biodiversity 3.1.1 → 3.1.2

data/CHANGELOG

@@ -1,6 +1,9 @@
-3.1.1 -- fixed problem with names ending on sp 
+3.1.2 -- fixed problems with infraspecies epithets starting with fo,
+for example Peristernia nassatula forskali Tapparone-Canefri 1875
 
-3.1.0 -- added surrogates: Genbank, Barcode of life names. 
+3.1.1 -- fixed problem with names ending on sp
+
+3.1.0 -- added surrogates: Genbank, Barcode of life names.
 Also cf., sp. spp are flagged as surrogates
 
 3.0.1 -- updated gems

data/VERSION

@@ -1 +1 @@
-3.1.1
+3.1.2

data/lib/biodiversity/parser/scientific_name_clean.treetop

@@ -560,7 +560,7 @@ grammar ScientificNameClean
   end
 
   rule rank
-    ("morph."/"f.sp."/"B "/"ssp."/"ssp "/"mut."/"nat "/"nothosubsp."/"convar."/"pseudovar."/"sect."/"ser."/"var."/"subvar."/ "[var.]" /"var "/"subsp."/"subsp "/"subf."/"race "/"forma "/"fma."/"fma "/"form."/"form "/"fo."/"fo"/"f."/"α"/"ββ"/"β"/"γ"/"δ"/"ε"/"φ"/"θ"/"μ"/"a."/"b."/"c."/"d."/"e."/"g."/"k."/"****"/"**"/"*")
+    ("morph."/"f.sp."/"B "/"ssp."/"ssp "/"mut."/"nat "/"nothosubsp."/"convar."/"pseudovar."/"sect."/"ser."/"var."/"subvar."/ "[var.]" /"var "/"subsp."/"subsp "/"subf."/"race "/"forma "/"fma."/"fma "/"form."/"form "/"fo."/"fo "/"f."/"α"/"ββ"/"β"/"γ"/"δ"/"ε"/"φ"/"θ"/"μ"/"a."/"b."/"c."/"d."/"e."/"g."/"k."/"****"/"**"/"*")
     {
       def value
         text_value.strip

data/spec/parser/scientific_name_clean.spec.rb

@@ -7,7 +7,7 @@ describe ScientificNameClean do
   before(:all) do
     set_parser(ScientificNameCleanParser.new)
   end
-  
+
   it 'should parse uninomial' do
     sn = 'Pseudocercospora'
     parse(sn).should_not be_nil
@@ -16,12 +16,12 @@ describe ScientificNameClean do
     details(sn).should == [{:uninomial=>{:string=>"Pseudocercospora"}}]
     pos(sn).should == {0=>["uninomial", 16]}
   end
-  
+
   it 'should parse uninomial with author and year' do
     sn = 'Pseudocercospora Speg.'
     parse(sn).should_not be_nil
     details(sn).should == [{:uninomial=>{:string=>"Pseudocercospora", :authorship=>"Speg.", :basionymAuthorTeam=>{:authorTeam=>"Speg.", :author=>["Speg."]}}}]
-    pos(sn).should == {0=>["uninomial", 16], 17=>["author_word", 22]}    
+    pos(sn).should == {0=>["uninomial", 16], 17=>["author_word", 22]}
     sn = 'Pseudocercospora Spegazzini, 1910'
     parse(sn).should_not be_nil
     value(sn).should == 'Pseudocercospora Spegazzini 1910'
@@ -34,7 +34,7 @@ describe ScientificNameClean do
     parse(sn).should_not be_nil
     details(sn).should == [{:uninomial=>{:string=>"Epacridaceae"}, :rank_uninomials=>"trib.", :uninomial2=>{:string=>"Archerieae", :authorship=>"Crayn & Quinn", :basionymAuthorTeam=>{:authorTeam=>"Crayn & Quinn", :author=>["Crayn", "Quinn"]}}}]
   end
-  
+
   it 'should parse names with a valid 2 letter genus' do
     ["Ca Dyar 1914",
     "Ea Distant 1911",
@@ -59,7 +59,7 @@ describe ScientificNameClean do
     end
     canonical('Quoyula').should == 'Quoyula'
   end
-  
+
   it 'should parse canonical' do
     sn = 'Pseudocercospora     dendrobii'
     parse(sn).should_not be_nil
@@ -78,8 +78,8 @@ describe ScientificNameClean do
     value(sn).should == 'Ps. dendrobii'
     details(sn).should == [{:genus=>{:string=>"Ps."}, :species=>{:string=>"dendrobii"}}]
   end
-  
-  
+
+
   it 'should parse species name with author and year' do
     sn = "Platypus bicaudatulus Schedl 1935"
     parse(sn).should_not be_nil
@@ -95,7 +95,7 @@ describe ScientificNameClean do
     details(sn).should == [{:genus=>{:string=>"Platypus"}, :species=>{:string=>"bicaudatulus", :authorship=>"Schedl (1935h)", :basionymAuthorTeam=>{:authorTeam=>"Schedl", :author=>["Schedl"], :year=>"1935"}}}]
     parse("Platypus bicaudatulus Schedl 1935").should_not be_nil
   end
-  
+
   it 'should parse species name with abbreviated genus, author and year' do
     sn = "P. bicaudatulus Schedl 1935"
     parse(sn).should_not be_nil
@@ -110,7 +110,7 @@ describe ScientificNameClean do
   end
 
   it "should parse species name with author's postfix f., filius (son of)" do
-    names = [ 
+    names = [
       [ "Platypus bicaudatulus Schedl f. 1935", [{:genus=>{:string=>"Platypus"}, :species=>{:string=>"bicaudatulus", :authorship=>"Schedl f. 1935", :basionymAuthorTeam=>{:authorTeam=>"Schedl f.", :author=>["Schedl f."], :year=>"1935"}}}], 'Platypus bicaudatulus Schedl f. 1935'],
       [ "Platypus bicaudatulus Schedl filius 1935", [{:genus=>{:string=>"Platypus"}, :species=>{:string=>"bicaudatulus", :authorship=>"Schedl filius 1935", :basionymAuthorTeam=>{:authorTeam=>"Schedl filius", :author=>["Schedl filius"], :year=>"1935"}}}], 'Platypus bicaudatulus Schedl filius 1935'],
       [ "Fimbristylis ovata (Burm. f.) J. Kern", [{:genus=>{:string=>"Fimbristylis"}, :species=>{:string=>"ovata", :authorship=>"(Burm. f.) J. Kern", :combinationAuthorTeam=>{:authorTeam=>"J. Kern", :author=>["J. Kern"]}, :basionymAuthorTeam=>{:authorTeam=>"Burm. f.", :author=>["Burm. f."]}}}], 'Fimbristylis ovata (Burm. f.) J. Kern'],
@@ -123,14 +123,15 @@ describe ScientificNameClean do
       ["Betula pendula fo. dalecarlica (L. f.) C.K. Schneid.", [{:infraspecies=>[{:basionymAuthorTeam=>{:author=>["L. f."], :authorTeam=>"L. f."}, :string=>"dalecarlica", :rank=>"fo.", :combinationAuthorTeam=>{:author=>["C.K. Schneid."], :authorTeam=>"C.K. Schneid."}, :authorship=>"(L. f.) C.K. Schneid."}], :genus=>{:string=>"Betula"}, :species=>{:string=>"pendula"}}], "Betula pendula fo. dalecarlica (L. f.) C.K. Schneid."],
       ["Racomitrium canescens f. ericoides (F. Weber ex Brid.) Mönk.", [{:genus=>{:string=>"Racomitrium"}, :species=>{:string=>"canescens"}, :infraspecies=>[{:string=>"ericoides", :rank=>"f.", :authorship=>"(F. Weber ex Brid.) Mönk.", :combinationAuthorTeam=>{:authorTeam=>"Mönk.", :author=>["Mönk."]}, :basionymAuthorTeam=>{:authorTeam=>"F. Weber", :author=>["F. Weber"], :exAuthorTeam=>{:authorTeam=>"Brid.", :author=>["Brid."]}}}]}], "Racomitrium canescens f. ericoides (F. Weber ex Brid.) Mönk."],
       ["Racomitrium canescens forma ericoides (F. Weber ex Brid.) Mönk.", [{:genus=>{:string=>"Racomitrium"}, :species=>{:string=>"canescens"}, :infraspecies=>[{:string=>"ericoides", :rank=>"forma", :authorship=>"(F. Weber ex Brid.) Mönk.", :combinationAuthorTeam=>{:authorTeam=>"Mönk.", :author=>["Mönk."]}, :basionymAuthorTeam=>{:authorTeam=>"F. Weber", :author=>["F. Weber"], :exAuthorTeam=>{:authorTeam=>"Brid.", :author=>["Brid."]}}}]}], "Racomitrium canescens forma ericoides (F. Weber ex Brid.) Mönk."],
+      ["Peristernia nassatula forskali Tapparone-Canefri 1875", [{:genus=>{:string=>"Peristernia"}, :species=>{:string=>"nassatula"}, :infraspecies=>[{:string=>"forskali", :rank=>"n/a", :authorship=>"Tapparone-Canefri 1875", :basionymAuthorTeam=>{:authorTeam=>"Tapparone-Canefri", :author=>["Tapparone-Canefri"], :year=>"1875"}}]}], "Peristernia nassatula forskali Tapparone-Canefri 1875"],
     ]
-    names.each do |sn, sn_details, sn_value|  
+    names.each do |sn, sn_details, sn_value|
       parse(sn).should_not be_nil
       details(sn).should == sn_details
       value(sn).should == sn_value
     end
   end
-  
+
   it 'should parse genus with "?"' do
     sn = "Ferganoconcha? oblonga"
     parse(sn).should_not be_nil
@@ -138,7 +139,7 @@ describe ScientificNameClean do
     details(sn).should == [{:genus=>{:string=>"Ferganoconcha"}, :species=>{:string=>"oblonga"}}]
     pos(sn).should == {0=>["genus", 14], 15=>["species", 22]}
   end
-  
+
   it 'should parse æ in the name' do
     names = [
       ["Læptura laetifica Dow, 1913", "Laeptura laetifica Dow 1913"],
@@ -157,7 +158,7 @@ describe ScientificNameClean do
       value(name_pair[0]).should == name_pair[1]
     end
   end
-  
+
   it 'should parse names with e-umlaut' do
    sn = 'Kalanchoë tuberosa'
    canonical(sn).should == 'Kalanchoe tuberosa'
@@ -174,7 +175,7 @@ describe ScientificNameClean do
     pos(sn).should == {0=>["genus", 7], 9=>["infragenus", 16], 18=>["species", 29], 30=>["author_word", 38], 39=>["author_word", 40], 41=>["year", 45]}
     sn = "Ixodes (Ixodes) hexagonus hexagonus Neumann, 1911"
     canonical(sn).should == "Ixodes hexagonus hexagonus"
-    sn = "Brachytrypus (B.) grandidieri" 
+    sn = "Brachytrypus (B.) grandidieri"
     canonical(sn).should == "Brachytrypus grandidieri"
     details(sn).should == [{:genus=>{:string=>"Brachytrypus"}, :infragenus=>{:string=>"B."}, :species=>{:string=>"grandidieri"}}]
     sn = "Empis (Argyrandrus) Bezzi 1909"
@@ -185,7 +186,7 @@ describe ScientificNameClean do
     sn = "Platydoris (B.)"
     details(sn).should == [{:uninomial=>{:string=>"Platydoris", :infragenus=>{:string=>"B."}}}]
   end
-  
+
   it 'should parse several authors without a year' do
     sn = "Pseudocercospora dendrobii U. Braun & Crous"
     parse(sn).should_not be_nil
@@ -199,14 +200,14 @@ describe ScientificNameClean do
     pos(sn).should == {0=>["genus", 16], 17=>["species", 26], 27=>["author_word", 29], 30=>["author_word", 35], 40=>["author_word", 45]}
     sn = "Pseudocercospora dendrobii U. Braun et Crous"
     parse(sn).should_not be_nil
-    value(sn).should == "Pseudocercospora dendrobii U. Braun & Crous"    
+    value(sn).should == "Pseudocercospora dendrobii U. Braun & Crous"
     sn = "Arthopyrenia hyalospora(Nyl.)R.C.     Harris"
     parse(sn).should_not be_nil
     value(sn).should == "Arthopyrenia hyalospora (Nyl.) R.C. Harris"
     canonical(sn).should == "Arthopyrenia hyalospora"
     details(sn).should == [{:genus=>{:string=>"Arthopyrenia"}, :species=>{:string=>"hyalospora", :authorship=>"(Nyl.)R.C.     Harris", :combinationAuthorTeam=>{:authorTeam=>"R.C.     Harris", :author=>["R.C. Harris"]}, :basionymAuthorTeam=>{:authorTeam=>"Nyl.", :author=>["Nyl."]}}}]
   end
-  
+
   it 'should parse several authors with a year' do
     sn = "Pseudocercospora dendrobii U. Braun & Crous 2003"
     parse(sn).should_not be_nil
@@ -217,7 +218,7 @@ describe ScientificNameClean do
     sn = "Pseudocercospora dendrobii Crous, 2003"
     parse(sn).should_not be_nil
   end
-  
+
   it 'should parse basionym authors in parenthesis' do
     sn = "Zophosis persis (Chatanay, 1914)"
     parse(sn).should_not be_nil
@@ -232,9 +233,9 @@ describe ScientificNameClean do
     pos(sn).should == {0=>["genus", 8], 9=>["species", 15], 17=>["author_word", 25], 28=>["year", 32]}
     parse("Zophosis persis (Chatanay) 1914").should_not be_nil
     #parse("Zophosis persis Chatanay (1914)").should_not be_nil
-  end  
+  end
 
-  it "should be able to parse name with identificaation annotation -- aff cf sp spp" do 
+  it "should be able to parse name with identificaation annotation -- aff cf sp spp" do
     sn = 'Diplocephalus aff. procerus Thaler, 1972'
     details(sn).should ==  [{:genus=>{:string=>"Diplocephalus"}, :annotation_identification=>"aff.", :ignored=>{:species=>{:string=>"procerus", :authorship=>"Thaler, 1972", :basionymAuthorTeam=>{:authorTeam=>"Thaler", :author=>["Thaler"], :year=>"1972"}}}}]
     sn = 'Diplocephalus aff procerus Thaler, 1972'
@@ -250,7 +251,7 @@ describe ScientificNameClean do
     sn = "Thryothorus leucotis spp. bogotensis"
     details(sn).should == [{:genus=>{:string=>"Thryothorus"}, :species=>{:string=>"leucotis"}, :infraspecies=>[{:annotation_identification=>"spp.", :ignored=>{:infraspecies=>{:string=>"bogotensis", :rank=>"n/a"}}}]}]
   end
-  
+
   it 'should parse scientific name' do
     sn = "Pseudocercospora dendrobii(H.C.     Burnett)U. Braun & Crous     2003"
     parse(sn).should_not be_nil
@@ -262,7 +263,7 @@ describe ScientificNameClean do
     value(sn).should == "Pseudocercospora dendrobii (H.C. Burnett 1873) U. Braun & Crous 2003"
     details(sn).should == [{:genus=>{:string=>"Pseudocercospora"}, :species=>{:string=>"dendrobii", :authorship=>"(H.C.     Burnett,1873)U. Braun & Crous     2003", :combinationAuthorTeam=>{:authorTeam=>"U. Braun & Crous", :author=>["U. Braun", "Crous"], :year=>"2003"}, :basionymAuthorTeam=>{:authorTeam=>"H.C.     Burnett", :author=>["H.C. Burnett"], :year=>"1873"}}}]
   end
-  
+
   it 'should parse several authors with several years' do
     sn = "Pseudocercospora dendrobii (H.C. Burnett 1883) U. Braun & Crous 2003"
     parse(sn).should_not be_nil
@@ -301,7 +302,7 @@ describe ScientificNameClean do
     sn = "Cassytha peninsularis J. Z. Weber var. flindersii"
     canonical(sn).should == "Cassytha peninsularis flindersii"
     sn = "Prunus armeniaca convar. budae (Pénzes) Soó"
-    
+
     canonical(sn).should == "Prunus armeniaca budae"
     sn = "Polypodium pectinatum L. f. typica Rosenst."
     canonical(sn).should == "Polypodium pectinatum typica"
@@ -330,8 +331,8 @@ describe ScientificNameClean do
     value(sn).should == "Lachenalia tricolor var. nelsonii (auct.) Baker"
     details(sn).should == [{:genus=>{:string=>"Lachenalia"}, :species=>{:string=>"tricolor"}, :infraspecies=>[{:string=>"nelsonii", :rank=>"var.", :authorship=>"(auct.) Baker", :combinationAuthorTeam=>{:authorTeam=>"Baker", :author=>["Baker"]}, :basionymAuthorTeam=>{:authorTeam=>"auct.", :author=>["unknown"]}}]}]
     pos(sn).should == {0=>["genus", 10], 11=>["species", 19], 20=>["infraspecific_type", 24], 25=>["infraspecies", 33], 35=>["unknown_author", 40], 42=>["author_word", 47]}
-  end  
-  
+  end
+
   it 'should parse unknown authors auct./anon./hort./ht.' do
     sn = "Puya acris ht."
     parse(sn).should_not be_nil
@@ -343,7 +344,7 @@ describe ScientificNameClean do
     pr = parse(sn).should_not be_nil
     pos(sn).should == {0=>["genus", 3], 4=>["species", 12], 13=>["infraspecies", 23]}
   end
-  
+
   it 'should parse real world examples' do
     sn = "Stagonospora polyspora M.T. Lucas & Sousa da Câmara 1934"
     parse(sn).should_not be_nil
@@ -358,7 +359,7 @@ describe ScientificNameClean do
     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 
+    #   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
@@ -411,7 +412,7 @@ describe ScientificNameClean do
     pos(sn).should == {0=>["genus", 13], 14=>["species", 25], 26=>["infraspecific_type", 32], 33=>["infraspecies", 41], 42=>["author_word", 47], 48=>["year", 52]}
   end
 
-  
+
   it "should parse name with forma/fo./form./f." do
     sn = "Caulerpa cupressoides forma nuda"
     parse(sn).should_not be_nil
@@ -440,18 +441,18 @@ describe ScientificNameClean do
     pos(sn).should == {0=>["genus", 12], 16=>["species", 25], 29=>["infraspecific_type", 31], 36=>["infraspecies", 43], 47=>["author_word", 53], 58=>["year", 62]}
     parse('Polypodium vulgare nothosubsp. mantoniae (Rothm.) Schidlay').should_not be_nil
   end
-  
+
   it "should parse name with several subspecies names NOT BOTANICAL CODE BUT NOT INFREQUENT" do
     sn = "Hydnellum scrobiculatum var. zonatum f. parvum (Banker) D. Hall & D.E. Stuntz 1972"
     parse(sn).should_not be_nil
     value(sn).should == "Hydnellum scrobiculatum var. zonatum f. parvum (Banker) D. Hall & D.E. Stuntz 1972"
     details(sn).should ==  [{:genus=>{:string=>"Hydnellum"}, :species=>{:string=>"scrobiculatum"}, :infraspecies=>[{:string=>"zonatum", :rank=>"var."}, {:string=>"parvum", :rank=>"f.", :authorship=>"(Banker) D. Hall & D.E. Stuntz 1972", :combinationAuthorTeam=>{:authorTeam=>"D. Hall & D.E. Stuntz", :author=>["D. Hall", "D.E. Stuntz"], :year=>"1972"}, :basionymAuthorTeam=>{:authorTeam=>"Banker", :author=>["Banker"]}}]}]
-    pos(sn).should == {0=>["genus", 9], 10=>["species", 23], 24=>["infraspecific_type", 28], 29=>["infraspecies", 36], 37=>["infraspecific_type", 39], 40=>["infraspecies", 46], 48=>["author_word", 54], 56=>["author_word", 58], 59=>["author_word", 63], 66=>["author_word", 70], 71=>["author_word", 77], 78=>["year", 82]} 
+    pos(sn).should == {0=>["genus", 9], 10=>["species", 23], 24=>["infraspecific_type", 28], 29=>["infraspecies", 36], 37=>["infraspecific_type", 39], 40=>["infraspecies", 46], 48=>["author_word", 54], 56=>["author_word", 58], 59=>["author_word", 63], 66=>["author_word", 70], 71=>["author_word", 77], 78=>["year", 82]}
     parse('Senecio fuchsii C.C.Gmel. subsp. fuchsii var. expansus (Boiss. & Heldr.) Hayek').should_not be_nil
     parse('Senecio fuchsii C.C.Gmel. subsp. fuchsii var. fuchsii').should_not be_nil
   end
-  
-  
+
+
   it "should parse status BOTANICAL RARE" do
     #it is always latin abbrev often 2 words
     sn = "Arthopyrenia hyalospora (Nyl.) R.C. Harris comb. nov."
@@ -461,7 +462,7 @@ describe ScientificNameClean do
     details(sn).should ==  [{:genus=>{:string=>"Arthopyrenia"}, :species=>{:string=>"hyalospora", :authorship=>"(Nyl.) R.C. Harris", :combinationAuthorTeam=>{:authorTeam=>"R.C. Harris", :author=>["R.C. Harris"]}, :basionymAuthorTeam=>{:authorTeam=>"Nyl.", :author=>["Nyl."]}}, :status=>"comb. nov."}]
     pos(sn).should == {0=>["genus", 12], 13=>["species", 23], 25=>["author_word", 29], 31=>["author_word", 35], 36=>["author_word", 42]}
   end
-  
+
   it "should parse revised (ex) names" do
     #invalidly published
     sn = "Arthopyrenia hyalospora (Nyl. ex Banker) R.C. Harris"
@@ -490,7 +491,7 @@ describe ScientificNameClean do
     details(sn).should == [{:genus=>{:string=>"Salmonella"}, :species=>{:string=>"werahensis", :authorship=>"(Castellani) Hauduroy and Ehringer in Hauduroy 1937", :combinationAuthorTeam=>{:authorTeam=>"Hauduroy and Ehringer", :author=>["Hauduroy", "Ehringer"], :exAuthorTeam=>{:authorTeam=>"Hauduroy", :author=>["Hauduroy"], :year=>"1937"}}, :basionymAuthorTeam=>{:authorTeam=>"Castellani", :author=>["Castellani"]}}}]
     pos(sn).should == {0=>["genus", 10], 11=>["species", 21], 23=>["author_word", 33], 35=>["author_word", 43], 48=>["author_word", 56], 60=>["author_word", 68], 69=>["year", 73]}
   end
-    
+
   it 'should parse named hybrids' do
     [
       ["×Agropogon P. Fourn. 1934", [{:uninomial=>{:string=>"Agropogon", :authorship=>"P. Fourn. 1934", :basionymAuthorTeam=>{:authorTeam=>"P. Fourn.", :author=>["P. Fourn."], :year=>"1934"}}}]],
@@ -504,12 +505,12 @@ describe ScientificNameClean do
       ["xHeucherella tiarelloides", [{:genus=>{:string=>"Heucherella"}, :species=>{:string=>"tiarelloides"}}]],
       ["x Heucherella tiarelloides", [{:genus=>{:string=>"Heucherella"}, :species=>{:string=>"tiarelloides"}}]],
       ["×Agropogon littoralis (Sm.) C. E. Hubb. 1946", [{:genus=>{:string=>"Agropogon"}, :species=>{:string=>"littoralis", :authorship=>"(Sm.) C. E. Hubb. 1946", :combinationAuthorTeam=>{:authorTeam=>"C. E. Hubb.", :author=>["C. E. Hubb."], :year=>"1946"}, :basionymAuthorTeam=>{:authorTeam=>"Sm.", :author=>["Sm."]}}}]]
-    ].each do |res| 
+    ].each do |res|
       parse(res[0]).should_not be_nil
       parse(res[0]).hybrid.should be_true
       details(res[0]).should == res[1]
     end
-   [ 
+   [
     ['Asplenium X inexpectatum (E.L. Braun 1940) Morton (1956)',[{:genus=>{:string=>"Asplenium"}, :species=>{:string=>"inexpectatum", :authorship=>"(E.L. Braun 1940) Morton (1956)", :combinationAuthorTeam=>{:authorTeam=>"Morton", :author=>["Morton"], :year=>"1956"}, :basionymAuthorTeam=>{:authorTeam=>"E.L. Braun", :author=>["E.L. Braun"], :year=>"1940"}}}]],
     ['Mentha ×smithiana R. A. Graham 1949',[{:genus=>{:string=>"Mentha"}, :species=>{:string=>"smithiana", :authorship=>"R. A. Graham 1949", :basionymAuthorTeam=>{:authorTeam=>"R. A. Graham", :author=>["R. A. Graham"], :year=>"1949"}}}]],
     ['Salix ×capreola Andersson (1867)',[{:genus=>{:string=>"Salix"}, :species=>{:string=>"capreola", :authorship=>"Andersson (1867)", :basionymAuthorTeam=>{:authorTeam=>"Andersson", :author=>["Andersson"], :year=>"1867"}}}]],
@@ -523,7 +524,7 @@ describe ScientificNameClean do
    canonical(sn).should == "Rosa alpina × pomifera"
    parse(sn).details.should == [{:genus=>{:string=>"Rosa"}, :species=>{:string=>"alpina"}}, {:species=>{:string=>"pomifera"}, :genus=>{:string=>"Rosa"}}]
   end
-  
+
   it "should parse hybrid combination" do
     sn = "Arthopyrenia hyalospora X Hydnellum scrobiculatum"
     parse(sn).should_not be_nil
@@ -538,7 +539,7 @@ describe ScientificNameClean do
     value(sn).should == "Arthopyrenia hyalospora (Banker) D. Hall \303\227 Hydnellum scrobiculatum D.E. Stuntz"
     canonical(sn).should == "Arthopyrenia hyalospora × Hydnellum scrobiculatum"
     pos(sn).should == {0=>["genus", 12], 13=>["species", 23], 25=>["author_word", 31], 33=>["author_word", 35], 36=>["author_word", 40], 43=>["genus", 52], 53=>["species", 66], 67=>["author_word", 71], 72=>["author_word", 78]}
-    value("Arthopyrenia hyalospora X").should == "Arthopyrenia hyalospora \303\227 ?"  
+    value("Arthopyrenia hyalospora X").should == "Arthopyrenia hyalospora \303\227 ?"
     sn = "Arthopyrenia hyalospora x"
     parse(sn).should_not be_nil
     parse(sn).hybrid.should be_true
@@ -551,7 +552,7 @@ describe ScientificNameClean do
     details(sn).should == [{:genus=>{:string=>"Arthopyrenia"}, :species=>{:string=>"hyalospora"}}, "?"]
     pos(sn).should == {0=>["genus", 12], 13=>["species", 23]}
   end
-  
+
   it 'should parse names with taxon concept' do
     sn = "Stenometope laevissimus sec. Eschmeyer 2004"
     details(sn).should == [{:genus=>{:string=>"Stenometope"}, :species=>{:string=>"laevissimus"}, :taxon_concept=>{:authorship=>"Eschmeyer 2004", :basionymAuthorTeam=>{:authorTeam=>"Eschmeyer", :author=>["Eschmeyer"], :year=>"2004"}}}]
@@ -561,12 +562,12 @@ describe ScientificNameClean do
     details(sn).should == [{:genus=>{:string=>"Stenometope"}, :species=>{:string=>"laevissimus", :authorship=>"Bibron 1855", :basionymAuthorTeam=>{:authorTeam=>"Bibron", :author=>["Bibron"], :year=>"1855"}}, :taxon_concept=>{:authorship=>"Eschmeyer 2004", :basionymAuthorTeam=>{:authorTeam=>"Eschmeyer", :author=>["Eschmeyer"], :year=>"2004"}}}]
     pos(sn).should == {0=>["genus", 11], 12=>["species", 23], 24=>["author_word", 30], 31=>["year", 35], 41=>["author_word", 50], 51=>["year", 55]}
   end
-  
+
   it 'should parse names with spaces inconsistencies at the start and the end and in the middle' do
     parse("   Asplenium X inexpectatum (E.L. Braun 1940) Morton (1956)   ").should_not be_nil
   end
-  
-  it 'should parse names with any number of spaces' do 
+
+  it 'should parse names with any number of spaces' do
     sn = "Trematosphaeria phaeospora (E. Müll.)         L.             Holm 1957"
     parse(sn).should_not be_nil
     value(sn).should == "Trematosphaeria phaeospora (E. Müll.) L. Holm 1957"
@@ -574,7 +575,7 @@ describe ScientificNameClean do
     details(sn).should == [{:genus=>{:string=>"Trematosphaeria"}, :species=>{:string=>"phaeospora", :authorship=>"(E. Müll.)         L.             Holm 1957", :combinationAuthorTeam=>{:authorTeam=>"L.             Holm", :author=>["L. Holm"], :year=>"1957"}, :basionymAuthorTeam=>{:authorTeam=>"E. Müll.", :author=>["E. Müll."]}}}]
     pos(sn).should == {0=>["genus", 15], 16=>["species", 26], 28=>["author_word", 30], 31=>["author_word", 36], 46=>["author_word", 48], 61=>["author_word", 65], 66=>["year", 70]}
   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
@@ -609,7 +610,7 @@ describe ScientificNameClean do
     sn = 'Deschampsia cespitosa ssp pumila'
     details(sn).should == [{:genus=>{:string=>"Deschampsia"}, :species=>{:string=>"cespitosa"}, :infraspecies=>[{:string=>"pumila", :rank=>"ssp"}]}]
   end
-  
+
   # Combination genus names should be merged without dash or capital letter
   it 'should parse hybrid names with capitalized second name in genus (botanical code error)' do
     sn = 'Anacampti-Platanthera P. Fourn.'
@@ -627,13 +628,13 @@ describe ScientificNameClean do
     canonical(sn).should == 'Oemona simplex'
   end
   #"Arthrosamanea eriorhachis (Harms & sine ref. ) Aubrév." -- ignore & sine ref. (means without reference)
-  
+
 =begin
   new stuff
 
    sn = "Orchidaceae × Asconopsis hort."
    canonical(sn).should == "Orchidaceae x Asconopsis"
-   sn 
+   sn
    Tamiops swinhoei near hainanus|Tamiops swinhoei near hainanus
    Conus textile form archiepiscopus|Conus textile form archiepiscopus|
    Crypticus pseudosericeus ssp. olivieri Desbrochers des Loges,1881|Crypticus pseudosericeus olivieri des

data/spec/parser/test_data.txt

@@ -414,6 +414,7 @@ Buteo borealis ? ventralis|{"scientificName":{"parsed":true, "parser_version":"t
 Cetraria islandica ? islandica|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Cetraria islandica ? islandica", "normalized":"Cetraria islandica", "canonical":"Cetraria islandica", "hybrid":false, "details":[{"genus":{"string":"Cetraria"}, "species":{"string":"islandica"}, "infraspecies":[{"annotation_identification":"?", "ignored":{"infraspecies":{"string":"islandica", "rank":"n/a"}}}]}], "parser_run":1, "positions":{"0":["genus", 8], "9":["species", 18], "19":["annotation_identification", 21]}}}
 Euxoa nr. idahoensis sp. 1clay|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Euxoa nr. idahoensis sp. 1clay", "normalized":"Euxoa idahoensis", "canonical":"Euxoa idahoensis", "hybrid":false, "details":[{"genus":{"string":"Euxoa"}, "species":{"string":"idahoensis"}, "infraspecies":[{"annotation_identification":"sp.", "ignored":{"infraspecies":{"string":"uniclay", "rank":"n/a"}}}]}], "parser_run":1, "positions":{"0":["genus", 5], "10":["species", 20], "21":["annotation_identification", 24]}, "surrogate": true}}
 Parus caeruleus species complex|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Parus caeruleus species complex", "normalized":"Parus caeruleus", "canonical":"Parus caeruleus", "hybrid":false, "details":[{"genus":{"string":"Parus"}, "species":{"string":"caeruleus"}}], "parser_run":1, "positions":{"0":["genus", 5], "6":["species", 15]}}}
+Peristernia nassatula forskali Tapparone-Canefri 1875|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Peristernia nassatula forskali Tapparone-Canefri 1875", "normalized":"Peristernia nassatula forskali Tapparone-Canefri 1875", "canonical":"Peristernia nassatula forskali", "hybrid":false, "details":[{"genus":{"string":"Peristernia"}, "species":{"string":"nassatula"}, "infraspecies":[{"string":"forskali", "rank":"n/a", "authorship":"Tapparone-Canefri 1875", "basionymAuthorTeam":{"authorTeam":"Tapparone-Canefri", "author":["Tapparone-Canefri"], "year":"1875"}}]}], "parser_run":1, "positions":{"0":["genus", 11], "12":["species", 21], "22":["infraspecies", 30], "31":["author_word", 48], "49":["year", 53]}}}
 
 #should flag surrogate names
 Coleoptera sp. BOLD:AAV0432|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Coleoptera sp. BOLD:AAV0432", "normalized":"Coleoptera", "canonical":"Coleoptera", "hybrid":false, "details":[{"genus":{"string":"Coleoptera"}, "annotation_identification":"sp.", "ignored":{"unparsed":"BOLD:AAV0432"}}], "parser_run":1, "positions":{"0":["genus", 10], "11":["annotation_identification", 14]}, "surrogate":true}}

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: biodiversity
 version: !ruby/object:Gem::Version
-  version: 3.1.1
+  version: 3.1.2
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-06-18 00:00:00.000000000 Z
+date: 2013-06-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -209,6 +209,9 @@ required_ruby_version: !ruby/object:Gem::Requirement
   - - ! '>='
     - !ruby/object:Gem::Version
       version: '0'
+      segments:
+      - 0
+      hash: 3336294247914629914
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: