+    assert_equal(Outer::Middle, Outer::Middle::C.parent_module, "Inner parent module incorrect")
+    assert_equal(Kernel, Outer.parent_module, "Outer parent module incorrect")
   end
 end

data/test/lib/caruby/util/partial_order_test.rb

@@ -6,36 +6,37 @@ require 'caruby/util/partial_order'
 class Queued
   include PartialOrder
 
-  attr_reader :value, :queue
+  attr_reader :queue
 
-  def initialize(value, on)
-    @value = value
+  def initialize(on)
     @queue = on.push(self)
   end
 
   def <=>(other)
-    value <=> other.value if queue.equal?(other.queue)
+    queue.index(self) <=> other.queue.index(other) if queue.equal?(other.queue)
   end
 end
 
 class PartialOrderTest < Test::Unit::TestCase
   def test_same_queue
-    @a = Queued.new(1, [])
-    assert_equal(@a, @a.dup, "Same value, queue not equal")
+    q = []
+    a = Queued.new(q)
+    assert_equal(a, a, "Same value, queue not equal")
   end
 
   def test_different_eql_queue
-    @a = Queued.new(1, [])
-    @b = Queued.new(1, [])
-    assert_nil(@a <=> @b, "Same value, different queue <=> not nil")
-    assert_not_equal(@a, @b, "Same value, different queue is equal")
+    a = Queued.new([])
+    @b = Queued.new([])
+    assert_nil(a <=> @b, "Same value, different queue <=> not nil")
+    assert_not_equal(a, @b, "Same value, different queue is equal")
   end
 
   def test_less_than
-    @a = Queued.new(1, [])
-    @b = Queued.new(2, @a.queue)
-    @c = Queued.new(2, [])
-    assert(@a < @b, "Comparison incorrect")
-    assert_nil(@a < @c, "Comparison incorrect")
+    q = []
+    a = Queued.new(q)
+    b = Queued.new(q)
+    c = Queued.new([])
+    assert(a < b, "Comparison incorrect")
+    assert_nil(a < c, "Comparison incorrect")
   end
 end

data/test/lib/caruby/util/visitor_test.rb

@@ -1,6 +1,6 @@
 $:.unshift 'lib'
 
-# JRuby alert - SyncEnumerator moved from generator to REXML in JRuby 1.5
+# JRuby SyncEnumerator moved from generator to REXML in JRuby 1.5
 require 'rexml/document'
 require "test/unit"
 require 'caruby/util/collection'

data/test/lib/examples/galena/clinical_trials/migration/test_case.rb

@@ -13,7 +13,7 @@ module Galena
       FIXTURES = 'examples/galena/data'
     
       # The migration input data directory.
-      SHIMS = 'examples/galena/lib/galena/migration'
+      SHIMS = 'examples/galena/lib/galena/clinical_trials/migration'
       
       # The migration configuration directory.
       CONFIGS = 'examples/galena/conf/migration'

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: caruby-core
 version: !ruby/object:Gem::Version 
-  hash: 21
+  hash: 1
   prerelease: false
   segments: 
   - 1
-  - 4
-  - 9
-  version: 1.4.9
+  - 5
+  - 1
+  version: 1.5.1
 platform: ruby
 authors: 
 - OHSU
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-05-09 00:00:00 -07:00
+date: 2011-07-05 00:00:00 -07:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -104,20 +104,22 @@ files:
 - lib/caruby/database/store_template_builder.rb
 - lib/caruby/database/writer.rb
 - lib/caruby/database.rb
-- lib/caruby/domain/attribute_metadata.rb
+- lib/caruby/domain/attribute.rb
+- lib/caruby/domain/attributes.rb
+- lib/caruby/domain/dependency.rb
 - lib/caruby/domain/id_alias.rb
+- lib/caruby/domain/importer.rb
+- lib/caruby/domain/introspection.rb
+- lib/caruby/domain/inverse.rb
 - lib/caruby/domain/inversible.rb
-- lib/caruby/domain/java_attribute_metadata.rb
+- lib/caruby/domain/java_attribute.rb
 - lib/caruby/domain/merge.rb
+- lib/caruby/domain/metadata.rb
+- lib/caruby/domain/mixin.rb
 - lib/caruby/domain/properties.rb
 - lib/caruby/domain/reference_visitor.rb
-- lib/caruby/domain/resource_attributes.rb
-- lib/caruby/domain/resource_dependency.rb
-- lib/caruby/domain/resource_introspection.rb
-- lib/caruby/domain/resource_inverse.rb
-- lib/caruby/domain/resource_metadata.rb
-- lib/caruby/domain/resource_module.rb
 - lib/caruby/domain/uniquify.rb
+- lib/caruby/domain.rb
 - lib/caruby/import/java.rb
 - lib/caruby/migration/migratable.rb
 - lib/caruby/migration/migrator.rb
@@ -154,7 +156,6 @@ files:
 - lib/caruby/util/visitor.rb
 - lib/caruby/util/weak_hash.rb
 - lib/caruby/version.rb
-- lib/caruby/yard/resource_metadata_handler.rb
 - lib/caruby.rb
 - test/lib/caruby/csv/csv_mapper_test.rb
 - test/lib/caruby/csv/csvio_test.rb
@@ -192,7 +193,7 @@ files:
 - test/lib/caruby/util/weak_hash_test.rb
 - test/lib/examples/galena/clinical_trials/migration/participant_test.rb
 - test/lib/examples/galena/clinical_trials/migration/test_case.rb
-- History.txt
+- History.md
 - LEGAL
 - LICENSE
 - README.md