dimus-biodiversity 0.0.1

data/spec/parser/scientific_name.spec.rb

@@ -0,0 +1,244 @@
+dir = File.dirname("__FILE__")
+require 'rubygems'
+require 'spec'
+require 'treetop'
+require 'biodiversity'
+Treetop.load(File.expand_path(dir + '../../lib/biodiversity/parser/scientific_name'))
+
+describe ScientificName do
+  before(:all) do
+    @parser = ScientificNameParser.new 
+  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
+  
+  it 'should parse uninomial' do
+    sn = 'Pseudocercospora'
+    parse(sn).should_not be_nil
+    value(sn).should == 'Pseudocercospora'
+    canonical(sn).should == 'Pseudocercospora'
+    details(sn).should == {:uninomial=>"Pseudocercospora", :name_type=>"Uninomial"}
+  end
+  
+  it 'should parse canonical' do
+    sn = 'Pseudocercospora     dendrobii'
+    parse(sn).should_not be_nil
+    value(sn).should == 'Pseudocercospora dendrobii'
+    canonical(sn).should == 'Pseudocercospora dendrobii'
+    details(sn).should == {:species=>"dendrobii", :genus=>"Pseudocercospora"}
+  end
+  
+  it 'should parse subgenus ZOOLOGICAL' do
+    sn = "Doriteuthis (Amerigo) pealeii Author 1999"
+    parse(sn).should_not be_nil
+    value(sn).should == "Doriteuthis (Amerigo) pealeii Author 1999"
+    canonical(sn).should == "Doriteuthis pealeii"
+    details(sn).should == {:subgenus=>"Amerigo", :authors=>{:year=>"1999", :names=>["Author"]}, :species=>"pealeii", :genus=>"Doriteuthis"}
+  end
+  
+  it 'should parse species autonym for complex subspecies authorships' do
+    #parse("Aus bus Linn. var. bus").should_not be_nil
+    # aus genus, bus species, Linn. author, var. rank, bus infraspecific epithet 
+  end
+  
+  it 'should parse several authors' do
+    sn = "Pseudocercospora dendrobii U. Braun & Crous"
+    parse(sn).should_not be_nil
+    value(sn).should == "Pseudocercospora dendrobii U. Braun & Crous"
+    canonical(sn).should == "Pseudocercospora dendrobii"
+    details(sn).should == {
+        :authors=>{:names=>["U. Braun","Crous"]},
+        :species=>"dendrobii", 
+        :genus=>"Pseudocercospora"}
+  end
+
+  it 'should parse several authors with a year' do
+    sn = "Pseudocercospora dendrobii U. Braun & Crous 2003"
+    parse(sn).should_not be_nil
+    value(sn).should == "Pseudocercospora dendrobii U. Braun & Crous 2003"
+    canonical(sn).should == "Pseudocercospora dendrobii"
+    details(sn).should == {
+        :authors=>{:names=>["U. Braun","Crous"], :year => "2003"},
+        :species=>"dendrobii", 
+        :genus=>"Pseudocercospora"}
+    sn = "Pseudocercospora dendrobii Crous, 2003"
+    parse(sn).should_not be_nil
+  end  
+  
+  it 'should parse scientific name' do
+    parse("Pseudocercospora dendrobii (H.C. Burnett) U. Braun & Crous 2003").should_not be_nil
+    value("Pseudocercospora dendrobii(H.C.     Burnett)U. Braun & Crous     2003").should == "Pseudocercospora dendrobii (H.C. Burnett) U. Braun & Crous 2003"
+    canonical("Pseudocercospora dendrobii(H.C.     Burnett)U. Braun & Crous     2003").should == "Pseudocercospora dendrobii"
+    {:orig_authors=>{:names=>["H.C. Burnett"]}, :species=>"dendrobii", :authors=>{:year=>"2003", :names=>["U. Braun", "Crous"]}, :genus=>"Pseudocercospora"}
+  
+    parse("Stagonospora polyspora M.T. Lucas & Sousa da Câmara 1934").should_not be_nil
+    value("Stagonospora polyspora M.T. Lucas & Sousa da Câmara 1934").should == "Stagonospora polyspora M.T. Lucas & Sousa da Câmara 1934"
+    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"}
+    
+    parse("Cladoniicola staurospora Diederich, van den Boom & Aptroot 2001").should_not be_nil
+    parse("Yarrowia lipolytica var. lipolytica (Wick., Kurtzman & E.A. Herrm.) Van der Walt & Arx 1981").should_not be_nil
+    parse("Physalospora rubiginosa (Fr.) anon.").should_not be_nil
+    parse("Pleurotus ëous (Berk.) Sacc. 1887").should_not be_nil
+    parse("Lecanora wetmorei Śliwa 2004").should_not be_nil
+    #   valid 
+    #   infraspecific
+    parse("Calicium furfuraceum * furfuraceum (L.) Pers. 1797").should_not be_nil
+    parse("Exobasidium vaccinii ** andromedae (P. Karst.) P. Karst. 1882").should_not be_nil
+    parse("Urceolaria scruposa **** clausa Flot. 1849").should_not be_nil
+    parse("Cortinarius angulatus B gracilescens Fr. 1838").should_not be_nil
+    parse("Cyathicula scelobelonium").should_not be_nil
+    #   single quote that did not show
+    #    parse("Phytophthora hedraiandra De Cock & Man in ?t Veld 2004"
+    #   Phthora vastatrix d?Hérelle 1909
+    #   author is exception
+    parse("Tuber liui A S. Xu 1999").should_not be_nil
+    parse("Agaricus squamula Berk. & M.A. Curtis 1860").should_not be_nil
+    parse("Peltula coriacea Büdel, Henssen & Wessels 1986").should_not be_nil
+  end
+  
+  
+  it 'should parse several authors with several years' do
+    parse("Pseudocercospora dendrobii (H.C. Burnett 1883) U. Braun & Crous 2003").should_not be_nil
+    value("Pseudocercospora dendrobii(H.C.     Burnett1883)U. Braun & Crous     2003").should == "Pseudocercospora dendrobii (H.C. Burnett 1883) U. Braun & Crous 2003"
+    canonical("Pseudocercospora dendrobii(H.C.     Burnett 1883)U. Braun & Crous     2003").should == "Pseudocercospora dendrobii"
+    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"}
+  end
+
+  it 'should not parse serveral authors groups with several years NOT CORRECT' do
+    parse("Pseudocercospora dendrobii (H.C. Burnett 1883) (Leight.) (Movss. 1967) U. Braun & Crous 2003").should be_nil
+  end
+
+    
+  it 'should parse utf-8 name' do
+    parse("Trematosphaeria phaeospora (E. Müll.) L. Holm 1957").should_not be_nil
+    value("Trematosphaeria         phaeospora (  E.      Müll.       )L.       Holm     1957").should == "Trematosphaeria phaeospora (E. Müll.) L. Holm 1957"
+    canonical("Trematosphaeria phaeospora(E. Müll.) L.       Holm 1957").should == "Trematosphaeria phaeospora"
+    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"} 
+  end
+  
+  it "should parse name with f." do
+    
+    parse("Sphaerotheca fuliginea f. dahliae Movss. 1967").should_not be_nil
+    value("   Sphaerotheca    fuliginea     f.    dahliae    Movss.   1967    ").should == "Sphaerotheca fuliginea f. dahliae Movss. 1967"
+    canonical("Sphaerotheca fuliginea f. dahliae Movss. 1967").should == "Sphaerotheca fuliginea dahliae"
+    details("Sphaerotheca fuliginea f. dahliae Movss. 1967").should ==  {:subspecies=>[{:type=>"f.", :value=>"dahliae"}], :authors=>{:year=>"1967", :names=>["Movss."]}, :species=>"fuliginea", :genus=>"Sphaerotheca"}
+  end
+  
+  it "should parse name with var." do
+    parse("Phaeographis inusta var. macularis (Leight.) A.L. Sm. 1861").should_not be_nil
+    value("Phaeographis     inusta    var. macularis(Leight.)  A.L.       Sm.     1861").should == "Phaeographis inusta var. macularis (Leight.) A.L. Sm. 1861"
+    canonical("Phaeographis     inusta    var. macularis(Leight.)  A.L.       Sm.     1861").should == "Phaeographis inusta macularis"
+  end
+  
+  it "should parse name with several subspecies names NOT BOTANICAL CODE BUT NOT INFREQUENT" do
+    parse("Hydnellum scrobiculatum var. zonatum f. parvum (Banker) D. Hall & D.E. Stuntz 1972").should_not be_nil
+    value("Hydnellum scrobiculatum var. zonatum f. parvum (Banker) D. Hall & D.E. Stuntz 1972").should == "Hydnellum scrobiculatum var. zonatum f. parvum (Banker) D. Hall & D.E. Stuntz 1972"
+    details("Hydnellum scrobiculatum var. zonatum f. parvum (Banker) D. Hall & D.E. Stuntz 1972").should == {:orig_authors=>{:names=>["Banker"]}, :subspecies=>[{:type=>"var.", :value=>"zonatum"}, {:type=>"f.", :value=>"parvum"}], :species=>"scrobiculatum", :authors=>{:year=>"1972", :names=>["D. Hall", "D.E. Stuntz"]}, :genus=>"Hydnellum", :is_valid=>false}  
+  end
+  
+  it "should parse status BOTANICAL RARE" do
+    #it is always latin abbrev often 2 words
+    parse("Arthopyrenia hyalospora (Nyl.) R.C. Harris comb. nov.").should_not be_nil
+    value("Arthopyrenia hyalospora (Nyl.) R.C. Harris comb. nov.").should == "Arthopyrenia hyalospora (Nyl.) R.C. Harris comb. nov."
+    canonical("Arthopyrenia hyalospora (Nyl.) R.C. Harris comb. nov.").should == "Arthopyrenia hyalospora"
+    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"}
+  end
+  
+  it "should parse name without a year but with authors" do 
+    parse("Arthopyrenia hyalospora (Nyl.) R.C. Harris").should_not be_nil
+    value("Arthopyrenia hyalospora(Nyl.)R.C.     Harris").should == "Arthopyrenia hyalospora (Nyl.) R.C. Harris"
+    canonical("Arthopyrenia hyalospora (Nyl.) R.C. Harris").should == "Arthopyrenia hyalospora"
+  end
+  
+  it "should parse revised (ex) names" do
+    #invalidly published
+    parse("Arthopyrenia hyalospora (Nyl. ex Banker) R.C. Harris").should_not be_nil
+    value("Arthopyrenia hyalospora (Nyl. ex Banker) R.C. Harris").should == "Arthopyrenia hyalospora (Nyl. ex Banker) R.C. Harris"
+    canonical("Arthopyrenia hyalospora (Nyl. ex Banker) R.C. Harris").should == "Arthopyrenia hyalospora"
+    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."]}}}    
+    parse("Arthopyrenia hyalospora Nyl. ex Banker").should_not be_nil
+    
+    parse("Glomopsis lonicerae Peck ex C.J. Gould 1945").should_not be_nil
+    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"}
+  
+    parse("Acanthobasidium delicatum (Wakef.) Oberw. ex Jülich 1979").should_not be_nil
+    parse("Mycosphaerella eryngii (Fr. ex Duby) Johanson ex Oudem. 1897").should_not be_nil
+    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"]}}}
+    #invalid but happens
+    parse("Mycosphaerella eryngii (Fr. Duby) ex Oudem. 1897").should_not be_nil
+    parse("Mycosphaerella eryngii (Fr.ex Duby) ex Oudem. 1897").should_not be_nil
+  end
+  
+  it "should parse multiplication sign" do
+    parse("Arthopyrenia x hyalospora (Nyl.) R.C. Harris").should_not be_nil
+    details("Arthopyrenia x 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=>"inside"}
+    parse("Arthopyrenia X hyalospora(Nyl. ex Banker) R.C. Harris").should_not be_nil
+    parse("x Arthopyrenia hyalospora (Nyl. ex Banker) R.C. Harris").should_not be_nil
+    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"}
+    parse("X Arthopyrenia (Nyl. ex Banker) R.C. Harris").should_not be_nil
+    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"}
+    #ascii for multiplication
+    parse("Melampsora × columbiana G. Newc. 2000").should_not be_nil
+  end
+  
+  it "should parse hybrid combination" do
+    parse("Arthopyrenia hyalospora X Hydnellum scrobiculatum").should_not be_nil
+    value("Arthopyrenia hyalospora X Hydnellum scrobiculatum").should == "Arthopyrenia hyalospora \303\227 Hydnellum scrobiculatum"
+    canonical("Arthopyrenia hyalospora X Hydnellum scrobiculatum").should == "Arthopyrenia hyalospora \303\227 Hydnellum scrobiculatum"
+    details("Arthopyrenia hyalospora x Hydnellum scrobiculatum").should == {:hybrid=>{:scientific_name1=>{:species=>"hyalospora", :genus=>"Arthopyrenia"}, :scientific_name2=>{:species=>"scrobiculatum", :genus=>"Hydnellum"}}}
+    
+    parse("Arthopyrenia hyalospora (Banker) D. Hall x Hydnellum scrobiculatum D.E. Stuntz").should_not be_nil
+    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"
+    canonical("Arthopyrenia hyalospora (Banker) D. Hall X Hydnellum scrobiculatum D.E. Stuntz").should == "Arthopyrenia hyalospora \303\227 Hydnellum scrobiculatum"
+    
+    parse("Arthopyrenia hyalospora x").should_not be_nil
+    value("Arthopyrenia hyalospora X").should == "Arthopyrenia hyalospora \303\227 ?"  
+    canonical("Arthopyrenia hyalospora x").should == "Arthopyrenia hyalospora"
+    details("Arthopyrenia hyalospora x").should == {:hybrid=>{:scientific_name1=>{:species=>"hyalospora", :genus=>"Arthopyrenia"}, :scientific_name2=>"?"}}  
+    parse("Arthopyrenia hyalospora × ?").should_not be_nil
+    details("Arthopyrenia hyalospora × ?").should == {:hybrid=>{:scientific_name1=>{:species=>"hyalospora", :genus=>"Arthopyrenia"}, :scientific_name2=>"?"}}
+  end
+
+  
+
+  it "should parse name with subspecies without rank selector NOT BOTANICAL" do
+    name = "Hydnellum scrobiculatum zonatum (Banker) D. Hall & D.E. Stuntz 1972"
+    parse(name).should_not be_nil
+    value(name).should == "Hydnellum scrobiculatum zonatum (Banker) D. Hall & D.E. Stuntz 1972"
+    canonical(name).should == "Hydnellum scrobiculatum zonatum"
+    details(name).should == {:orig_authors=>{:names=>["Banker"]}, :subspecies=>{:type=>"n/a", :value=>"zonatum"}, :species=>"scrobiculatum", :authors=>{:year=>"1972", :names=>["D. Hall", "D.E. Stuntz"]}, :genus=>"Hydnellum"}
+  end
+  
+  it "should not parse utf-8 chars in name part" do
+    parse("Érematosphaeria phaespora").should be_nil
+    parse("Trematosphaeria phaeáapora").should be_nil
+  end
+  
+  it "should parse some invalid names" do
+    parse("Acarospora cratericola 1929").should_not be_nil
+    parse("Agaricus acris var. (b.)").should_not be_nil  
+    value("Agaricus acris var. (b.)").should == "Agaricus acris var. (b.)"  
+    parse("Agaricus acris var. (b.)").should_not be_nil 
+    value("Agaricus acris var. (b.&c.)").should == "Agaricus acris var. (b.c.)"  
+    details("Agaricus acris var. (b.&c.)").should == {:editorial_markup=>"(b.c.)", :subspecies=>[{:type=>"var.", :value=>nil}], :species=>"acris", :genus=>"Agaricus", :is_valid=>false}
+
+  end
+  
+  it "should not have this problems, but it has them" do
+    parse("Saccharomyces drosophilae anon.").should be_nil
+  end
+end

metadata

@@ -0,0 +1,76 @@
+--- !ruby/object:Gem::Specification 
+name: dimus-biodiversity
+version: !ruby/object:Gem::Version 
+  version: 0.0.1
+platform: ruby
+authors: 
+- Dmitry Mozzherin
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2008-10-21 00:00:00 -07:00
+default_executable: 
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: treetop
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 1.2.4
+    version: 
+description: Biodiversity library provides a parser tool for scientific species names
+email: dmozzherin {et} eol {dt} org
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- README.rdoc
+- LICENSE
+files: 
+- LICENSE
+- README.rdoc
+- Rakefile
+- spec/parser
+- spec/parser/scientific_name.spec.rb
+- lib/biodiversity
+- lib/biodiversity/parser
+- lib/biodiversity/parser/scientific_name.rb
+- lib/biodiversity/parser/scientific_name.treetop
+- lib/biodiversity/parser.rb
+- lib/biodiversity.rb
+- bin/nnparse
+has_rdoc: true
+homepage: http://github.com/dimus/biodiversity/wikis
+post_install_message: 
+rdoc_options: 
+- --main
+- README.rdoc
+- --inline-source
+- --charset=UTF-8
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+  version: 
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+  version: 
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.2.0
+signing_key: 
+specification_version: 2
+summary: scientific species name parser
+test_files: []
+