columns_matcher 0.0.1

data/.gitignore

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+*.gem
+*.rbc
+.bundle
+.config
+.yardoc
+Gemfile.lock
+InstalledFiles
+_yardoc
+coverage
+doc/
+lib/bundler/man
+pkg
+rdoc
+spec/reports
+test/tmp
+test/version_tmp
+tmp

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in columns-matcher.gemspec
+gemspec

data/LICENSE.txt

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+Copyright (c) 2012 David Pham
+
+MIT License
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

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+# Columns::Matcher
+
+TODO: Write a gem description
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+    gem 'columns-matcher'
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install columns-matcher
+
+## Usage
+
+TODO: Write usage instructions here
+
+## Contributing
+
+1. Fork it
+2. Create your feature branch (`git checkout -b my-new-feature`)
+3. Commit your changes (`git commit -am 'Add some feature'`)
+4. Push to the branch (`git push origin my-new-feature`)
+5. Create new Pull Request

data/Rakefile

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+require 'bundler/gem_tasks'

data/columns_matcher.gemspec

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+# -*- encoding: utf-8 -*-
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'columns_matcher/version'
+
+Gem::Specification.new do |gem|
+  gem.name          = 'columns_matcher'
+  gem.version       = ColumnsMatcher::VERSION
+  gem.authors       = ['David Pham']
+  gem.email         = ['hello@khoi.co']
+  gem.description   = %q{Determine the mappings between 2 sets of data}
+  gem.summary       = %q{Determine the mappings between 2 sets of data}
+  gem.homepage      = ''
+
+  gem.files         = `git ls-files`.split($/)
+  gem.executables   = gem.files.grep(%r{^bin/}).map{ |f| File.basename(f) }
+  gem.test_files    = gem.files.grep(%r{^(test|spec|features)/})
+  gem.require_paths = ['lib']
+
+  gem.add_dependency 'gratr19', '~> 0.4.4.1'
+  gem.add_dependency 'rserve-client', '~> 0.3.0'
+  gem.add_dependency 'rserve-simpler', '~> 0.0.6'
+  gem.add_dependency 'munkres', '~> 0.1.0'
+end

data/lib/columns_matcher/converter.rb

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+module ColumnsMatcher
+	module Converter
+		# values is an array of any type
+		# Returns an array of numeric types
+		def self.convert_from_array_to_numeric_array(values)
+			values.collect {|value| value.is_a?(String) ? value.sum : value }
+		end
+
+		# values is an array of numeric types
+		# Returns an R vector
+		def self.convert_from_array_to_r_vector(values)
+			"c(#{values.join(',')})"
+		end
+
+		# graph is an UndirectedGraph
+		# Returns an array of vectors in the format of [Vertex weight, [Edges' weights in descending order]]
+		# for input into calculation of Euclidian distance
+		def self.convert_from_vertices_to_vectors(graph)
+			graph_vectors = []
+
+			graph.vertices.each do |vertex|
+        graph_vectors << [graph[vertex]] + graph.adjacent(vertex, { type: :edges }).collect{|edge| edge.label }.sort {|first, second| second <=> first }
+      end
+
+      graph_vectors
+		end
+
+		# first_vectors and second_vectors are arrays of vectors in the format of [Vertex weight, [Edges' weights in descending order]]
+		# Returns a square cost matrix - cost calculated using Euclidian distance - for input into Munkres assignment algorithm
+		def self.convert_from_vectors_to_euclidian_distance_cost_matrix(first_vectors, second_vectors)
+			combinations_of_vectors = first_vectors.product(second_vectors)
+      euclidian_distances = combinations_of_vectors.map {|combination_of_vector| Statistics::euclidian_distance(combination_of_vector.first, combination_of_vector.last) }
+
+      squared_vector = nil
+      cost_matrix = nil
+
+      size = first_vectors.size >= second_vectors.size ? first_vectors.size : second_vectors.size
+
+      squared_vector = Array.new(size ** 2) { Graph::STUB_VALUE }
+
+      (0..(first_vectors.size - 1)).each do |row|
+        (0..(second_vectors.size - 1)).each do |column|
+          index = (row * size) + column
+
+          squared_vector[index] = euclidian_distances[index]
+        end
+      end
+
+      cost_matrix = squared_vector.each_slice(size).to_a
+		end
+	end
+end

data/lib/columns_matcher/graph.rb

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+require 'gratr'
+
+module ColumnsMatcher
+  module Graph
+    include GRATR
+
+    STUB_VALUE = 1000
+
+  	# columns is a hash with
+    # column names as the keys and column values as the values
+    # Returns a graph of vertices and edges, with weights
+  	def self.build_dependency_graph(columns)
+  		combinations_of_column_names = Utilities::get_combinations(columns.keys)
+
+      graph = UndirectedGraph.new
+
+    	combinations_of_column_names.map do |combination_of_column_names|
+        first_column_name = combination_of_column_names.first
+        second_column_name = combination_of_column_names.last
+
+    		first_column_values = columns[first_column_name]
+    		second_column_values = columns[second_column_name]
+
+        if first_column_name == second_column_name
+          entropy_of_column = Statistics::entropy(first_column_values)
+
+          graph[first_column_name] = entropy_of_column
+        else
+          mutual_information_between_columns = Statistics::mutual_information(first_column_values, second_column_values)
+
+          graph.add_edge!(first_column_name, second_column_name, mutual_information_between_columns)
+        end
+    	end
+
+      graph
+  	end
+
+    # graph_to_match_against and graph_to_match are are UndirectedGraph's
+    # Returns mappings of columns with the keys as columns to match and values as columns to match against
+  	def self.match_graphs(graph_to_match_against, graph_to_match)
+      graph_to_match_against_vectors = Converter::convert_from_vertices_to_vectors(graph_to_match_against)
+      graph_to_match_vectors = Converter::convert_from_vertices_to_vectors(graph_to_match)
+
+      cost_matrix = Converter::convert_from_vectors_to_euclidian_distance_cost_matrix(graph_to_match_vectors, graph_to_match_against_vectors)
+
+      pairings = Statistics::munkres_assignment_algorithm(cost_matrix)
+
+      mappings = Graph::get_mappings(pairings, graph_to_match_against, graph_to_match)
+
+      mappings
+  	end
+
+
+    # pairings is a 2D array of sub-arrays of size 2 - the results of the Munkres assignment algorithm
+    # first_graph and second_graph are UndirectedGraph's
+    # Returns mappings of columns with the keys as columns to match and values as columns to match against
+    def self.get_mappings(pairings, first_graph, second_graph)
+      first_graph_vertices = first_graph.vertices
+      second_graph_vertices = second_graph.vertices
+
+      mappings = Hash.new
+
+      pairings.each do |pair|
+        first_graph_vertex = first_graph_vertices[pair.last]
+        second_graph_vertex = second_graph_vertices[pair.first]
+
+        mappings[second_graph_vertex] = first_graph_vertex
+      end
+
+      mappings
+    end
+  end
+end

data/lib/columns_matcher/statistics.rb

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+require 'munkres'
+
+module ColumnsMatcher
+	module Statistics
+		# values is an array of values
+		# Returns entropy statistic
+		def self.entropy(values)
+			r = Rserve::Simpler.new
+
+			r.converse("library(\"entropy\")")
+
+			numeric_values = Converter::convert_from_array_to_numeric_array(values)
+
+			values_in_r_vector = Converter::convert_from_array_to_r_vector(numeric_values)
+
+			entropy = r.converse("entropy(table(#{values_in_r_vector}))")
+
+			entropy
+		end
+
+		# first_values and second_values are arrays of values
+		# Returns mutual information statistic
+	  def self.mutual_information(first_values, second_values)
+			r = Rserve::Simpler.new
+
+			r.converse("library(\"entropy\")")
+
+			first_numeric_values = Converter::convert_from_array_to_numeric_array(first_values)
+			second_numeric_values = Converter::convert_from_array_to_numeric_array(second_values)
+
+			first_values_in_r_vector = Converter::convert_from_array_to_r_vector(first_numeric_values)
+			second_values_in_r_vector = Converter::convert_from_array_to_r_vector(second_numeric_values)
+
+			mutual_information = r.converse("mi.plugin(rbind(#{first_values_in_r_vector}, #{second_values_in_r_vector}))")
+
+			mutual_information
+		end
+
+		# first_vector and second_vector are two arrays of two potentially different sizes
+		# Returns Euclidian distance between the two vectors
+		def self.euclidian_distance(first_vector, second_vector)
+	  	sum = 0
+
+	  	size = (first_vector.size >= second_vector.size) ? first_vector.size : second_vector.size
+
+	  	equalized_first_vector = Array.new(size) { 0 }.fill {|index| first_vector[index] }
+	  	equalized_second_vector = Array.new(size) { 0 }.fill {|index| second_vector[index] }
+
+	  	equalized_first_vector.zip(equalized_second_vector).each do |first, second|
+	    	component = (first - second) ** 2
+
+	    	sum += component
+	  	end
+	  	
+	  	Math.sqrt(sum)
+		end
+
+		# cost_matrix is a square matrix of costs
+		# Returns pairings that optimize costs - lowest overall cost
+		def self.munkres_assignment_algorithm(cost_matrix)
+			munkres = Munkres.new(cost_matrix)
+      
+      pairings = munkres.find_pairings
+		end
+	end
+end

data/lib/columns_matcher/utilities.rb

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+module ColumnsMatcher
+	module Utilities
+	  # column_names is an array
+	  # Returns combinations of column names
+	  def self.get_combinations(column_names)
+	  	column_names.product(column_names)
+	  end
+	end
+end

data/lib/columns_matcher/version.rb

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+module ColumnsMatcher
+  VERSION = '0.0.1'
+end

data/lib/columns_matcher.rb

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+require 'columns_matcher/version'
+require 'columns_matcher/utilities'
+require 'columns_matcher/converter'
+require 'columns_matcher/statistics'
+require 'columns_matcher/graph'
+require 'rserve/simpler'
+
+module ColumnsMatcher
+	# columns_to_match_against and columns_to_match are hashes with
+	# column names as the keys and column values as the values
+	# Returns mappings of columns with the keys as columns to match and values as columns to match against
+  def self.match(columns_to_match_against, columns_to_match)
+  	columns_to_match_against_graph = Graph::build_dependency_graph(columns_to_match_against)
+  	columns_to_match_graph = Graph::build_dependency_graph(columns_to_match)
+
+  	column_mappings = Graph::match_graphs(columns_to_match_against_graph, columns_to_match_graph)
+
+  	column_mappings
+  end
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: columns_matcher
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+  prerelease: 
+platform: ruby
+authors:
+- David Pham
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2012-09-23 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: gratr19
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.4.4.1
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.4.4.1
+- !ruby/object:Gem::Dependency
+  name: rserve-client
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.3.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.3.0
+- !ruby/object:Gem::Dependency
+  name: rserve-simpler
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.0.6
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.0.6
+- !ruby/object:Gem::Dependency
+  name: munkres
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.1.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.1.0
+description: Determine the mappings between 2 sets of data
+email:
+- hello@khoi.co
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- .DS_Store
+- .gitignore
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- columns_matcher.gemspec
+- lib/.DS_Store
+- lib/columns_matcher.rb
+- lib/columns_matcher/converter.rb
+- lib/columns_matcher/graph.rb
+- lib/columns_matcher/statistics.rb
+- lib/columns_matcher/utilities.rb
+- lib/columns_matcher/version.rb
+homepage: ''
+licenses: []
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.24
+signing_key: 
+specification_version: 3
+summary: Determine the mappings between 2 sets of data
+test_files: []