dimus-biodiversity 0.0.12 → 0.0.13
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- data/Rakefile +3 -1
- data/bin/nnparse +2 -1
- data/lib/biodiversity/parser.rb +19 -1
- data/lib/biodiversity/parser/scientific_name_canonical.rb +214 -0
- data/lib/biodiversity/parser/scientific_name_canonical.treetop +40 -0
- data/lib/biodiversity/parser/{scientific_name.rb → scientific_name_clean.rb} +1432 -369
- data/lib/biodiversity/parser/{scientific_name.treetop → scientific_name_clean.treetop} +197 -18
- data/lib/biodiversity/parser/scientific_name_dirty.rb +473 -0
- data/lib/biodiversity/parser/scientific_name_dirty.treetop +80 -0
- data/spec/parser/scientific_name.spec.rb +14 -252
- data/spec/parser/scientific_name_canonical.spec.rb +43 -0
- data/spec/parser/scientific_name_clean.spec.rb +393 -0
- data/spec/parser/scientific_name_dirty.spec.rb +90 -0
- metadata +10 -3
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grammar ScientificNameDirty
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include ScientificNameClean
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rule composite_scientific_name
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super
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end
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# rule original_authors_names_full
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# super
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# end
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#
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# rule incorrect_original_authors_names
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# "[" space a:authors_names_full space "]" {
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# def value
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# "(" + a.value + ")"
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# end
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# def details
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# {:orig_authors => a.details[:authors]}
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# end
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# }
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# end
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rule year
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a:[\d]+ space b:approximate_year {
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def value
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a.text_value + " " + b.text_value
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end
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def details
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{:ambiguous_year => value}
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end
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}
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/
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a:[\d]+ page_number
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{
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def value
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a.text_value
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end
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def details
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{:year => value}
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end
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}
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/
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double_year
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/
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approximate_year
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/
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super
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end
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rule approximate_year
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"[" space a:([\d] [\d] [\d] [\d\?]+) space "]"+ {
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def value
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"(" + a.text_value + ")"
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end
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def details
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{:approximate_year => value}
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end
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}
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end
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rule double_year
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[0-9] [0-9A-Za-z\?\-]+ {
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def value
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text_value
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end
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def details
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{:year => value}
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end
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}
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end
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rule page_number
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":" space [\d]+
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{
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def value
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end
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}
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end
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end
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@@ -1,12 +1,13 @@
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# encoding: UTF-8
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dir = File.dirname("__FILE__")
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require 'rubygems'
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require 'spec'
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require 'treetop'
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require 'yaml'
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-
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#NOTE: this spec needs compiled treetop files.
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dir = File.dirname("__FILE__")
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require File.expand_path(dir + '../../lib/biodiversity/parser')
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describe
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describe ScientificNameClean do
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before(:all) do
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@parser = ScientificNameParser.new
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end
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@@ -27,263 +28,24 @@ describe ScientificName do
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parse(input).details
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end
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it 'should parse
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sn = 'Pseudocercospora'
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parse(sn).should_not be_nil
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value(sn).should == 'Pseudocercospora'
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canonical(sn).should == 'Pseudocercospora'
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details(sn).should == {:uninomial=>"Pseudocercospora"}
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end
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-
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it 'should parse canonical' do
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it 'should parse accurate name' do
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sn = 'Pseudocercospora dendrobii'
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parse(sn).should_not be_nil
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value(sn).should == 'Pseudocercospora dendrobii'
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canonical(sn).should == 'Pseudocercospora dendrobii'
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details(sn).should == {:species=>"dendrobii", :genus=>"Pseudocercospora"}
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canonical('Quoyula').should == 'Quoyula'
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parse('Perissandra laotica').should_not be_nil
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end
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it 'should parse
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parse(sn).should_not be_nil
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value(sn).should == "Doriteuthis (Amerigo) pealeii Author 1999"
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canonical(sn).should == "Doriteuthis pealeii"
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details(sn).should == {:subgenus=>"Amerigo", :authors=>{:year=>"1999", :names=>["Author"]}, :species=>"pealeii", :genus=>"Doriteuthis"}
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end
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-
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it 'should parse æ in the name' do
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names = [
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["Læptura laetifica Dow, 1913", "Laeptura laetifica Dow 1913"],
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["Leptura lætifica Dow, 1913", "Leptura laetifica Dow 1913"],
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["Leptura leætifica Dow, 1913", "Leptura leaetifica Dow 1913"],
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["Leæptura laetifica Dow, 1913", "Leaeptura laetifica Dow 1913"],
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["Leœptura laetifica Dow, 1913", "Leoeptura laetifica Dow 1913"]
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]
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names.each do |name_pair|
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parse(name_pair[0]).should_not be_nil
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value(name_pair[0]).should == name_pair[1]
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end
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end
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-
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it 'should parse year' do
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sn = "Platypus bicaudatulus Schedl 1935"
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parse(sn).should_not be_nil
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value(sn).should == "Platypus bicaudatulus Schedl 1935"
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sn = "Platypus bicaudatulus Schedl, 1935h"
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parse(sn).should_not be_nil
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value(sn).should == "Platypus bicaudatulus Schedl 1935"
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details(sn).should == {:genus=>"Platypus", :species=>"bicaudatulus", :authors=>{:names=>["Schedl"], :year=>"1935"}}
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parse("Platypus bicaudatulus Schedl, 1935B").should_not be_nil
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end
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it 'should parse species autonym for complex subspecies authorships' do
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parse("Aus bus Linn. var. bus").should_not be_nil
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details("Aus bus Linn. var. bus").should == {:species=>"bus", :species_authors=>{:authors=>{:names=>["Linn."]}}, :genus=>"Aus", :subspecies=>[{:rank=>"var.", :value=>"bus"}]}
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parse("Agalinis purpurea (L.) Briton var. borealis (Berg.) Peterson 1987").should_not be_nil
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details("Agalinis purpurea (L.) Briton var. borealis (Berg.) Peterson 1987").should == {:species=>"purpurea", :genus=>"Agalinis", :species_authors=>{:orig_authors=>{:names=>["L."]}, :authors=>{:names=>["Briton"]}}, :subspecies_authors=>{:orig_authors=>{:names=>["Berg."]}, :authors=>{:year=>"1987", :names=>["Peterson"]}}, :subspecies=>[{:value=>"borealis", :rank=>"var."}]}
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end
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it 'should parse several authors' do
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sn = "Pseudocercospora dendrobii U. Braun & Crous"
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parse(sn).should_not be_nil
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value(sn).should == "Pseudocercospora dendrobii U. Braun et Crous"
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canonical(sn).should == "Pseudocercospora dendrobii"
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details(sn).should == {
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:authors=>{:names=>["U. Braun","Crous"]},
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:species=>"dendrobii",
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:genus=>"Pseudocercospora"}
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sn = "Pseudocercospora dendrobii U. Braun and Crous"
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parse(sn).should_not be_nil
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value(sn).should == "Pseudocercospora dendrobii U. Braun et Crous"
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sn = "Pseudocercospora dendrobii U. Braun et Crous"
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parse(sn).should_not be_nil
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value(sn).should == "Pseudocercospora dendrobii U. Braun et Crous"
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end
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it 'should parse several authors with a year' do
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sn = "Pseudocercospora dendrobii U. Braun & Crous 2003"
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parse(sn).should_not be_nil
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value(sn).should == "Pseudocercospora dendrobii U. Braun et Crous 2003"
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canonical(sn).should == "Pseudocercospora dendrobii"
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details(sn).should == {
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:authors=>{:names=>["U. Braun","Crous"], :year => "2003"},
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:species=>"dendrobii",
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:genus=>"Pseudocercospora"}
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sn = "Pseudocercospora dendrobii Crous, 2003"
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parse(sn).should_not be_nil
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parse("Zophosis persis (Chatanay, 1914)").should_not be_nil
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parse("Zophosis persis (Chatanay 1914)").should_not be_nil
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parse("Zophosis persis (Chatanay), 1914").should_not be_nil
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value("Zophosis persis (Chatanay), 1914").should == "Zophosis persis (Chatanay 1914)"
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details("Zophosis persis (Chatanay), 1914").should == {:genus=>"Zophosis", :species=>"persis", :orig_authors=>{:names=>["Chatanay"]}, :year=>"1914"}
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parse("Zophosis persis (Chatanay) 1914").should_not be_nil
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#parse("Zophosis persis Chatanay (1914)").should_not be_nil
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end
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it 'should parse scientific name' do
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parse("Pseudocercospora dendrobii (H.C. Burnett) U. Braun & Crous 2003").should_not be_nil
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value("Pseudocercospora dendrobii(H.C. Burnett)U. Braun & Crous 2003").should == "Pseudocercospora dendrobii (H.C. Burnett) U. Braun et Crous 2003"
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canonical("Pseudocercospora dendrobii(H.C. Burnett)U. Braun & Crous 2003").should == "Pseudocercospora dendrobii"
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{:orig_authors=>{:names=>["H.C. Burnett"]}, :species=>"dendrobii", :authors=>{:year=>"2003", :names=>["U. Braun", "Crous"]}, :genus=>"Pseudocercospora"}
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parse("Stagonospora polyspora M.T. Lucas & Sousa da Câmara 1934").should_not be_nil
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value("Stagonospora polyspora M.T. Lucas & Sousa da Câmara 1934").should == "Stagonospora polyspora M.T. Lucas et Sousa da Câmara 1934"
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details("Stagonospora polyspora M.T. Lucas & Sousa da Câmara 1934").should == {:authors=>{:year=>"1934", :names=>["M.T. Lucas", "Sousa da C\303\242mara"]}, :species=>"polyspora", :genus=>"Stagonospora"}
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parse("Cladoniicola staurospora Diederich, van den Boom & Aptroot 2001").should_not be_nil
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parse("Yarrowia lipolytica var. lipolytica (Wick., Kurtzman & E.A. Herrm.) Van der Walt & Arx 1981").should_not be_nil
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value("Yarrowia lipolytica var. lipolytica (Wick., Kurtzman & E.A. Herrm.) Van der Walt & Arx 1981").should == "Yarrowia lipolytica var. lipolytica (Wick., Kurtzman et E.A. Herrm.) Van der Walt et Arx 1981"
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parse("Physalospora rubiginosa (Fr.) anon.").should_not be_nil
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parse("Pleurotus ëous (Berk.) Sacc. 1887").should_not be_nil
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parse("Lecanora wetmorei Śliwa 2004").should_not be_nil
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# valid
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# infraspecific
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parse("Calicium furfuraceum * furfuraceum (L.) Pers. 1797").should_not be_nil
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parse("Exobasidium vaccinii ** andromedae (P. Karst.) P. Karst. 1882").should_not be_nil
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parse("Urceolaria scruposa **** clausa Flot. 1849").should_not be_nil
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parse("Cortinarius angulatus B gracilescens Fr. 1838").should_not be_nil
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parse("Cyathicula scelobelonium").should_not be_nil
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# single quote that did not show
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# parse("Phytophthora hedraiandra De Cock & Man in ?t Veld 2004"
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# Phthora vastatrix d?Hérelle 1909
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# author is exception
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parse("Tuber liui A S. Xu 1999").should_not be_nil
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parse("Agaricus squamula Berk. & M.A. Curtis 1860").should_not be_nil
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parse("Peltula coriacea Büdel, Henssen & Wessels 1986").should_not be_nil
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#had to add no dot rule for trinomials without a rank to make it to work
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parse("Saccharomyces drosophilae anon.").should_not be_nil
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details("Saccharomyces drosophilae anon.").should == {:genus=>"Saccharomyces", :species=>"drosophilae", :authors=>{:names=>["anon."]}}
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end
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-
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it 'should parse several authors with several years' do
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parse("Pseudocercospora dendrobii (H.C. Burnett 1883) U. Braun & Crous 2003").should_not be_nil
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value("Pseudocercospora dendrobii(H.C. Burnett1883)U. Braun & Crous 2003").should == "Pseudocercospora dendrobii (H.C. Burnett 1883) U. Braun et Crous 2003"
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canonical("Pseudocercospora dendrobii(H.C. Burnett 1883)U. Braun & Crous 2003").should == "Pseudocercospora dendrobii"
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details("Pseudocercospora dendrobii(H.C. Burnett 1883)U. Braun & Crous 2003").should == {:orig_authors=>{:year=>"1883", :names=>["H.C. Burnett"]}, :species=>"dendrobii", :authors=>{:year=>"2003", :names=>["U. Braun", "Crous"]}, :genus=>"Pseudocercospora"}
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end
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-
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it 'should not parse serveral authors groups with several years NOT CORRECT' do
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parse("Pseudocercospora dendrobii (H.C. Burnett 1883) (Leight.) (Movss. 1967) U. Braun & Crous 2003").should be_nil
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end
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-
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-
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it 'should parse utf-8 name' do
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parse("Trematosphaeria phaeospora (E. Müll.) L. Holm 1957").should_not be_nil
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value("Trematosphaeria phaeospora ( E. Müll. )L. Holm 1957").should == "Trematosphaeria phaeospora (E. Müll.) L. Holm 1957"
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canonical("Trematosphaeria phaeospora(E. Müll.) L. Holm 1957").should == "Trematosphaeria phaeospora"
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details("Trematosphaeria phaeospora(E. Müll.) L. Holm 1957 ").should == {:orig_authors=>{:names=>["E. M\303\274ll."]}, :species=>"phaeospora", :authors=>{:year=>"1957", :names=>["L. Holm"]}, :genus=>"Trematosphaeria"}
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end
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-
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it "should parse name with f." do
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parse("Sphaerotheca fuliginea f. dahliae Movss. 1967").should_not be_nil
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value(" Sphaerotheca fuliginea f. dahliae Movss. 1967 ").should == "Sphaerotheca fuliginea f. dahliae Movss. 1967"
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canonical("Sphaerotheca fuliginea f. dahliae Movss. 1967").should == "Sphaerotheca fuliginea dahliae"
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details("Sphaerotheca fuliginea f. dahliae Movss. 1967").should == {:subspecies=>[{:rank=>"f.", :value=>"dahliae"}], :authors=>{:year=>"1967", :names=>["Movss."]}, :species=>"fuliginea", :genus=>"Sphaerotheca"}
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-
end
|
|
184
|
-
|
|
185
|
-
it "should parse name with var." do
|
|
186
|
-
parse("Phaeographis inusta var. macularis (Leight.) A.L. Sm. 1861").should_not be_nil
|
|
187
|
-
value("Phaeographis inusta var. macularis(Leight.) A.L. Sm. 1861").should == "Phaeographis inusta var. macularis (Leight.) A.L. Sm. 1861"
|
|
188
|
-
canonical("Phaeographis inusta var. macularis(Leight.) A.L. Sm. 1861").should == "Phaeographis inusta macularis"
|
|
189
|
-
end
|
|
190
|
-
|
|
191
|
-
it "should parse name with several subspecies names NOT BOTANICAL CODE BUT NOT INFREQUENT" do
|
|
192
|
-
parse("Hydnellum scrobiculatum var. zonatum f. parvum (Banker) D. Hall & D.E. Stuntz 1972").should_not be_nil
|
|
193
|
-
value("Hydnellum scrobiculatum var. zonatum f. parvum (Banker) D. Hall & D.E. Stuntz 1972").should == "Hydnellum scrobiculatum var. zonatum f. parvum (Banker) D. Hall et D.E. Stuntz 1972"
|
|
194
|
-
details("Hydnellum scrobiculatum var. zonatum f. parvum (Banker) D. Hall & D.E. Stuntz 1972").should == {:orig_authors=>{:names=>["Banker"]}, :subspecies=>[{:rank=>"var.", :value=>"zonatum"}, {:rank=>"f.", :value=>"parvum"}], :species=>"scrobiculatum", :authors=>{:year=>"1972", :names=>["D. Hall", "D.E. Stuntz"]}, :genus=>"Hydnellum", :is_valid=>false}
|
|
195
|
-
end
|
|
196
|
-
|
|
197
|
-
it "should parse status BOTANICAL RARE" do
|
|
198
|
-
#it is always latin abbrev often 2 words
|
|
199
|
-
parse("Arthopyrenia hyalospora (Nyl.) R.C. Harris comb. nov.").should_not be_nil
|
|
200
|
-
value("Arthopyrenia hyalospora (Nyl.) R.C. Harris comb. nov.").should == "Arthopyrenia hyalospora (Nyl.) R.C. Harris comb. nov."
|
|
201
|
-
canonical("Arthopyrenia hyalospora (Nyl.) R.C. Harris comb. nov.").should == "Arthopyrenia hyalospora"
|
|
202
|
-
details("Arthopyrenia hyalospora (Nyl.) R.C. Harris comb. nov.").should == {:status=>"comb. nov.", :orig_authors=>{:names=>["Nyl."]}, :species=>"hyalospora", :authors=>{:names=>["R.C. Harris"]}, :genus=>"Arthopyrenia"}
|
|
203
|
-
end
|
|
204
|
-
|
|
205
|
-
it "should parse name without a year but with authors" do
|
|
206
|
-
parse("Arthopyrenia hyalospora (Nyl.) R.C. Harris").should_not be_nil
|
|
207
|
-
value("Arthopyrenia hyalospora(Nyl.)R.C. Harris").should == "Arthopyrenia hyalospora (Nyl.) R.C. Harris"
|
|
208
|
-
canonical("Arthopyrenia hyalospora (Nyl.) R.C. Harris").should == "Arthopyrenia hyalospora"
|
|
209
|
-
end
|
|
210
|
-
|
|
211
|
-
it "should parse revised (ex) names" do
|
|
212
|
-
#invalidly published
|
|
213
|
-
parse("Arthopyrenia hyalospora (Nyl. ex Banker) R.C. Harris").should_not be_nil
|
|
214
|
-
value("Arthopyrenia hyalospora (Nyl. ex Banker) R.C. Harris").should == "Arthopyrenia hyalospora (Nyl. ex Banker) R.C. Harris"
|
|
215
|
-
canonical("Arthopyrenia hyalospora (Nyl. ex Banker) R.C. Harris").should == "Arthopyrenia hyalospora"
|
|
216
|
-
details("Arthopyrenia hyalospora (Nyl. ex Banker) R.C. Harris").should == {:species=>"hyalospora", :authors=>{:names=>["R.C. Harris"]}, :genus=>"Arthopyrenia", :original_revised_name_authors=>{:authors=>{:names=>["Banker"]}, :revised_authors=>{:names=>["Nyl."]}}}
|
|
217
|
-
parse("Arthopyrenia hyalospora Nyl. ex Banker").should_not be_nil
|
|
218
|
-
|
|
219
|
-
parse("Glomopsis lonicerae Peck ex C.J. Gould 1945").should_not be_nil
|
|
220
|
-
details("Glomopsis lonicerae Peck ex C.J. Gould 1945").should == {:revised_name_authors=>{:authors=>{:year=>"1945", :names=>["C.J. Gould"]}, :revised_authors=>{:names=>["Peck"]}}, :species=>"lonicerae", :genus=>"Glomopsis"}
|
|
221
|
-
|
|
222
|
-
parse("Acanthobasidium delicatum (Wakef.) Oberw. ex Jülich 1979").should_not be_nil
|
|
223
|
-
parse("Mycosphaerella eryngii (Fr. ex Duby) Johanson ex Oudem. 1897").should_not be_nil
|
|
224
|
-
details("Mycosphaerella eryngii (Fr. ex Duby) Johanson ex Oudem. 1897").should == {:original_revised_name_authors=>{:authors=>{:names=>["Duby"]}, :revised_authors=>{:names=>["Fr."]}}, :species=>"eryngii", :genus=>"Mycosphaerella", :revised_name_authors=>{:authors=>{:year=>"1897", :names=>["Oudem."]}, :revised_authors=>{:names=>["Johanson"]}}}
|
|
225
|
-
#invalid but happens
|
|
226
|
-
parse("Mycosphaerella eryngii (Fr. Duby) ex Oudem. 1897").should_not be_nil
|
|
227
|
-
parse("Mycosphaerella eryngii (Fr.ex Duby) ex Oudem. 1897").should_not be_nil
|
|
228
|
-
parse("Salmonella werahensis (Castellani) Hauduroy and Ehringer in Hauduroy 1937").should_not be_nil
|
|
41
|
+
it 'should parse inaccurate name' do
|
|
42
|
+
parse("Tridentella tangeroae Bruce, 198?").should_not be_nil
|
|
229
43
|
end
|
|
230
44
|
|
|
231
|
-
it
|
|
232
|
-
parse("
|
|
233
|
-
|
|
234
|
-
parse("Arthopyrenia X hyalospora(Nyl. ex Banker) R.C. Harris").should_not be_nil
|
|
235
|
-
parse("x Arthopyrenia hyalospora (Nyl. ex Banker) R.C. Harris").should_not be_nil
|
|
236
|
-
details("x Arthopyrenia hyalospora (Nyl. ex Banker) R.C. Harris").should == {:original_revised_name_authors=>{:authors=>{:names=>["Banker"]}, :revised_authors=>{:names=>["Nyl."]}}, :species=>"hyalospora", :authors=>{:names=>["R.C. Harris"]}, :genus=>"Arthopyrenia", :cross=>"before"}
|
|
237
|
-
parse("X Arthopyrenia (Nyl. ex Banker) R.C. Harris").should_not be_nil
|
|
238
|
-
details("X Arthopyrenia (Nyl. ex Banker) R.C. Harris").should == {:uninomial=>"Arthopyrenia", :original_revised_name_authors=>{:authors=>{:names=>["Banker"]}, :revised_authors=>{:names=>["Nyl."]}}, :authors=>{:names=>["R.C. Harris"]}, :cross=>"before"}
|
|
239
|
-
#ascii for multiplication
|
|
240
|
-
parse("Melampsora × columbiana G. Newc. 2000").should_not be_nil
|
|
45
|
+
it 'should parse name that cannot be fully parsed' do
|
|
46
|
+
parse("Plantago major ESEFDSlj sdafsladjfasd fd ;asldfjasfas#&^&*^*^&}}").should_not be_nil
|
|
47
|
+
canonical('Plantago major ESEFDSlj sdafsladjfasd fd ;asldfjasfas#&^&*^*^&}}').should == 'Plantago major'
|
|
241
48
|
end
|
|
242
49
|
|
|
243
|
-
it "should parse hybrid combination" do
|
|
244
|
-
parse("Arthopyrenia hyalospora X Hydnellum scrobiculatum").should_not be_nil
|
|
245
|
-
value("Arthopyrenia hyalospora X Hydnellum scrobiculatum").should == "Arthopyrenia hyalospora \303\227 Hydnellum scrobiculatum"
|
|
246
|
-
canonical("Arthopyrenia hyalospora X Hydnellum scrobiculatum").should == "Arthopyrenia hyalospora \303\227 Hydnellum scrobiculatum"
|
|
247
|
-
details("Arthopyrenia hyalospora x Hydnellum scrobiculatum").should == {:hybrid=>{:scientific_name1=>{:species=>"hyalospora", :genus=>"Arthopyrenia"}, :scientific_name2=>{:species=>"scrobiculatum", :genus=>"Hydnellum"}}}
|
|
248
|
-
|
|
249
|
-
parse("Arthopyrenia hyalospora (Banker) D. Hall x Hydnellum scrobiculatum D.E. Stuntz").should_not be_nil
|
|
250
|
-
value("Arthopyrenia hyalospora (Banker) D. Hall X Hydnellum scrobiculatum D.E. Stuntz").should == "Arthopyrenia hyalospora (Banker) D. Hall \303\227 Hydnellum scrobiculatum D.E. Stuntz"
|
|
251
|
-
canonical("Arthopyrenia hyalospora (Banker) D. Hall X Hydnellum scrobiculatum D.E. Stuntz").should == "Arthopyrenia hyalospora \303\227 Hydnellum scrobiculatum"
|
|
252
50
|
|
|
253
|
-
|
|
254
|
-
value("Arthopyrenia hyalospora X").should == "Arthopyrenia hyalospora \303\227 ?"
|
|
255
|
-
canonical("Arthopyrenia hyalospora x").should == "Arthopyrenia hyalospora"
|
|
256
|
-
details("Arthopyrenia hyalospora x").should == {:hybrid=>{:scientific_name1=>{:species=>"hyalospora", :genus=>"Arthopyrenia"}, :scientific_name2=>"?"}}
|
|
257
|
-
parse("Arthopyrenia hyalospora × ?").should_not be_nil
|
|
258
|
-
details("Arthopyrenia hyalospora × ?").should == {:hybrid=>{:scientific_name1=>{:species=>"hyalospora", :genus=>"Arthopyrenia"}, :scientific_name2=>"?"}}
|
|
259
|
-
end
|
|
260
|
-
|
|
261
|
-
|
|
262
|
-
|
|
263
|
-
it "should parse name with subspecies without rank NOT BOTANICAL" do
|
|
264
|
-
name = "Hydnellum scrobiculatum zonatum (Banker) D. Hall & D.E. Stuntz 1972"
|
|
265
|
-
parse(name).should_not be_nil
|
|
266
|
-
value(name).should == "Hydnellum scrobiculatum zonatum (Banker) D. Hall et D.E. Stuntz 1972"
|
|
267
|
-
canonical(name).should == "Hydnellum scrobiculatum zonatum"
|
|
268
|
-
details(name).should == {:orig_authors=>{:names=>["Banker"]}, :subspecies=>{:rank=>"n/a", :value=>"zonatum"}, :species=>"scrobiculatum", :authors=>{:year=>"1972", :names=>["D. Hall", "D.E. Stuntz"]}, :genus=>"Hydnellum"}
|
|
269
|
-
sp = "Begonia pingbienensis angustior"
|
|
270
|
-
parse(sp).should_not be_nil
|
|
271
|
-
details(sp).should == {:genus=>"Begonia", :species=>"pingbienensis", :subspecies=>{:rank=>"n/a", :value=>"angustior"}}
|
|
272
|
-
end
|
|
273
|
-
|
|
274
|
-
it "should not parse utf-8 chars in name part" do
|
|
275
|
-
parse("Érematosphaeria phaespora").should be_nil
|
|
276
|
-
parse("Trematosphaeria phaeáapora").should be_nil
|
|
277
|
-
end
|
|
278
|
-
|
|
279
|
-
it "should parse some invalid names" do
|
|
280
|
-
parse("Acarospora cratericola 1929").should_not be_nil
|
|
281
|
-
parse("Agaricus acris var. (b.)").should_not be_nil
|
|
282
|
-
value("Agaricus acris var. (b.)").should == "Agaricus acris var. (b.)"
|
|
283
|
-
parse("Agaricus acris var. (b.)").should_not be_nil
|
|
284
|
-
value("Agaricus acris var. (b.&c.)").should == "Agaricus acris var. (b.c.)"
|
|
285
|
-
details("Agaricus acris var. (b.&c.)").should == {:editorial_markup=>"(b.c.)", :subspecies=>[{:rank=>"var.", :value=>nil}], :species=>"acris", :genus=>"Agaricus", :is_valid=>false}
|
|
286
|
-
|
|
287
|
-
end
|
|
288
|
-
|
|
289
|
-
end
|
|
51
|
+
end
|
|
@@ -0,0 +1,43 @@
|
|
|
1
|
+
dir = File.dirname("__FILE__")
|
|
2
|
+
require 'rubygems'
|
|
3
|
+
require 'spec'
|
|
4
|
+
require 'treetop'
|
|
5
|
+
require 'yaml'
|
|
6
|
+
|
|
7
|
+
Treetop.load(File.expand_path(dir + '../../lib/biodiversity/parser/scientific_name_clean'))
|
|
8
|
+
Treetop.load(File.expand_path(dir + '../../lib/biodiversity/parser/scientific_name_dirty'))
|
|
9
|
+
Treetop.load(File.expand_path(dir + '../../lib/biodiversity/parser/scientific_name_canonical'))
|
|
10
|
+
|
|
11
|
+
|
|
12
|
+
describe ScientificNameCanonical do
|
|
13
|
+
before(:all) do
|
|
14
|
+
@parser = ScientificNameCanonicalParser.new
|
|
15
|
+
end
|
|
16
|
+
|
|
17
|
+
def parse(input)
|
|
18
|
+
@parser.parse(input)
|
|
19
|
+
end
|
|
20
|
+
|
|
21
|
+
def value(input)
|
|
22
|
+
parse(input).value
|
|
23
|
+
end
|
|
24
|
+
|
|
25
|
+
def canonical(input)
|
|
26
|
+
parse(input).canonical
|
|
27
|
+
end
|
|
28
|
+
|
|
29
|
+
def details(input)
|
|
30
|
+
parse(input).details
|
|
31
|
+
end
|
|
32
|
+
|
|
33
|
+
it 'should parse names with valid name part and unparseable rest' do
|
|
34
|
+
[
|
|
35
|
+
['Moraea spathulata ( (L. f. Klatt','Moraea spathulata',{:genus=>"Moraea", :species=>"spathulata", :name_part_verbatim=>"Moraea spathulata", :auth_part_verbatim=>"( (L. f. Klatt"} ],
|
|
36
|
+
['Verpericola megasoma ""Dall" Pils.','Verpericola megasoma',{:genus=>"Verpericola", :species=>"megasoma", :name_part_verbatim=>"Verpericola megasoma", :auth_part_verbatim=>"\"\"Dall\" Pils."}]
|
|
37
|
+
].each do |n|
|
|
38
|
+
parse(n[0]).should_not be_nil
|
|
39
|
+
value(n[0]).should == n[1]
|
|
40
|
+
details(n[0]).should == n[2]
|
|
41
|
+
end
|
|
42
|
+
end
|
|
43
|
+
end
|
|
@@ -0,0 +1,393 @@
|
|
|
1
|
+
# encoding: UTF-8
|
|
2
|
+
dir = File.dirname("__FILE__")
|
|
3
|
+
require 'rubygems'
|
|
4
|
+
require 'spec'
|
|
5
|
+
require 'treetop'
|
|
6
|
+
|
|
7
|
+
Treetop.load(File.expand_path(dir + '../../lib/biodiversity/parser/scientific_name_clean'))
|
|
8
|
+
|
|
9
|
+
describe ScientificNameClean do
|
|
10
|
+
before(:all) do
|
|
11
|
+
@parser = ScientificNameCleanParser.new
|
|
12
|
+
end
|
|
13
|
+
|
|
14
|
+
def parse(input)
|
|
15
|
+
@parser.parse(input)
|
|
16
|
+
end
|
|
17
|
+
|
|
18
|
+
def value(input)
|
|
19
|
+
parse(input).value
|
|
20
|
+
end
|
|
21
|
+
|
|
22
|
+
def canonical(input)
|
|
23
|
+
parse(input).canonical
|
|
24
|
+
end
|
|
25
|
+
|
|
26
|
+
def details(input)
|
|
27
|
+
parse(input).details
|
|
28
|
+
end
|
|
29
|
+
|
|
30
|
+
it 'should parse uninomial' do
|
|
31
|
+
sn = 'Pseudocercospora'
|
|
32
|
+
parse(sn).should_not be_nil
|
|
33
|
+
value(sn).should == 'Pseudocercospora'
|
|
34
|
+
canonical(sn).should == 'Pseudocercospora'
|
|
35
|
+
details(sn).should == {:uninomial=>"Pseudocercospora"}
|
|
36
|
+
end
|
|
37
|
+
|
|
38
|
+
it 'should parse canonical' do
|
|
39
|
+
sn = 'Pseudocercospora dendrobii'
|
|
40
|
+
parse(sn).should_not be_nil
|
|
41
|
+
value(sn).should == 'Pseudocercospora dendrobii'
|
|
42
|
+
canonical(sn).should == 'Pseudocercospora dendrobii'
|
|
43
|
+
details(sn).should == {:species=>"dendrobii", :genus=>"Pseudocercospora"}
|
|
44
|
+
end
|
|
45
|
+
|
|
46
|
+
it 'should parse subgenus ZOOLOGICAL' do
|
|
47
|
+
sn = "Doriteuthis (Amerigo) pealeii Author 1999"
|
|
48
|
+
parse(sn).should_not be_nil
|
|
49
|
+
value(sn).should == "Doriteuthis (Amerigo) pealeii Author 1999"
|
|
50
|
+
canonical(sn).should == "Doriteuthis pealeii"
|
|
51
|
+
details(sn).should == {:genus=>"Doriteuthis", :subgenus=>"Amerigo", :species=>"pealeii", :authors=>{:names=>["Author"], :year=>"1999"}, :name_part_verbatim=>"Doriteuthis (Amerigo) pealeii", :auth_part_verbatim=>"Author 1999"}
|
|
52
|
+
end
|
|
53
|
+
|
|
54
|
+
it 'should parse æ in the name' do
|
|
55
|
+
names = [
|
|
56
|
+
["Læptura laetifica Dow, 1913", "Laeptura laetifica Dow 1913"],
|
|
57
|
+
["Leptura lætifica Dow, 1913", "Leptura laetifica Dow 1913"],
|
|
58
|
+
["Leptura leætifica Dow, 1913", "Leptura leaetifica Dow 1913"],
|
|
59
|
+
["Leæptura laetifica Dow, 1913", "Leaeptura laetifica Dow 1913"],
|
|
60
|
+
["Leœptura laetifica Dow, 1913", "Leoeptura laetifica Dow 1913"],
|
|
61
|
+
['Ærenea cognata Lacordaire, 1872', 'Ærenea cognata Lacordaire 1872'],
|
|
62
|
+
['Œdicnemus capensis ehrenbergi', 'Œdicnemus capensis ehrenbergi'],
|
|
63
|
+
['Œnanthe œnanthe œnanthe','Œnanthe oenanthe oenanthe']
|
|
64
|
+
]
|
|
65
|
+
names.each do |name_pair|
|
|
66
|
+
parse(name_pair[0]).should_not be_nil
|
|
67
|
+
value(name_pair[0]).should == name_pair[1]
|
|
68
|
+
end
|
|
69
|
+
end
|
|
70
|
+
|
|
71
|
+
it 'should parse names with "common" utf-8 charactes' do
|
|
72
|
+
names = ["Rühlella","Sténométope laevissimus Bibron 1855"].each do |name|
|
|
73
|
+
parse(name).should_not be_nil
|
|
74
|
+
end
|
|
75
|
+
end
|
|
76
|
+
|
|
77
|
+
it 'should parse names with a valid 2 letter genus' do
|
|
78
|
+
["Ca Dyar 1914",
|
|
79
|
+
"Ea Distant 1911",
|
|
80
|
+
"Ge Nicéville 1895",
|
|
81
|
+
"Ia Thomas 1902",
|
|
82
|
+
"Io Lea 1831",
|
|
83
|
+
"Io Blanchard 1852",
|
|
84
|
+
"Ix Bergroth 1916",
|
|
85
|
+
"Lo Seale 1906",
|
|
86
|
+
"Oa Girault 1929",
|
|
87
|
+
"Ra Whitley 1931",
|
|
88
|
+
"Ty Bory de St. Vincent 1827",
|
|
89
|
+
"Ua Girault 1929",
|
|
90
|
+
"Aa Baker 1940",
|
|
91
|
+
#"Mc",
|
|
92
|
+
"Ja Uéno 1955",
|
|
93
|
+
"Zu Walters & Fitch 1960",
|
|
94
|
+
"La Bleszynski 1966",
|
|
95
|
+
"Qu Durkoop",
|
|
96
|
+
"As Slipinski 1982",
|
|
97
|
+
"Ba Solem 1983"].each do |name|
|
|
98
|
+
parse(name).should_not be_nil
|
|
99
|
+
end
|
|
100
|
+
canonical('Quoyula').should == 'Quoyula'
|
|
101
|
+
end
|
|
102
|
+
|
|
103
|
+
it 'should parse year' do
|
|
104
|
+
sn = "Platypus bicaudatulus Schedl 1935"
|
|
105
|
+
parse(sn).should_not be_nil
|
|
106
|
+
value(sn).should == "Platypus bicaudatulus Schedl 1935"
|
|
107
|
+
sn = "Platypus bicaudatulus Schedl, 1935h"
|
|
108
|
+
parse(sn).should_not be_nil
|
|
109
|
+
value(sn).should == "Platypus bicaudatulus Schedl 1935"
|
|
110
|
+
details(sn).should == {:genus=>"Platypus", :species=>"bicaudatulus", :authors=>{:names=>["Schedl"], :year=>"1935"}, :name_part_verbatim=>"Platypus bicaudatulus", :auth_part_verbatim=>"Schedl, 1935h"}
|
|
111
|
+
parse("Platypus bicaudatulus Schedl, 1935B").should_not be_nil
|
|
112
|
+
end
|
|
113
|
+
|
|
114
|
+
it 'should parse species autonym for complex subspecies authorships' do
|
|
115
|
+
parse("Aus bus Linn. var. bus").should_not be_nil
|
|
116
|
+
details("Aus bus Linn. var. bus").should == {:genus=>"Aus", :species=>"bus", :subspecies=>[{:rank=>"var.", :value=>"bus"}], :species_authors=>{:authors=>{:names=>["Linn."]}}, :name_part_verbatim=>"Aus bus", :auth_part_verbatim=>"Linn. var. bus"}
|
|
117
|
+
parse("Agalinis purpurea (L.) Briton var. borealis (Berg.) Peterson 1987").should_not be_nil
|
|
118
|
+
details("Agalinis purpurea (L.) Briton var. borealis (Berg.) Peterson 1987").should == {:genus=>"Agalinis", :species=>"purpurea", :subspecies=>[{:rank=>"var.", :value=>"borealis"}], :species_authors=>{:orig_authors=>{:names=>["L."]}, :authors=>{:names=>["Briton"]}}, :subspecies_authors=>{:orig_authors=>{:names=>["Berg."]}, :authors=>{:names=>["Peterson"], :year=>"1987"}}, :name_part_verbatim=>"Agalinis purpurea", :auth_part_verbatim=>"(L.) Briton var. borealis (Berg.) Peterson 1987"}
|
|
119
|
+
end
|
|
120
|
+
|
|
121
|
+
it 'should parse several authors' do
|
|
122
|
+
sn = "Pseudocercospora dendrobii U. Braun & Crous"
|
|
123
|
+
parse(sn).should_not be_nil
|
|
124
|
+
value(sn).should == "Pseudocercospora dendrobii U. Braun et Crous"
|
|
125
|
+
canonical(sn).should == "Pseudocercospora dendrobii"
|
|
126
|
+
details(sn).should == {:genus=>"Pseudocercospora", :species=>"dendrobii", :authors=>{:names=>["U. Braun", "Crous"]}, :name_part_verbatim=>"Pseudocercospora dendrobii", :auth_part_verbatim=>"U. Braun & Crous"}
|
|
127
|
+
sn = "Pseudocercospora dendrobii U. Braun and Crous"
|
|
128
|
+
parse(sn).should_not be_nil
|
|
129
|
+
value(sn).should == "Pseudocercospora dendrobii U. Braun et Crous"
|
|
130
|
+
sn = "Pseudocercospora dendrobii U. Braun et Crous"
|
|
131
|
+
parse(sn).should_not be_nil
|
|
132
|
+
value(sn).should == "Pseudocercospora dendrobii U. Braun et Crous"
|
|
133
|
+
end
|
|
134
|
+
|
|
135
|
+
it 'should parse several authors with a year' do
|
|
136
|
+
sn = "Pseudocercospora dendrobii U. Braun & Crous 2003"
|
|
137
|
+
parse(sn).should_not be_nil
|
|
138
|
+
value(sn).should == "Pseudocercospora dendrobii U. Braun et Crous 2003"
|
|
139
|
+
canonical(sn).should == "Pseudocercospora dendrobii"
|
|
140
|
+
details(sn).should == {:genus=>"Pseudocercospora", :species=>"dendrobii", :authors=>{:names=>["U. Braun", "Crous"], :year=>"2003"}, :name_part_verbatim=>"Pseudocercospora dendrobii", :auth_part_verbatim=>"U. Braun & Crous 2003"}
|
|
141
|
+
sn = "Pseudocercospora dendrobii Crous, 2003"
|
|
142
|
+
parse(sn).should_not be_nil
|
|
143
|
+
parse("Zophosis persis (Chatanay, 1914)").should_not be_nil
|
|
144
|
+
parse("Zophosis persis (Chatanay 1914)").should_not be_nil
|
|
145
|
+
parse("Zophosis persis (Chatanay), 1914").should_not be_nil
|
|
146
|
+
value("Zophosis persis (Chatanay), 1914").should == "Zophosis persis (Chatanay 1914)"
|
|
147
|
+
details("Zophosis persis (Chatanay), 1914").should == {:genus=>"Zophosis", :species=>"persis", :orig_authors=>{:names=>["Chatanay"]}, :year=>"1914", :name_part_verbatim=>"Zophosis persis", :auth_part_verbatim=>"(Chatanay), 1914"}
|
|
148
|
+
|
|
149
|
+
parse("Zophosis persis (Chatanay) 1914").should_not be_nil
|
|
150
|
+
#parse("Zophosis persis Chatanay (1914)").should_not be_nil
|
|
151
|
+
end
|
|
152
|
+
|
|
153
|
+
it 'should parse scientific name' do
|
|
154
|
+
parse("Pseudocercospora dendrobii (H.C. Burnett) U. Braun & Crous 2003").should_not be_nil
|
|
155
|
+
value("Pseudocercospora dendrobii(H.C. Burnett)U. Braun & Crous 2003").should == "Pseudocercospora dendrobii (H.C. Burnett) U. Braun et Crous 2003"
|
|
156
|
+
canonical("Pseudocercospora dendrobii(H.C. Burnett)U. Braun & Crous 2003").should == "Pseudocercospora dendrobii"
|
|
157
|
+
{:orig_authors=>{:names=>["H.C. Burnett"]}, :species=>"dendrobii", :authors=>{:year=>"2003", :names=>["U. Braun", "Crous"]}, :genus=>"Pseudocercospora"}
|
|
158
|
+
|
|
159
|
+
parse("Stagonospora polyspora M.T. Lucas & Sousa da Câmara 1934").should_not be_nil
|
|
160
|
+
value("Stagonospora polyspora M.T. Lucas & Sousa da Câmara 1934").should == "Stagonospora polyspora M.T. Lucas et Sousa da Câmara 1934"
|
|
161
|
+
details("Stagonospora polyspora M.T. Lucas & Sousa da Câmara 1934").should == {:genus=>"Stagonospora", :species=>"polyspora", :authors=>{:names=>["M.T. Lucas", "Sousa da Câmara"], :year=>"1934"}, :name_part_verbatim=>"Stagonospora polyspora", :auth_part_verbatim=>"M.T. Lucas & Sousa da Câmara 1934"}
|
|
162
|
+
|
|
163
|
+
parse("Cladoniicola staurospora Diederich, van den Boom & Aptroot 2001").should_not be_nil
|
|
164
|
+
parse("Yarrowia lipolytica var. lipolytica (Wick., Kurtzman & E.A. Herrm.) Van der Walt & Arx 1981").should_not be_nil
|
|
165
|
+
value("Yarrowia lipolytica var. lipolytica (Wick., Kurtzman & E.A. Herrm.) Van der Walt & Arx 1981").should == "Yarrowia lipolytica var. lipolytica (Wick., Kurtzman et E.A. Herrm.) Van der Walt et Arx 1981"
|
|
166
|
+
parse("Physalospora rubiginosa (Fr.) anon.").should_not be_nil
|
|
167
|
+
parse("Pleurotus ëous (Berk.) Sacc. 1887").should_not be_nil
|
|
168
|
+
parse("Lecanora wetmorei Śliwa 2004").should_not be_nil
|
|
169
|
+
# valid
|
|
170
|
+
# infraspecific
|
|
171
|
+
parse("Calicium furfuraceum * furfuraceum (L.) Pers. 1797").should_not be_nil
|
|
172
|
+
parse("Exobasidium vaccinii ** andromedae (P. Karst.) P. Karst. 1882").should_not be_nil
|
|
173
|
+
parse("Urceolaria scruposa **** clausa Flot. 1849").should_not be_nil
|
|
174
|
+
parse("Cortinarius angulatus B gracilescens Fr. 1838").should_not be_nil
|
|
175
|
+
parse("Cyathicula scelobelonium").should_not be_nil
|
|
176
|
+
# single quote that did not show
|
|
177
|
+
# parse("Phytophthora hedraiandra De Cock & Man in ?t Veld 2004"
|
|
178
|
+
# Phthora vastatrix d?Hérelle 1909
|
|
179
|
+
# author is exception
|
|
180
|
+
parse('Xylaria potentillae A S. Xu').should_not be_nil
|
|
181
|
+
parse("Tuber liui A S. Xu 1999").should_not be_nil
|
|
182
|
+
details("Tuber liui A S. Xu 1999").should == {:genus=>"Tuber", :species=>"liui", :authors=>{:names=>["A S. Xu"], :year=>"1999"}, :name_part_verbatim=>"Tuber liui", :auth_part_verbatim=>"A S. Xu 1999"}
|
|
183
|
+
parse('Xylaria potentillae A S. Xu').should_not be_nil
|
|
184
|
+
parse("Agaricus squamula Berk. & M.A. Curtis 1860").should_not be_nil
|
|
185
|
+
parse("Peltula coriacea Büdel, Henssen & Wessels 1986").should_not be_nil
|
|
186
|
+
#had to add no dot rule for trinomials without a rank to make it to work
|
|
187
|
+
parse("Saccharomyces drosophilae anon.").should_not be_nil
|
|
188
|
+
details("Saccharomyces drosophilae anon.").should == {:genus=>"Saccharomyces", :species=>"drosophilae", :authors=>{:names=>["anon."]}, :name_part_verbatim=>"Saccharomyces drosophilae", :auth_part_verbatim=>"anon."}
|
|
189
|
+
end
|
|
190
|
+
|
|
191
|
+
it 'should parse several authors with several years' do
|
|
192
|
+
parse("Pseudocercospora dendrobii (H.C. Burnett 1883) U. Braun & Crous 2003").should_not be_nil
|
|
193
|
+
value("Pseudocercospora dendrobii(H.C. Burnett1883)U. Braun & Crous 2003").should == "Pseudocercospora dendrobii (H.C. Burnett 1883) U. Braun et Crous 2003"
|
|
194
|
+
canonical("Pseudocercospora dendrobii(H.C. Burnett 1883)U. Braun & Crous 2003").should == "Pseudocercospora dendrobii"
|
|
195
|
+
details("Pseudocercospora dendrobii(H.C. Burnett 1883)U. Braun & Crous 2003").should == {:genus=>"Pseudocercospora", :species=>"dendrobii", :orig_authors=>{:names=>["H.C. Burnett"], :year=>"1883"}, :authors=>{:names=>["U. Braun", "Crous"], :year=>"2003"}, :name_part_verbatim=>"Pseudocercospora dendrobii", :auth_part_verbatim=>"(H.C. Burnett 1883)U. Braun & Crous 2003"}
|
|
196
|
+
end
|
|
197
|
+
|
|
198
|
+
it 'should parse unknown original authors (auct.)/(hort.)/(?)' do
|
|
199
|
+
parse("Tragacantha leporina (?) Kuntze").should_not be_nil
|
|
200
|
+
value("Tragacantha leporina ( ? ) Kuntze").should == "Tragacantha leporina (?) Kuntze"
|
|
201
|
+
parse("Lachenalia tricolor var. nelsonii (auct.) Baker").should_not be_nil
|
|
202
|
+
value("Lachenalia tricolor var. nelsonii ( auct. ) Baker").should == "Lachenalia tricolor var. nelsonii (auct.) Baker"
|
|
203
|
+
details("Lachenalia tricolor var. nelsonii ( auct. ) Baker").should == {:genus=>"Lachenalia", :species=>"tricolor", :subspecies=>[{:rank=>"var.", :value=>"nelsonii"}], :orig_authors=>"unknown", :authors=>{:names=>["Baker"]}, :name_part_verbatim=>"Lachenalia tricolor var. nelsonii", :auth_part_verbatim=>"( auct. ) Baker"}
|
|
204
|
+
end
|
|
205
|
+
|
|
206
|
+
it 'should parse unknown authors auct./anon./hort./ht.' do
|
|
207
|
+
parse("Puya acris ht. ex Gentil").should_not be_nil
|
|
208
|
+
end
|
|
209
|
+
|
|
210
|
+
|
|
211
|
+
it 'should not parse serveral authors groups with several years NOT CORRECT' do
|
|
212
|
+
parse("Pseudocercospora dendrobii (H.C. Burnett 1883) (Leight.) (Movss. 1967) U. Braun & Crous 2003").should be_nil
|
|
213
|
+
end
|
|
214
|
+
|
|
215
|
+
it 'should parse names with taxon concept sec. part' do
|
|
216
|
+
parse("Sténométope laevissimus sec. Eschmeyer 2004").should_not be_nil
|
|
217
|
+
details('Sténométope laevissimus sec. Eschmeyer 2004').should == {:genus=>"Sténométope", :species=>"laevissimus", :taxon_concept=>{:authors=>{:names=>["Eschmeyer"], :year=>"2004"}}, :name_part_verbatim=>"Sténométope laevissimus", :auth_part_verbatim=>"sec. Eschmeyer 2004"}
|
|
218
|
+
parse("Sténométope laevissimus Bibron 1855 sec. Eschmeyer 2004").should_not be_nil
|
|
219
|
+
details('Sténométope laevissimus Bibron 1855 sec. Eschmeyer 2004').should == {:genus=>"Sténométope", :species=>"laevissimus", :authors=>{:names=>["Bibron"], :year=>"1855"}, :taxon_concept=>{:authors=>{:names=>["Eschmeyer"], :year=>"2004"}}, :name_part_verbatim=>"Sténométope laevissimus", :auth_part_verbatim=>"Bibron 1855 sec. Eschmeyer 2004"}
|
|
220
|
+
#
|
|
221
|
+
# puts "<pre>"
|
|
222
|
+
# puts @parser.failure_reason
|
|
223
|
+
# #puts @parser.public_methods.select{|r| r.match /fail/}
|
|
224
|
+
# puts "</pre>"
|
|
225
|
+
end
|
|
226
|
+
|
|
227
|
+
|
|
228
|
+
it 'should parse utf-8 name' do
|
|
229
|
+
parse("Trematosphaeria phaeospora (E. Müll.) L. Holm 1957").should_not be_nil
|
|
230
|
+
value("Trematosphaeria phaeospora ( E. Müll. )L. Holm 1957").should == "Trematosphaeria phaeospora (E. Müll.) L. Holm 1957"
|
|
231
|
+
canonical("Trematosphaeria phaeospora(E. Müll.) L. Holm 1957").should == "Trematosphaeria phaeospora"
|
|
232
|
+
details("Trematosphaeria phaeospora(E. Müll.) L. Holm 1957 ").should == {:genus=>"Trematosphaeria", :species=>"phaeospora", :orig_authors=>{:names=>["E. Müll."]}, :authors=>{:names=>["L. Holm"], :year=>"1957"}, :name_part_verbatim=>"Trematosphaeria phaeospora", :auth_part_verbatim=>"(E. Müll.) L. Holm 1957"}
|
|
233
|
+
end
|
|
234
|
+
|
|
235
|
+
it "should parse name with var." do
|
|
236
|
+
parse("Phaeographis inusta var. macularis (Leight.) A.L. Sm. 1861").should_not be_nil
|
|
237
|
+
value("Phaeographis inusta var. macularis(Leight.) A.L. Sm. 1861").should == "Phaeographis inusta var. macularis (Leight.) A.L. Sm. 1861"
|
|
238
|
+
canonical("Phaeographis inusta var. macularis(Leight.) A.L. Sm. 1861").should == "Phaeographis inusta macularis"
|
|
239
|
+
end
|
|
240
|
+
|
|
241
|
+
it "should parse name with morph." do
|
|
242
|
+
val = "Callideriphus flavicollis morph. reductus Fuchs 1961"
|
|
243
|
+
parse(val).should_not be_nil
|
|
244
|
+
value(val).should == "Callideriphus flavicollis morph. reductus Fuchs 1961"
|
|
245
|
+
canonical(val).should == "Callideriphus flavicollis reductus"
|
|
246
|
+
#details(val).should == {}
|
|
247
|
+
end
|
|
248
|
+
|
|
249
|
+
# "subsect."/"subtrib."/"subgen."/"trib."/
|
|
250
|
+
#Stipa Speg. subgen. Leptostipa
|
|
251
|
+
#Sporobolus subgen. Sporobolus R.Br.
|
|
252
|
+
|
|
253
|
+
# it 'should parse name with "subsect."/"subtrib."/"subgen."/"trib."' do
|
|
254
|
+
# val = "Sporobolus subgen. Sporobolus R.Br."
|
|
255
|
+
# parse(val).should_not be_nil
|
|
256
|
+
# # value(val).should == val
|
|
257
|
+
# # canonical(val).should == "Callideriphus flavicollis reductus"
|
|
258
|
+
# # details(val).should == {}
|
|
259
|
+
# end
|
|
260
|
+
|
|
261
|
+
it "should parse name with forma/fo./form./f." do
|
|
262
|
+
parse("Caulerpa cupressoides forma nuda").should_not be_nil
|
|
263
|
+
value("Caulerpa cupressoides forma nuda").should == "Caulerpa cupressoides f. nuda"
|
|
264
|
+
canonical("Caulerpa cupressoides forma nuda").should == "Caulerpa cupressoides nuda"
|
|
265
|
+
details("Caulerpa cupressoides forma nuda").should == {:genus=>"Caulerpa", :species=>"cupressoides", :subspecies=>[{:rank=>"f.", :value=>"nuda"}]}
|
|
266
|
+
parse("Chlorocyperus glaber form. fasciculariforme (Lojac.) Soó").should_not be_nil
|
|
267
|
+
value("Chlorocyperus glaber form. fasciculariforme (Lojac.) Soó").should == "Chlorocyperus glaber f. fasciculariforme (Lojac.) Soó"
|
|
268
|
+
canonical("Chlorocyperus glaber form. fasciculariforme (Lojac.) Soó").should == "Chlorocyperus glaber fasciculariforme"
|
|
269
|
+
details("Chlorocyperus glaber form. fasciculariforme (Lojac.) Soó").should == {:genus=>"Chlorocyperus", :species=>"glaber", :subspecies=>[{:rank=>"f.", :value=>"fasciculariforme"}], :orig_authors=>{:names=>["Lojac."]}, :authors=>{:names=>["Soó"]}, :name_part_verbatim=>"Chlorocyperus glaber form. fasciculariforme", :auth_part_verbatim=>"(Lojac.) Soó"}
|
|
270
|
+
parse("Bambusa nana Roxb. fo. alphonse-karri (Mitford ex Satow) Makino ex Shiros.").should_not be_nil
|
|
271
|
+
value("Bambusa nana Roxb. fo. alphonse-karri (Mitford ex Satow) Makino ex Shiros.").should == "Bambusa nana Roxb. f. alphonse-karri (Mitford ex Satow) Makino ex Shiros."
|
|
272
|
+
canonical("Bambusa nana Roxb. fo. alphonse-karri (Mitford ex Satow) Makino ex Shiros.").should == "Bambusa nana alphonse-karri"
|
|
273
|
+
details("Bambusa nana Roxb. fo. alphonse-karri (Mitford ex Satow) Makino ex Shiros.").should == {:genus=>"Bambusa", :species=>"nana", :subspecies=>[{:rank=>"f.", :value=>"alphonse-karri"}], :species_authors=>{:authors=>{:names=>["Roxb."]}}, :subspecies_authors=>{:original_revised_name_authors=>{:revised_authors=>{:names=>["Mitford"]}, :authors=>{:names=>["Satow"]}}, :revised_name_authors=>{:revised_authors=>{:names=>["Makino"]}, :authors=>{:names=>["Shiros."]}}}, :name_part_verbatim=>"Bambusa nana", :auth_part_verbatim=>"Roxb. fo. alphonse-karri (Mitford ex Satow) Makino ex Shiros."}
|
|
274
|
+
parse("Sphaerotheca fuliginea f. dahliae Movss. 1967").should_not be_nil
|
|
275
|
+
value(" Sphaerotheca fuliginea f. dahliae Movss. 1967 ").should == "Sphaerotheca fuliginea f. dahliae Movss. 1967"
|
|
276
|
+
canonical("Sphaerotheca fuliginea f. dahliae Movss. 1967").should == "Sphaerotheca fuliginea dahliae"
|
|
277
|
+
details("Sphaerotheca fuliginea f. dahliae Movss. 1967").should == {:genus=>"Sphaerotheca", :species=>"fuliginea", :subspecies=>[{:rank=>"f.", :value=>"dahliae"}], :authors=>{:names=>["Movss."], :year=>"1967"}, :name_part_verbatim=>"Sphaerotheca fuliginea f. dahliae", :auth_part_verbatim=>"Movss. 1967"}
|
|
278
|
+
end
|
|
279
|
+
|
|
280
|
+
it "should parse name with several subspecies names NOT BOTANICAL CODE BUT NOT INFREQUENT" do
|
|
281
|
+
parse("Hydnellum scrobiculatum var. zonatum f. parvum (Banker) D. Hall & D.E. Stuntz 1972").should_not be_nil
|
|
282
|
+
value("Hydnellum scrobiculatum var. zonatum f. parvum (Banker) D. Hall & D.E. Stuntz 1972").should == "Hydnellum scrobiculatum var. zonatum f. parvum (Banker) D. Hall et D.E. Stuntz 1972"
|
|
283
|
+
details("Hydnellum scrobiculatum var. zonatum f. parvum (Banker) D. Hall & D.E. Stuntz 1972").should == {:genus=>"Hydnellum", :species=>"scrobiculatum", :subspecies=>[{:rank=>"var.", :value=>"zonatum"}, {:rank=>"f.", :value=>"parvum"}], :is_valid=>false, :orig_authors=>{:names=>["Banker"]}, :authors=>{:names=>["D. Hall", "D.E. Stuntz"], :year=>"1972"}, :name_part_verbatim=>"Hydnellum scrobiculatum var. zonatum f. parvum", :auth_part_verbatim=>"(Banker) D. Hall & D.E. Stuntz 1972"}
|
|
284
|
+
end
|
|
285
|
+
|
|
286
|
+
it "should parse status BOTANICAL RARE" do
|
|
287
|
+
#it is always latin abbrev often 2 words
|
|
288
|
+
parse("Arthopyrenia hyalospora (Nyl.) R.C. Harris comb. nov.").should_not be_nil
|
|
289
|
+
value("Arthopyrenia hyalospora (Nyl.) R.C. Harris comb. nov.").should == "Arthopyrenia hyalospora (Nyl.) R.C. Harris comb. nov."
|
|
290
|
+
canonical("Arthopyrenia hyalospora (Nyl.) R.C. Harris comb. nov.").should == "Arthopyrenia hyalospora"
|
|
291
|
+
details("Arthopyrenia hyalospora (Nyl.) R.C. Harris comb. nov.").should == {:genus=>"Arthopyrenia", :species=>"hyalospora", :orig_authors=>{:names=>["Nyl."]}, :authors=>{:names=>["R.C. Harris"]}, :status=>"comb. nov.", :name_part_verbatim=>"Arthopyrenia hyalospora", :auth_part_verbatim=>"(Nyl.) R.C. Harris comb. nov."}
|
|
292
|
+
end
|
|
293
|
+
|
|
294
|
+
it "should parse name without a year but with authors" do
|
|
295
|
+
parse("Arthopyrenia hyalospora (Nyl.) R.C. Harris").should_not be_nil
|
|
296
|
+
value("Arthopyrenia hyalospora(Nyl.)R.C. Harris").should == "Arthopyrenia hyalospora (Nyl.) R.C. Harris"
|
|
297
|
+
canonical("Arthopyrenia hyalospora (Nyl.) R.C. Harris").should == "Arthopyrenia hyalospora"
|
|
298
|
+
end
|
|
299
|
+
|
|
300
|
+
it "should parse revised (ex) names" do
|
|
301
|
+
#invalidly published
|
|
302
|
+
parse("Arthopyrenia hyalospora (Nyl. ex Banker) R.C. Harris").should_not be_nil
|
|
303
|
+
value("Arthopyrenia hyalospora (Nyl. ex Banker) R.C. Harris").should == "Arthopyrenia hyalospora (Nyl. ex Banker) R.C. Harris"
|
|
304
|
+
canonical("Arthopyrenia hyalospora (Nyl. ex Banker) R.C. Harris").should == "Arthopyrenia hyalospora"
|
|
305
|
+
details("Arthopyrenia hyalospora (Nyl. ex Banker) R.C. Harris").should == {:genus=>"Arthopyrenia", :species=>"hyalospora", :original_revised_name_authors=>{:revised_authors=>{:names=>["Nyl."]}, :authors=>{:names=>["Banker"]}}, :authors=>{:names=>["R.C. Harris"]}, :name_part_verbatim=>"Arthopyrenia hyalospora", :auth_part_verbatim=>"(Nyl. ex Banker) R.C. Harris"}
|
|
306
|
+
parse("Arthopyrenia hyalospora Nyl. ex Banker").should_not be_nil
|
|
307
|
+
|
|
308
|
+
parse("Glomopsis lonicerae Peck ex C.J. Gould 1945").should_not be_nil
|
|
309
|
+
details("Glomopsis lonicerae Peck ex C.J. Gould 1945").should == {:genus=>"Glomopsis", :species=>"lonicerae", :revised_name_authors=>{:revised_authors=>{:names=>["Peck"]}, :authors=>{:names=>["C.J. Gould"], :year=>"1945"}}, :name_part_verbatim=>"Glomopsis lonicerae", :auth_part_verbatim=>"Peck ex C.J. Gould 1945"}
|
|
310
|
+
|
|
311
|
+
parse("Acanthobasidium delicatum (Wakef.) Oberw. ex Jülich 1979").should_not be_nil
|
|
312
|
+
parse("Mycosphaerella eryngii (Fr. ex Duby) Johanson ex Oudem. 1897").should_not be_nil
|
|
313
|
+
details("Mycosphaerella eryngii (Fr. ex Duby) Johanson ex Oudem. 1897").should == {:genus=>"Mycosphaerella", :species=>"eryngii", :original_revised_name_authors=>{:revised_authors=>{:names=>["Fr."]}, :authors=>{:names=>["Duby"]}}, :revised_name_authors=>{:revised_authors=>{:names=>["Johanson"]}, :authors=>{:names=>["Oudem."], :year=>"1897"}}, :name_part_verbatim=>"Mycosphaerella eryngii", :auth_part_verbatim=>"(Fr. ex Duby) Johanson ex Oudem. 1897"}
|
|
314
|
+
#invalid but happens
|
|
315
|
+
parse("Mycosphaerella eryngii (Fr. Duby) ex Oudem. 1897").should_not be_nil
|
|
316
|
+
parse("Mycosphaerella eryngii (Fr.ex Duby) ex Oudem. 1897").should_not be_nil
|
|
317
|
+
parse("Salmonella werahensis (Castellani) Hauduroy and Ehringer in Hauduroy 1937").should_not be_nil
|
|
318
|
+
end
|
|
319
|
+
|
|
320
|
+
it "should parse multiplication sign" do
|
|
321
|
+
parse("Arthopyrenia x hyalospora (Nyl.) R.C. Harris").should_not be_nil
|
|
322
|
+
details("Arthopyrenia x hyalospora (Nyl. ex Banker) R.C. Harris").should == {:genus=>"Arthopyrenia", :species=>"hyalospora", :cross=>"inside", :original_revised_name_authors=>{:revised_authors=>{:names=>["Nyl."]}, :authors=>{:names=>["Banker"]}}, :authors=>{:names=>["R.C. Harris"]}, :name_part_verbatim=>"Arthopyrenia x hyalospora", :auth_part_verbatim=>"(Nyl. ex Banker) R.C. Harris"}
|
|
323
|
+
parse("Arthopyrenia X hyalospora(Nyl. ex Banker) R.C. Harris").should_not be_nil
|
|
324
|
+
parse("x Arthopyrenia hyalospora (Nyl. ex Banker) R.C. Harris").should_not be_nil
|
|
325
|
+
details("x Arthopyrenia hyalospora (Nyl. ex Banker) R.C. Harris").should == {:genus=>"Arthopyrenia", :species=>"hyalospora", :cross=>"before", :original_revised_name_authors=>{:revised_authors=>{:names=>["Nyl."]}, :authors=>{:names=>["Banker"]}}, :authors=>{:names=>["R.C. Harris"]}, :name_part_verbatim=>"x Arthopyrenia hyalospora", :auth_part_verbatim=>"(Nyl. ex Banker) R.C. Harris"}
|
|
326
|
+
parse("X Arthopyrenia (Nyl. ex Banker) R.C. Harris").should_not be_nil
|
|
327
|
+
details("X Arthopyrenia (Nyl. ex Banker) R.C. Harris").should == {:uninomial=>"Arthopyrenia", :cross=>"before", :original_revised_name_authors=>{:revised_authors=>{:names=>["Nyl."]}, :authors=>{:names=>["Banker"]}}, :authors=>{:names=>["R.C. Harris"]}, :name_part_verbatim=>"X Arthopyrenia", :auth_part_verbatim=>"(Nyl. ex Banker) R.C. Harris"}
|
|
328
|
+
#ascii for multiplication
|
|
329
|
+
parse("Melampsora × columbiana G. Newc. 2000").should_not be_nil
|
|
330
|
+
end
|
|
331
|
+
|
|
332
|
+
it "should parse hybrid combination" do
|
|
333
|
+
parse("Arthopyrenia hyalospora X Hydnellum scrobiculatum").should_not be_nil
|
|
334
|
+
value("Arthopyrenia hyalospora X Hydnellum scrobiculatum").should == "Arthopyrenia hyalospora \303\227 Hydnellum scrobiculatum"
|
|
335
|
+
canonical("Arthopyrenia hyalospora X Hydnellum scrobiculatum").should == "Arthopyrenia hyalospora \303\227 Hydnellum scrobiculatum"
|
|
336
|
+
details("Arthopyrenia hyalospora x Hydnellum scrobiculatum").should == {:hybrid=>{:scientific_name1=>{:species=>"hyalospora", :genus=>"Arthopyrenia"}, :scientific_name2=>{:species=>"scrobiculatum", :genus=>"Hydnellum"}}}
|
|
337
|
+
|
|
338
|
+
parse("Arthopyrenia hyalospora (Banker) D. Hall x Hydnellum scrobiculatum D.E. Stuntz").should_not be_nil
|
|
339
|
+
value("Arthopyrenia hyalospora (Banker) D. Hall X Hydnellum scrobiculatum D.E. Stuntz").should == "Arthopyrenia hyalospora (Banker) D. Hall \303\227 Hydnellum scrobiculatum D.E. Stuntz"
|
|
340
|
+
canonical("Arthopyrenia hyalospora (Banker) D. Hall X Hydnellum scrobiculatum D.E. Stuntz").should == "Arthopyrenia hyalospora \303\227 Hydnellum scrobiculatum"
|
|
341
|
+
|
|
342
|
+
parse("Arthopyrenia hyalospora x").should_not be_nil
|
|
343
|
+
value("Arthopyrenia hyalospora X").should == "Arthopyrenia hyalospora \303\227 ?"
|
|
344
|
+
canonical("Arthopyrenia hyalospora x").should == "Arthopyrenia hyalospora"
|
|
345
|
+
details("Arthopyrenia hyalospora x").should == {:hybrid=>{:scientific_name1=>{:species=>"hyalospora", :genus=>"Arthopyrenia"}, :scientific_name2=>"?"}}
|
|
346
|
+
parse("Arthopyrenia hyalospora × ?").should_not be_nil
|
|
347
|
+
details("Arthopyrenia hyalospora × ?").should == {:hybrid=>{:scientific_name1=>{:species=>"hyalospora", :genus=>"Arthopyrenia"}, :scientific_name2=>"?"}}
|
|
348
|
+
end
|
|
349
|
+
|
|
350
|
+
|
|
351
|
+
|
|
352
|
+
it "should parse name with subspecies without rank NOT BOTANICAL" do
|
|
353
|
+
name = "Hydnellum scrobiculatum zonatum (Banker) D. Hall & D.E. Stuntz 1972"
|
|
354
|
+
parse(name).should_not be_nil
|
|
355
|
+
value(name).should == "Hydnellum scrobiculatum zonatum (Banker) D. Hall et D.E. Stuntz 1972"
|
|
356
|
+
canonical(name).should == "Hydnellum scrobiculatum zonatum"
|
|
357
|
+
details(name).should == {:genus=>"Hydnellum", :species=>"scrobiculatum", :subspecies=>{:rank=>"n/a", :value=>"zonatum"}, :orig_authors=>{:names=>["Banker"]}, :authors=>{:names=>["D. Hall", "D.E. Stuntz"], :year=>"1972"}, :name_part_verbatim=>"Hydnellum scrobiculatum zonatum", :auth_part_verbatim=>"(Banker) D. Hall & D.E. Stuntz 1972"}
|
|
358
|
+
sp = "Begonia pingbienensis angustior"
|
|
359
|
+
parse(sp).should_not be_nil
|
|
360
|
+
details(sp).should == {:genus=>"Begonia", :species=>"pingbienensis", :subspecies=>{:rank=>"n/a", :value=>"angustior"}}
|
|
361
|
+
end
|
|
362
|
+
|
|
363
|
+
it "should not parse utf-8 chars in name part" do
|
|
364
|
+
parse("Érematosphaeria phaespora").should be_nil
|
|
365
|
+
parse("Trematosphaeria phaeáapora").should be_nil
|
|
366
|
+
end
|
|
367
|
+
|
|
368
|
+
it "should parse some invalid names" do
|
|
369
|
+
parse("Acarospora cratericola 1929").should_not be_nil
|
|
370
|
+
parse("Agaricus acris var. (b.)").should_not be_nil
|
|
371
|
+
value("Agaricus acris var. (b.)").should == "Agaricus acris var. (b.)"
|
|
372
|
+
parse("Agaricus acris var. (b.)").should_not be_nil
|
|
373
|
+
value("Agaricus acris var. (b.&c.)").should == "Agaricus acris var. (b.c.)"
|
|
374
|
+
details("Agaricus acris var. (b.&c.)").should == {:editorial_markup=>"(b.c.)", :subspecies=>[{:rank=>"var.", :value=>nil}], :species=>"acris", :genus=>"Agaricus", :is_valid=>false}
|
|
375
|
+
|
|
376
|
+
end
|
|
377
|
+
|
|
378
|
+
it 'should parse double parenthesis' do
|
|
379
|
+
val = "Eichornia crassipes ( (Martius) ) Solms-Laub."
|
|
380
|
+
parse(val).should_not be_nil
|
|
381
|
+
value(val).should == "Eichornia crassipes (Martius) Solms-Laub."
|
|
382
|
+
details(val).should == {:genus=>"Eichornia", :species=>"crassipes", :orig_authors=>{:names=>["Martius"]}, :authors=>{:names=>["Solms-Laub."]}, :name_part_verbatim=>"Eichornia crassipes", :auth_part_verbatim=>"( (Martius) ) Solms-Laub."}
|
|
383
|
+
end
|
|
384
|
+
|
|
385
|
+
# val = "Ferganoconcha? oblonga"
|
|
386
|
+
it 'should parse genus?' do
|
|
387
|
+
val = "Ferganoconcha? oblonga"
|
|
388
|
+
parse(val).should_not be_nil
|
|
389
|
+
value(val).should == "Ferganoconcha oblonga"
|
|
390
|
+
details(val).should == {:genus=>"Ferganoconcha", :species=>"oblonga"}
|
|
391
|
+
end
|
|
392
|
+
|
|
393
|
+
end
|