biodiversity19 1.0.10 → 1.0.11

data/VERSION

@@ -1 +1 @@
-1.0.10
+1.0.11

data/lib/biodiversity/parser/scientific_name_clean.treetop

@@ -403,8 +403,7 @@ grammar ScientificNameClean
   end
   
   rule rank
-    ("morph."/"f.sp."/"B"/"ssp."/"mut."/"nat"/"nothosubsp."/"convar."/"pseudovar."/"sect."/"ser."/"var."/"subvar."/ "[var.]" /"var"/"subsp."/"subsp"/"subf."/"race"/"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"/"form."/"form"/"fo."/"f."/"α"/"ββ"/"β"/"γ"/"δ"/"ε"/"φ"/"θ"/"μ"/"a."/"b."/"c."/"d."/"e."/"g."/"k."/"****"/"**"/"*")
     {
       def value
         text_value.strip
@@ -430,27 +429,6 @@ grammar ScientificNameClean
     rank_forma
   end
   
-  rule rank_forma
-    ("forma"/"form."/"form"/"fo."/"f.")
-    {
-      def value
-        "f."
-      end
-      def apply(a)
-        " " + value + " " + a.value
-      end
-      def canonical(a)
-        " " + a.value
-      end
-      def pos(a)
-        {interval.begin => ['infraspecific_type', interval.end], a.interval.begin => ['infraspecies', a.interval.end]}
-      end
-      def details(a = nil)
-        {:infraspecies => {:string => (a.value rescue nil), :rank => value}}
-      end
-    }
-  end
-  
   rule species
     a:species_string space b:authorship {
       def value

data/lib/biodiversity/parser.rb

@@ -10,7 +10,7 @@ module PreProcessor
   NOTES = /\s+(species\s+group|species\s+complex|group|author)\b.*$/i
   TAXON_CONCEPTS1 = /\s+(sensu\.|sensu|auct\.|auct)\b.*$/i
   TAXON_CONCEPTS2 = /\s+(\(?s\.\s?s\.|\(?s\.\s?l\.|\(?s\.\s?str\.|\(?s\.\s?lat\.|sec\.|sec|near)\b.*$/
-  TAXON_CONCEPTS3 = /(,\s*|\s+)(pro parte|p.\s?p.)\s*$/i  
+  TAXON_CONCEPTS3 = /(,\s*|\s+)(pro parte|p\.\s?p\.)\s*$/i  
   NOMEN_CONCEPTS  = /(,\s*|\s+)(\(?nomen|\(?nom\.|\(?comb\.).*$/i
   LAST_WORD_JUNK  = /(,\s*|\s+)(von|van|sensu|new|non|nec|cf|ssp|subsp|subgen|hybrid|hort.|hort)\s*$/i
   

data/spec/parser/scientific_name_clean.spec.rb

@@ -91,9 +91,9 @@ describe ScientificNameClean do
       [ "Cerastium arvense var. fuegianum Hook.f.", [{:genus=>{:string=>"Cerastium"}, :species=>{:string=>"arvense"}, :infraspecies=>[{:string=>"fuegianum", :rank=>"var.", :authorship=>"Hook.f.", :basionymAuthorTeam=>{:authorTeam=>"Hook.f.", :author=>["Hook.f."]}}]}], 'Cerastium arvense var. fuegianum Hook.f.'],
       [ "Cerastium arvense ssp. velutinum var. velutinum (Raf.) Britton f.", [{:genus=>{:string=>"Cerastium"}, :species=>{:string=>"arvense"}, :infraspecies=>[{:string=>"velutinum", :rank=>"ssp."}, {:string=>"velutinum", :rank=>"var.", :authorship=>"(Raf.) Britton f.", :combinationAuthorTeam=>{:authorTeam=>"Britton f.", :author=>["Britton f."]}, :basionymAuthorTeam=>{:authorTeam=>"Raf.", :author=>["Raf."]}}]}], "Cerastium arvense ssp. velutinum var. velutinum (Raf.) Britton f."],
       ["Amelanchier arborea f. hirsuta (Michx. f.) Fernald", [{:infraspecies=>[{:basionymAuthorTeam=>{:author=>["Michx. f."], :authorTeam=>"Michx. f."}, :string=>"hirsuta", :rank=>"f.", :combinationAuthorTeam=>{:author=>["Fernald"], :authorTeam=>"Fernald"}, :authorship=>"(Michx. f.) Fernald"}], :genus=>{:string=>"Amelanchier"}, :species=>{:string=>"arborea"}}], "Amelanchier arborea f. hirsuta (Michx. f.) Fernald"],
-      ["Betula pendula fo. dalecarlica (L. f.) C.K. Schneid.", [{:infraspecies=>[{:basionymAuthorTeam=>{:author=>["L. f."], :authorTeam=>"L. f."}, :string=>"dalecarlica", :rank=>"f.", :combinationAuthorTeam=>{:author=>["C.K. Schneid."], :authorTeam=>"C.K. Schneid."}, :authorship=>"(L. f.) C.K. Schneid."}], :genus=>{:string=>"Betula"}, :species=>{:string=>"pendula"}}], "Betula pendula f. dalecarlica (L. f.) C.K. Schneid."],
+      ["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=>"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."],
     ]
     names.each do |sn, sn_details, sn_value|  
       parse(sn).should_not be_nil
@@ -363,21 +363,21 @@ describe ScientificNameClean do
   it "should parse name with forma/fo./form./f." do
     sn = "Caulerpa cupressoides forma nuda"
     parse(sn).should_not be_nil
-    value(sn).should == "Caulerpa cupressoides f. nuda"
+    value(sn).should == "Caulerpa cupressoides forma nuda"
     canonical(sn).should == "Caulerpa cupressoides nuda"
-    details(sn).should == [{:genus=>{:string=>"Caulerpa"}, :species=>{:string=>"cupressoides"}, :infraspecies=>[{:string=>"nuda", :rank=>"f."}]}]
+    details(sn).should == [{:genus=>{:string=>"Caulerpa"}, :species=>{:string=>"cupressoides"}, :infraspecies=>[{:string=>"nuda", :rank=>"forma"}]}]
     pos(sn).should == {0=>["genus", 8], 9=>["species", 21], 22=>["infraspecific_type", 27], 28=>["infraspecies", 32]}
     sn = "Chlorocyperus glaber form. fasciculariforme (Lojac.) Soó"
     parse(sn).should_not be_nil
-    value("Chlorocyperus glaber form. fasciculariforme (Lojac.) Soó").should == "Chlorocyperus glaber f. fasciculariforme (Lojac.) Soó"
+    value("Chlorocyperus glaber form. fasciculariforme (Lojac.) Soó").should == "Chlorocyperus glaber form. fasciculariforme (Lojac.) Soó"
     canonical(sn).should == "Chlorocyperus glaber fasciculariforme"
-    details(sn).should == [{:genus=>{:string=>"Chlorocyperus"}, :species=>{:string=>"glaber"}, :infraspecies=>[{:string=>"fasciculariforme", :rank=>"f.", :authorship=>"(Lojac.) Soó", :combinationAuthorTeam=>{:authorTeam=>"Soó", :author=>["Soó"]}, :basionymAuthorTeam=>{:authorTeam=>"Lojac.", :author=>["Lojac."]}}]}]
+    details(sn).should == [{:genus=>{:string=>"Chlorocyperus"}, :species=>{:string=>"glaber"}, :infraspecies=>[{:string=>"fasciculariforme", :rank=>"form.", :authorship=>"(Lojac.) Soó", :combinationAuthorTeam=>{:authorTeam=>"Soó", :author=>["Soó"]}, :basionymAuthorTeam=>{:authorTeam=>"Lojac.", :author=>["Lojac."]}}]}]
     pos(sn).should == {0=>["genus", 13], 14=>["species", 20], 21=>["infraspecific_type", 26], 27=>["infraspecies", 43], 45=>["author_word", 51], 53=>["author_word", 56]}
     sn = "Bambusa nana Roxb. fo. alphonse-karri (Mitford ex Satow) Makino ex Shiros."
     parse(sn).should_not be_nil
-    value(sn).should == "Bambusa nana Roxb. f. alphonse-karri (Mitford ex Satow) Makino ex Shiros."
+    value(sn).should == "Bambusa nana Roxb. fo. alphonse-karri (Mitford ex Satow) Makino ex Shiros."
     canonical(sn).should == "Bambusa nana alphonse-karri"
-    details(sn).should == [{:genus=>{:string=>"Bambusa"}, :species=>{:string=>"nana", :authorship=>"Roxb.", :basionymAuthorTeam=>{:authorTeam=>"Roxb.", :author=>["Roxb."]}}, :infraspecies=>[{:string=>"alphonse-karri", :rank=>"f.", :authorship=>"(Mitford ex Satow) Makino ex Shiros.", :combinationAuthorTeam=>{:authorTeam=>"Makino", :author=>["Makino"], :exAuthorTeam=>{:authorTeam=>"Shiros.", :author=>["Shiros."]}}, :basionymAuthorTeam=>{:authorTeam=>"Mitford", :author=>["Mitford"], :exAuthorTeam=>{:authorTeam=>"Satow", :author=>["Satow"]}}}]}]
+    details(sn).should == [{:genus=>{:string=>"Bambusa"}, :species=>{:string=>"nana", :authorship=>"Roxb.", :basionymAuthorTeam=>{:authorTeam=>"Roxb.", :author=>["Roxb."]}}, :infraspecies=>[{:string=>"alphonse-karri", :rank=>"fo.", :authorship=>"(Mitford ex Satow) Makino ex Shiros.", :combinationAuthorTeam=>{:authorTeam=>"Makino", :author=>["Makino"], :exAuthorTeam=>{:authorTeam=>"Shiros.", :author=>["Shiros."]}}, :basionymAuthorTeam=>{:authorTeam=>"Mitford", :author=>["Mitford"], :exAuthorTeam=>{:authorTeam=>"Satow", :author=>["Satow"]}}}]}]
     pos(sn).should == {0=>["genus", 7], 8=>["species", 12], 13=>["author_word", 18], 19=>["infraspecific_type", 22], 23=>["infraspecies", 37], 39=>["author_word", 46], 50=>["author_word", 55], 57=>["author_word", 63], 67=>["author_word", 74]}
     sn = "   Sphaerotheca    fuliginea     f.    dahliae    Movss.   1967    "
     sn = "Sphaerotheca    fuliginea    f.     dahliae    Movss.     1967"
@@ -556,6 +556,8 @@ describe ScientificNameClean do
     details(sn).should == [{:genus=>{:string=>"Flexibacter"}, :species=>{:string=>"elegans", :authorship=>"Soriano 1945, non Lewin 1969", :basionymAuthorTeam=>{:authorTeam=>"Soriano", :author=>["Soriano"], :year=>"1945"}}}]
     sn = 'Schottera nicaeënsis (J.V. Lamouroux ex Duby) Guiry & Hollenberg'
     details(sn).should == [{:genus=>{:string=>"Schottera"}, :species=>{:string=>"nicaeënsis", :authorship=>"(J.V. Lamouroux ex Duby) Guiry & Hollenberg", :combinationAuthorTeam=>{:authorTeam=>"Guiry & Hollenberg", :author=>["Guiry", "Hollenberg"]}, :basionymAuthorTeam=>{:authorTeam=>"J.V. Lamouroux", :author=>["J.V. Lamouroux"], :exAuthorTeam=>{:authorTeam=>"Duby", :author=>["Duby"]}}}}]
+    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

data/spec/parser/test_data.txt

@@ -41,6 +41,7 @@ Ba Solem 1983|{"scientificName":{"parsed":true, "parser_version":"test_version",
 
 #canonical binomial
 Pseudocercospora     dendrobii|{"scientificName":{"parsed":true, "parser_version":"test_version", "parser_run":1,"verbatim":"Pseudocercospora     dendrobii","normalized":"Pseudocercospora dendrobii","canonical":"Pseudocercospora dendrobii","hybrid":false,"details":[{"genus":{"string":"Pseudocercospora"},"species":{"string":"dendrobii"}}],"positions":{"0":["genus",16],"21":["species",30]}}}
+Cucurbita pepo|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Cucurbita pepo", "normalized":"Cucurbita pepo", "canonical":"Cucurbita pepo", "hybrid":false, "details":[{"genus":{"string":"Cucurbita"}, "species":{"string":"pepo"}}], "parser_run":1, "positions":{"0":["genus", 9], "10":["species", 14]}}}
 
 #binomial with author and a year
 Platypus bicaudatulus Schedl 1935|{"scientificName":{"parsed":true, "parser_version":"test_version", "parser_run":1,"verbatim":"Platypus bicaudatulus Schedl 1935","normalized":"Platypus bicaudatulus Schedl 1935","canonical":"Platypus bicaudatulus","hybrid":false,"details":[{"genus":{"string":"Platypus"},"species":{"string":"bicaudatulus","authorship":"Schedl 1935","basionymAuthorTeam":{"authorTeam":"Schedl","author":["Schedl"],"year":"1935"}}}],"positions":{"0":["genus",8],"9":["species",21],"22":["author_word",28],"29":["year",33]}}}
@@ -105,8 +106,8 @@ Hydnellum scrobiculatum zonatum|{"scientificName":{"parsed":true, "parser_versio
 Aus bus Linn. var. bus|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Aus bus Linn. var. bus", "normalized":"Aus bus Linn. var. bus", "canonical":"Aus bus bus", "hybrid":false, "details":[{"genus":{"string":"Aus"}, "species":{"string":"bus", "authorship":"Linn.", "basionymAuthorTeam":{"authorTeam":"Linn.", "author":["Linn."]}}, "infraspecies":[{"string":"bus", "rank":"var."}]}], "parser_run":1, "positions":{"0":["genus", 3], "4":["species", 7], "8":["author_word", 13], "14":["infraspecific_type", 18], "19":["infraspecies", 22]}}}
 Agalinis purpurea (L.) Briton var. borealis (Berg.) Peterson 1987|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Agalinis purpurea (L.) Briton var. borealis (Berg.) Peterson 1987", "normalized":"Agalinis purpurea (L.) Briton var. borealis (Berg.) Peterson 1987", "canonical":"Agalinis purpurea borealis", "hybrid":false, "details":[{"genus":{"string":"Agalinis"}, "species":{"string":"purpurea", "authorship":"(L.) Briton", "combinationAuthorTeam":{"authorTeam":"Briton", "author":["Briton"]}, "basionymAuthorTeam":{"authorTeam":"L.", "author":["L."]}}, "infraspecies":[{"string":"borealis", "rank":"var.", "authorship":"(Berg.) Peterson 1987", "combinationAuthorTeam":{"authorTeam":"Peterson", "author":["Peterson"], "year":"1987"}, "basionymAuthorTeam":{"authorTeam":"Berg.", "author":["Berg."]}}]}], "parser_run":1, "positions":{"0":["genus", 8], "9":["species", 17], "19":["author_word", 21], "23":["author_word", 29], "30":["infraspecific_type", 34], "35":["infraspecies", 43], "45":["author_word", 50], "52":["author_word", 60], "61":["year", 65]}}}
 Callideriphus flavicollis morph. reductus Fuchs 1961|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Callideriphus flavicollis morph. reductus Fuchs 1961", "normalized":"Callideriphus flavicollis morph. reductus Fuchs 1961", "canonical":"Callideriphus flavicollis reductus", "hybrid":false, "details":[{"genus":{"string":"Callideriphus"}, "species":{"string":"flavicollis"}, "infraspecies":[{"string":"reductus", "rank":"morph.", "authorship":"Fuchs 1961", "basionymAuthorTeam":{"authorTeam":"Fuchs", "author":["Fuchs"], "year":"1961"}}]}], "parser_run":1, "positions":{"0":["genus", 13], "14":["species", 25], "26":["infraspecific_type", 32], "33":["infraspecies", 41], "42":["author_word", 47], "48":["year", 52]}}}
-Caulerpa cupressoides forma nuda|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Caulerpa cupressoides forma nuda", "normalized":"Caulerpa cupressoides f. nuda", "canonical":"Caulerpa cupressoides nuda", "hybrid":false, "details":[{"genus":{"string":"Caulerpa"}, "species":{"string":"cupressoides"}, "infraspecies":[{"string":"nuda", "rank":"f."}]}], "parser_run":1, "positions":{"0":["genus", 8], "9":["species", 21], "22":["infraspecific_type", 27], "28":["infraspecies", 32]}}}
-Chlorocyperus glaber form. fasciculariforme (Lojac.) Soó|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Chlorocyperus glaber form. fasciculariforme (Lojac.) Soó", "normalized":"Chlorocyperus glaber f. fasciculariforme (Lojac.) Soó", "canonical":"Chlorocyperus glaber fasciculariforme", "hybrid":false, "details":[{"genus":{"string":"Chlorocyperus"}, "species":{"string":"glaber"}, "infraspecies":[{"string":"fasciculariforme", "rank":"f.", "authorship":"(Lojac.) Soó", "combinationAuthorTeam":{"authorTeam":"Soó", "author":["Soó"]}, "basionymAuthorTeam":{"authorTeam":"Lojac.", "author":["Lojac."]}}]}], "parser_run":1, "positions":{"0":["genus", 13], "14":["species", 20], "21":["infraspecific_type", 26], "27":["infraspecies", 43], "45":["author_word", 51], "53":["author_word", 56]}}}
+Caulerpa cupressoides forma nuda|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Caulerpa cupressoides forma nuda", "normalized":"Caulerpa cupressoides forma nuda", "canonical":"Caulerpa cupressoides nuda", "hybrid":false, "details":[{"genus":{"string":"Caulerpa"}, "species":{"string":"cupressoides"}, "infraspecies":[{"string":"nuda", "rank":"forma"}]}], "parser_run":1, "positions":{"0":["genus", 8], "9":["species", 21], "22":["infraspecific_type", 27], "28":["infraspecies", 32]}}}
+Chlorocyperus glaber form. fasciculariforme (Lojac.) Soó|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Chlorocyperus glaber form. fasciculariforme (Lojac.) Soó", "normalized":"Chlorocyperus glaber form. fasciculariforme (Lojac.) Soó", "canonical":"Chlorocyperus glaber fasciculariforme", "hybrid":false, "details":[{"genus":{"string":"Chlorocyperus"}, "species":{"string":"glaber"}, "infraspecies":[{"string":"fasciculariforme", "rank":"form.", "authorship":"(Lojac.) Soó", "combinationAuthorTeam":{"authorTeam":"Soó", "author":["Soó"]}, "basionymAuthorTeam":{"authorTeam":"Lojac.", "author":["Lojac."]}}]}], "parser_run":1, "positions":{"0":["genus", 13], "14":["species", 20], "21":["infraspecific_type", 26], "27":["infraspecies", 43], "45":["author_word", 51], "53":["author_word", 56]}}}
 Sphaerotheca    fuliginea    f.     dahliae    Movss.     1967|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Sphaerotheca    fuliginea    f.     dahliae    Movss.     1967", "normalized":"Sphaerotheca fuliginea f. dahliae Movss. 1967", "canonical":"Sphaerotheca fuliginea dahliae", "hybrid":false, "details":[{"genus":{"string":"Sphaerotheca"}, "species":{"string":"fuliginea"}, "infraspecies":[{"string":"dahliae", "rank":"f.", "authorship":"Movss.     1967", "basionymAuthorTeam":{"authorTeam":"Movss.", "author":["Movss."], "year":"1967"}}]}], "parser_run":1, "positions":{"0":["genus", 12], "16":["species", 25], "29":["infraspecific_type", 31], "36":["infraspecies", 43], "47":["author_word", 53], "58":["year", 62]}}}
 Polypodium vulgare nothosubsp. mantoniae (Rothm.) Schidlay|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Polypodium vulgare nothosubsp. mantoniae (Rothm.) Schidlay", "normalized":"Polypodium vulgare nothosubsp. mantoniae (Rothm.) Schidlay", "canonical":"Polypodium vulgare mantoniae", "hybrid":false, "details":[{"genus":{"string":"Polypodium"}, "species":{"string":"vulgare"}, "infraspecies":[{"string":"mantoniae", "rank":"nothosubsp.", "authorship":"(Rothm.) Schidlay", "combinationAuthorTeam":{"authorTeam":"Schidlay", "author":["Schidlay"]}, "basionymAuthorTeam":{"authorTeam":"Rothm.", "author":["Rothm."]}}]}], "parser_run":1, "positions":{"0":["genus", 10], "11":["species", 18], "19":["infraspecific_type", 30], "31":["infraspecies", 40], "42":["author_word", 48], "50":["author_word", 58]}}}
 Allophylus amazonicus var amazonicus|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Allophylus amazonicus var amazonicus", "normalized":"Allophylus amazonicus var amazonicus", "canonical":"Allophylus amazonicus amazonicus", "hybrid":false, "details":[{"genus":{"string":"Allophylus"}, "species":{"string":"amazonicus"}, "infraspecies":[{"string":"amazonicus", "rank":"var"}]}], "parser_run":1, "positions":{"0":["genus", 10], "11":["species", 21], "22":["infraspecific_type", 25], "26":["infraspecies", 36]}}}
@@ -294,9 +295,9 @@ Cerastium arvense var. fuegianum Hook. f.|{"scientificName":{"parsed":true, "par
 Cerastium arvense var. fuegianum Hook.f.|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Cerastium arvense var. fuegianum Hook.f.", "normalized":"Cerastium arvense var. fuegianum Hook.f.", "canonical":"Cerastium arvense fuegianum", "hybrid":false, "details":[{"genus":{"string":"Cerastium"}, "species":{"string":"arvense"}, "infraspecies":[{"string":"fuegianum", "rank":"var.", "authorship":"Hook.f.", "basionymAuthorTeam":{"authorTeam":"Hook.f.", "author":["Hook.f."]}}]}], "parser_run":1, "positions":{"0":["genus", 9], "10":["species", 17], "18":["infraspecific_type", 22], "23":["infraspecies", 32], "33":["author_word", 40]}}}
 Cerastium arvense ssp. velutinum var. velutinum (Raf.) Britton f.|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Cerastium arvense ssp. velutinum var. velutinum (Raf.) Britton f.", "normalized":"Cerastium arvense ssp. velutinum var. velutinum (Raf.) Britton f.", "canonical":"Cerastium arvense velutinum velutinum", "hybrid":false, "details":[{"genus":{"string":"Cerastium"}, "species":{"string":"arvense"}, "infraspecies":[{"string":"velutinum", "rank":"ssp."}, {"string":"velutinum", "rank":"var.", "authorship":"(Raf.) Britton f.", "combinationAuthorTeam":{"authorTeam":"Britton f.", "author":["Britton f."]}, "basionymAuthorTeam":{"authorTeam":"Raf.", "author":["Raf."]}}]}], "parser_run":1, "positions":{"0":["genus", 9], "10":["species", 17], "18":["infraspecific_type", 22], "23":["infraspecies", 32], "33":["infraspecific_type", 37], "38":["infraspecies", 47], "49":["author_word", 53], "55":["author_word", 62], "63":["author_word", 65]}}}
 Amelanchier arborea f. hirsuta (Michx. f.) Fernald|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Amelanchier arborea f. hirsuta (Michx. f.) Fernald", "normalized":"Amelanchier arborea f. hirsuta (Michx. f.) Fernald", "canonical":"Amelanchier arborea hirsuta", "hybrid":false, "details":[{"genus":{"string":"Amelanchier"}, "species":{"string":"arborea"}, "infraspecies":[{"string":"hirsuta", "rank":"f.", "authorship":"(Michx. f.) Fernald", "combinationAuthorTeam":{"authorTeam":"Fernald", "author":["Fernald"]}, "basionymAuthorTeam":{"authorTeam":"Michx. f.", "author":["Michx. f."]}}]}], "parser_run":1, "positions":{"0":["genus", 11], "12":["species", 19], "20":["infraspecific_type", 22], "23":["infraspecies", 30], "32":["author_word", 38], "39":["author_word", 41], "43":["author_word", 50]}}}
-Betula pendula fo. dalecarlica (L. f.) C.K. Schneid.|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Betula pendula fo. dalecarlica (L. f.) C.K. Schneid.", "normalized":"Betula pendula f. dalecarlica (L. f.) C.K. Schneid.", "canonical":"Betula pendula dalecarlica", "hybrid":false, "details":[{"genus":{"string":"Betula"}, "species":{"string":"pendula"}, "infraspecies":[{"string":"dalecarlica", "rank":"f.", "authorship":"(L. f.) C.K. Schneid.", "combinationAuthorTeam":{"authorTeam":"C.K. Schneid.", "author":["C.K. Schneid."]}, "basionymAuthorTeam":{"authorTeam":"L. f.", "author":["L. f."]}}]}], "parser_run":1, "positions":{"0":["genus", 6], "7":["species", 14], "15":["infraspecific_type", 18], "19":["infraspecies", 30], "32":["author_word", 34], "35":["author_word", 37], "39":["author_word", 43], "44":["author_word", 52]}}}
+Betula pendula fo. dalecarlica (L. f.) C.K. Schneid.|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Betula pendula fo. dalecarlica (L. f.) C.K. Schneid.", "normalized":"Betula pendula fo. dalecarlica (L. f.) C.K. Schneid.", "canonical":"Betula pendula dalecarlica", "hybrid":false, "details":[{"genus":{"string":"Betula"}, "species":{"string":"pendula"}, "infraspecies":[{"string":"dalecarlica", "rank":"fo.", "authorship":"(L. f.) C.K. Schneid.", "combinationAuthorTeam":{"authorTeam":"C.K. Schneid.", "author":["C.K. Schneid."]}, "basionymAuthorTeam":{"authorTeam":"L. f.", "author":["L. f."]}}]}], "parser_run":1, "positions":{"0":["genus", 6], "7":["species", 14], "15":["infraspecific_type", 18], "19":["infraspecies", 30], "32":["author_word", 34], "35":["author_word", 37], "39":["author_word", 43], "44":["author_word", 52]}}}
 Racomitrium canescens f. ericoides (F. Weber ex Brid.) Mönk.|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Racomitrium canescens f. ericoides (F. Weber ex Brid.) Mönk.", "normalized":"Racomitrium canescens f. ericoides (F. Weber ex Brid.) Mönk.", "canonical":"Racomitrium canescens ericoides", "hybrid":false, "details":[{"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."]}}}]}], "parser_run":1, "positions":{"0":["genus", 11], "12":["species", 21], "22":["infraspecific_type", 24], "25":["infraspecies", 34], "36":["author_word", 38], "39":["author_word", 44], "48":["author_word", 53], "55":["author_word", 60]}}}
-Racomitrium canescens forma ericoides (F. Weber ex Brid.) Mönk.|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Racomitrium canescens forma ericoides (F. Weber ex Brid.) Mönk.", "normalized":"Racomitrium canescens f. ericoides (F. Weber ex Brid.) Mönk.", "canonical":"Racomitrium canescens ericoides", "hybrid":false, "details":[{"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."]}}}]}], "parser_run":1, "positions":{"0":["genus", 11], "12":["species", 21], "22":["infraspecific_type", 27], "28":["infraspecies", 37], "39":["author_word", 41], "42":["author_word", 47], "51":["author_word", 56], "58":["author_word", 63]}}}
+Racomitrium canescens forma ericoides (F. Weber ex Brid.) Mönk.|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Racomitrium canescens forma ericoides (F. Weber ex Brid.) Mönk.", "normalized":"Racomitrium canescens forma ericoides (F. Weber ex Brid.) Mönk.", "canonical":"Racomitrium canescens ericoides", "hybrid":false, "details":[{"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."]}}}]}], "parser_run":1, "positions":{"0":["genus", 11], "12":["species", 21], "22":["infraspecific_type", 27], "28":["infraspecies", 37], "39":["author_word", 41], "42":["author_word", 47], "51":["author_word", 56], "58":["author_word", 63]}}}
 Polypodium pectinatum L. f., Rosenst.|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Polypodium pectinatum L. f., Rosenst.", "normalized":"Polypodium pectinatum L. f., Rosenst.", "canonical":"Polypodium pectinatum", "hybrid":false, "details":[{"genus":{"string":"Polypodium"}, "species":{"string":"pectinatum", "authorship":"L. f., Rosenst.", "basionymAuthorTeam":{"authorTeam":"L. f., Rosenst.", "author":["L. f.", "Rosenst."]}}}], "parser_run":1, "positions":{"0":["genus", 10], "11":["species", 21], "22":["author_word", 24], "25":["author_word", 27], "29":["author_word", 37]}}}
 Polypodium pectinatum L. f.|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Polypodium pectinatum L. f.", "normalized":"Polypodium pectinatum L. f.", "canonical":"Polypodium pectinatum", "hybrid":false, "details":[{"genus":{"string":"Polypodium"}, "species":{"string":"pectinatum", "authorship":"L. f.", "basionymAuthorTeam":{"authorTeam":"L. f.", "author":["L. f."]}}}], "parser_run":1, "positions":{"0":["genus", 10], "11":["species", 21], "22":["author_word", 24], "25":["author_word", 27]}}}
 Polypodium pectinatum (L. f.) typica Rosent|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Polypodium pectinatum (L. f.) typica Rosent", "normalized":"Polypodium pectinatum (L. f.) typica Rosent", "canonical":"Polypodium pectinatum typica", "hybrid":false, "details":[{"genus":{"string":"Polypodium"}, "species":{"string":"pectinatum", "authorship":"(L. f.)", "basionymAuthorTeam":{"authorTeam":"L. f.", "author":["L. f."]}}, "infraspecies":[{"string":"typica", "rank":"n/a", "authorship":"Rosent", "basionymAuthorTeam":{"authorTeam":"Rosent", "author":["Rosent"]}}]}], "parser_run":1, "positions":{"0":["genus", 10], "11":["species", 21], "23":["author_word", 25], "26":["author_word", 28], "30":["infraspecies", 36], "37":["author_word", 43]}}}

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: biodiversity19
 version: !ruby/object:Gem::Version
-  version: 1.0.10
+  version: 1.0.11
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-01-25 00:00:00.000000000Z
+date: 2012-06-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: treetop
-  requirement: &70227647806880 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,10 +21,15 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *70227647806880
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: parallel
-  requirement: &70227647806400 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -32,10 +37,15 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *70227647806400
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &70227647805920 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -43,10 +53,15 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *70227647805920
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: treetop
-  requirement: &70227647805440 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -54,10 +69,15 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *70227647805440
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: parallel
-  requirement: &70227647804960 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -65,10 +85,15 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *70227647804960
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &70227647804480 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -76,7 +101,12 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *70227647804480
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 description: Tools for biodiversity informatics
 email: dmozzherin@gmail.com
 executables:
@@ -137,7 +167,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.10
+rubygems_version: 1.8.24
 signing_key: 
 specification_version: 3
 summary: Parser of scientific names