biodiversity 5.3.0 → 5.3.4

checksums.yaml

@@ -1,7 +1,7 @@
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data/.rubocop.yml

@@ -14,6 +14,10 @@ Metrics/MethodLength:
 Metrics/BlockLength:
   Exclude:
     - spec/**/*
+Metrics/CyclomaticComplexity:
+  Enabled: false
+Metrics/PerceivedComplexity:
+  Enabled: false
 Style/HashEachMethods:
   Enabled: true
 Style/HashTransformKeys:

data/.ruby-version

@@ -1 +1 @@
-3.0.1
+3.0.2

data/README.md

@@ -1,6 +1,6 @@
 # Biodiversity
 
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3569596.svg)](https://doi.org/10.5281/zenodo.3569596)
+[![DOI](https://zenodo.org/badge/764046.svg)](https://zenodo.org/badge/latestdoi/764046)
 [![Gem Version][gem_svg]][gem_link]
 [![Continuous Integration Status][ci_svg]][ci_link]
 

data/biodiversity.gemspec

@@ -25,4 +25,5 @@ Gem::Specification.new do |gem|
   gem.add_development_dependency 'rake', '~> 13.0'
   gem.add_development_dependency 'rspec', '~> 3.10'
   gem.add_development_dependency 'rubocop', '~> 1.8'
+  gem.add_development_dependency 'solargraph', '~> 0.43'
 end

data/lib/biodiversity/parser.rb

@@ -57,11 +57,14 @@ module Biodiversity
                                  with_details, with_cultivars)
       free_mem(ptr)
       if simple
-        CSV.new(parsed).map do |row|
+        CSV.new(parsed.force_encoding('UTF-8')).map do |row|
           csv_row(row)
         end
       else
-        JSON.parse(parsed, symbolize_names: true)
+        JSON.parse(parsed, symbolize_names: true).map do |item|
+          item[:parserVersion] = Biodiversity.gnparser_version
+          item
+        end
       end
     end
 

data/lib/biodiversity/version.rb

@@ -2,8 +2,8 @@
 
 # Biodiversity module provides a namespace for scientific name parser.
 module Biodiversity
-  VERSION = '5.3.0'
-  GNPARSER_VERSION = 'GNparser 1.3.0+'
+  VERSION = '5.3.4'
+  GNPARSER_VERSION = 'GNparser 1.4.2'
 
   def self.version
     VERSION

data/spec/lib/parser_spec.rb

@@ -49,18 +49,25 @@ describe Biodiversity::Parser do
   describe('parse_ary') do
     it 'parses names in simple format' do
       parsed = subject.parse_ary(
-        ['Homo sapiens Linn.', 'Pardosa moesta'],
-        simple: true
+        ['Homo sapiens Linn.', 'Pardosa moesta', 'Aus bus "White Russian"'],
+        simple: true, with_cultivars: true
       )
       expect(parsed[0][:canonical][:simple]).to eq 'Homo sapiens'
       expect(parsed[0][:normalized]).to be_nil
 
       expect(parsed[1][:canonical][:simple]).to eq 'Pardosa moesta'
+      expect(parsed[2][:canonical][:simple]).to eq 'Aus bus ‘White Russian’'
+      expect(parsed[2][:quality]).to eq 1
     end
 
     it 'parsed name in full format' do
       parsed = subject.parse_ary(
-        ['Homo sapiens  Linn.', 'Tobacco Mosaic Virus']
+        [
+          'Homo sapiens  Linn.',
+          'Tobacco Mosaic Virus',
+          "Aus bus 'White Russian'"
+        ],
+        with_cultivars: true
       )
       expect(parsed[0][:canonical][:simple]).to eq 'Homo sapiens'
       expect(parsed[0][:normalized]).to eq 'Homo sapiens Linn.'
@@ -68,6 +75,9 @@ describe Biodiversity::Parser do
       expect(parsed[1][:parsed]).to be false
       expect(parsed[1][:virus]).to be true
       expect(parsed[1][:words]).to be_nil
+      expect(parsed[2][:canonical][:simple]).to eq 'Aus bus ‘White Russian’'
+      expect(parsed[2][:quality]).to eq 1
+      expect(parsed[2][:parserVersion]).to match(/GNparser/)
     end
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: biodiversity
 version: !ruby/object:Gem::Version
-  version: 5.3.0
+  version: 5.3.4
 platform: ruby
 authors:
 - Dmitry Mozzherin
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2021-07-03 00:00:00.000000000 Z
+date: 2021-10-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ffi
@@ -94,6 +94,20 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '1.8'
+- !ruby/object:Gem::Dependency
+  name: solargraph
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.43'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.43'
 description: Parsing tool for biodiversity informatics
 email: dmozzherin@gmail.com
 executables: []
@@ -142,7 +156,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.2.15
+rubygems_version: 3.2.22
 signing_key:
 specification_version: 4
 summary: Parser of scientific names