biodiversity 0.5.15 → 0.5.16

data/lib/biodiversity/parser/scientific_name_clean.treetop

@@ -22,6 +22,10 @@ grammar ScientificNameClean
       def details
         a.details.class == Array ? a.details : [a.details]
       end
+
+      def parser_run
+        1
+      end
     }
   end
   
@@ -509,7 +513,7 @@ grammar ScientificNameClean
   end
   
   rule genus
-    a:cap_latin_word !(space_hard author_prefix_word space_hard author_word) {
+    a:(cap_latin_word_pair/cap_latin_word) !(space_hard author_prefix_word space_hard author_word) {
       def value
         a.value
       end
@@ -555,7 +559,7 @@ grammar ScientificNameClean
   end
 
   rule uninomial_string
-    cap_latin_word {
+    (cap_latin_word_pair/cap_latin_word) {
       def canonical
         value
       end
@@ -938,6 +942,14 @@ grammar ScientificNameClean
     }
   end
   
+  rule cap_latin_word_pair
+    a:cap_latin_word "-" b:cap_latin_word {
+      def value
+        a.value + b.value.downcase
+      end
+    }
+  end
+  
   rule cap_latin_word
     a:([A-Z]/cap_digraph) b:latin_word "?" {
       def value
@@ -951,6 +963,12 @@ grammar ScientificNameClean
       end
     }
     /
+    a:("AE"/"OE") b:latin_word {
+      def value
+        a.text_value[0..0] + 'e' + b.value
+      end
+    }
+    /
     ("Ca"/"Ea"/"Ge"/"Ia"/"Io"/"Io"/"Ix"/"Lo"/"Oa"/"Ra"/"Ty"/"Ua"/"Aa"/"Ja"/"Zu"/"La"/"Qu"/"As"/"Ba") {
       def value
         text_value
@@ -1041,42 +1059,32 @@ grammar ScientificNameClean
   end
 
   rule latin_word
-    a:[a-zëüäöïéåóç] b:full_name_letters {
-      def value
-        a.text_value + b.value
-      end
-     }
-     /
-     a:digraph b:full_name_letters {
+    a:[a-zëæœ] b:valid_name_letters {
       def value
-        a.value + b.value
+        l = a.text_value
+        l = 'ae' if l == 'æ'
+        l = 'oe' if l == 'œ'
+        l + b.value
       end
      }
   end
 
-  rule full_name_letters
-    a:digraph b:full_name_letters {
-      def value
-        a.value + b.value
-      end
-    }
-    /
-    a:valid_name_letters b:digraph c:full_name_letters {
-      def value
-        a.value + b.value + c.value
-      end
-    }
-    /
-    valid_name_letters
-  end
-
   rule valid_name_letters
-    [a-z\-ëüäöïéåóç]+ {
+    [a-z\-ëæœ]+ {
       def value
-        text_value
+        res = ''
+        text_value.split('').each do |l|
+          l = 'ae' if l == 'æ'
+          l = 'oe' if l == 'œ'
+          # not sure if we should normalize ë as well. It is legal in botanical code, but it 
+          # might be beneficial to normalize it for the reconsiliation purposes
+          # l = 'e' if l == 'ë' 
+          res << l
+        end
+        res
       end
     }
-  end 
+  end
 
   rule cap_digraph
     "Æ" {
@@ -1092,20 +1100,6 @@ grammar ScientificNameClean
     }  
   end
 
-  rule digraph
-    "æ" {
-      def value
-      'ae'
-      end
-    }   
-    /
-    "œ" {
-      def value
-      'oe'
-      end
-    }
-  end
-
   rule year
     b:left_paren space a:(year_number_with_character/year_number) space c:right_paren {
       def value
@@ -1177,9 +1171,9 @@ grammar ScientificNameClean
   end
   
   rule multiplication_sign
-    "×" {
+    ("×"/"*") {
       def value
-        text_value
+        "×"
       end
     }
   end

data/lib/biodiversity/parser/scientific_name_dirty.rb

@@ -8,15 +8,76 @@ module ScientificNameDirty
 
   include ScientificNameClean
 
+  module Root0
+    def space1
+      elements[0]
+    end
+
+    def a
+      elements[1]
+    end
+
+    def space2
+      elements[2]
+    end
+  end
+
+  module Root1
+    def value
+      a.value.gsub(/\s{2,}/, ' ').strip
+    end
+    
+    def canonical
+      a.canonical.gsub(/\s{2,}/, ' ').strip
+    end
+    
+    def pos
+      a.pos
+    end
+    
+    def hybrid
+      a.hybrid
+    end
+    
+    def details
+      a.details.class == Array ? a.details : [a.details]
+    end
+
+    def parser_run
+      2
+    end
+  end
+
   def _nt_root
     start_index = index
     if node_cache[:root].has_key?(index)
       cached = node_cache[:root][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
-    r0 = super
+    i0, s0 = index, []
+    r1 = _nt_space
+    s0 << r1
+    if r1
+      r2 = _nt_scientific_name_5
+      s0 << r2
+      if r2
+        r3 = _nt_space
+        s0 << r3
+      end
+    end
+    if s0.last
+      r0 = instantiate_node(SyntaxNode,input, i0...index, s0)
+      r0.extend(Root0)
+      r0.extend(Root1)
+    else
+      @index = i0
+      r0 = nil
+    end
 
     node_cache[:root][start_index] = r0
 
@@ -55,7 +116,10 @@ module ScientificNameDirty
     start_index = index
     if node_cache[:scientific_name_5].has_key?(index)
       cached = node_cache[:scientific_name_5][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -129,7 +193,7 @@ module ScientificNameDirty
       elements[0]
     end
 
-    def space
+    def space1
       elements[1]
     end
 
@@ -137,7 +201,7 @@ module ScientificNameDirty
       elements[2]
     end
 
-    def space
+    def space2
       elements[3]
     end
 
@@ -168,7 +232,10 @@ module ScientificNameDirty
     start_index = index
     if node_cache[:infraspecies].has_key?(index)
       cached = node_cache[:infraspecies][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -276,7 +343,10 @@ module ScientificNameDirty
     start_index = index
     if node_cache[:species].has_key?(index)
       cached = node_cache[:species][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -317,6 +387,161 @@ module ScientificNameDirty
     r0
   end
 
+  module LatinWord0
+    def a
+      elements[0]
+    end
+
+    def b
+      elements[1]
+    end
+  end
+
+  module LatinWord1
+    def value
+      res = ''
+      text_value.split('').each do |l|
+        l = 'ae' if l == 'æ'
+        l = 'oe' if l == 'œ'
+        res << l
+      end
+      res.tr('àâåãäáçčéèíìïňññóòôøõöúùürŕřŗššşž',
+             'aaaaaacceeiiinnnoooooouuurrrrsssz')
+    end
+  end
+
+  def _nt_latin_word
+    start_index = index
+    if node_cache[:latin_word].has_key?(index)
+      cached = node_cache[:latin_word][index]
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
+      return cached
+    end
+
+    i0, s0 = index, []
+    if has_terminal?('\G[a-z\\-ëæœàâåãäáçčéèíìïňññóòôøõöúùürŕřŗššşž]', true, index)
+      r1 = true
+      @index += 1
+    else
+      r1 = nil
+    end
+    s0 << r1
+    if r1
+      r2 = _nt_valid_name_letters
+      s0 << r2
+    end
+    if s0.last
+      r0 = instantiate_node(SyntaxNode,input, i0...index, s0)
+      r0.extend(LatinWord0)
+      r0.extend(LatinWord1)
+    else
+      @index = i0
+      r0 = nil
+    end
+
+    node_cache[:latin_word][start_index] = r0
+
+    r0
+  end
+
+  module ValidNameLetters0
+    def value
+      res = ''
+      text_value.split('').each do |l|
+        l = 'ae' if l == 'æ'
+        l = 'oe' if l == 'œ'
+        res << l
+      end
+      res.tr('àâåãäáçčéèíìïňññóòôøõöúùürŕřŗššşž',
+             'aaaaaacceeiiinnnoooooouuurrrrsssz')
+    end
+  end
+
+  def _nt_valid_name_letters
+    start_index = index
+    if node_cache[:valid_name_letters].has_key?(index)
+      cached = node_cache[:valid_name_letters][index]
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
+      return cached
+    end
+
+    s0, i0 = [], index
+    loop do
+      if has_terminal?('\G[a-z\\-ëæœàâåãäáçčéèíìïňññóòôøõöúùürŕřŗššşž]', true, index)
+        r1 = true
+        @index += 1
+      else
+        r1 = nil
+      end
+      if r1
+        s0 << r1
+      else
+        break
+      end
+    end
+    if s0.empty?
+      @index = i0
+      r0 = nil
+    else
+      r0 = instantiate_node(SyntaxNode,input, i0...index, s0)
+      r0.extend(ValidNameLetters0)
+    end
+
+    node_cache[:valid_name_letters][start_index] = r0
+
+    r0
+  end
+
+  module ValidNameLetters0
+    def value
+      text_value
+    end
+  end
+
+  def _nt_valid_name_letters
+    start_index = index
+    if node_cache[:valid_name_letters].has_key?(index)
+      cached = node_cache[:valid_name_letters][index]
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
+      return cached
+    end
+
+    s0, i0 = [], index
+    loop do
+      if has_terminal?('\G[a-z\\-ëüäöïéåóç]', true, index)
+        r1 = true
+        @index += 1
+      else
+        r1 = nil
+      end
+      if r1
+        s0 << r1
+      else
+        break
+      end
+    end
+    if s0.empty?
+      @index = i0
+      r0 = nil
+    else
+      r0 = instantiate_node(SyntaxNode,input, i0...index, s0)
+      r0.extend(ValidNameLetters0)
+    end
+
+    node_cache[:valid_name_letters][start_index] = r0
+
+    r0
+  end
+
   module RightParen0
     def space
       elements[1]
@@ -328,7 +553,10 @@ module ScientificNameDirty
     start_index = index
     if node_cache[:right_paren].has_key?(index)
       cached = node_cache[:right_paren][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -391,7 +619,10 @@ module ScientificNameDirty
     start_index = index
     if node_cache[:left_paren].has_key?(index)
       cached = node_cache[:left_paren][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -503,7 +734,10 @@ module ScientificNameDirty
     start_index = index
     if node_cache[:year].has_key?(index)
       cached = node_cache[:year][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -583,7 +817,7 @@ module ScientificNameDirty
   end
 
   module ApproximateYear0
-    def space
+    def space1
       elements[1]
     end
 
@@ -591,7 +825,7 @@ module ScientificNameDirty
       elements[2]
     end
 
-    def space
+    def space2
       elements[3]
     end
 
@@ -615,7 +849,10 @@ module ScientificNameDirty
     start_index = index
     if node_cache[:approximate_year].has_key?(index)
       cached = node_cache[:approximate_year][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -703,7 +940,10 @@ module ScientificNameDirty
     start_index = index
     if node_cache[:double_year].has_key?(index)
       cached = node_cache[:double_year][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -723,7 +963,7 @@ module ScientificNameDirty
         s3, i3 = [], index
         loop do
           if has_terminal?('\G[0-9]', true, index)
-            r4 = instantiate_node(SyntaxNode,input, index...(index + 1))
+            r4 = true
             @index += 1
           else
             r4 = nil
@@ -743,7 +983,7 @@ module ScientificNameDirty
         s0 << r3
         if r3
           if has_terminal?('\G[A-Za-z]', true, index)
-            r6 = instantiate_node(SyntaxNode,input, index...(index + 1))
+            r6 = true
             @index += 1
           else
             r6 = nil
@@ -756,7 +996,7 @@ module ScientificNameDirty
           s0 << r5
           if r5
             if has_terminal?('\G[\\?]', true, index)
-              r8 = instantiate_node(SyntaxNode,input, index...(index + 1))
+              r8 = true
               @index += 1
             else
               r8 = nil
@@ -810,7 +1050,10 @@ module ScientificNameDirty
     start_index = index
     if node_cache[:year_number_with_punctuation].has_key?(index)
       cached = node_cache[:year_number_with_punctuation][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -857,7 +1100,10 @@ module ScientificNameDirty
     start_index = index
     if node_cache[:page_number].has_key?(index)
       cached = node_cache[:page_number][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -877,7 +1123,7 @@ module ScientificNameDirty
         s3, i3 = [], index
         loop do
           if has_terminal?('\G[\\d]', true, index)
-            r4 = instantiate_node(SyntaxNode,input, index...(index + 1))
+            r4 = true
             @index += 1
           else
             r4 = nil
@@ -915,7 +1161,10 @@ module ScientificNameDirty
     start_index = index
     if node_cache[:string_authorship_inconsistencies].has_key?(index)
       cached = node_cache[:string_authorship_inconsistencies][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -933,11 +1182,11 @@ module ScientificNameDirty
   end
 
   module Garbage0
-    def space
+    def space1
       elements[0]
     end
 
-    def space
+    def space2
       elements[2]
     end
 
@@ -954,7 +1203,10 @@ module ScientificNameDirty
     start_index = index
     if node_cache[:garbage].has_key?(index)
       cached = node_cache[:garbage][index]
-      @index = cached.interval.end if cached
+      if cached
+        cached = SyntaxNode.new(input, index...(index + 1)) if cached == true
+        @index = cached.interval.end
+      end
       return cached
     end
 
@@ -964,7 +1216,7 @@ module ScientificNameDirty
     s1 << r2
     if r2
       if has_terminal?('\G["\',.]', true, index)
-        r3 = instantiate_node(SyntaxNode,input, index...(index + 1))
+        r3 = true
         @index += 1
       else
         r3 = nil
@@ -977,7 +1229,7 @@ module ScientificNameDirty
           s5, i5 = [], index
           loop do
             if has_terminal?('\G[^щ]', true, index)
-              r6 = instantiate_node(SyntaxNode,input, index...(index + 1))
+              r6 = true
               @index += 1
             else
               r6 = nil
@@ -1010,7 +1262,7 @@ module ScientificNameDirty
         s9, i9 = [], index
         loop do
           if has_terminal?('\G[^ш]', true, index)
-            r10 = instantiate_node(SyntaxNode,input, index...(index + 1))
+            r10 = true
             @index += 1
           else
             r10 = nil
@@ -1054,3 +1306,4 @@ end
 class ScientificNameDirtyParser < Treetop::Runtime::CompiledParser
   include ScientificNameDirty
 end
+