caruby-core 1.4.7 → 1.4.9

data/test/lib/caruby/test_case.rb

@@ -0,0 +1,231 @@
+$:.unshift  '../caruby/lib'
+
+# open the logger
+LOG_FILE = 'test/results/log/catissue.log' unless defined?(LOG_FILE)
+require 'caruby/util/log' and
+  CaRuby::Log.instance.open(LOG_FILE, :shift_age => 10, :shift_size => 1048576, :debug => true)
+
+require 'caruby'
+
+module CaRuby
+  module TestCase
+    attr_reader :database
+
+    def setup(database=nil)
+      super()
+      logger.info("Testing #{name}...")
+      @database = database
+    end
+
+    def teardown
+      super
+      @database.close if @database
+      logger.info("Test #{name} completed.")
+    end
+    
+    def defaults
+      @defaults ||= CaTissueTest.defaults.uniquify
+    end
+    
+    # Tests the domain object +add_defaults_local+ method.
+    # Subclasses are responsible for setting every attribute that is a pre-condition for default value initialization.
+    def verify_defaults(subject)
+      subject.add_defaults
+      msg = "#{subject.qp} with default attributes fails validation"
+      assert_nothing_raised(ValidationError, msg) { subject.validate }
+    end
+
+    # Tests saving the subject. Calls {Database#save} on the subject and verifies that subject and its
+    # references were persisted.
+    #
+    # @param [Resource] subject the object to save
+    def verify_save(subject)
+      logger.debug{ "Verifying #{subject.qp} save with content:\n#{dump(subject)}" }
+      # capture the save operation time
+      @database.clear
+      st = Stopwatch.measure { @database.open { |db| db.save(subject) } }.elapsed
+      # the database execution time
+      dt = @database.execution_time
+      logger.debug { "#{subject.qp} save took #{'%.2f' % st} seconds, of which #{'%.2f' % dt} were database operations." }
+      verify_saved(subject)
+    end
+
+    # Verifies that the given subject and its references were persisted.
+    #
+    # @param [Resource] subject the saved object to verify
+    def verify_saved(subject)
+      logger.debug { "Verifying saved content of #{subject}..." }
+      subject.dependent? ? verify_saved_dependent(subject) : verify_saved_independent(subject)
+      logger.debug { "Verified saved content of #{subject}." }
+    end
+    
+    # Tests a query on the given template.
+    # The block given to this method is called on the query result.
+    def verify_query(template, *path) # :yields: result
+      yield database.query(template, *path)
+    end
+
+    # Returns the Ruby date as determined by setting a Java Date property.
+    def date(year, month, day)
+      jdate = java.util.Calendar.instance
+      jdate.clear
+      jdate.set(year, month - 1, day)
+      jdate.time.to_ruby_date
+    end
+
+    private
+    
+    def dump(obj)
+      @database.lazy_loader.suspend { obj.dump }
+    end
+  
+    # @param (see #mock_storable_template)
+    # @return (see #mock_storable_template)
+    def mock_create_template(obj)
+      mock_storable_template(obj) { |ref| ref.class.creatable_domain_attributes }
+    end
+  
+    # @param (see #mock_storable_template)
+    # @return (see #mock_storable_template)
+    def mock_update_template(obj)
+      mock_storable_template(obj) { |ref| ref.class.updatable_domain_attributes }
+    end
+    
+    # @param [Resource] obj the domain object to "save"
+    # @return [Resource] the template to use in the save operation
+    # @yield [ref] the storable attributes
+    # @yieldparam [Resource] ref the domain object to "save"
+    def mock_storable_template(obj, &selector)
+      # add fake identifiers to prerequisite references
+      obj.class.storable_prerequisite_attributes.each do |attr|
+        obj.send(attr).enumerate { |ref| ref.identifier = 1 }
+      end
+      # the template builder
+      bldr = CaRuby::StoreTemplateBuilder.new(@database, &selector)
+      # the save template
+      bldr.build_template(obj)
+    end
+
+    def verify_saved_dependent(dependent)
+      verify_dependency(dependent)
+      verify_saved_content(dependent)
+    end
+    
+    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
+      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}")
+      # a dependent collection reference must be refetched
+      if ownr.class.collection_attribute?(attribute) then
+        verify_saved_dependent_collection_member(dependent, ownr, attribute)
+      else
+        assert_not_nil(dependent.identifier, "Stored dependent #{dependent} identifier is not set")
+      end
+    end
+
+    # 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
+    # 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)
+      assert(deps.detect { |dep| dep == dependent }, "Owner #{owner.qp} #{attribute} value #{deps.pp_s} does not contain #{dependent}")
+      assert_not_nil(dependent.identifier, "Identifier not set for stored owner #{owner.qp} #{attribute} dependent collection member #{dependent}")
+    end
+
+    # Verifies the subject stored content.
+    def verify_saved_independent(subject)
+      subject_id = subject.identifier
+      assert_not_nil(subject_id, "#{subject.class.qp} identifier not set")
+      verify_saved_content(subject)
+    end
+
+    # Verifies that the given subject matches the database content. Does not verify subject unless it has
+    # a secondary key.
+    def verify_saved_content(subject)
+      attrs = subject.class.secondary_key_attributes
+      return if attrs.empty?
+      rqd = attrs & subject.class.mandatory_attributes
+      missing = rqd.reject { |attr| subject.send(attr) }
+      assert(missing.empty?, "#{subject} is missing values for secondary key attributes #{missing.to_series}")
+      # make a secondary key search template
+      vh = attrs.to_compact_hash do |attr|
+         v = subject.send(attr)
+         Resource === v ? v.copy : v
+      end
+      tmpl = subject.class.new(vh)
+      # find the template in the database
+      logger.debug  { "Verifying #{subject.qp} by finding and comparing template #{tmpl.pp_s}..." }
+      assert_not_nil(tmpl.find, "#{subject} not found in database")
+      # compare the subject to the fetched template
+      verify_that_saved_matches_fetched(subject, tmpl)
+    end
+
+    # 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.
+    #
+    # @param [Resource] expected the saved value
+    # @param [Resource] actual the fetched value
+    def verify_that_saved_matches_fetched(expected, actual)
+      expected.class.saved_nondomain_attributes.each do |attr|
+        # TODO - available_quantity broken for spc type Not Specified
+        # compare attributes that are fetched and set on create
+        attr_md = expected.class.attribute_metadata(attr)
+        if verify_saved_attribute?(attr_md) then
+          eval = expected.database.lazy_loader.suspend { expected.send(attr) }
+          next if eval.nil_or_empty?
+          aval = actual.send(attr)
+          if eval.nil? then
+            assert_nil(aval, "#{expected.qp} was saved without a #{attr} value, but was stored in the database with value #{actual.qp}")
+          else
+            assert_not_nil(aval, "#{expected.qp} was saved with #{attr} value #{eval.qp}, but this value was not found in the database.")
+            if attr == :available_quantity and expected.specimen_type == 'Not Specified' and eval != aval then
+              logger.warn("Skipped broken caTissue unspecified specimen type available comparison.")
+            else
+              assert(CaRuby::Resource.value_equal?(eval, aval), "#{expected.qp} was saved with #{attr} value #{eval.qp} that does not match the database value #{aval.qp}")
+            end
+          end
+        end
+      end
+      verify_dependents_match(expected, actual)
+    end
+    
+    # @param [AttributeMetadata] 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?
+    end
+
+    # Verifies that each expected dependent matches an actual dependent and has the same content.
+    def verify_dependents_match(expected, actual)
+      expected.class.dependent_attributes.each do |attr|
+        edeps = expected.database.lazy_loader.suspend { expected.send(attr) }
+        next if edeps.nil_or_empty?
+        adeps = actual.send(attr)
+        logger.debug { "Verifying #{expected.qp} dependent #{attr} #{edeps.qp} against #{actual.qp} #{adeps.qp}..." } unless edeps.nil_or_empty?
+        if edeps.collection? then
+          edeps.each do |edep|
+            adep = edep.match_in_owner_scope(adeps)
+            assert_not_nil(adep, "#{expected} #{attr} dependent #{edep} not found in fetched #{adeps.pp_s}")
+            verify_that_saved_matches_fetched(edep, adep)
+          end
+        else
+          edep = edeps; adep = adeps;
+          assert_not_nil(adep, "#{expected} #{attr} dependent #{edep} not found in database")
+          verify_that_saved_matches_fetched(edep, adep)
+        end
+      end
+    end
+  end
+end

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

@@ -24,8 +24,8 @@ class ClassTest < Test::Unit::TestCase
   class Person
     attr_reader :social_security_number
     attr_accessor :postal_code
-    define_attribute_alias(:ssn, :social_security_number)
-    define_attribute_alias(:zip_code, :postal_code)
+    alias_attribute(:ssn, :social_security_number)
+    alias_attribute(:zip_code, :postal_code)
   end
 
   def test_attribute_alias

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

@@ -1,6 +1,7 @@
 $:.unshift 'lib'
 
-require 'generator'
+# JRuby alert - SyncEnumerator moved from generator to REXML in JRuby 1.5
+require 'rexml/document'
 require "test/unit"
 require 'caruby/util/collection'
 require 'caruby/util/visitor'
@@ -101,7 +102,7 @@ class VistorTest < Test::Unit::TestCase
     child = Node.new(2, p1)
     p2 = Node.new(3)
     p2.children << child
-    result = CaRuby::Visitor.new { |pair| SyncEnumerator.new(pair.first.children, pair.last.children).to_a }.to_enum([p1, p2]).map { |pair| [pair.first.value, pair.last.value] }
+    result = CaRuby::Visitor.new { |pair| REXML::SyncEnumerator.new(pair.first.children, pair.last.children).to_a }.to_enum([p1, p2]).map { |pair| [pair.first.value, pair.last.value] }
     assert_equal([[1, 3], [2, 2]], result.to_a, "Collection visit result incorrect")
   end
 

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

@@ -0,0 +1,28 @@
+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

@@ -0,0 +1,40 @@
+$:.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/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

metadata

@@ -1,62 +1,79 @@
 --- !ruby/object:Gem::Specification 
 name: caruby-core
 version: !ruby/object:Gem::Version 
-  prerelease: 
-  version: 1.4.7
+  hash: 21
+  prerelease: false
+  segments: 
+  - 1
+  - 4
+  - 9
+  version: 1.4.9
 platform: ruby
 authors: 
-  - OHSU
+- OHSU
 autorequire: 
 bindir: bin
 cert_chain: []
 
-date: 2011-03-04 00:00:00 -08:00
+date: 2011-05-09 00:00:00 -07:00
 default_executable: 
 dependencies: 
-  - !ruby/object:Gem::Dependency 
-    name: dbi
-    prerelease: false
-    requirement: &id001 !ruby/object:Gem::Requirement 
-      none: false
-      requirements: 
-        - - ">="
-          - !ruby/object:Gem::Version 
-            version: "0"
-    type: :runtime
-    version_requirements: *id001
-  - !ruby/object:Gem::Dependency 
-    name: dbd-jdbc
-    prerelease: false
-    requirement: &id002 !ruby/object:Gem::Requirement 
-      none: false
-      requirements: 
-        - - ">="
-          - !ruby/object:Gem::Version 
-            version: "0"
-    type: :runtime
-    version_requirements: *id002
-  - !ruby/object:Gem::Dependency 
-    name: fastercsv
-    prerelease: false
-    requirement: &id003 !ruby/object:Gem::Requirement 
-      none: false
-      requirements: 
-        - - ">="
-          - !ruby/object:Gem::Version 
-            version: "0"
-    type: :runtime
-    version_requirements: *id003
-  - !ruby/object:Gem::Dependency 
-    name: uom
-    prerelease: false
-    requirement: &id004 !ruby/object:Gem::Requirement 
-      none: false
-      requirements: 
-        - - ">="
-          - !ruby/object:Gem::Version 
-            version: "0"
-    type: :runtime
-    version_requirements: *id004
+- !ruby/object:Gem::Dependency 
+  name: dbi
+  prerelease: false
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  type: :runtime
+  version_requirements: *id001
+- !ruby/object:Gem::Dependency 
+  name: dbd-jdbc
+  prerelease: false
+  requirement: &id002 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  type: :runtime
+  version_requirements: *id002
+- !ruby/object:Gem::Dependency 
+  name: fastercsv
+  prerelease: false
+  requirement: &id003 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  type: :runtime
+  version_requirements: *id003
+- !ruby/object:Gem::Dependency 
+  name: uom
+  prerelease: false
+  requirement: &id004 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  type: :runtime
+  version_requirements: *id004
 description: "    caRuby is a JRuby facade for interaction with caBIG applications.\n"
 email: caruby.org@gmail.com
 executables: []
@@ -66,142 +83,150 @@ extensions: []
 extra_rdoc_files: []
 
 files: 
-  - lib/caruby.rb
-  - lib/caruby/database.rb
-  - lib/caruby/resource.rb
-  - lib/caruby/version.rb
-  - lib/caruby/active_support/inflections.rb
-  - lib/caruby/active_support/inflector.rb
-  - lib/caruby/active_support/README.txt
-  - lib/caruby/active_support/core_ext/string.rb
-  - lib/caruby/active_support/core_ext/string/inflections.rb
-  - lib/caruby/cli/application.rb
-  - lib/caruby/cli/command.rb
-  - lib/caruby/csv/csv_mapper.rb
-  - lib/caruby/csv/csvio.rb
-  - lib/caruby/database/fetched_matcher.rb
-  - lib/caruby/database/lazy_loader.rb
-  - lib/caruby/database/persistable.rb
-  - lib/caruby/database/persistence_service.rb
-  - lib/caruby/database/persistifier.rb
-  - lib/caruby/database/reader.rb
-  - lib/caruby/database/saved_matcher.rb
-  - lib/caruby/database/search_template_builder.rb
-  - lib/caruby/database/sql_executor.rb
-  - lib/caruby/database/store_template_builder.rb
-  - lib/caruby/database/writer.rb
-  - lib/caruby/domain/attribute_initializer.rb
-  - lib/caruby/domain/attribute_metadata.rb
-  - lib/caruby/domain/id_alias.rb
-  - lib/caruby/domain/inversible.rb
-  - lib/caruby/domain/java_attribute_metadata.rb
-  - lib/caruby/domain/merge.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/import/java.rb
-  - lib/caruby/migration/migratable.rb
-  - lib/caruby/migration/migrator.rb
-  - lib/caruby/migration/resource_module.rb
-  - lib/caruby/migration/uniquify.rb
-  - lib/caruby/util/attribute_path.rb
-  - lib/caruby/util/cache.rb
-  - lib/caruby/util/class.rb
-  - lib/caruby/util/collection.rb
-  - lib/caruby/util/controlled_value.rb
-  - lib/caruby/util/coordinate.rb
-  - lib/caruby/util/domain_extent.rb
-  - lib/caruby/util/file_separator.rb
-  - lib/caruby/util/inflector.rb
-  - lib/caruby/util/log.rb
-  - lib/caruby/util/math.rb
-  - lib/caruby/util/merge.rb
-  - lib/caruby/util/module.rb
-  - lib/caruby/util/options.rb
-  - lib/caruby/util/partial_order.rb
-  - lib/caruby/util/person.rb
-  - lib/caruby/util/pretty_print.rb
-  - lib/caruby/util/properties.rb
-  - lib/caruby/util/roman.rb
-  - lib/caruby/util/stopwatch.rb
-  - lib/caruby/util/topological_sync_enumerator.rb
-  - lib/caruby/util/transitive_closure.rb
-  - lib/caruby/util/tree.rb
-  - lib/caruby/util/trie.rb
-  - lib/caruby/util/uniquifier.rb
-  - lib/caruby/util/validation.rb
-  - lib/caruby/util/version.rb
-  - lib/caruby/util/visitor.rb
-  - lib/caruby/util/weak_hash.rb
-  - lib/caruby/yard/resource_metadata_handler.rb
-  - test/lib/caruby/csv/csv_mapper_test.rb
-  - test/lib/caruby/csv/csvio_test.rb
-  - test/lib/caruby/database/persistable_test.rb
-  - test/lib/caruby/domain/domain_test.rb
-  - test/lib/caruby/domain/inversible_test.rb
-  - test/lib/caruby/domain/reference_visitor_test.rb
-  - test/lib/caruby/import/java_test.rb
-  - test/lib/caruby/util/cache_test.rb
-  - test/lib/caruby/util/class_test.rb
-  - test/lib/caruby/util/collection_test.rb
-  - test/lib/caruby/util/command_test.rb
-  - test/lib/caruby/util/controlled_value_test.rb
-  - test/lib/caruby/util/domain_extent_test.rb
-  - test/lib/caruby/util/file_separator_test.rb
-  - test/lib/caruby/util/inflector_test.rb
-  - test/lib/caruby/util/lazy_hash_test.rb
-  - test/lib/caruby/util/merge_test.rb
-  - test/lib/caruby/util/module_test.rb
-  - test/lib/caruby/util/options_test.rb
-  - test/lib/caruby/util/partial_order_test.rb
-  - test/lib/caruby/util/person_test.rb
-  - test/lib/caruby/util/pretty_print_test.rb
-  - test/lib/caruby/util/properties_test.rb
-  - test/lib/caruby/util/roman_test.rb
-  - test/lib/caruby/util/stopwatch_test.rb
-  - test/lib/caruby/util/topological_sync_enumerator_test.rb
-  - test/lib/caruby/util/transitive_closure_test.rb
-  - test/lib/caruby/util/tree_test.rb
-  - test/lib/caruby/util/trie_test.rb
-  - test/lib/caruby/util/validation_test.rb
-  - test/lib/caruby/util/version_test.rb
-  - test/lib/caruby/util/visitor_test.rb
-  - test/lib/caruby/util/weak_hash_test.rb
-  - History.txt
-  - LEGAL
-  - LICENSE
-  - README.md
-has_rdoc: true
-homepage: http://rubyforge.org/projects/caruby
+- lib/caruby/active_support/core_ext/string/inflections.rb
+- lib/caruby/active_support/core_ext/string.rb
+- lib/caruby/active_support/inflections.rb
+- lib/caruby/active_support/inflector.rb
+- lib/caruby/active_support/README.txt
+- lib/caruby/cli/application.rb
+- lib/caruby/cli/command.rb
+- lib/caruby/csv/csv_mapper.rb
+- lib/caruby/csv/csvio.rb
+- lib/caruby/database/fetched_matcher.rb
+- lib/caruby/database/lazy_loader.rb
+- lib/caruby/database/persistable.rb
+- lib/caruby/database/persistence_service.rb
+- lib/caruby/database/persistifier.rb
+- lib/caruby/database/reader.rb
+- lib/caruby/database/saved_matcher.rb
+- lib/caruby/database/search_template_builder.rb
+- lib/caruby/database/sql_executor.rb
+- 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/id_alias.rb
+- lib/caruby/domain/inversible.rb
+- lib/caruby/domain/java_attribute_metadata.rb
+- lib/caruby/domain/merge.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/import/java.rb
+- lib/caruby/migration/migratable.rb
+- lib/caruby/migration/migrator.rb
+- lib/caruby/migration/resource_module.rb
+- lib/caruby/migration/uniquify.rb
+- lib/caruby/resource.rb
+- lib/caruby/util/attribute_path.rb
+- lib/caruby/util/cache.rb
+- lib/caruby/util/class.rb
+- lib/caruby/util/collection.rb
+- lib/caruby/util/controlled_value.rb
+- lib/caruby/util/coordinate.rb
+- lib/caruby/util/domain_extent.rb
+- lib/caruby/util/file_separator.rb
+- lib/caruby/util/inflector.rb
+- lib/caruby/util/log.rb
+- lib/caruby/util/math.rb
+- lib/caruby/util/merge.rb
+- lib/caruby/util/module.rb
+- lib/caruby/util/options.rb
+- lib/caruby/util/partial_order.rb
+- lib/caruby/util/person.rb
+- lib/caruby/util/pretty_print.rb
+- lib/caruby/util/properties.rb
+- lib/caruby/util/roman.rb
+- lib/caruby/util/stopwatch.rb
+- lib/caruby/util/topological_sync_enumerator.rb
+- lib/caruby/util/transitive_closure.rb
+- lib/caruby/util/tree.rb
+- lib/caruby/util/trie.rb
+- lib/caruby/util/uniquifier.rb
+- lib/caruby/util/validation.rb
+- lib/caruby/util/version.rb
+- 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
+- test/lib/caruby/database/persistable_test.rb
+- test/lib/caruby/domain/domain_test.rb
+- test/lib/caruby/domain/inversible_test.rb
+- test/lib/caruby/domain/reference_visitor_test.rb
+- test/lib/caruby/import/java_test.rb
+- test/lib/caruby/migration/test_case.rb
+- test/lib/caruby/test_case.rb
+- test/lib/caruby/util/cache_test.rb
+- test/lib/caruby/util/class_test.rb
+- test/lib/caruby/util/collection_test.rb
+- test/lib/caruby/util/command_test.rb
+- test/lib/caruby/util/controlled_value_test.rb
+- test/lib/caruby/util/domain_extent_test.rb
+- test/lib/caruby/util/file_separator_test.rb
+- test/lib/caruby/util/inflector_test.rb
+- test/lib/caruby/util/lazy_hash_test.rb
+- test/lib/caruby/util/merge_test.rb
+- test/lib/caruby/util/module_test.rb
+- test/lib/caruby/util/options_test.rb
+- test/lib/caruby/util/partial_order_test.rb
+- test/lib/caruby/util/person_test.rb
+- test/lib/caruby/util/pretty_print_test.rb
+- test/lib/caruby/util/properties_test.rb
+- test/lib/caruby/util/roman_test.rb
+- test/lib/caruby/util/stopwatch_test.rb
+- test/lib/caruby/util/topological_sync_enumerator_test.rb
+- test/lib/caruby/util/transitive_closure_test.rb
+- test/lib/caruby/util/tree_test.rb
+- test/lib/caruby/util/trie_test.rb
+- 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
+- History.txt
+- LEGAL
+- LICENSE
+- README.md
+has_rdoc: yard
+homepage: http://caruby.rubyforge.org
 licenses: 
-  - MIT
+- MIT
 post_install_message: 
 rdoc_options: []
 
 require_paths: 
-  - lib
+- lib
 required_ruby_version: !ruby/object:Gem::Requirement 
   none: false
   requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        version: "0"
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
+      - 0
+      version: "0"
 required_rubygems_version: !ruby/object:Gem::Requirement 
   none: false
   requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        version: "0"
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
+      - 0
+      version: "0"
 requirements: []
 
 rubyforge_project: caruby
-rubygems_version: 1.5.3
+rubygems_version: 1.3.7
 signing_key: 
 specification_version: 3
 summary: Ruby facade for caBIG applications.