caruby-core 1.5.3 → 1.5.4

data/lib/caruby/resource.rb

@@ -46,9 +46,11 @@ module CaRuby
     #
     # @return [Resource] self
     def add_defaults
-      # apply owner defaults
-      if owner and owner.identifier.nil? then
-        owner.add_defaults
+      # If there is an owner, then delegate to the owner.
+      # Otherwise, add defaults to this object.
+      par = owner
+      if par and par.identifier.nil? then
+        par.add_defaults
       else
         logger.debug { "Adding defaults to #{qp} and its dependents..." }
         # apply the local and dependent defaults

data/lib/caruby/util/collection.rb

@@ -625,14 +625,6 @@ module Hashable
     filter_on_value { |value| not value.nil? }
   end
   
-  # Partitions this Hashable into two Hashables based on the given filter block
-  #
-  # @yield [key, value] the partition block
-  # @return [(Hashable, Hashable)] the partitioned result
-  def hash_partition(&block)
-    [filter(&block), filter { |k, v| not yield(k, v) }]
-  end
-  
   # Returns the difference between this Hashable and the other Hashable in a Hash of the form:
   #
   # _key_ => [_mine_, _theirs_]
@@ -753,14 +745,14 @@ module Hashable
   def flatten
     Flattener.new(self).to_a
   end
-
+  
   # @yield [key, value] hash splitter
-  # @return [Hash] two hashes split by whether calling the block on the
+  # @return [(Hash, Hash)] two hashes split by whether calling the block on the
   #   entry returns a non-nil, non-false value
   # @example
-  #   {:a => 1, :b => 2}.partition { |key, value| value < 2 } #=> [{:a => 1}, {:b => 2}]
-  def partition(&block)
-    super(&block).map { |pairs| pairs.to_assoc_hash }
+  #   {:a => 1, :b => 2}.split { |key, value| value < 2 } #=> [{:a => 1}, {:b => 2}]
+  def split(&block)
+    partition(&block).map { |pairs| pairs.to_assoc_hash }
   end
 
   # Returns a new Hash that recursively copies this hash's values. Values of type hash are copied using copy_recursive.
@@ -1065,10 +1057,11 @@ class Array
   # element is associated with the second element. If there is less than two elements in the member,
   # the first element is associated with nil. An empty array is ignored.
   #
-  # Example:
+  # @example
   #   [[:a, 1], [:b, 2, 3], [:c], []].to_assoc_hash #=> { :a => 1, :b => [2,3], :c => nil }
+  # @return [Hash] the first => rest hash
   def to_assoc_hash
-    hash = Hash.new
+    hash = {}
     each do |item|
       raise ArgumentError.new("Array member must be an array: #{item.pp_s(:single_line)}") unless Array === item
       key = item.first

data/lib/caruby/util/log.rb

@@ -50,7 +50,7 @@ module CaRuby
       shift_age = Options.get(:shift_age, options, 4)
       shift_size = Options.get(:shift_size, options, 16 * 1048576)
       @logger = MultilineLogger.new(dev, shift_age, shift_size)
-      @logger.level = Options.get(:debug, options, ENV['DEBUG']) ? Logger::DEBUG : Logger::INFO
+      @logger.level = Options.get(:debug, options, ENV['DEBUG'] == 'true') ? Logger::DEBUG : Logger::INFO
       @logger.info('============================================')
       @logger.info('Logging started.')
       @dev = dev

data/lib/caruby/util/properties.rb

@@ -86,7 +86,7 @@ module CaRuby
       end
       # if the key is a merge property key, then perform a deep merge.
       # otherwise, do a shallow merge of the property value into this property hash.
-      deep, shallow = properties.partition { |key, value| @merge_properties.include?(key) }
+      deep, shallow = properties.split { |key, value| @merge_properties.include?(key) }
       merge!(deep, :deep)
       merge!(shallow)
     end

data/lib/caruby/util/topological_sync_enumerator.rb

@@ -1,5 +1,8 @@
 require 'caruby/util/collection'
 
+# A TopologicalSyncEnumerator iterates over (target, source) pairs with the target matched
+# to the source with a matcher block. Child targets are matched to child sources based on
+# a topological order reference method. The iteration is performed in depth-first order.
 class TopologicalSyncEnumerator
   include Enumerable
 
@@ -14,7 +17,7 @@ class TopologicalSyncEnumerator
     @matcher = matcher || lambda { |tgt, srcs| srcs.first }
   end
 
-  # Calls the given block on each matching target and source.
+  # Calls the given block on each matching target and source in depth-first order.
   #
   # @yield [target, source] the objects to synchronize
   # @return [Hash] the matching target => source hash

data/lib/caruby/util/transitive_closure.rb

@@ -1,7 +1,18 @@
 require 'caruby/util/visitor'
 
 class Object
-  # Returns the transitive closure over a method or block, e.g.:
+  # Returns the transitive closure over a method or block. This method returns an array partially ordered
+  # by the children method or block, i.e. each node occurs before all other nodes referenced directly or
+  # indirectly by the children.
+  #
+  # If a method symbol or name is provided, then that method is called. Otherwise, the block is called.
+  # In either case, the call is expected to return an object or Enumerable of objects which also respond
+  # to the method or block.
+  #
+  # @param [Symbol, nil] method the child reference, or nil if a block is given
+  # @yield [node] the parent node's children
+  # @yieldparam node the parent node
+  # @example
   #   class Node
   #     attr_reader :parent, :children
   #     def initialize(name, parent=nil)
@@ -17,16 +28,15 @@ class Object
   #   a = Node.new('a'); b = Node.new('b', a), c = Node.new('c', a); d = Node.new('d', c)
   #   a.transitive_closure { |node| node.children }.to_a.join(", ") #=> a, b, c, d
   #   a.transitive_closure(:children).to_a.join(", ") #=> a, b, c, d
-  # This method returns an array partially ordered by the closure method, i.e.
-  # each node occurs before all other nodes referenced directly or indirectly by the closure method.
-  #
-  # If a method symbol or name is provided, then that method is called. Otherwise, the block is called.
-  # In either case, the call is expected to return an object or Enumerable of objects which also respond
-  # to the method or block.
   def transitive_closure(method=nil)
     raise ArgumentError.new("Missing both a method argument and a block") if method.nil? and not block_given?
-    return transitive_closure() { |node| node.send(method) } if method
-    CaRuby::Visitor.new(:depth_first) { |node| yield node }.to_enum(self).to_a.reverse
+    # If there is a method argument, then the transitive closure is based on that method.
+    # Otherwise, visit the closure in reverse depth-first order.
+    if method then
+      transitive_closure() { |node| node.send(method) }
+    else
+      CaRuby::Visitor.new(:depth_first) { |node| yield node }.to_enum(self).to_a.reverse
+    end
   end
 end
 

data/lib/caruby/version.rb

@@ -1,3 +1,3 @@
 module CaRuby
-  VERSION = "1.5.3"
+  VERSION = "1.5.4"
 end

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

@@ -60,7 +60,7 @@ class CollectionTest < Test::Unit::TestCase
 
   def test_detect_value
    assert_equal(4, [1, 2, 3].detect_value { |item| item * 2 if item > 1 }, "Detect value incorrect")
-   assert_nil([1, 2, 3].detect_value { |item| iitem * 2 if item > 3 }, "Value incorrectly detected")
+   assert_nil([1, 2, 3].detect_value { |item| item * 2 if item > 3 }, "Value incorrectly detected")
   end
 
   def test_detect_with_value
@@ -202,10 +202,6 @@ class CollectionTest < Test::Unit::TestCase
     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
@@ -231,7 +227,7 @@ class CollectionTest < Test::Unit::TestCase
   end
 
   def test_hash_partition
-    assert_equal([{:a => 1, :c => 3}, {:b => 2}], {:a => 1, :b => 2, :c => 3}.hash_partition { |k, v| k == :a or v == 3 }, "Hash partition incorrect")
+    assert_equal([{:a => 1, :c => 3}, {:b => 2}], {:a => 1, :b => 2, :c => 3}.split { |k, v| k == :a or v == 3 }, "Hash partition incorrect")
   end
 
   def test_hash_filter_on_key

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

@@ -23,37 +23,45 @@ class TransitiveClosureTest < Test::Unit::TestCase
     alias :inspect :to_s
   end
 
+  # Verifies closure iteration for the following hierarchy:
+  #  root -> a, e
+  #  a -> b, c
+  #  c -> d
+  # The expected iteration is +root+ preceding +a+ and +e+, +a+ preceding +b+ and +c+, +c+ preceding +d+.
   def test_hierarchy
     root= Node.new('root'); a = Node.new('a', root); b = Node.new('b', a); c = Node.new('c', a); d = Node.new('d', c); e = Node.new('e', root)
-    expected = [root, a, b, c, d, e].to_set
-    closure = root.transitive_closure(:children)
-    assert_equal(expected, closure.to_set, "Hierarchy closure incorrect")
-    closure.each_with_index { |node, index| closure[index..-1].each { |other| assert(!other.children.include?(node), "Order incorrect") } }
-    closure.reject { |node| node.parent.nil? }.each_with_index { |node, index| assert(closure[0..index].detect { |other| other.children.include?(node) }, "Order incorrect") }
+    verify_closure([root, a, b, c, d, e], root.transitive_closure(:children))
   end
 
   def test_internal
     root= Node.new('root'); a = Node.new('a', root); b = Node.new('b', a); c = Node.new('c', a); d = Node.new('d', c); e = Node.new('e', root)
-    expected = [a, b, c, d].to_set
-    closure = a.transitive_closure(:children)
-    assert_equal(expected, closure.to_set, "Hierarchy closure incorrect")
+    verify_closure([a, b, c, d], a.transitive_closure(:children))
   end
 
   def test_leaf
     leaf = Node.new(1)
-    assert_equal([leaf], leaf.transitive_closure(:children), "Leaf closure incorrect")
+    verify_closure([leaf], leaf.transitive_closure(:children))
   end
 
   def test_collection
     a = Node.new('a'); b = Node.new('b'); c = Node.new('c', a); d = Node.new('d', b); e = Node.new('e', c)
-    expected = [a, b, c, d, e].to_set
-    closure = [a, b].transitive_closure(:children)
-    assert_equal(expected, closure.to_set, "Hierarchy closure incorrect")
+    verify_closure([a, b, c, d, e], [a, b].transitive_closure(:children))
   end
 
   def test_cycle
     root= Node.new('root'); a = Node.new('a', root); b = Node.new('b', a); c = Node.new('c', a); c.children << root
     expected = [root, a, b, c].to_set
-    assert_equal(expected, a.transitive_closure(:children).to_set, "Cycle closure incorrect")
+    verify_closure([root, a, b, c], root.transitive_closure(:children))
+  end
+  
+  def verify_closure(content, closure)
+    assert_equal(content.to_set, closure.to_set, "Hierarchy closure incorrect")
+    # Verify that no child succeeds the parent.
+    closure.each_with_index do |node, index|
+      par = node.parent
+      if content.include?(par) then
+        assert(closure.index(par) < index, "Child #{node} precedes parent #{par}")
+      end
+    end
   end
 end

data/test/lib/examples/clinical_trials/migration/migration_test.rb

@@ -0,0 +1,58 @@
+require 'test/lib/caruby/migration/test_case'
+require 'examples/clinical_trials/lib/clinical_trials'
+
+module ClinicalTrials
+  # Tests the ClinicalTrials example migration.
+  class MigrationTest < Test::Unit::TestCase
+    include CaRuby::MigrationTestCase
+    
+    def setup
+      super(FIXTURES)
+    end
+    
+#    def test_subject
+#      verify_target(:subject, :target => ClinicalTrials::Subject, :mapping=> SUBJECT_MAPPING) do |sbj|
+#        assert_not_nil(sbj.ssn, "Missing SSN")
+#      end
+#    end
+#    
+#    def test_ssn_filter
+#      verify_target(:ssn_filter, :target => ClinicalTrials::Subject, :mapping=> SUBJECT_MAPPING, :shims => SSN_SHIMS) do |sbj|
+#        assert_not_nil(sbj.ssn, "Missing SSN")
+#      end
+#    end
+    
+    def test_activity_filter
+      verify_target(:activity_filter, :target => ClinicalTrials::Study, :mapping=> STUDY_MAPPING, :defaults => STUDY_DEFAULTS, :filters => STUDY_FILTERS) do |std|
+        expected = std.name.split(' ').first
+        assert_equal(expected, std.activity_status, "Incorrect activity status")
+      end
+    end
+    
+    private
+    
+    # The migration input data directory.
+    FIXTURES = 'examples/clinical_trials/data'
+  
+    # The migration input shim directory.
+    SHIMS = 'examples/clinical_trials/lib/clinical_trials/migration'
+    
+    # The migration configuration directory.
+    CONFIGS = 'examples/clinical_trials/conf/migration'
+    
+    # The subject input file.
+    SUBJECT_MAPPING = File.join(CONFIGS, "subject_fields.yaml")
+    
+    # The study input file.
+    STUDY_MAPPING = File.join(CONFIGS, "study_fields.yaml")
+    
+    # The study default values.
+    STUDY_DEFAULTS = File.join(CONFIGS, "study_defaults.yaml")
+    
+    # The study default values.
+    STUDY_FILTERS = File.join(CONFIGS, "study_filters.yaml")
+    
+    # The filter shims file.
+    SSN_SHIMS = File.join(SHIMS, "ssn_shim.rb")
+  end
+end

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

@@ -0,0 +1,38 @@
+require 'test/lib/caruby/migration/test_case'
+require 'examples/clinical_trials/lib/clinical_trials'
+
+# Tests the ClinicalTrials example migration.
+module ClinicalTrials
+  module MigrationTestCase
+    include CaRuby::MigrationTestCase
+    
+    def setup
+      super(FIXTURES)
+    end
+    
+    # Adds the +:target+, +:mapping+ and +:shims+ to the options and delegates
+    # to the superclass.
+    #
+    # @see {CaTissue::MigrationTestCase#create_migrator}
+    def create_migrator(fixture, opts={})
+      opts[:mapping] ||= File.join(CONFIGS, "#{fixture}_fields.yaml")
+      shims = File.join(SHIMS, "#{fixture}_shims.rb")
+      if File.exists?(shims) then
+        sopt = opts[:shims] ||= []
+        sopt << shims
+      end
+      super
+    end
+    
+    private
+    
+    # The migration input data directory.
+    FIXTURES = 'examples/clinical_trials/data'
+  
+    # The migration input shim directory.
+    SHIMS = 'examples/clinical_trials/lib/clinical_trials/migration'
+    
+    # The migration configuration directory.
+    CONFIGS = 'examples/clinical_trials/conf/migration'
+  end
+end

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: caruby-core
 version: !ruby/object:Gem::Version 
-  hash: 5
+  hash: 11
   prerelease: false
   segments: 
   - 1
   - 5
-  - 3
-  version: 1.5.3
+  - 4
+  version: 1.5.4
 platform: ruby
 authors: 
 - OHSU
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-07-08 00:00:00 -07:00
+date: 2011-09-22 00:00:00 -07:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -121,6 +121,8 @@ files:
 - lib/caruby/domain/uniquify.rb
 - lib/caruby/domain.rb
 - lib/caruby/import/java.rb
+- lib/caruby/json/deserializer.rb
+- lib/caruby/json/serializer.rb
 - lib/caruby/migration/migratable.rb
 - lib/caruby/migration/migrator.rb
 - lib/caruby/migration/resource_module.rb
@@ -191,8 +193,8 @@ files:
 - test/lib/caruby/util/version_test.rb
 - test/lib/caruby/util/visitor_test.rb
 - 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
+- test/lib/examples/clinical_trials/migration/migration_test.rb
+- test/lib/examples/clinical_trials/migration/test_case.rb
 - History.md
 - LEGAL
 - LICENSE

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

@@ -1,28 +0,0 @@
-require File.join(File.dirname(__FILE__), 'test_case')
-
-# Tests the ClinicalTrials example migration.
-module Galena
-  module ClinicalTrials
-    class ParticipantMigrationTest < Test::Unit::TestCase
-      include MigrationTestCase
-      
-      def test_target
-        verify_target(:participant, :target => ClinicalTrials::Participant) do |pnt|
-          assert_not_nil(pnt.ssn, "Missing SSN")
-        end
-      end
-      
-      def test_filter
-        verify_target(:participant, :target => ClinicalTrials::Participant, :input => FILTER_DATA, :shims => [FILTER_SHIMS]) do |pnt|
-          assert_not_nil(pnt.ssn, "Missing SSN")
-        end
-      end
-      
-      private
-      
-      FILTER_DATA = 'examples/galena/data/filter.csv'
-      
-      FILTER_SHIMS = 'examples/galena/lib/galena/migration/filter_shims.rb'
-    end
-  end
-end

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

@@ -1,40 +0,0 @@
-$:.unshift 'examples/clinical_trials/lib'
-
-require 'test/lib/caruby/migration/test_case'
-require 'clinical_trials'
-
-# Tests the ClinicalTrials example migration.
-module Galena
-  module ClinicalTrials
-    module MigrationTestCase
-      include CaRuby::MigrationTestCase
-      
-      # The migration input data directory.
-      FIXTURES = 'examples/galena/data'
-    
-      # The migration input data directory.
-      SHIMS = 'examples/galena/lib/galena/clinical_trials/migration'
-      
-      # The migration configuration directory.
-      CONFIGS = 'examples/galena/conf/migration'
-      
-      def setup
-        super(FIXTURES)
-      end
-      
-      # Adds the +:target+, +:mapping+ and +:shims+ to the options and delegates
-      # to the superclass.
-      #
-      # @see {CaTissue::MigrationTestCase#create_migrator}
-      def create_migrator(fixture, opts={})
-        opts[:mapping] ||= File.join(CONFIGS, "#{fixture}_fields.yaml")
-        shims = File.join(SHIMS, "#{fixture}_shims.rb")
-        if File.exists?(shims) then
-          sopt = opts[:shims] ||= []
-          sopt << shims
-        end
-        super
-      end
-    end
-  end
-end