biodiversity 1.0.9 → 1.0.10

data/LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2009 Dmitry Mozzherin
+Copyright (c) 2009-2012 Marine Biological Laboratory
 
 Permission is hereby granted, free of charge, to any person obtaining
 a copy of this software and associated documentation files (the

data/README.rdoc

@@ -31,9 +31,9 @@ to return a canonical form of the name string
 
   parserver --output=canonical_with_rank
 
-the same as above, but infracpecies' rank is shown if available
+the same as above, but infraspecies' rank is shown if available
 
-  praserver --port 5555
+  parserver --port 5555
 
 run socket server on a different port
 
@@ -88,7 +88,9 @@ You can use it as a library
   # to parse using several CPUs (4 seem to be optimal)
   parser = ParallelParser.new # ParallelParser.new(4) will try to run 4 processes if hardware allows
   array_of_names = ["Betula alba", "Homo sapiens"....]
-  parser.parse(array_of_names) # -> {"Betula alba" => "{scientificName...}", "Homo sapiens" => "{scientificName...}", ...}
+  parser.parse(array_of_names) # -> {"Betula alba" => {:scientificName...}, "Homo sapiens" => {:scientificName...}, ...}
+
+  parallel parser takes list of names and returns back a hash with names as keys and parsed data as values
 
   # to resolve lsid and get back RDF file
   LsidResolver.resolve("urn:lsid:ubio.org:classificationbank:2232671")

data/VERSION

@@ -1 +1 @@
-1.0.9
+1.0.10

data/lib/biodiversity/parser.rb

@@ -47,7 +47,7 @@ class ParallelParser
   private
   def parse_process(name)
     p = ScientificNameParser.new
-    p.parse(name).to_json rescue {'scientificName' => {'parsed' => false, 'verbatim' => name,  'error' => 'Parser error'}}.to_json
+    p.parse(name) rescue {:scientificName => {:parsed => false, :verbatim => name,  :error => 'Parser error'}}
   end
 end
 

data/lib/biodiversity/parser/scientific_name_clean.treetop

@@ -909,7 +909,7 @@ grammar ScientificNameClean
   end
 
   rule author_name
-    space a:author_name_without_postfix space b:author_postix_word {
+    space a:author_name_without_postfix space b:author_postfix_word space !latin_word {
       def value
         a.value + ' ' + b.value
       end
@@ -1032,8 +1032,8 @@ grammar ScientificNameClean
     }
   end
 
-  rule author_postix_word
-    space ("f."/"filius") space {
+  rule author_postfix_word
+    ("f."/"filius") {
       def value 
         text_value.strip
       end

data/spec/parser/scientific_name.spec.rb

@@ -70,4 +70,16 @@ describe ParallelParser do
     names.size.should > 100
     res.keys.size.should == names.size
   end
+
+  it "should have parsed name in native ruby format and in returned as a hash with name as a key and parsed data as value" do
+    names = []
+    read_test_file { |n| names << (n[:name]) if n[:name] }
+    names.uniq!
+    pparser = ParallelParser.new(4)
+    res = pparser.parse(names)
+    names.each_with_index do |name, i|
+      res[name].is_a?(Hash).should be_true
+      res[name][:scientificName][:verbatim].should == name
+    end
+  end
 end

data/spec/parser/scientific_name_clean.spec.rb

@@ -255,7 +255,23 @@ 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"
+    # might get confused with forma vs filius
+    sn = "Polypodium pectinatum L.f. typica Rosenst."
+    canonical(sn).should == "Polypodium pectinatum typica"
+    sn = "Polypodium pectinatum (L.) f. typica Rosenst."
+    canonical(sn).should == "Polypodium pectinatum typica"
+    sn = "Polypodium pectinatum L. f., Rosenst."
+    canonical(sn).should == "Polypodium pectinatum"
+    sn = "Polypodium pectinatum L. f."
+    canonical(sn).should == "Polypodium pectinatum"
+    sn = "Polypodium pectinatum (L. f.) typica Rosent."
+    canonical(sn).should == "Polypodium pectinatum typica"
+    sn = "Polypodium pectinatum L. f. thisisjunk Rosent."
+    canonical(sn).should == "Polypodium pectinatum thisisjunk"
   end
 
   it 'should parse unknown original authors (auct.)/(hort.)/(?)' do

data/spec/parser/scientific_name_dirty.spec.rb

@@ -93,7 +93,7 @@ describe ScientificNameDirty do
   end
   
   it 'should parse names with "common" utf-8 charactes' do
-    names = ["Rühlella","Sténométope laevissimus Bibron 1855"].each do |name|
+    names = ["Rühlella","Sténométope laevissimus Bibron 1855", "Döringina Ihering 1929"].each do |name|
       parse(name).should_not be_nil
     end
   end

data/spec/parser/test_data.txt

@@ -9,6 +9,7 @@ Pseudocercospora|{"scientificName":{"parsed":true, "parser_version":"test_versio
 
 #uninomial with author
 Pseudocercospora Speg.|{"scientificName":{"parsed":true, "parser_version":"test_version", "parser_run":1,"verbatim":"Pseudocercospora Speg.","normalized":"Pseudocercospora Speg.","canonical":"Pseudocercospora","hybrid":false,"details":[{"uninomial":{"string":"Pseudocercospora","authorship":"Speg.","basionymAuthorTeam":{"authorTeam":"Speg.","author":["Speg."]}}}],"positions":{"0":["uninomial",16],"17":["author_word",22]}}}
+Döringina Ihering 1929|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Döringina Ihering 1929", "normalized":"Doringina Ihering 1929", "canonical":"Doringina", "hybrid":false, "details":[{"uninomial":{"string":"Doringina", "authorship":"Ihering 1929", "basionymAuthorTeam":{"authorTeam":"Ihering", "author":["Ihering"], "year":"1929"}}}], "parser_run":2, "positions":{"0":["uninomial", 9], "10":["author_word", 17], "18":["year", 22]}}}
 
 #uninomial with author and year
 Pseudocercospora Speg. 1910|{"scientificName":{"parsed":true, "parser_version":"test_version", "parser_run":1,"verbatim":"Pseudocercospora Speg. 1910","normalized":"Pseudocercospora Speg. 1910","canonical":"Pseudocercospora","hybrid":false,"details":[{"uninomial":{"string":"Pseudocercospora","authorship":"Speg. 1910","basionymAuthorTeam":{"authorTeam":"Speg.","author":["Speg."],"year":"1910"}}}],"positions":{"0":["uninomial",16],"17":["author_word",22],"23":["year",27]}}}
@@ -110,6 +111,13 @@ Sphaerotheca    fuliginea    f.     dahliae    Movss.     1967|{"scientificName"
 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]}}}
 Prunus armeniaca convar. budae (Pénzes) Soó|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Prunus armeniaca convar. budae (Pénzes) Soó", "normalized":"Prunus armeniaca convar. budae (Pénzes) Soó", "canonical":"Prunus armeniaca budae", "hybrid":false, "details":[{"genus":{"string":"Prunus"}, "species":{"string":"armeniaca"}, "infraspecies":[{"string":"budae", "rank":"convar.", "authorship":"(Pénzes) Soó", "combinationAuthorTeam":{"authorTeam":"Soó", "author":["Soó"]}, "basionymAuthorTeam":{"authorTeam":"Pénzes", "author":["Pénzes"]}}]}], "parser_run":1, "positions":{"0":["genus", 6], "7":["species", 16], "17":["infraspecific_type", 24], "25":["infraspecies", 30], "32":["author_word", 38], "40":["author_word", 43]}}}
+Polypodium pectinatum (L.) f. typica Rosenst.|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Polypodium pectinatum (L.) f. typica Rosenst.", "normalized":"Polypodium pectinatum (L.) f. typica Rosenst.", "canonical":"Polypodium pectinatum typica", "hybrid":false, "details":[{"genus":{"string":"Polypodium"}, "species":{"string":"pectinatum", "authorship":"(L.)", "basionymAuthorTeam":{"authorTeam":"L.", "author":["L."]}}, "infraspecies":[{"string":"typica", "rank":"f.", "authorship":"Rosenst.", "basionymAuthorTeam":{"authorTeam":"Rosenst.", "author":["Rosenst."]}}]}], "parser_run":1, "positions":{"0":["genus", 10], "11":["species", 21], "23":["author_word", 25], "27":["infraspecific_type", 29], "30":["infraspecies", 36], "37":["author_word", 45]}}}
+Polypodium pectinatum L. f. typica Rosenst.|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Polypodium pectinatum L. f. typica Rosenst.", "normalized":"Polypodium pectinatum L. f. typica Rosenst.", "canonical":"Polypodium pectinatum typica", "hybrid":false, "details":[{"genus":{"string":"Polypodium"}, "species":{"string":"pectinatum", "authorship":"L.", "basionymAuthorTeam":{"authorTeam":"L.", "author":["L."]}}, "infraspecies":[{"string":"typica", "rank":"f.", "authorship":"Rosenst.", "basionymAuthorTeam":{"authorTeam":"Rosenst.", "author":["Rosenst."]}}]}], "parser_run":1, "positions":{"0":["genus", 10], "11":["species", 21], "22":["author_word", 24], "25":["infraspecific_type", 27], "28":["infraspecies", 34], "35":["author_word", 43]}}}
+# TODO: the following phrasing can be ambiguous. Does f mean forma or filius? Currently capturing it as filius
+Polypodium pectinatum L.f. typica Rosenst.|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Polypodium pectinatum L.f. typica Rosenst.", "normalized":"Polypodium pectinatum L.f. typica Rosenst.", "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":"Rosenst.", "basionymAuthorTeam":{"authorTeam":"Rosenst.", "author":["Rosenst."]}}]}], "parser_run":1, "positions":{"0":["genus", 10], "11":["species", 21], "22":["author_word", 26], "27":["infraspecies", 33], "34":["author_word", 42]}}}
+Polypodium pectinatum L. f. thisisjunk Rosent.|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Polypodium pectinatum L. f. thisisjunk Rosent.", "normalized":"Polypodium pectinatum L. f. thisisjunk Rosent.", "canonical":"Polypodium pectinatum thisisjunk", "hybrid":false, "details":[{"genus":{"string":"Polypodium"}, "species":{"string":"pectinatum", "authorship":"L.", "basionymAuthorTeam":{"authorTeam":"L.", "author":["L."]}}, "infraspecies":[{"string":"thisisjunk", "rank":"f.", "authorship":"Rosent.", "basionymAuthorTeam":{"authorTeam":"Rosent.", "author":["Rosent."]}}]}], "parser_run":1, "positions":{"0":["genus", 10], "11":["species", 21], "22":["author_word", 24], "25":["infraspecific_type", 27], "28":["infraspecies", 38], "39":["author_word", 46]}}}
+Polypodium lineare C.Chr. f. caudatoattenuatum Takeda|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Polypodium lineare C.Chr. f. caudatoattenuatum Takeda", "normalized":"Polypodium lineare C.Chr. f. caudatoattenuatum Takeda", "canonical":"Polypodium lineare caudatoattenuatum", "hybrid":false, "details":[{"genus":{"string":"Polypodium"}, "species":{"string":"lineare", "authorship":"C.Chr.", "basionymAuthorTeam":{"authorTeam":"C.Chr.", "author":["C.Chr."]}}, "infraspecies":[{"string":"caudatoattenuatum", "rank":"f.", "authorship":"Takeda", "basionymAuthorTeam":{"authorTeam":"Takeda", "author":["Takeda"]}}]}], "parser_run":1, "positions":{"0":["genus", 10], "11":["species", 18], "19":["author_word", 25], "26":["infraspecific_type", 28], "29":["infraspecies", 46], "47":["author_word", 53]}}}
+Rhododendron weyrichii Maxim. f. albiflorum T.Yamaz.|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Rhododendron weyrichii Maxim. f. albiflorum T.Yamaz.", "normalized":"Rhododendron weyrichii Maxim. f. albiflorum T.Yamaz.", "canonical":"Rhododendron weyrichii albiflorum", "hybrid":false, "details":[{"genus":{"string":"Rhododendron"}, "species":{"string":"weyrichii", "authorship":"Maxim.", "basionymAuthorTeam":{"authorTeam":"Maxim.", "author":["Maxim."]}}, "infraspecies":[{"string":"albiflorum", "rank":"f.", "authorship":"T.Yamaz.", "basionymAuthorTeam":{"authorTeam":"T.Yamaz.", "author":["T.Yamaz."]}}]}], "parser_run":1, "positions":{"0":["genus", 12], "13":["species", 22], "23":["author_word", 29], "30":["infraspecific_type", 32], "33":["infraspecies", 43], "44":["author_word", 52]}}}
 
 #infraspecies_multiple
 Hydnellum scrobiculatum var. zonatum f. parvum (Banker) D. Hall & D.E. Stuntz 1972|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Hydnellum scrobiculatum var. zonatum f. parvum (Banker) D. Hall & D.E. Stuntz 1972", "normalized":"Hydnellum scrobiculatum var. zonatum f. parvum (Banker) D. Hall et D.E. Stuntz 1972", "canonical":"Hydnellum scrobiculatum zonatum parvum", "hybrid":false, "details":[{"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"]}}]}], "parser_run":1, "positions":{"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]}}}
@@ -277,8 +285,8 @@ Eichornia crassipes ( (Martius) ) Solms-Laub.|{"scientificName":{"parsed":true,
 Acarospora cratericola 1929|{"scientificName":{"parsed":true, "parser_version":"test_version", "parser_run":2,"verbatim":"Acarospora cratericola 1929","normalized":"Acarospora cratericola 1929","canonical":"Acarospora cratericola","hybrid":false,"details":[{"genus":{"string":"Acarospora"},"species":{"string":"cratericola","year":"1929"}}],"positions":{"0":["genus",10],"11":["species",22],"23":["year",27]}}}
 
 #authorship with filius (son of)
-Platypus bicaudatulus Schedl f. 1935|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Platypus bicaudatulus Schedl f. 1935", "normalized":"Platypus bicaudatulus Schedl f. 1935", "canonical":"Platypus bicaudatulus", "hybrid":false, "details":[{"genus":{"string":"Platypus"}, "species":{"string":"bicaudatulus", "authorship":"Schedl f. 1935", "basionymAuthorTeam":{"authorTeam":"Schedl f.", "author":["Schedl f."], "year":"1935"}}}], "parser_run":1, "positions":{"0":["genus", 8], "9":["species", 21], "22":["author_word", 28], "29":["author_word", 32], "32":["year", 36]}}}
-Platypus bicaudatulus Schedl filius 1935|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Platypus bicaudatulus Schedl filius 1935", "normalized":"Platypus bicaudatulus Schedl filius 1935", "canonical":"Platypus bicaudatulus", "hybrid":false, "details":[{"genus":{"string":"Platypus"}, "species":{"string":"bicaudatulus", "authorship":"Schedl filius 1935", "basionymAuthorTeam":{"authorTeam":"Schedl filius", "author":["Schedl filius"], "year":"1935"}}}], "parser_run":1, "positions":{"0":["genus", 8], "9":["species", 21], "22":["author_word", 28], "29":["author_word", 36], "36":["year", 40]}}}
+Platypus bicaudatulus Schedl f. 1935|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Platypus bicaudatulus Schedl f. 1935", "normalized":"Platypus bicaudatulus Schedl f. 1935", "canonical":"Platypus bicaudatulus", "hybrid":false, "details":[{"genus":{"string":"Platypus"}, "species":{"string":"bicaudatulus", "authorship":"Schedl f. 1935", "basionymAuthorTeam":{"authorTeam":"Schedl f.", "author":["Schedl f."], "year":"1935"}}}], "parser_run":1, "positions":{"0":["genus", 8], "9":["species", 21], "22":["author_word", 28], "29":["author_word", 31], "32":["year", 36]}}}
+Platypus bicaudatulus Schedl filius 1935|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Platypus bicaudatulus Schedl filius 1935", "normalized":"Platypus bicaudatulus Schedl filius 1935", "canonical":"Platypus bicaudatulus", "hybrid":false, "details":[{"genus":{"string":"Platypus"}, "species":{"string":"bicaudatulus", "authorship":"Schedl filius 1935", "basionymAuthorTeam":{"authorTeam":"Schedl filius", "author":["Schedl filius"], "year":"1935"}}}], "parser_run":1, "positions":{"0":["genus", 8], "9":["species", 21], "22":["author_word", 28], "29":["author_word", 35], "36":["year", 40]}}}
 Fimbristylis ovata (Burm. f.) J. Kern|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Fimbristylis ovata (Burm. f.) J. Kern", "normalized":"Fimbristylis ovata (Burm. f.) J. Kern", "canonical":"Fimbristylis ovata", "hybrid":false, "details":[{"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."]}}}], "parser_run":1, "positions":{"0":["genus", 12], "13":["species", 18], "20":["author_word", 25], "26":["author_word", 28], "30":["author_word", 32], "33":["author_word", 37]}}}
 Carex chordorrhiza Ehrh. ex L. f.|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Carex chordorrhiza Ehrh. ex L. f.", "normalized":"Carex chordorrhiza Ehrh. ex L. f.", "canonical":"Carex chordorrhiza", "hybrid":false, "details":[{"genus":{"string":"Carex"}, "species":{"string":"chordorrhiza", "authorship":"Ehrh. ex L. f.", "basionymAuthorTeam":{"authorTeam":"Ehrh.", "author":["Ehrh."], "exAuthorTeam":{"authorTeam":"L. f.", "author":["L. f."]}}}}], "parser_run":1, "positions":{"0":["genus", 5], "6":["species", 18], "19":["author_word", 24], "28":["author_word", 30], "31":["author_word", 33]}}}
 Amelanchier arborea var. arborea (Michx. f.) Fernald|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Amelanchier arborea var. arborea (Michx. f.) Fernald", "normalized":"Amelanchier arborea var. arborea (Michx. f.) Fernald", "canonical":"Amelanchier arborea arborea", "hybrid":false, "details":[{"genus":{"string":"Amelanchier"}, "species":{"string":"arborea"}, "infraspecies":[{"string":"arborea", "rank":"var.", "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", 24], "25":["infraspecies", 32], "34":["author_word", 40], "41":["author_word", 43], "45":["author_word", 52]}}}
@@ -289,6 +297,9 @@ Amelanchier arborea f. hirsuta (Michx. f.) Fernald|{"scientificName":{"parsed":t
 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]}}}
 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]}}}
+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]}}}
 
 #year range
 Tridentella tangeroae Bruce, 1987-92|{"scientificName":{"parsed":true, "parser_version":"test_version", "parser_run":2,"verbatim":"Tridentella tangeroae Bruce, 1987-92","normalized":"Tridentella tangeroae Bruce 1987-92","canonical":"Tridentella tangeroae","hybrid":false,"details":[{"genus":{"string":"Tridentella"},"species":{"string":"tangeroae","authorship":"Bruce, 1987-92","basionymAuthorTeam":{"authorTeam":"Bruce","author":["Bruce"],"year":"1987-92"}}}],"positions":{"0":["genus",11],"12":["species",21],"22":["author_word",27],"29":["year",36]}}}

data/spec/parser/todo.txt

@@ -0,0 +1,28 @@
+Rana aurora Baird and Girard, 1852; H.B. Shaffer et al., 2004 <---- WRONG CANONICAL FORM!!!!!!!!
+
+Gemmula cf. cosmoi NP-2008 <--- WRONG CANONICAL FORM
+Eupithecia cf. E. maestosa
+Eupithecia cf. maestosa
+Aleiodes Tetrasphaeropyx chumashanus => Aleiodes [subgenus] chumashanus
+
+Cucurbita pepo subsp. ovifera x subsp. fraterna
+
+Döringina Ihering 1929 (synonym)          Dzzringina
+Doringina Ihering, 1929 (synonym)          Döringina
+
+Lacanobia nr. subjuncta Bold:Aab, 0925       Lacanobia nr
+Lacanobia sp. nr. subjuncta Bold:Aab, 0925     Lacanobia sp
+
+Agropyron pectiniforme var. karabaljikji ined.?          Agropyron pectiniforme
+Shaanxilithes Xing, Yue & Zhang, 1984       Shaanxilithes ing
+Parapandorina Xue, Tang, Yu & Zhou 1995          Parapandorina ue
+
+Potamogeton iilinoensis var. ventanicola (Hicken) Horn af Rantzien       Potamogeton iilinoensis var. ventanicola af
+Rhododendron weyrichii Maxim. f. albiflorum T.Yamaz.       Rhododendron
+
+Polypodium pectinatum L. f. typica Rosenst.             Polypodium
+Polypodium lineare C.Chr. f. caudatoattenuatum Takeda   Polypodium
+
+
+Rosa gallica × tomentosa var. eglandulosa R.Keller      Rosa gallica
+Rosa gallica × afzeliana subsp. vosagiaca forma subcomplicata R.Keller        Rosa gallica

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: biodiversity
 version: !ruby/object:Gem::Version 
-  hash: 5
+  hash: 3
   prerelease: 
   segments: 
   - 1
   - 0
-  - 9
-  version: 1.0.9
+  - 10
+  version: 1.0.10
 platform: ruby
 authors: 
 - Dmitry Mozzherin
@@ -15,10 +15,10 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-11-30 00:00:00 Z
+date: 2012-01-25 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
-  requirement: &id001 !ruby/object:Gem::Requirement 
+  version_requirements: &id001 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
@@ -27,12 +27,12 @@ dependencies:
         segments: 
         - 0
         version: "0"
-  version_requirements: *id001
-  name: treetop
+  requirement: *id001
   prerelease: false
+  name: treetop
   type: :runtime
 - !ruby/object:Gem::Dependency 
-  requirement: &id002 !ruby/object:Gem::Requirement 
+  version_requirements: &id002 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
@@ -41,12 +41,12 @@ dependencies:
         segments: 
         - 0
         version: "0"
-  version_requirements: *id002
-  name: parallel
+  requirement: *id002
   prerelease: false
+  name: parallel
   type: :runtime
 - !ruby/object:Gem::Dependency 
-  requirement: &id003 !ruby/object:Gem::Requirement 
+  version_requirements: &id003 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
@@ -55,12 +55,12 @@ dependencies:
         segments: 
         - 0
         version: "0"
-  version_requirements: *id003
-  name: jeweler
+  requirement: *id003
   prerelease: false
+  name: jeweler
   type: :development
 - !ruby/object:Gem::Dependency 
-  requirement: &id004 !ruby/object:Gem::Requirement 
+  version_requirements: &id004 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
@@ -69,12 +69,12 @@ dependencies:
         segments: 
         - 0
         version: "0"
-  version_requirements: *id004
-  name: treetop
+  requirement: *id004
   prerelease: false
+  name: treetop
   type: :runtime
 - !ruby/object:Gem::Dependency 
-  requirement: &id005 !ruby/object:Gem::Requirement 
+  version_requirements: &id005 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
@@ -83,12 +83,12 @@ dependencies:
         segments: 
         - 0
         version: "0"
-  version_requirements: *id005
-  name: parallel
+  requirement: *id005
   prerelease: false
+  name: parallel
   type: :runtime
 - !ruby/object:Gem::Dependency 
-  requirement: &id006 !ruby/object:Gem::Requirement 
+  version_requirements: &id006 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
@@ -97,12 +97,12 @@ dependencies:
         segments: 
         - 0
         version: "0"
-  version_requirements: *id006
-  name: json
+  requirement: *id006
   prerelease: false
+  name: json
   type: :runtime
 - !ruby/object:Gem::Dependency 
-  requirement: &id007 !ruby/object:Gem::Requirement 
+  version_requirements: &id007 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
@@ -111,9 +111,9 @@ dependencies:
         segments: 
         - 0
         version: "0"
-  version_requirements: *id007
-  name: rspec
+  requirement: *id007
   prerelease: false
+  name: rspec
   type: :development
 description: Tools for biodiversity informatics
 email: dmozzherin@gmail.com
@@ -154,6 +154,7 @@ files:
 - spec/parser/scientific_name_dirty.spec.rb
 - spec/parser/spec_helper.rb
 - spec/parser/test_data.txt
+- spec/parser/todo.txt
 - spec/spec_helper.rb
 homepage: http://github.com/GlobalNamesArchitecture/biodiversity
 licenses: []