gn_crossmap 0.1.1

checksums.yaml

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+SHA1:
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+  data.tar.gz: 4ebf72afdfe65e37148d19dd2234d771cb3db951
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data/.gitignore

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+/.bundle/
+/.yardoc
+/Gemfile.lock
+/_yardoc/
+/coverage/
+/doc/
+/pkg/
+/spec/reports/
+/tmp/
+output.csv

data/.rspec

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+--format documentation
+--color
+--require spec_helper

data/.rubocop.yml

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+AllCops:
+  Exclude:
+    - db/**/*
+    - bundle_bin/**/*
+  Include:
+    - exe/crossmap
+Style/StringLiterals:
+  EnforcedStyle: double_quotes
+Style/DotPosition:
+  EnforcedStyle: trailing

data/.travis.yml

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+language: ruby
+rvm:
+  - 2.1
+  - 2.2
+script:
+  - bundle exec rake
+branches:
+  only:
+      - master

data/CHANGELOG.md

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+gn_crossmap CHANGELOG
+=====================
+
+0.1.1
+-----
+- [Dmitry Mozzherin][dimus] - first official release -- works for full names
+                              and names entered in rank fields
+
+0.1.0
+-----
+- [Dmitry Mozzherin][dimus] - initial version
+
+[dimus]: https://github.com/dimus

data/Gemfile

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+source "https://rubygems.org"
+
+# Specify your gem's dependencies in gn_crossmap.gemspec
+gemspec

data/LICENSE

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+Copyright (c) 2015 Marine Biological Laboratory
+
+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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+# GnCrossmap
+[![Gem Version][gem_badge]][gem_link]
+[![Continuous Integration Status][ci_badge]][ci_link]
+[![Coverage Status][cov_badge]][cov_link]
+[![CodeClimate][code_badge]][code_link]
+[![Dependency Status][dep_badge]][dep_link]
+
+This gem crossmaps a checklist of scientific names to names from a data source
+in [GN Resolver][resolver].
+
+Checklist has to be in a CSV format.
+
+Compatibility
+-------------
+
+This gem is compatible with Ruby versions higher or equal to 2.1.0
+
+Installation
+------------
+
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'gn_crossmap'
+```
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install gn_crossmap
+
+Usage
+-----
+
+### Input file format
+
+- Comma Separated File with names of fields in first row.
+- Columns can be separated by tab, comma or semicolon
+- At least some columns should have recognizable fields
+
+    taxonID kingdom phylum class order family genus species
+    subspecies variety form scientificNameAuthorship scientificName
+    taxonRank
+
+#### Simple Example
+
+    taxonID;scientificName
+    1;Macrobiotus echinogenitus subsp. areolatus Murray, 1907
+    ...
+
+#### Rank Example
+
+    taxonID;scientificName;taxonRank
+    1;Macrobiotus echinogenitus f. areolatus Murray, 1907;form
+    ...
+
+#### Family and Authorship Example
+
+    taxonID;family;scientificName;scientificNameAuthorship
+    1;Macrobiotidae;Macrobiotus echinogenitus subsp. areolatus;Murray, 1907
+    ...
+
+#### Fine-grained Example
+
+    TaxonId;kingdom;subkingdom;phylum;subphylum;superclass;class;subclass;cohort;superorder;order;suborder;infraorder;superfamily;family;subfamily;tribe;subtribe;genus;subgenus;section;species;subspecies;variety;form;ScientificNameAuthorship
+    1;Animalia;;Tardigrada;;;Eutardigrada;;;;Parachela;;;Macrobiotoidea;Macrobiotidae;;;;Macrobiotus;;;harmsworthi;obscurus;;;Dastych, 1985
+
+### Usage from command line
+
+    # to see help
+    $ crossmap --help
+
+    # to compare with default source (Catalogue of Life)
+    $ crossmap -i my_list.csv -o my_list_col.csv
+
+    # to compare with other source (Index Fungorum in this example)
+    $ crossmap -i my_list.csv -o my_list_if.csv -d 5
+
+### Usage as Ruby Library
+
+```ruby
+require "gn_crossmap"
+
+# If you want to change logger -- default Logging is to standard output
+GnCrossmap.logger = MyCustomLogger.new
+
+GnCrossmap.run("path/to/input.csv", "path/to/output.csv", 5)
+```
+
+Development
+-----------
+
+After checking out the repo, run `bin/setup` to install dependencies. Then, run
+`bin/console` for an interactive prompt that will allow you to experiment.
+
+To install this gem onto your local machine, run `bundle exec rake install`. To
+release a new version, update the version number in `version.rb`, and then run
+`bundle exec rake release` to create a git tag for the version, push git
+commits and tags, and push the `.gem` file to
+[rubygems.org][rubygems]
+
+Contributing
+------------
+
+1. Fork it ( https://github.com/[my-github-username]/gn_crossmap/fork )
+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 a new Pull Request
+
+Copyright
+---------
+
+Author -- [Dmitry Mozzherin][dimus]
+
+Copyright (c) 2015 [Marine Biological Laboratory][mbl].
+See [LICENSE][license] for details.
+
+[gem_badge]: https://badge.fury.io/rb/gn_crossmap.png
+[gem_link]: http://badge.fury.io/rb/gn_crossmap
+[ci_badge]: https://secure.travis-ci.org/GlobalNamesArchitecture/gn_crossmap.png
+[ci_link]: http://travis-ci.org/GlobalNamesArchitecture/gn_crossmap
+[cov_badge]: https://coveralls.io/repos/GlobalNamesArchitecture/gn_crossmap/badge.png?branch=master
+[cov_link]: https://coveralls.io/r/GlobalNamesArchitecture/gn_crossmap?branch=master
+[code_badge]: https://codeclimate.com/github/GlobalNamesArchitecture/gn_crossmap.png
+[code_link]: https://codeclimate.com/github/GlobalNamesArchitecture/gn_crossmap
+[dep_badge]: https://gemnasium.com/GlobalNamesArchitecture/gn_crossmap.png
+[dep_link]: https://gemnasium.com/GlobalNamesArchitecture/gn_crossmap
+[resolver]: http://resolver.globalnames.org
+[rubygems]: https://rubygems.org
+[dimus]: https://github.com/dimus
+[mbl]: http://mbl.edu
+[license]: https://github.com/GlobalNamesArchitecture/gn_crossmap/blob/master/LICENSE
+[terms]: http://rs.tdwg.org/dwc/terms

data/Rakefile

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+require "bundler/gem_tasks"
+require "rspec/core/rake_task"
+require "rubocop/rake_task"
+
+RSpec::Core::RakeTask.new(:rspec) do |rspec|
+  rspec.pattern = "spec/**/*_spec.rb"
+end
+
+RuboCop::RakeTask.new
+
+task default: [:rubocop, :rspec]

data/bin/console

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+#!/usr/bin/env ruby
+
+require "bundler/setup"
+require "gn_crossmap"
+
+# You can add fixtures and/or initialization code here to make experimenting
+# with your gem easier. You can also use a different console, if you like.
+
+# (If you use this, don't forget to add pry to your Gemfile!)
+# require "pry"
+# Pry.start
+
+require "irb"
+IRB.start

data/bin/setup

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+#!/bin/bash
+set -euo pipefail
+IFS=$'\n\t'
+
+bundle install
+
+# Do any other automated setup that you need to do here

data/exe/crossmap

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+#!/usr/bin/env ruby
+require "trollop"
+require "gn_crossmap"
+
+puts "This program requires Ruby >= v. 2.1.0" if RUBY_VERSION < "2.1.0"
+
+CATALOGUE_OF_LIFE = 1
+OUTPUT = "output.csv"
+opts = Trollop.options do
+  banner "Compares a list of scientific names to scientific names from a " \
+    "data source from Global Names Resolver\n\n " \
+    "Usage:\n  crossmap [options]\n\noptions:"
+
+  opt(:input, "Path to intput file", type: :string)
+  opt(:output, "Path to output file", default: OUTPUT)
+  opt(:data_source_id, "Data source id from GN Resolver",
+      default: CATALOGUE_OF_LIFE)
+end
+
+Trollop.die :input, "must be set" if opts[:input].nil?
+Trollop.die :input, "file must exist" unless File.exist?(opts[:input])
+
+GnCrossmap.run(opts[:input], opts[:output], opts[:data_source_id])

data/gn_crossmap.gemspec

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+# coding: utf-8
+lib = File.expand_path("../lib", __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require "gn_crossmap/version"
+
+Gem::Specification.new do |gem|
+  gem.name          = "gn_crossmap"
+  gem.version       = GnCrossmap::VERSION
+  gem.authors       = ["Dmitry Mozzherin"]
+  gem.email         = ["dmozzherin@gmail.com"]
+
+  gem.summary       = "Crossmaps a list of scientific names to names from " \
+                       "a data source in GN Index"
+  gem.description   = "User supplies a comma-separated file which breaks " \
+                       "contains in one row a hierarchy path of known ranks, " \
+                       "scientific name which can be split into its semantic " \
+                       "elements and include authorship and taxon concept " \
+                       "reference. User also supplies an id of a data source "\
+                       "from global names resolver/index. User gets back a " \
+                       "new comma-separated file where scientific names from " \
+                       "her list match data from the given data source."
+  gem.homepage      = "https://github.com/GlobalNamesArchitecture/gn_crossmap"
+
+  gem.files         = `git ls-files -z`.split("\x0").
+    reject { |f| f.match(%r{^(test|spec|features)/}) }
+  gem.bindir        = "exe"
+  gem.executables   = gem.files.grep(%r{^exe/}) { |f| File.basename(f) }
+  gem.require_paths = ["lib"]
+
+  gem.add_dependency "trollop", "~> 2.1"
+  gem.add_dependency "biodiversity", "~> 3.1"
+
+  gem.add_development_dependency "bundler", "~> 1.7"
+  gem.add_development_dependency "rake", "~> 10.0"
+  gem.add_development_dependency "rspec", "~> 3.2"
+  gem.add_development_dependency "rubocop", "~> 0.31"
+  gem.add_development_dependency "coveralls", "~> 0.8"
+  gem.add_development_dependency "byebug"
+end

data/lib/gn_crossmap.rb

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+require "csv"
+require "rest_client"
+require "logger"
+require "biodiversity"
+require "gn_crossmap/version"
+require "gn_crossmap/reader"
+require "gn_crossmap/writer"
+require "gn_crossmap/collector"
+require "gn_crossmap/column_collector"
+require "gn_crossmap/sci_name_collector"
+require "gn_crossmap/resolver"
+require "gn_crossmap/result_processor"
+
+# Namespace module for crossmapping checklists wth GN sources
+module GnCrossmap
+  class << self
+    attr_writer :logger
+
+    def run(input, output, data_source_id)
+      data = Reader.new(input).read
+      writer = Writer.new(output)
+      Resolver.new(writer, data_source_id).resolve(data)
+      output
+    end
+
+    def logger
+      @logger ||= Logger.new($stdout)
+    end
+
+    def log(message)
+      logger.info(message)
+    end
+  end
+end

data/lib/gn_crossmap/collector.rb

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+module GnCrossmap
+  # Assemble data from CSV reader by checking column fields
+  class Collector
+    RANKS = %i(kingdom subkingdom phylum subphylum superclass class
+               subclass cohort superorder order suborder infraorder superfamily
+               family subfamily tribe subtribe genus subgenus section species
+               subspecies variety form)
+    SPECIES_RANKS = %i(genus species subspecies variety form)
+
+    attr_reader :data
+
+    def initialize
+      @data = []
+      @fields = nil
+      @collector = nil
+    end
+
+    def process_row(row)
+      @row = row
+      @fields ? collect_data : init_fields_collector
+    end
+
+    private
+
+    def init_fields_collector
+      @fields = @row.map { |f| f.downcase.to_sym }
+      @collector = collector_factory
+    end
+
+    def collect_data
+      @row = @fields.zip(@row).to_h
+      data = @collector.id_name_rank(@row)
+      @data << data if data
+    end
+
+    def collector_factory
+      if @fields.include?(:scientificname)
+        SciNameCollector.new(@fields)
+      else
+        ColumnCollector.new(@fields)
+      end
+    end
+  end
+end

data/lib/gn_crossmap/column_collector.rb

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+module GnCrossmap
+  # Assemble data from CSV reader by checking column fields
+  class ColumnCollector
+    RANKS = %i(kingdom subkingdom phylum subphylum superclass class
+               subclass cohort superorder order suborder infraorder superfamily
+               family subfamily tribe subtribe genus subgenus section species
+               subspecies variety form)
+    SPECIES_RANKS = %i(genus species subspecies variety form)
+
+    attr_reader :data
+
+    def initialize(fields)
+      @fields = fields
+    end
+
+    def id_name_rank(row)
+      @row = row
+      id = @row[:taxonid]
+      return nil if id.to_s.strip == ""
+      rank = find_rank
+      return nil unless rank
+      name = assemble_name(rank)
+      return nil unless name
+      { id: id, name: name, rank: rank.to_s }
+    end
+
+    private
+
+    def find_rank
+      name_rank = nil
+      RANKS.reverse_each do  |rank|
+        next if @row[rank].to_s.strip == ""
+        name_rank = rank
+        break
+      end
+      name_rank
+    end
+
+    def assemble_name(name_rank)
+      name = @row[name_rank]
+      if SPECIES_RANKS[1..-1].include?(name_rank)
+        name = assemble_species_name(name, name_rank)
+      end
+      name
+    end
+
+    def assemble_species_name(name, name_rank)
+      ending = [add_infrarank(name, name_rank), @row[:scientificnameauthorship]]
+      ranks = SPECIES_RANKS[0...SPECIES_RANKS.index(name_rank)]
+      starting = name_start(ranks)
+      (starting + ending).flatten.join(" ").strip.gsub(/\s+/, " ")
+    end
+
+    def name_start(ranks)
+      ranks.each_with_object([]) do |rank, ary|
+        next unless @row[rank]
+        ary << add_infrarank(@row[rank], rank)
+      end
+    end
+
+    def add_infrarank(name, rank)
+      case rank
+      when :subspecies
+        "subsp. #{name}"
+      when :variety
+        "var. #{name}"
+      when :form
+        "f. #{name}"
+      else
+        name
+      end
+    end
+  end
+end

data/lib/gn_crossmap/reader.rb

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+module GnCrossmap
+  # Reads supplied csv file and creates ruby structure to compare
+  # with a Global Names Resolver source
+  class Reader
+    def initialize(csv_path)
+      @csv_file = csv_path
+      @col_sep = col_sep
+    end
+
+    def read
+      GnCrossmap.log("Read input file '#{File.basename(@csv_file)}'")
+      parse_input
+    end
+
+    private
+
+    def col_sep
+      line = open(@csv_file, &:readline)
+      [";", ",", "\t"].map { |s| [line.count(s), s] }.sort.last.last
+    end
+
+    def parse_input
+      dc = Collector.new
+      CSV.open(@csv_file, col_sep: @col_sep).each do |row|
+        dc.process_row(row)
+      end
+      dc.data
+    end
+  end
+end

data/lib/gn_crossmap/resolver.rb

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+module GnCrossmap
+  # Sends data to GN Resolver and collects results
+  class Resolver
+    URL = "http://resolver.globalnames.org/name_resolvers.json"
+
+    def initialize(writer, data_source_id)
+      @processor = GnCrossmap::ResultProcessor.new(writer)
+      @ds_id = data_source_id
+      @count = 0
+      @batch = 200
+    end
+
+    def resolve(data)
+      data_size = data.size
+      data.each_slice(@batch) do |slice|
+        with_log(data_size) do
+          names = collect_names(slice)
+          remote_resolve(names)
+        end
+      end
+      @processor.writer.close
+    end
+
+    private
+
+    def with_log(size)
+      s = @count + 1
+      @count += @batch
+      e = [@count, size].min
+      GnCrossmap.log("Resolve #{s}-#{e} out of #{size} records")
+      yield
+    end
+
+    def collect_names(slice)
+      slice.each_with_object("") do |row, str|
+        @processor.input[row[:id]] = { rank: row[:rank] }
+        str << "#{row[:id]}|#{row[:name]}\n"
+      end
+    end
+
+    def remote_resolve(names)
+      res = RestClient.post(URL, data: names, data_source_ids: @ds_id)
+      @processor.process(res)
+    rescue RestClient::Exception
+      single_remote_resolve(names)
+    end
+
+    def single_remote_resolve(names)
+      names.split("\n").each do |name|
+        begin
+          res = RestClient.post(URL, data: name, data_source_ids: @ds_id)
+          @processor.process(res)
+        rescue RestClient::Exception => e
+          GnCrossmap.log("Resolver broke on '#{name}': #{e}")
+          next
+        end
+      end
+    end
+  end
+end

data/lib/gn_crossmap/result_processor.rb

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+module GnCrossmap
+  # Processes data received from the GN Resolver
+  class ResultProcessor
+    MATCH_TYPES = {
+      1 => "Exact match",
+      2 => "Canonical form exact match",
+      3 => "Canonical form fuzzy match",
+      4 => "Partial canonical form match",
+      5 => "Partial canonical form fuzzy match",
+      6 => "Genus part match"
+    }
+
+    attr_reader :input, :writer
+
+    def initialize(writer)
+      @writer = writer
+      @input = {}
+    end
+
+    def process(result)
+      res = rubyfy(result)
+      res[:data].each do |d|
+        d[:results].nil? ? write_empty_result(d) : write_result(d)
+      end
+    end
+
+    private
+
+    def rubyfy(result)
+      JSON.parse(result, symbolize_names: true)
+    end
+
+    def write_empty_result(datum)
+      res = [datum[:supplied_id], datum[:supplied_name_string], nil, nil,
+             @input[datum[:supplied_id]][:rank], nil, nil, nil, nil]
+      @writer.write(res)
+    end
+
+    def write_result(datum)
+      datum[:results].each do |r|
+        res = [datum[:supplied_id], datum[:supplied_name_string],
+               r[:name_string], r[:canonical_form],
+               @input[datum[:supplied_id]][:rank],
+               matched_rank(r), matched_type(r),
+               r[:edit_distance], r[:score]]
+        @writer.write(res)
+      end
+    end
+
+    def matched_rank(record)
+      record[:classification_path_ranks].split("|").last
+    end
+
+    def matched_type(record)
+      MATCH_TYPES[record[:match_type]]
+    end
+  end
+end

data/lib/gn_crossmap/sci_name_collector.rb

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+module GnCrossmap
+  # Assemble data from CSV reader by parsing scientificName field
+  class SciNameCollector
+    def initialize(fields)
+      @fields = fields
+      @parser = ScientificNameParser.new
+    end
+
+    def id_name_rank(row)
+      @row = row
+      id = @row[:taxonid]
+      name = find_name
+      rank = @row[:taxonRank]
+      rank = parse_rank if rank.nil?
+      (id && name) ? { id: id, name: name, rank: rank } : nil
+    end
+
+    private
+
+    def find_name
+      name = @row[:scientificname].strip
+      authorship = @row[:scientificnameauthorship].to_s.strip
+      name = "#{name} #{authorship}" if authorship != ""
+      name
+    end
+
+    def parse_rank
+      @parsed_name = @parser.parse(@row[:scientificname])[:scientificName]
+      return nil if !@parsed_name[:canonical] || @parsed_name[:hybrid]
+      words_num = @parsed_name[:canonical].split(" ").size
+      infer_rank(words_num)
+    rescue RuntimeError
+      @parser = ScientificNameParser.new
+      nil
+    end
+
+    def infer_rank(words_in_canonical_form)
+      case words_in_canonical_form
+      when 1
+        nil
+      when 2
+        "species"
+      else
+        normalize_rank(@parsed_name[:details][0][:infraspecies][-1][:rank])
+      end
+    end
+
+    def normalize_rank(rank)
+      case rank
+      when /^f/
+        "form"
+      when /^var/
+        "variety"
+      when /^sub/
+        "subspicies"
+      else
+        rank
+      end
+    end
+  end
+end

data/lib/gn_crossmap/version.rb

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+# Namespace module for crossmapping checklists to GN sources
+module GnCrossmap
+  VERSION = "0.1.1"
+
+  def self.version
+    VERSION
+  end
+end

data/lib/gn_crossmap/writer.rb

@@ -0,0 +1,22 @@
+module GnCrossmap
+  # Saves output from GN Resolver to disk
+  class Writer
+    def initialize(output_path)
+      @path = output_path
+      @output = CSV.open(@path, "w:utf-8")
+      @output << [:taxonID, :scientificName, :matchedScientificName,
+                  :matchedCanonicalForm, :rank, :matchedRank, :matchType,
+                  :editDistance, :score]
+      GnCrossmap.log("Open output file '#{@path}'")
+    end
+
+    def write(record)
+      @output << record
+    end
+
+    def close
+      GnCrossmap.log("Close output file '#{@path}'")
+      @output.close
+    end
+  end
+end

metadata

@@ -0,0 +1,182 @@
+--- !ruby/object:Gem::Specification
+name: gn_crossmap
+version: !ruby/object:Gem::Version
+  version: 0.1.1
+platform: ruby
+authors:
+- Dmitry Mozzherin
+autorequire: 
+bindir: exe
+cert_chain: []
+date: 2015-05-11 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: trollop
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.1'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.1'
+- !ruby/object:Gem::Dependency
+  name: biodiversity
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.1'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.1'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.7'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.7'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.2'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.2'
+- !ruby/object:Gem::Dependency
+  name: rubocop
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.31'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.31'
+- !ruby/object:Gem::Dependency
+  name: coveralls
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.8'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.8'
+- !ruby/object:Gem::Dependency
+  name: byebug
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+description: User supplies a comma-separated file which breaks contains in one row
+  a hierarchy path of known ranks, scientific name which can be split into its semantic
+  elements and include authorship and taxon concept reference. User also supplies
+  an id of a data source from global names resolver/index. User gets back a new comma-separated
+  file where scientific names from her list match data from the given data source.
+email:
+- dmozzherin@gmail.com
+executables:
+- crossmap
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- ".rspec"
+- ".rubocop.yml"
+- ".travis.yml"
+- CHANGELOG.md
+- Gemfile
+- LICENSE
+- README.md
+- Rakefile
+- bin/console
+- bin/setup
+- exe/crossmap
+- gn_crossmap.gemspec
+- lib/gn_crossmap.rb
+- lib/gn_crossmap/collector.rb
+- lib/gn_crossmap/column_collector.rb
+- lib/gn_crossmap/reader.rb
+- lib/gn_crossmap/resolver.rb
+- lib/gn_crossmap/result_processor.rb
+- lib/gn_crossmap/sci_name_collector.rb
+- lib/gn_crossmap/version.rb
+- lib/gn_crossmap/writer.rb
+homepage: https://github.com/GlobalNamesArchitecture/gn_crossmap
+licenses: []
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.2.3
+signing_key: 
+specification_version: 4
+summary: Crossmaps a list of scientific names to names from a data source in GN Index
+test_files: []