biodiversity 3.5.1 → 4.0.0

data/lib/biodiversity/version.rb

@@ -1,3 +1,10 @@
+# frozen_string_literal: true
+
+# Biodiversity module provides a namespace for scientific name parser.
 module Biodiversity
-  VERSION = "3.5.1"
+  VERSION = '4.0.0'
+
+  def self.version
+    VERSION
+  end
 end

data/spec/lib/biodiversity_spec.rb

@@ -0,0 +1,9 @@
+# frozen_string_literal: true
+
+describe Biodiversity do
+  describe 'version' do
+    it 'returns version of Biodiversity gem' do
+      expect(subject.version).to match(/\d+\.\d+\.\d+/)
+    end
+  end
+end

data/spec/lib/parser_spec.rb

@@ -0,0 +1,38 @@
+# frozen_string_literal: true
+
+# s frozen_string_literal: true
+
+describe Biodiversity::Parser do
+  describe('parse') do
+    it 'parses name in simple format' do
+      parsed = subject.parse('Homo sapiens Linn.', true)
+      expect(parsed[:canonicalName][:simple]).to eq 'Homo sapiens'
+      expect(parsed[:normalized]).to be_nil
+    end
+
+    it 'parsed name in full format' do
+      parsed = subject.parse('Homo sapiens  Linn.')
+      expect(parsed[:canonicalName][:simple]).to eq 'Homo sapiens'
+      expect(parsed[:normalized]).to eq 'Homo sapiens Linn.'
+    end
+  end
+
+  describe('parse_ary') do
+    it 'parses names in simple format' do
+      parsed = subject.parse_ary(['Homo sapiens Linn.', 'Pardosa moesta'], true)
+      expect(parsed[0][:canonicalName][:simple]).to eq 'Homo sapiens'
+      expect(parsed[1][:canonicalName][:simple]).to eq 'Pardosa moesta'
+      expect(parsed[0][:normalized]).to be_nil
+    end
+
+    it 'parsed name in full format' do
+      parsed = subject.parse_ary(
+        ['Homo sapiens  Linn.', 'Tobacco Mosaic Virus']
+      )
+      expect(parsed[0][:canonicalName][:simple]).to eq 'Homo sapiens'
+      expect(parsed[0][:normalized]).to eq 'Homo sapiens Linn.'
+      expect(parsed[1][:parsed]).to be false
+      expect(parsed[1][:virus]).to be true
+    end
+  end
+end

data/spec/spec_helper.rb

@@ -1,82 +1,5 @@
-require "yaml"
-require "treetop"
-require "json"
-require "biodiversity"
-require "webmock/rspec"
-
-
-RSpec.configure do |c|
-  c.mock_with :rr
-end
-
-dir = File.dirname(__FILE__)
-Treetop.load(File.expand_path(File.join(dir,
-             "../lib/biodiversity/parser/scientific_name_clean")))
-Treetop.load(File.expand_path(File.join(dir,
-             "../lib/biodiversity/parser/scientific_name_dirty")))
-Treetop.load(File.expand_path(File.join(dir,
-             "../lib/biodiversity/parser/scientific_name_canonical")))
-
-PARSER_TEST_VERSION = "test_version"
-
-def set_parser(parser)
-  @parser = parser
-end
-
-def parse(input)
-  @parser.parse(input)
-end
-
-def value(input)
-  parse(input).value
-end
-
-def canonical(input)
-  parse(input).canonical
-end
-
-def details(input)
-  parse(input).details
-end
-
-def pos(input)
-  parse(input).pos
-end
-
-def json(input)
-  parse(input).
-    to_json.gsub(/"parser_version":"[^"]*"/,
-                 %Q["parser_version":"#{PARSER_TEST_VERSION}"])
-end
-
-def debug(input)
-  res = parse(input)
-  puts "<pre>"
-    if res
-      puts "success!"
-      puts res.inspect
-    else
-      puts input
-      val = @parser.failure_reason.to_s.match(/column [0-9]*/).
-        to_s.gsub(/column /, "").to_i
-      print ("-" * (val - 1))
-      print "^   Computer says 'ni'!\n"
-      puts @parser.failure_reason
-      puts @parser.to_yaml
-    end
-  puts "</pre>"
-end
-
-def read_test_file
-  f = open(File.expand_path("../files/test_data.txt", __FILE__))
-  f.each do |line|
-    name, jsn = line.split("|")
-    if line.match(/^\s*#/) == nil && name && jsn
-      yield({ name: name, jsn: jsn })
-    else
-      yield({ comment: line })
-    end
-  end
-end
-
+# frozen_string_literal: true
 
+require 'rspec'
+require 'json'
+require 'biodiversity'

metadata

@@ -1,165 +1,105 @@
 --- !ruby/object:Gem::Specification
 name: biodiversity
 version: !ruby/object:Gem::Version
-  version: 3.5.1
+  version: 4.0.0
 platform: ruby
 authors:
 - Dmitry Mozzherin
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-09-14 00:00:00.000000000 Z
+date: 2019-11-18 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
-  name: treetop
+  name: ffi
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.6'
+        version: '1.11'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.6'
-- !ruby/object:Gem::Dependency
-  name: parallel
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '1.12'
-  type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '1.12'
-- !ruby/object:Gem::Dependency
-  name: unicode_utils
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '1.4'
-  type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '1.4'
-- !ruby/object:Gem::Dependency
-  name: gn_uuid
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '0.5'
-  type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '0.5'
+        version: '1.11'
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.16'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '1.16'
-- !ruby/object:Gem::Dependency
-  name: rake
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '12.3'
+        version: '2.0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '12.3'
+        version: '2.0'
 - !ruby/object:Gem::Dependency
-  name: rspec
+  name: byebug
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.7'
+        version: '11.0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.7'
+        version: '11.0'
 - !ruby/object:Gem::Dependency
-  name: webmock
+  name: rake
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.3'
+        version: '13.0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.3'
+        version: '13.0'
 - !ruby/object:Gem::Dependency
-  name: rr
+  name: rspec
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.2'
+        version: '3.9'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.2'
+        version: '3.9'
 - !ruby/object:Gem::Dependency
   name: rubocop
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.52'
+        version: '0.76'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.52'
-description: Tools for biodiversity informatics
+        version: '0.76'
+description: Parsing tool for biodiversity informatics
 email: dmozzherin@gmail.com
-executables:
-- nnparse
-- parserver
+executables: []
 extensions: []
 extra_rdoc_files: []
 files:
-- ".byebug_history"
-- ".document"
 - ".gitignore"
 - ".rspec"
 - ".rubocop.yml"
@@ -170,31 +110,16 @@ files:
 - LICENSE
 - README.md
 - Rakefile
-- bin/nnparse
-- bin/parserver
 - biodiversity.gemspec
-- examples/socket_client.rb
+- clib/linux/libgnparser.h
+- clib/linux/libgnparser.so
+- clib/mac/libgnparser.h
+- clib/mac/libgnparser.so
 - lib/biodiversity.rb
-- lib/biodiversity/guid.rb
-- lib/biodiversity/guid/lsid.rb
 - lib/biodiversity/parser.rb
-- lib/biodiversity/parser/scientific_name_canonical.rb
-- lib/biodiversity/parser/scientific_name_canonical.treetop
-- lib/biodiversity/parser/scientific_name_clean.rb
-- lib/biodiversity/parser/scientific_name_clean.treetop
-- lib/biodiversity/parser/scientific_name_dirty.rb
-- lib/biodiversity/parser/scientific_name_dirty.treetop
 - lib/biodiversity/version.rb
-- pkg/.gitkeep
-- spec/biodiversity_spec.rb
-- spec/files/lsid.xml
-- spec/files/test_data.txt
-- spec/files/todo.txt
-- spec/guid/lsid.spec.rb
-- spec/parser/scientific_name_canonical_spec.rb
-- spec/parser/scientific_name_clean_spec.rb
-- spec/parser/scientific_name_dirty_spec.rb
-- spec/parser/scientific_name_spec.rb
+- spec/lib/biodiversity_spec.rb
+- spec/lib/parser_spec.rb
 - spec/spec_helper.rb
 homepage: https://github.com/GlobalNamesArchitecture/biodiversity
 licenses:
@@ -216,7 +141,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.6.14.1
+rubygems_version: 2.7.6.2
 signing_key: 
 specification_version: 4
 summary: Parser of scientific names

data/.byebug_history

@@ -1,18 +0,0 @@
-q
-res[:scientificName][:tail]
-res[:scientificName]
-q
-res[:tail]
-res[:scientificName][:tail]
-res[:scientificName]
-res
-c
-q
-res
-q
-res
-q
-@ss
-@2tt
-@tail
-res

data/.document

@@ -1,5 +0,0 @@
-README.rdoc
-lib/**/*.rb
-bin/*
-features/**/*.feature
-LICENSE

data/examples/socket_client.rb

@@ -1,25 +0,0 @@
-#!/usr/bin/env ruby
-require 'socket'
-
-host = 'localhost'
-port = 4334
-
-f = open('10000_names.txt')
-w = open('output.txt', 'w')
-s = TCPSocket.open(host, port)
-
-f.each_with_index do |line, i|
-  puts i if i % 1000 == 0
-  line = line.strip
-  s.puts(line.strip)
-  res = s.gets
-  if res && res.split(" ").size > 3
-    res = res.strip
-    w.write(line + "\n")
-    w.write(res + "\n")
-    w.write("\n")
-  end
-end
-
-s.close
-

data/lib/biodiversity/guid.rb

@@ -1 +0,0 @@
-require_relative 'guid/lsid'

data/lib/biodiversity/guid/lsid.rb

@@ -1,16 +0,0 @@
-class LsidResolver
-  def self.resolve(lsid)
-    http_get_rdf(lsid)
-  end
-  
-protected
-  def self.http_get_rdf(lsid)
-    rdf = ''
-    open(Biodiversity::LSID_RESOLVER_URL + lsid) do |f|
-      f.each do |line|
-        rdf += line if !line.strip.blank?
-      end
-    end
-    rdf
-  end
-end