dimus-biodiversity 0.0.1

data/lib/biodiversity/parser/scientific_name.treetop

@@ -0,0 +1,507 @@
+grammar ScientificName
+
+  rule composite_scientific_name
+    a:scientific_name space hybrid_separator space b:scientific_name space {
+      def value
+        a.value + " × " + b.value
+      end
+      def canonical
+        a.canonical + " × " + b.canonical
+      end
+      def details
+        {:hybrid => {:scientific_name1 => a.details, :scientific_name2 => b.details}}
+      end
+    }
+    /
+    a:scientific_name space hybrid_separator space [\?]? {
+      def value
+        a.value + " × ?"
+      end
+      
+      def canonical
+        a.canonical
+      end
+      
+      def details
+        {:hybrid => {:scientific_name1 => a.details, :scientific_name2 => "?"}}
+      end
+    }
+    /
+    scientific_name
+  end
+  
+  rule scientific_name
+    space a:name_part space b:authors_part space c:status_part space {
+      def value
+        a.value + " " + b.value + " " + c.value
+      end
+      def canonical
+        a.canonical
+      end
+      def details
+        a.details.merge(b.details).merge(c.details)
+      end
+    }
+    /
+    space a:name_part space b:authors_part space {
+      def value
+        a.value + " " + b.value
+      end
+      def canonical
+        a.canonical
+      end
+      def details
+        a.details.merge(b.details)
+      end
+    }
+    /
+    space a:name_part space b:year space {
+      def value
+        a.value + " " + b.value
+      end
+      
+      def canonical
+        a.canonical
+      end
+      
+      def details
+        a.details.merge(b.details).merge({:is_valid => false})
+      end
+    }
+    /
+    name_part
+  end
+  
+  rule status_part
+    a:status_word space b:status_part {
+      def value
+        a.value + " " + b.value
+      end
+      def details
+        {:status => value}
+      end
+    }
+    /
+    status_word
+  end
+  
+  rule status_word
+    latin_word [\.] {
+      def value
+        text_value.strip
+      end
+      def details
+        {:status => value}
+      end
+    }
+    /
+    latin_word
+  end
+  
+  rule authors_part
+    a:original_authors_revised_name space b:authors_revised_name {
+      def value 
+        a.value + " " + b.value
+      end
+    
+      def details
+        a.details.merge(b.details)
+      end
+    }
+    /
+    a:simple_authors_part space "ex" space b:simple_authors_part {
+      def value 
+        a.value + " ex " + b.value
+      end
+      
+      def details
+        {:revised_name_authors => {:revised_authors => a.details[:authors], :authors => b.details[:authors]}}
+      end
+    }
+    /
+    a:original_authors_revised_name space b:authors_names_full {
+      def value
+        a.value + " " + b.value
+      end
+      def details
+        a.details.merge(b.details)
+      end
+    }
+    /
+    authors_revised_name
+    /
+    original_authors_revised_name
+    /
+    simple_authors_part
+  end
+  
+  rule simple_authors_part
+    a:original_authors_names_full space b:authors_names_full {
+      def value
+        a.value + " " + b.value
+      end
+      def details
+        a.details.merge(b.details)
+      end
+    }
+    /
+    original_authors_names_full
+    /
+    authors_names_full
+  end
+  
+  rule original_authors_names_full
+    "(" space a:authors_names_full space ")" {
+      def value
+        "(" + a.value + ")"
+      end
+      def details
+        {:orig_authors => a.details[:authors]}
+      end
+    }
+  end
+    
+  rule original_authors_revised_name
+    "(" space a:authors_revised_name space ")" {
+      def value
+        "(" + a.value + ")"
+      end
+      
+      def details
+        {:original_revised_name_authors => a.details[:revised_name_authors]}
+      end
+    }
+  end
+  
+  rule authors_revised_name
+    a:authors_names_full space "ex" space b:authors_names_full {
+      def value
+        a.value + " ex " + b.value
+      end
+      def details
+        {:revised_name_authors =>{:revised_authors => a.details[:authors], :authors => b.details[:authors]}}
+      end
+    } 
+  end
+
+  rule authors_names_full
+    a:authors_names space [,]? space b:year {
+      def value 
+        a.value + " " + b.value
+      end
+      def details
+        {:authors => {:names => a.details[:authors][:names]}.merge(b.details)}
+      end
+    }
+    /
+    authors_names
+  end
+      
+  rule authors_names
+    a:author_name space sep:author_name_separator space b:authors_names {
+      def value
+        sep.apply(a,b)
+      end
+      
+      def details
+        sep.details(a,b)
+      end
+    }
+    /
+    author_name
+  end  
+  
+  rule author_name_separator
+    ("&"/",") {
+      def apply(a,b)
+        a.value + " " + text_value + " " + b.value
+      end
+
+      def details(a,b)
+        {:authors => {:names => a.details[:authors][:names] + b.details[:authors][:names]}}
+      end
+    }
+  end
+  
+  rule author_name
+    space a:author_word space b:author_name space {
+      def value
+        a.value + " " + b.value
+      end
+
+      def details
+        {:authors => {:names => [value]}}
+      end
+    }
+    /
+    author_word
+  end
+  
+  rule author_word
+    "A S. Xu"
+    /
+    ("anon."/"f."/"bis"/"arg."/"da"/"der"/"den"/"de"/"du"/"la"/"ter"/"van"/"et al.\{\?\}"/"et al.") {
+      def value
+        text_value.strip
+      end
+      def details
+        {:authors => {:names => [value]}}
+      end
+    }
+    / 
+    ("Å"/"Ö"/"Á"/"Ø"/"Ô"/"Š"/"Ś"/"Č"/"Ķ"/"Ł"/"É"/"Ž"/[A-Z]) [^0-9()\s&,]+ {
+      def value
+        text_value.gsub(/\s+/, " ").strip
+      end
+      def details
+        {:authors => {:names => [value]}}
+      end
+    }
+  end
+  
+  rule name_part
+    space a:species_name space b:selector space_hard c:editorials_full {
+      def value
+        a.value + " " + b.value + " " + c.value
+      end
+      def canonical
+        a.canonical
+      end
+      def details
+        a.details.merge(b.details).merge(c.details)
+      end
+    }
+    /
+    space a:species_name space b:subspecies_names {
+      def value
+        a.value + b.value
+      end
+      def canonical
+        a.canonical + b.canonical
+      end
+      
+      def details
+        a.details.merge(b.details)
+      end
+    }
+    /
+    space a:species_name space b:latin_word {
+      def value
+        a.value + " " + b.value
+      end
+      
+      def canonical
+        value
+      end
+      
+      def details
+        a.details.merge({:subspecies => {:type => "n/a", :value =>b.value}})
+      end
+    }
+    /
+    species_name
+    / 
+    cap_latin_word
+  end
+  
+  rule subspecies_names
+    a:subspecies_name space b:subspecies_names {
+      def value
+        a.value + b.value
+      end
+      
+      def canonical
+        a.canonical + b.canonical
+      end
+      
+      def details
+        c = a.details[:subspecies] + b.details_subspecies
+        a.details.merge({:subspecies => c, :is_valid => false})
+      end
+    }
+    /
+    subspecies_name
+  end
+  
+  rule subspecies_name
+    sel:selector space_hard a:latin_word {
+      def value 
+        sel.apply(a)
+      end
+      def canonical
+        sel.canonical(a)
+      end
+      def details
+        sel.details(a)
+      end
+      def details_subspecies
+        details[:subspecies]
+      end
+    }
+  end
+  
+  rule editorials_full 
+    "(" space a:editorials space ")" {
+      def value
+        "(" + a.value + ")"
+      end
+      def details
+        {:editorial_markup => value, :is_valid => false}
+      end
+    }
+  end
+  
+  rule editorials
+    space a:selector space [&]? space b:editorials {
+      def value
+        a.value + b.value
+      end 
+    }
+    /
+    selector
+  end
+  
+  rule selector
+    ("f.sp."/"f."/"B"/"ssp."/"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
+        text_value.strip
+      end
+      def apply(a)
+        " " + text_value + " " + a.value
+      end
+      def canonical(a)
+        " " + a.value
+      end
+      def details(a = nil)
+        {:subspecies => [{:type => text_value, :value => (a.value rescue nil)}]}
+      end
+    }
+  end
+  
+  rule species_name
+    hybrid_separator space_hard  a:cap_latin_word space_hard b:latin_word {
+      def value
+        "× " + a.value + " " + b.value
+      end
+      def canonical
+        a.value + " " + b.value
+      end
+      def details
+        {:genus => a.value, :species => b.value, :cross => 'before'}
+      end
+    }
+    /
+    hybrid_separator space_hard  a:cap_latin_word {
+      def value
+        "× " + a.value
+      end
+      def canonical
+        a.value
+      end
+      def details
+        {:uninomial => a.value, :cross => 'before'}
+      end
+    }
+    /
+    a:cap_latin_word space_hard hybrid_separator space_hard b:latin_word {
+      def value
+        a.value + " × " + b.value
+      end
+      def canonical
+        a.value + " " + b.value
+      end
+      def details
+        {:genus => a.value, :species => b.value, :cross => 'inside'}
+      end
+    }
+    /
+    a:cap_latin_word space_hard b:subgenus space_hard c:latin_word {
+      def value
+        a.value + " " + b.value + " " + c.value
+      end
+      def canonical
+        a.value + " " + c.value
+      end
+      def details
+        {:genus => a.value, :subgenus => b.details, :species => c.value}
+      end
+    } 
+    /
+    a:cap_latin_word space_hard b:latin_word {
+      def value
+        a.value + " " + b.value 
+      end
+      def canonical
+        value
+      end
+      
+      def details
+        {:genus => a.value, :species => b.value}
+      end
+    }
+  end
+  
+  rule subgenus
+    "(" space a:cap_latin_word space ")" {
+      def value
+        "(" + a.value + ")"
+      end
+      def details
+        a.value
+      end
+    }
+  end
+
+  rule latin_word
+    [a-zë] [a-z\-ëüäöï]+ {
+      def value 
+        text_value.strip
+      end
+    }
+  end
+  
+  rule cap_latin_word
+    [A-Z] [a-zë] [a-z\-ëüäöï]+ {
+      def value
+        text_value.strip
+      end
+      
+      def canonical 
+        text_value.strip
+      end
+      
+      def details 
+        {:name_type => "Uninomial", :uninomial => value}
+      end
+    }
+  end
+  
+  rule hybrid_separator
+    ("x"/"X"/"×") {
+      def value
+        "x"
+      end
+    }
+  end
+  
+  rule year
+    [0-9\?]+ {
+      def value
+        text_value.strip
+      end
+      def details
+        {:year => value}
+      end
+    }
+  end
+    
+  rule space
+    [\s]*
+  end
+
+  rule space_hard
+    [\s]+
+  end
+end