family-reunion 0.1.1

data/.document

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+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/.rspec

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+--color

data/.rvmrc

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+rvm use ruby-1.9.2-p0

data/Gemfile

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+source "http://rubygems.org"
+require 'yaml'
+YAML::ENGINE.yamler= 'syck'
+
+
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+
+gem "dwc-archive", ">= 0.5.13"
+gem "taxamatch_rb", ">= 0.6.5"
+
+
+group :development do
+  gem "rspec", "~> 2.3.0"
+  gem "cucumber", ">= 0"
+  gem "bundler", "~> 1.0.0"
+  gem "jeweler", "~> 1.6.0"
+  gem "rcov", ">= 0"
+  gem "ruby-debug19"
+  gem "ruby-prof"
+  gem "shoulda"
+  gem "mocha"
+end

data/Gemfile.lock

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+GEM
+  remote: http://rubygems.org/
+  specs:
+    RubyInline (3.9.0)
+      ZenTest (~> 4.3)
+    ZenTest (4.5.0)
+    archive-tar-minitar (0.5.2)
+    biodiversity (0.7.3)
+      json
+      treetop
+    builder (3.0.0)
+    columnize (0.3.2)
+    cucumber (0.10.2)
+      builder (>= 2.1.2)
+      diff-lcs (>= 1.1.2)
+      gherkin (>= 2.3.5)
+      json (>= 1.4.6)
+      term-ansicolor (>= 1.0.5)
+    diff-lcs (1.1.2)
+    dwc-archive (0.5.13)
+      parsley-store (>= 0.2.0)
+    gherkin (2.3.7)
+      json (>= 1.4.6)
+    git (1.2.5)
+    jeweler (1.6.0)
+      bundler (~> 1.0.0)
+      git (>= 1.2.5)
+      rake
+    json (1.5.1)
+    linecache19 (0.5.11)
+      ruby_core_source (>= 0.1.4)
+    mocha (0.9.8)
+      rake
+    parsley-store (0.2.2)
+      biodiversity
+      redis
+    polyglot (0.3.1)
+    rake (0.8.7)
+    rcov (0.9.9)
+    redis (2.2.0)
+    rspec (2.3.0)
+      rspec-core (~> 2.3.0)
+      rspec-expectations (~> 2.3.0)
+      rspec-mocks (~> 2.3.0)
+    rspec-core (2.3.1)
+    rspec-expectations (2.3.0)
+      diff-lcs (~> 1.1.2)
+    rspec-mocks (2.3.0)
+    ruby-debug-base19 (0.11.24)
+      columnize (>= 0.3.1)
+      linecache19 (>= 0.5.11)
+      ruby_core_source (>= 0.1.4)
+    ruby-debug19 (0.11.6)
+      columnize (>= 0.3.1)
+      linecache19 (>= 0.5.11)
+      ruby-debug-base19 (>= 0.11.19)
+    ruby-prof (0.10.7)
+    ruby_core_source (0.1.4)
+      archive-tar-minitar (>= 0.5.2)
+    shoulda (2.11.3)
+    taxamatch_rb (0.6.5)
+      RubyInline
+      biodiversity (>= 0.5.13)
+    term-ansicolor (1.0.5)
+    treetop (1.4.9)
+      polyglot (>= 0.3.1)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  bundler (~> 1.0.0)
+  cucumber
+  dwc-archive (>= 0.5.13)
+  jeweler (~> 1.6.0)
+  mocha
+  rcov
+  rspec (~> 2.3.0)
+  ruby-debug19
+  ruby-prof
+  shoulda
+  taxamatch_rb (>= 0.6.5)

data/LICENSE.txt

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+Copyright (c) 2011 Dmitry Mozzherin
+
+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.rdoc

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+= family-reunion
+
+Description goes here.
+
+== Contributing to family-reunion
+ 
+* Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet
+* Check out the issue tracker to make sure someone already hasn't requested it and/or contributed it
+* Fork the project
+* Start a feature/bugfix branch
+* Commit and push until you are happy with your contribution
+* Make sure to add tests for it. This is important so I don't break it in a future version unintentionally.
+* Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.
+
+== Copyright
+
+Copyright (c) 2011 Marine Biological Laboratory. See LICENSE.txt for
+further details.
+

data/Rakefile

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+# encoding: utf-8
+
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
+  gem.name = "family-reunion"
+  gem.homepage = "http://github.com/dimus/family-reunion"
+  gem.license = "MIT"
+  gem.summary = %Q{An algorithm to merge related nodes of two taxonomic hierarchies}
+  gem.description = %Q{An algorithm to merge related nodes of two taxonomic hierarchies with synonym information}
+  gem.email = "dmozzherin@gmail.com"
+  gem.authors = ["Dmitry Mozzherin", "David Shorthouse"]
+  # dependencies defined in Gemfile
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rspec/core'
+require 'rspec/core/rake_task'
+RSpec::Core::RakeTask.new(:spec) do |spec|
+  spec.pattern = FileList['spec/**/*_spec.rb']
+end
+
+RSpec::Core::RakeTask.new(:rcov) do |spec|
+  spec.pattern = 'spec/**/*_spec.rb'
+  spec.rcov = true
+end
+
+require 'cucumber/rake/task'
+Cucumber::Rake::Task.new(:features)
+
+task :default => :spec
+
+require 'rake/rdoctask'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "family-reunion #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.1.1

data/family-reunion.gemspec

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+# Generated by jeweler
+# DO NOT EDIT THIS FILE DIRECTLY
+# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |s|
+  s.name = %q{family-reunion}
+  s.version = "0.1.1"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = ["Dmitry Mozzherin", "David Shorthouse"]
+  s.date = %q{2011-06-07}
+  s.description = %q{An algorithm to merge related nodes of two taxonomic hierarchies with synonym information}
+  s.email = %q{dmozzherin@gmail.com}
+  s.extra_rdoc_files = [
+    "LICENSE.txt",
+    "README.rdoc"
+  ]
+  s.files = [
+    ".document",
+    ".rspec",
+    ".rvmrc",
+    "Gemfile",
+    "Gemfile.lock",
+    "LICENSE.txt",
+    "README.rdoc",
+    "Rakefile",
+    "VERSION",
+    "family-reunion.gemspec",
+    "features/family-reunion.feature",
+    "features/step_definitions/family-reunion_steps.rb",
+    "features/support/env.rb",
+    "lib/family-reunion.rb",
+    "lib/family-reunion/cache.rb",
+    "lib/family-reunion/exact_matcher.rb",
+    "lib/family-reunion/fuzzy_matcher.rb",
+    "lib/family-reunion/matcher_helper.rb",
+    "lib/family-reunion/nomatch_organizer.rb",
+    "lib/family-reunion/taxamatch_preprocessor.rb",
+    "lib/family-reunion/taxamatch_wrapper.rb",
+    "lib/family-reunion/top_node.rb",
+    "scripts/dwca2fr.rb",
+    "spec/family-reunion_spec.rb",
+    "spec/fixtures/ants_primary.json",
+    "spec/fixtures/ants_secondary.json",
+    "spec/fixtures/matched_merges.json",
+    "spec/fixtures/nodes_to_match.json",
+    "spec/fixtures/synonyms_strings_primary.json",
+    "spec/fixtures/synonyms_strings_secondary.json",
+    "spec/fixtures/valid_names_strings_primary.json",
+    "spec/fixtures/valid_names_strings_secondary.json",
+    "spec/fuzzy_matcher_spec.rb",
+    "spec/node_spec.rb",
+    "spec/nomatch_organizer_spec.rb",
+    "spec/spec_helper.rb",
+    "spec/taxamatch_preprocessor_spec.rb",
+    "spec/taxamatch_wrapper_spec.rb"
+  ]
+  s.homepage = %q{http://github.com/dimus/family-reunion}
+  s.licenses = ["MIT"]
+  s.require_paths = ["lib"]
+  s.rubygems_version = %q{1.3.7}
+  s.summary = %q{An algorithm to merge related nodes of two taxonomic hierarchies}
+
+  if s.respond_to? :specification_version then
+    current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
+    s.specification_version = 3
+
+    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
+      s.add_runtime_dependency(%q<dwc-archive>, [">= 0.5.13"])
+      s.add_runtime_dependency(%q<taxamatch_rb>, [">= 0.6.5"])
+      s.add_development_dependency(%q<rspec>, ["~> 2.3.0"])
+      s.add_development_dependency(%q<cucumber>, [">= 0"])
+      s.add_development_dependency(%q<bundler>, ["~> 1.0.0"])
+      s.add_development_dependency(%q<jeweler>, ["~> 1.6.0"])
+      s.add_development_dependency(%q<rcov>, [">= 0"])
+      s.add_development_dependency(%q<ruby-debug19>, [">= 0"])
+      s.add_development_dependency(%q<ruby-prof>, [">= 0"])
+      s.add_development_dependency(%q<shoulda>, [">= 0"])
+      s.add_development_dependency(%q<mocha>, [">= 0"])
+    else
+      s.add_dependency(%q<dwc-archive>, [">= 0.5.13"])
+      s.add_dependency(%q<taxamatch_rb>, [">= 0.6.5"])
+      s.add_dependency(%q<rspec>, ["~> 2.3.0"])
+      s.add_dependency(%q<cucumber>, [">= 0"])
+      s.add_dependency(%q<bundler>, ["~> 1.0.0"])
+      s.add_dependency(%q<jeweler>, ["~> 1.6.0"])
+      s.add_dependency(%q<rcov>, [">= 0"])
+      s.add_dependency(%q<ruby-debug19>, [">= 0"])
+      s.add_dependency(%q<ruby-prof>, [">= 0"])
+      s.add_dependency(%q<shoulda>, [">= 0"])
+      s.add_dependency(%q<mocha>, [">= 0"])
+    end
+  else
+    s.add_dependency(%q<dwc-archive>, [">= 0.5.13"])
+    s.add_dependency(%q<taxamatch_rb>, [">= 0.6.5"])
+    s.add_dependency(%q<rspec>, ["~> 2.3.0"])
+    s.add_dependency(%q<cucumber>, [">= 0"])
+    s.add_dependency(%q<bundler>, ["~> 1.0.0"])
+    s.add_dependency(%q<jeweler>, ["~> 1.6.0"])
+    s.add_dependency(%q<rcov>, [">= 0"])
+    s.add_dependency(%q<ruby-debug19>, [">= 0"])
+    s.add_dependency(%q<ruby-prof>, [">= 0"])
+    s.add_dependency(%q<shoulda>, [">= 0"])
+    s.add_dependency(%q<mocha>, [">= 0"])
+  end
+end
+

data/features/family-reunion.feature

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+Feature: something something
+  In order to something something
+  A user something something
+  something something something
+
+  Scenario: something something
+    Given inspiration
+    When I create a sweet new gem
+    Then everyone should see how awesome I am

data/features/support/env.rb

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+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+
+$LOAD_PATH.unshift(File.dirname(__FILE__) + '/../../lib')
+require 'family-reunion'
+
+require 'rspec/expectations'

data/lib/family-reunion.rb

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+require 'json'
+require 'taxamatch_rb'
+require 'family-reunion/cache'
+require 'family-reunion/top_node'
+require 'family-reunion/matcher_helper'
+require 'family-reunion/exact_matcher'
+require 'family-reunion/fuzzy_matcher'
+require 'family-reunion/taxamatch_wrapper'
+require 'family-reunion/taxamatch_preprocessor'
+require 'family-reunion/nomatch_organizer'
+
+
+class FamilyReunion
+  attr :primary_node, :secondary_node, :merges
+  attr :primary_valid_names_set, :secondary_valid_names_set
+  attr :primary_synonyms_set, :secondary_synonyms_set
+
+  def initialize(primary_node, secondary_node)
+    @primary_node = FamilyReunion::TopNode.new(primary_node)
+    @secondary_node = FamilyReunion::TopNode.new(secondary_node)
+    @primary_valid_names_set = Set.new(@primary_node.valid_names_hash.keys)
+    @secondary_valid_names_set = Set.new(@secondary_node.valid_names_hash.keys)
+    @primary_synonyms_set = Set.new(@primary_node.synonyms_hash.keys)
+    @secondary_synonyms_set = Set.new(@secondary_node.synonyms_hash.keys)
+    @merges = {}
+  end
+
+  def merge(with_fuzzy_matching = true)
+    merge_exact_matches
+    merge_fuzzy_matches if with_fuzzy_matching
+    merge_no_matches
+    @merges
+  end
+
+  private
+
+  def merge_exact_matches
+    ExactMatcher.new(self).merge
+  end
+
+  def merge_fuzzy_matches
+    FuzzyMatcher.new(self).merge
+  end
+  
+  def merge_no_matches
+    NomatchOrganizer.new(self).merge
+  end
+
+end

data/lib/family-reunion/cache.rb

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+class FamilyReunion
+  class Cache
+    attr :word_letters, :similar_words
+
+    def initialize
+      @word_letters = {}
+      @similar_words = {}
+      @taxamatch_genus = {}
+      @taxamatch_species = {}
+    end
+
+  end
+end

data/lib/family-reunion/exact_matcher.rb

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+class FamilyReunion
+  class ExactMatcher
+    include MatcherHelper
+
+    def initialize(family_reunion)
+      @fr = family_reunion
+    end
+
+    def merge
+      add_valid_matches(get_valid_matches)
+      add_synonym_matches(get_valid_to_synonym_matches, :valid_to_synonym)
+      add_synonym_matches(get_synonym_to_valid_matches, :synonym_to_valid)
+      add_synonym_matches(get_synonym_to_synonym_matches, :synonym_to_synonym)
+    end
+
+    private
+
+    def get_valid_matches
+      valid_matches = @fr.primary_valid_names_set & @fr.secondary_valid_names_set
+    end
+
+    def add_valid_matches(valid_matches)
+      # Homonyms are treated separately, and are not matched by the algorithm,
+      # they are excluded from valid_matches
+      valid_matches.each do |name|
+        primary_id = @fr.primary_node.valid_names_hash[name][:id]
+        secondary_id = @fr.secondary_node.valid_names_hash[name][:id]
+        @fr.merges[primary_id] = {:matches => {secondary_id.to_s => {:match_type => :valid_to_valid}}, :nonmatches => []}
+      end
+    end
+
+    def get_valid_to_synonym_matches
+      @fr.primary_valid_names_set & @fr.secondary_synonyms_set
+    end
+
+    def get_synonym_to_valid_matches
+      @fr.primary_synonyms_set & @fr.secondary_valid_names_set
+    end
+    
+    def get_synonym_to_synonym_matches
+      @fr.primary_synonyms_set & @fr.secondary_synonyms_set
+    end
+
+    def add_synonym_matches(match_set, match_type)
+      match_set.each do |name|
+        primary_ids, secondary_ids = get_valid_name_ids(name)
+        secondary_id_matches = format_secondary_id_for_merge(secondary_ids, match_type)
+        primary_ids.each do |primary_id|
+          add_record_to_merges(primary_id, secondary_id_matches)
+        end
+      end
+    end
+
+    def get_valid_name_ids(name)
+      primary_ids = get_ids_from_node(name, @fr.primary_node)
+      secondary_ids = get_ids_from_node(name, @fr.secondary_node)
+      [primary_ids, secondary_ids]
+    end
+
+    def get_ids_from_node(name, node)
+      valid_names = node.valid_names_hash
+      synonyms = node.synonyms_hash
+      if valid_names.has_key?(name)
+        return [valid_names[name][:id]]
+      else
+        return synonyms[name].map {|n| n[:id]}
+      end
+    end
+
+  end
+end
+