dimus-biodiversity 0.0.16 → 0.0.18

data/lib/biodiversity/parser/scientific_name_clean.treetop

@@ -469,7 +469,7 @@ grammar ScientificNameClean
       end
     }
     /
-    ("anon."/"f."/"bis"/"arg."/"da"/"der"/"den"/"de"/"du"/"la"/"ter"/"van"/"et al.\{\?\}"/"et al.") {
+    ("anon."/"f."/"bis"/"arg."/author_prefix/"et al.\{\?\}"/"et al.") {
       def value
         text_value.strip
       end
@@ -498,6 +498,10 @@ grammar ScientificNameClean
       end
     }
   end
+
+  rule author_prefix
+    "da"/"der"/"den"/"de"/"du"/"la"/"ter"/"van"/"von"
+  end
   
   rule name_part
     space a:species_name space b:rank space_hard c:editorials_full {
@@ -517,6 +521,24 @@ grammar ScientificNameClean
       end
     }
     /
+    space a:species_name &(space author_prefix) {
+      def value
+        a.value
+      end
+      
+      def canonical
+        a.canonical
+      end
+
+      def pos
+        a.pos
+      end
+
+      def details
+        a.details
+      end
+    }
+    /
     space a:species_name space b:subspecies_names {
       def value
         a.value + b.value
@@ -534,13 +556,13 @@ grammar ScientificNameClean
       end
     }
     /
-    space a:species_name space b:latin_word ![\.] {
+    space a:species_name space b:species_word ![\.] {
       def value
         a.value + " " + b.value
       end
       
       def canonical
-        value
+        a.canonical + " " + b.value
       end
       
       def pos
@@ -581,7 +603,7 @@ grammar ScientificNameClean
   end
   
   rule subspecies_name
-    sel:rank space_hard a:latin_word {
+    sel:rank space_hard a:species_word {
       def value 
         sel.apply(a)
       end
@@ -626,7 +648,7 @@ grammar ScientificNameClean
   end
   
   rule rank
-    ("morph."/"f.sp."/"B"/"ssp."/"mut."/"pseudovar."/"sect."/"ser."/"var."/"subvar."/ "[var.]" /"subsp."/"subf."/"race"/"α" 
+    ("morph."/"f.sp."/"B"/"ssp."/"nat"/"mut."/"pseudovar."/"sect."/"ser."/"var."/"subvar."/ "[var.]" /"subsp."/"subf."/"race"/"α" 
     /"ββ"/"β"/"γ"/"δ"/"ε"/"φ"/"θ"/"μ"/"a."/"b."/"c."/"d."/"e."/"g."/"k."/"****"/"**"/"*")
     {
       def value
@@ -665,7 +687,7 @@ grammar ScientificNameClean
   end
   
   rule species_name
-    hybrid_separator space_hard a:cap_latin_word space_hard b:latin_word {
+    hybrid_separator space_hard a:cap_latin_word space_hard b:species_word {
       def value
         "× " + a.value + " " + b.value
       end
@@ -699,7 +721,7 @@ grammar ScientificNameClean
       end
     }
     /
-    a:cap_latin_word space_hard hybrid_separator space_hard b:latin_word {
+    a:cap_latin_word space_hard hybrid_separator space_hard b:species_word {
       def value
         a.value + " × " + b.value
       end
@@ -716,7 +738,7 @@ grammar ScientificNameClean
       end
     }
     /
-    a:cap_latin_word space b:subgenus space c:latin_word {
+    a:cap_latin_word space b:subgenus space c:species_word {
       def value
         a.value + " " + b.value + " " + c.value
       end
@@ -733,7 +755,7 @@ grammar ScientificNameClean
       end
     } 
     /
-    a:cap_latin_word space_hard b:latin_word {
+    a:cap_latin_word space_hard b:species_word {
       def value
         a.value + " " + b.value 
       end
@@ -757,6 +779,10 @@ grammar ScientificNameClean
         "(" + a.value + ")"
       end
       
+      def canonical
+        ''
+      end
+      
       def pos
         {a.interval.begin => ['subgenus', a.interval.end]}
       end
@@ -792,7 +818,7 @@ grammar ScientificNameClean
         " " + text_value + " " + a.value
       end
       def canonical(a)
-        " " + a.value
+        ""
       end
       def details(a = nil)
         {:subgenus => [{:rank => text_value, :value => (a.value rescue nil)}]}
@@ -800,7 +826,6 @@ grammar ScientificNameClean
     }
   end
   
-  
   rule cap_latin_word
     a:([A-Z]/cap_digraph) b:latin_word "?" {
       def value
@@ -856,6 +881,16 @@ grammar ScientificNameClean
       end
     }
   end
+  
+  rule species_word
+    a:[0-9]+ "-"? b:latin_word {
+      def value
+        a.text_value + "-"+ b.value
+      end
+    }
+    /
+    latin_word
+  end
 
   rule latin_word
     a:[a-zëüäöïé] b:full_name_letters {
@@ -1021,4 +1056,4 @@ grammar ScientificNameClean
       end
     }
   end
-end
+end

data/spec/parser/scientific_name_canonical.spec.rb

@@ -36,13 +36,15 @@ describe ScientificNameCanonical do
     
   it 'should parse names with valid name part and unparseable rest' do
     [
-      ['Moraea spathulata ( (L. f. Klatt','Moraea spathulata',{:genus=>"Moraea", :species=>"spathulata", :name_part_verbatim=>"Moraea spathulata", :auth_part_verbatim=>"( (L. f. Klatt"}, {0=>["genus", 6], 7=>["species", 17]} ],
-      ['Verpericola megasoma ""Dall" Pils.','Verpericola megasoma',{:genus=>"Verpericola", :species=>"megasoma", :name_part_verbatim=>"Verpericola megasoma", :auth_part_verbatim=>"\"\"Dall\" Pils."}, {0=>["genus", 11], 12=>["species", 20]}] 
+      ['Moraea spathulata ( (L. f. Klatt','Moraea spathulata','Moraea spathulata',{:genus=>"Moraea", :species=>"spathulata", :name_part_verbatim=>"Moraea spathulata", :auth_part_verbatim=>"( (L. f. Klatt"}, {0=>["genus", 6], 7=>["species", 17]} ],
+      ['Verpericola megasoma ""Dall" Pils.','Verpericola megasoma','Verpericola megasoma',{:genus=>"Verpericola", :species=>"megasoma", :name_part_verbatim=>"Verpericola megasoma", :auth_part_verbatim=>"\"\"Dall\" Pils."}, {0=>["genus", 11], 12=>["species", 20]}],
+      ['Nesticus cellulanus affinis Kulczynski, in Chyzer & Kulczynski, 1894','Nesticus cellulanus affinis','Nesticus cellulanus affinis',{:genus=>"Nesticus", :species=>"cellulanus", :subspecies=>{:rank=>"n/a", :value=>"affinis"}, :name_part_verbatim=>"Nesticus cellulanus", :auth_part_verbatim=>"Kulczynski, in Chyzer & Kulczynski, 1894"},{0=>["genus", 8], 9=>["species", 19], 20=>["subspecies", 27]}]
     ].each do |n|
       parse(n[0]).should_not be_nil
       value(n[0]).should == n[1]
-      details(n[0]).should == n[2]
-      pos(n[0]).should == n[3]
+      canonical(n[0]).should == n[2]
+      details(n[0]).should == n[3]
+      pos(n[0]).should == n[4]
     end
   end  
 end

data/spec/parser/scientific_name_clean.spec.rb

@@ -175,7 +175,7 @@ describe ScientificNameClean do
   it 'should parse scientific name' do
     sn = "Abacetus laevicollis de Chaudoir, 1869"
     parse(sn).should_not be_nil
-    #TODO!!!!!! canonical(sn).should == 'Abacetus laevicollis'
+    canonical(sn).should == 'Abacetus laevicollis'
     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 et Crous 2003"
     canonical("Pseudocercospora dendrobii(H.C.     Burnett)U. Braun & Crous     2003").should == "Pseudocercospora dendrobii"
@@ -474,4 +474,25 @@ end
     pos(sn).should == {0=>["genus", 14], 15=>["species", 22]}
   end
   
+  it 'should parse new additions' do
+    sn = "Abacetus laevicollis de Chaudoir, 1869"
+    parse(sn).should_not be_nil
+    canonical(sn).should == 'Abacetus laevicollis'
+    sn = "Gastrosericus eremorum van Beaumont 1955"
+    canonical(sn).should == 'Gastrosericus eremorum'
+    sn = "Gastrosericus eremorum von Beaumont 1955"
+    canonical(sn).should == 'Gastrosericus eremorum'
+    sn = "Cypraeovula (Luponia) amphithales perdentata"
+    canonical(sn).should == 'Cypraeovula amphithales perdentata'
+    details(sn).should == {:genus=>"Cypraeovula", :subgenus=>"Luponia", :species=>"amphithales", :subspecies=>{:rank=>"n/a", :value=>"perdentata"}}
+    sn = "Polyrhachis orsyllus nat musculus Forel 1901"
+    canonical(sn).should == "Polyrhachis orsyllus musculus"
+    sn = 'Latrodectus 13-guttatus Thorell, 1875'
+    canonical(sn).should == 'Latrodectus 13-guttatus'
+    value(sn).should == 'Latrodectus 13-guttatus Thorell 1875'
+    sn = 'Latrodectus 3guttatus Thorell, 1875'
+    canonical(sn).should == 'Latrodectus 3-guttatus'
+    value(sn).should == 'Latrodectus 3-guttatus Thorell 1875'
+  end
+  
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: dimus-biodiversity
 version: !ruby/object:Gem::Version 
-  version: 0.0.16
+  version: 0.0.18
 platform: ruby
 authors: 
 - Dmitry Mozzherin
@@ -9,7 +9,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2009-04-11 00:00:00 -07:00
+date: 2009-06-12 00:00:00 -07:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency