dimus-biodiversity 0.5.2 → 0.5.3

data/lib/biodiversity.rb

@@ -7,5 +7,3 @@ BIODIVERSITY_ROOT = File.join(dir, 'biodiversity')
 require File.join(dir, "/../conf/environment")
 require File.join(BIODIVERSITY_ROOT, "parser")
 require File.join(BIODIVERSITY_ROOT, "guid")
-
-

data/lib/biodiversity/parser.rb

@@ -23,17 +23,14 @@ class ScientificNameParser
       parsed = self.class != Hash
       res = {:parsed => parsed}
       if parsed
+        hybrid = self.hybrid rescue false
         res.merge!({
           :verbatim => self.text_value,
           :normalized => self.value,
-          :canonical => self.canonical
+          :canonical => self.canonical,
+          :hybrid => hybrid,
+          :details => self.details
           })
-        data = self.details
-        if data[:species] && data[:species][:namedHybrid]
-          data[:species].delete(:namedHybrid)
-          data = {:namedHybrid => data}
-        end
-        res.merge!(data)
       else
         res.merge!(self)
       end

data/lib/biodiversity/parser/scientific_name_canonical.rb

@@ -10,6 +10,26 @@ module ScientificNameCanonical
 
   include ScientificNameDirty
 
+  module Root0
+    def hybrid
+      false
+    end
+
+    def details
+      [super]
+    end
+  end
+
+  module Root1
+    def hybrid
+      false
+    end
+    
+    def details
+      [super]
+    end
+  end
+
   def _nt_root
     start_index = index
     if node_cache[:root].has_key?(index)
@@ -20,10 +40,12 @@ module ScientificNameCanonical
 
     i0 = index
     r1 = _nt_multinomial_with_garbage
+    r1.extend(Root0)
     if r1
       r0 = r1
     else
       r2 = _nt_uninomial_with_garbage
+      r2.extend(Root1)
       if r2
         r0 = r2
       else

data/lib/biodiversity/parser/scientific_name_canonical.treetop

@@ -4,9 +4,25 @@ grammar ScientificNameCanonical
   include ScientificNameDirty
 
   rule root
-    multinomial_with_garbage
+    multinomial_with_garbage {
+      def hybrid
+        false
+      end
+
+      def details
+        [super]
+      end
+    }
     /
-    uninomial_with_garbage
+    uninomial_with_garbage {
+      def hybrid
+        false
+      end
+      
+      def details
+        [super]
+      end
+    }
   end
   
   rule multinomial_with_garbage

data/lib/biodiversity/parser/scientific_name_clean.rb

@@ -33,8 +33,12 @@ module ScientificNameClean
       a.pos
     end
     
+    def hybrid
+      a.hybrid
+    end
+    
     def details
-      a.details
+      a.details.class == Array ? a.details : [a.details]
     end
   end
 
@@ -105,7 +109,11 @@ module ScientificNameClean
     def pos
       a.pos.merge(c.pos)
     end
-  
+    
+    def hybrid
+      a.hybrid
+    end
+    
     def details
       a.details.merge(b.details(c))
     end
@@ -199,8 +207,12 @@ module ScientificNameClean
       a.pos.merge(b.pos)
     end
     
+    def hybrid
+      true
+    end
+    
     def details
-      {:hybridFormula => [a.details, b.details]}
+      [a.details, b.details]
     end
   end
 
@@ -236,8 +248,12 @@ module ScientificNameClean
       a.pos
     end
     
+    def hybrid
+      true
+    end
+    
     def details
-      {:hybridFormula => [a.details, "?"]}
+      [a.details, "?"]
     end
   end
 
@@ -362,8 +378,12 @@ module ScientificNameClean
       b.pos
     end
     
+    def hybrid
+      true
+    end
+    
     def details
-      {:namedHybrid => b.details}
+      b.details
     end
   end
 
@@ -439,6 +459,10 @@ module ScientificNameClean
       a.pos
     end
     
+    def hybrid
+      a.hybrid rescue false
+    end
+    
     def details
       a.details.merge(b.details)
     end
@@ -680,6 +704,10 @@ module ScientificNameClean
     def pos
       a.pos.merge(b.pos).merge(c.pos).merge(d.pos)
     end
+    
+    def hybrid
+      c.hybrid rescue false
+    end
   
     def details
       a.details.merge(b.details).merge(c.details).merge(d.details)
@@ -725,6 +753,10 @@ module ScientificNameClean
       a.pos.merge(b.pos).merge(c.pos)
     end
     
+    def hybrid
+      c.hybrid rescue false
+    end
+    
     def details
       a.details.merge(b.details).merge(c.details)
     end
@@ -768,6 +800,10 @@ module ScientificNameClean
     def pos
       a.pos.merge(b.pos).merge(c.pos)
     end
+    
+    def hybrid
+      b.hybrid rescue false
+    end
   
     def details
       a.details.merge(b.details).merge(c.details)
@@ -805,6 +841,10 @@ module ScientificNameClean
       a.pos.merge(b.pos)
     end
     
+    def hybrid
+      b.hybrid rescue false
+    end
+    
     def details
       a.details.merge(b.details)
     end
@@ -1037,6 +1077,12 @@ module ScientificNameClean
     end
   end
 
+  module InfraspeciesMult2
+    def details
+      {:infraspecies => [super[:infraspecies]]}
+    end
+  end
+
   def _nt_infraspecies_mult
     start_index = index
     if node_cache[:infraspecies_mult].has_key?(index)
@@ -1069,6 +1115,7 @@ module ScientificNameClean
       r0 = r1
     else
       r5 = _nt_infraspecies
+      r5.extend(InfraspeciesMult2)
       if r5
         r0 = r5
       else
@@ -1544,8 +1591,8 @@ module ScientificNameClean
                                     r1.extend(Rank0)
                                   else
                                     if input.index("α", index) == index
-                                      r18 = instantiate_node(SyntaxNode,input, index...(index + 1))
-                                      @index += 1
+                                      r18 = instantiate_node(SyntaxNode,input, index...(index + 2))
+                                      @index += 2
                                     else
                                       terminal_parse_failure("α")
                                       r18 = nil
@@ -1555,8 +1602,8 @@ module ScientificNameClean
                                       r1.extend(Rank0)
                                     else
                                       if input.index("ββ", index) == index
-                                        r19 = instantiate_node(SyntaxNode,input, index...(index + 2))
-                                        @index += 2
+                                        r19 = instantiate_node(SyntaxNode,input, index...(index + 4))
+                                        @index += 4
                                       else
                                         terminal_parse_failure("ββ")
                                         r19 = nil
@@ -1566,8 +1613,8 @@ module ScientificNameClean
                                         r1.extend(Rank0)
                                       else
                                         if input.index("β", index) == index
-                                          r20 = instantiate_node(SyntaxNode,input, index...(index + 1))
-                                          @index += 1
+                                          r20 = instantiate_node(SyntaxNode,input, index...(index + 2))
+                                          @index += 2
                                         else
                                           terminal_parse_failure("β")
                                           r20 = nil
@@ -1577,8 +1624,8 @@ module ScientificNameClean
                                           r1.extend(Rank0)
                                         else
                                           if input.index("γ", index) == index
-                                            r21 = instantiate_node(SyntaxNode,input, index...(index + 1))
-                                            @index += 1
+                                            r21 = instantiate_node(SyntaxNode,input, index...(index + 2))
+                                            @index += 2
                                           else
                                             terminal_parse_failure("γ")
                                             r21 = nil
@@ -1588,8 +1635,8 @@ module ScientificNameClean
                                             r1.extend(Rank0)
                                           else
                                             if input.index("δ", index) == index
-                                              r22 = instantiate_node(SyntaxNode,input, index...(index + 1))
-                                              @index += 1
+                                              r22 = instantiate_node(SyntaxNode,input, index...(index + 2))
+                                              @index += 2
                                             else
                                               terminal_parse_failure("δ")
                                               r22 = nil
@@ -1599,8 +1646,8 @@ module ScientificNameClean
                                               r1.extend(Rank0)
                                             else
                                               if input.index("ε", index) == index
-                                                r23 = instantiate_node(SyntaxNode,input, index...(index + 1))
-                                                @index += 1
+                                                r23 = instantiate_node(SyntaxNode,input, index...(index + 2))
+                                                @index += 2
                                               else
                                                 terminal_parse_failure("ε")
                                                 r23 = nil
@@ -1610,8 +1657,8 @@ module ScientificNameClean
                                                 r1.extend(Rank0)
                                               else
                                                 if input.index("φ", index) == index
-                                                  r24 = instantiate_node(SyntaxNode,input, index...(index + 1))
-                                                  @index += 1
+                                                  r24 = instantiate_node(SyntaxNode,input, index...(index + 2))
+                                                  @index += 2
                                                 else
                                                   terminal_parse_failure("φ")
                                                   r24 = nil
@@ -1621,8 +1668,8 @@ module ScientificNameClean
                                                   r1.extend(Rank0)
                                                 else
                                                   if input.index("θ", index) == index
-                                                    r25 = instantiate_node(SyntaxNode,input, index...(index + 1))
-                                                    @index += 1
+                                                    r25 = instantiate_node(SyntaxNode,input, index...(index + 2))
+                                                    @index += 2
                                                   else
                                                     terminal_parse_failure("θ")
                                                     r25 = nil
@@ -1632,8 +1679,8 @@ module ScientificNameClean
                                                     r1.extend(Rank0)
                                                   else
                                                     if input.index("μ", index) == index
-                                                      r26 = instantiate_node(SyntaxNode,input, index...(index + 1))
-                                                      @index += 1
+                                                      r26 = instantiate_node(SyntaxNode,input, index...(index + 2))
+                                                      @index += 2
                                                     else
                                                       terminal_parse_failure("μ")
                                                       r26 = nil
@@ -1909,6 +1956,10 @@ module ScientificNameClean
       a.canonical
     end
     
+    def hybrid
+      a.hybrid rescue false
+    end
+    
     def pos
       a.pos.merge(b.pos)
     end
@@ -1992,6 +2043,10 @@ module ScientificNameClean
     def canonical
       a.value
     end
+    
+    def hybrid
+      a.hybrid rescue false
+    end
   
     def pos
       {a.interval.begin => ['species', a.interval.end]}
@@ -2011,6 +2066,10 @@ module ScientificNameClean
       {interval.begin => ['species', interval.end]}
     end
     
+    def hybrid
+      false
+    end
+    
     def details
       {:species => {:epitheton => value}}
     end
@@ -2295,6 +2354,10 @@ module ScientificNameClean
       a.pos.merge(b.pos)
     end
     
+    def hybrid
+      false
+    end
+    
     def details
       {:uninomial => a.details[:uninomial].merge(b.details)}
     end
@@ -2354,6 +2417,10 @@ module ScientificNameClean
       {interval.begin => ['uninomial', interval.end]}
     end
     
+    def hybrid
+      false
+    end
+    
     def details 
       {:uninomial => {:epitheton => value}}
     end
@@ -3932,8 +3999,8 @@ module ScientificNameClean
         i6, s6 = index, []
         i7 = index
         if input.index("Å", index) == index
-          r8 = instantiate_node(SyntaxNode,input, index...(index + 1))
-          @index += 1
+          r8 = instantiate_node(SyntaxNode,input, index...(index + 2))
+          @index += 2
         else
           terminal_parse_failure("Å")
           r8 = nil
@@ -3942,8 +4009,8 @@ module ScientificNameClean
           r7 = r8
         else
           if input.index("Ö", index) == index
-            r9 = instantiate_node(SyntaxNode,input, index...(index + 1))
-            @index += 1
+            r9 = instantiate_node(SyntaxNode,input, index...(index + 2))
+            @index += 2
           else
             terminal_parse_failure("Ö")
             r9 = nil
@@ -3952,8 +4019,8 @@ module ScientificNameClean
             r7 = r9
           else
             if input.index("Á", index) == index
-              r10 = instantiate_node(SyntaxNode,input, index...(index + 1))
-              @index += 1
+              r10 = instantiate_node(SyntaxNode,input, index...(index + 2))
+              @index += 2
             else
               terminal_parse_failure("Á")
               r10 = nil
@@ -3962,8 +4029,8 @@ module ScientificNameClean
               r7 = r10
             else
               if input.index("Ø", index) == index
-                r11 = instantiate_node(SyntaxNode,input, index...(index + 1))
-                @index += 1
+                r11 = instantiate_node(SyntaxNode,input, index...(index + 2))
+                @index += 2
               else
                 terminal_parse_failure("Ø")
                 r11 = nil
@@ -3972,8 +4039,8 @@ module ScientificNameClean
                 r7 = r11
               else
                 if input.index("Ô", index) == index
-                  r12 = instantiate_node(SyntaxNode,input, index...(index + 1))
-                  @index += 1
+                  r12 = instantiate_node(SyntaxNode,input, index...(index + 2))
+                  @index += 2
                 else
                   terminal_parse_failure("Ô")
                   r12 = nil
@@ -3982,8 +4049,8 @@ module ScientificNameClean
                   r7 = r12
                 else
                   if input.index("Š", index) == index
-                    r13 = instantiate_node(SyntaxNode,input, index...(index + 1))
-                    @index += 1
+                    r13 = instantiate_node(SyntaxNode,input, index...(index + 2))
+                    @index += 2
                   else
                     terminal_parse_failure("Š")
                     r13 = nil
@@ -3992,8 +4059,8 @@ module ScientificNameClean
                     r7 = r13
                   else
                     if input.index("Ś", index) == index
-                      r14 = instantiate_node(SyntaxNode,input, index...(index + 1))
-                      @index += 1
+                      r14 = instantiate_node(SyntaxNode,input, index...(index + 2))
+                      @index += 2
                     else
                       terminal_parse_failure("Ś")
                       r14 = nil
@@ -4002,8 +4069,8 @@ module ScientificNameClean
                       r7 = r14
                     else
                       if input.index("Č", index) == index
-                        r15 = instantiate_node(SyntaxNode,input, index...(index + 1))
-                        @index += 1
+                        r15 = instantiate_node(SyntaxNode,input, index...(index + 2))
+                        @index += 2
                       else
                         terminal_parse_failure("Č")
                         r15 = nil
@@ -4012,8 +4079,8 @@ module ScientificNameClean
                         r7 = r15
                       else
                         if input.index("Ķ", index) == index
-                          r16 = instantiate_node(SyntaxNode,input, index...(index + 1))
-                          @index += 1
+                          r16 = instantiate_node(SyntaxNode,input, index...(index + 2))
+                          @index += 2
                         else
                           terminal_parse_failure("Ķ")
                           r16 = nil
@@ -4022,8 +4089,8 @@ module ScientificNameClean
                           r7 = r16
                         else
                           if input.index("Ł", index) == index
-                            r17 = instantiate_node(SyntaxNode,input, index...(index + 1))
-                            @index += 1
+                            r17 = instantiate_node(SyntaxNode,input, index...(index + 2))
+                            @index += 2
                           else
                             terminal_parse_failure("Ł")
                             r17 = nil
@@ -4032,8 +4099,8 @@ module ScientificNameClean
                             r7 = r17
                           else
                             if input.index("É", index) == index
-                              r18 = instantiate_node(SyntaxNode,input, index...(index + 1))
-                              @index += 1
+                              r18 = instantiate_node(SyntaxNode,input, index...(index + 2))
+                              @index += 2
                             else
                               terminal_parse_failure("É")
                               r18 = nil
@@ -4042,8 +4109,8 @@ module ScientificNameClean
                               r7 = r18
                             else
                               if input.index("Ž", index) == index
-                                r19 = instantiate_node(SyntaxNode,input, index...(index + 1))
-                                @index += 1
+                                r19 = instantiate_node(SyntaxNode,input, index...(index + 2))
+                                @index += 2
                               else
                                 terminal_parse_failure("Ž")
                                 r19 = nil
@@ -4785,12 +4852,16 @@ module ScientificNameClean
       b.value
     end
     
+    def hybrid
+      true
+    end
+    
     def pos
       {b.interval.begin => ['species', b.interval.end]}
     end
     
     def details
-      {:species => {:epitheton => b.value, :namedHybrid => true}}
+      {:species => {:epitheton => b.value}}
     end
   end
 
@@ -4817,12 +4888,16 @@ module ScientificNameClean
       b.value
     end
     
+    def hybrid
+      true
+    end
+    
     def pos
       {b.interval.begin => ['species', b.interval.end]}
     end
     
     def details
-      {:species => {:epitheton => b.value, :namedHybrid => true}}
+      {:species => {:epitheton => b.value}}
     end
   end
 
@@ -4849,12 +4924,16 @@ module ScientificNameClean
       b.value
     end
     
+    def hybrid
+      true
+    end
+    
     def pos
       {b.interval.begin => ['species', b.interval.end]}
     end
     
     def details
-      {:species => {:epitheton => b.value, :namedHybrid => true}}
+      {:species => {:epitheton => b.value}}
     end
   end
 
@@ -5375,9 +5454,9 @@ module ScientificNameClean
 
     i0 = index
     if input.index("Æ", index) == index
-      r1 = instantiate_node(SyntaxNode,input, index...(index + 1))
+      r1 = instantiate_node(SyntaxNode,input, index...(index + 2))
       r1.extend(CapDigraph0)
-      @index += 1
+      @index += 2
     else
       terminal_parse_failure("Æ")
       r1 = nil
@@ -5386,9 +5465,9 @@ module ScientificNameClean
       r0 = r1
     else
       if input.index("Œ", index) == index
-        r2 = instantiate_node(SyntaxNode,input, index...(index + 1))
+        r2 = instantiate_node(SyntaxNode,input, index...(index + 2))
         r2.extend(CapDigraph1)
-        @index += 1
+        @index += 2
       else
         terminal_parse_failure("Œ")
         r2 = nil
@@ -5428,9 +5507,9 @@ module ScientificNameClean
 
     i0 = index
     if input.index("æ", index) == index
-      r1 = instantiate_node(SyntaxNode,input, index...(index + 1))
+      r1 = instantiate_node(SyntaxNode,input, index...(index + 2))
       r1.extend(Digraph0)
-      @index += 1
+      @index += 2
     else
       terminal_parse_failure("æ")
       r1 = nil
@@ -5439,9 +5518,9 @@ module ScientificNameClean
       r0 = r1
     else
       if input.index("œ", index) == index
-        r2 = instantiate_node(SyntaxNode,input, index...(index + 1))
+        r2 = instantiate_node(SyntaxNode,input, index...(index + 2))
         r2.extend(Digraph1)
-        @index += 1
+        @index += 2
       else
         terminal_parse_failure("œ")
         r2 = nil
@@ -5829,9 +5908,9 @@ module ScientificNameClean
     end
 
     if input.index("×", index) == index
-      r0 = instantiate_node(SyntaxNode,input, index...(index + 1))
+      r0 = instantiate_node(SyntaxNode,input, index...(index + 2))
       r0.extend(MultiplicationSign0)
-      @index += 1
+      @index += 2
     else
       terminal_parse_failure("×")
       r0 = nil