biodiversity 0.5.14

data/lib/biodiversity/parser/scientific_name_clean.treetop

@@ -0,0 +1,1195 @@
+# encoding: UTF-8
+grammar ScientificNameClean
+
+  rule root
+    space a:scientific_name_5 space {
+      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
+    }
+  end
+  
+  rule scientific_name_5
+    a:scientific_name_1 space b:taxon_concept_rank space c:authorship {
+      def value
+        a.value + " " + b.apply(c)
+      end
+    
+      def canonical
+        a.canonical
+      end
+      
+      def pos
+        a.pos.merge(c.pos)
+      end
+      
+      def hybrid
+        a.hybrid
+      end
+      
+      def details
+        a.details.merge(b.details(c))
+      end
+    }
+    /
+    scientific_name_4
+  end
+  
+  rule scientific_name_4
+    a:scientific_name_1 space hybrid_character space b:scientific_name_1 {
+      def value
+        a.value + " × " + b.value
+      end
+      
+      def canonical
+        a.canonical + " " + b.canonical
+      end
+      
+      def pos
+        a.pos.merge(b.pos)
+      end
+      
+      def hybrid
+        true
+      end
+      
+      def details
+        [a.details, b.details]
+      end
+    }
+    /
+    a:scientific_name_1 space hybrid_character space [\?]? {
+      def value
+        a.value + " × ?"
+      end
+      
+      def canonical
+        a.canonical
+      end
+      
+      def pos
+        a.pos
+      end
+      
+      def hybrid
+        true
+      end
+      
+      def details
+        [a.details, "?"]
+      end
+    }
+    /
+    scientific_name_3
+  end
+  
+  rule scientific_name_3
+    a:hybrid_character space b:scientific_name_2 {
+      def  value
+        a.value + " " + b.value
+      end
+      
+      def canonical
+        b.canonical
+      end
+      
+      def pos
+        b.pos
+      end
+      
+      def hybrid
+        true
+      end
+      
+      def details
+        b.details
+      end
+    }
+    /
+    scientific_name_2
+  end
+  
+  rule scientific_name_2
+    a:scientific_name_1 space b:status_part {
+      def value
+        a.value + " " + b.value
+      end
+      
+      def canonical
+        a.canonical
+      end
+      
+      def pos
+        a.pos
+      end
+      
+      def hybrid
+        a.hybrid rescue false
+      end
+      
+      def details
+        a.details.merge(b.details)
+      end
+    }
+    /
+    scientific_name_1
+  end
+
+  rule scientific_name_1
+    multinomial_name
+    /
+    uninomial_name  
+  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 multinomial_name
+    a:genus space b:subgenus space species_prefix? space c:species space_hard d:infraspecies_mult {
+      def value
+        a.value + " " + b.value + " " + c.value + " " + d.value
+      end
+    
+      def canonical
+        a.canonical + " " + b.canonical + " " + c.canonical + " " + d.canonical
+      end
+    
+      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)
+      end
+    }
+    /  
+    a:genus space b:subgenus space species_prefix? space c:species {
+      def value
+        a.value + " " + b.value + " " + c.value
+      end
+      
+      def canonical
+        a.canonical + " " + c.canonical
+      end
+      
+      def pos
+        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
+    }
+    /
+    a:genus space species_prefix? space b:species space_hard c:infraspecies_mult {
+      def value
+        a.value + " " + b.value + " " + c.value 
+      end
+
+      def canonical
+        a.canonical + " " + b.canonical + " " + c.canonical
+      end
+    
+      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)
+      end
+    }
+    /
+    a:genus space species_prefix? space b:species {
+      def value
+        a.value + " " + b.value 
+      end
+
+      def canonical
+        a.canonical + " " + b.canonical
+      end
+      
+      def pos
+        a.pos.merge(b.pos)
+      end
+      
+      def hybrid
+        b.hybrid rescue false
+      end
+      
+      def details
+        a.details.merge(b.details)
+      end
+    }
+  end
+  
+  rule infraspecies_mult
+    a:infraspecies space b:infraspecies_mult {
+      def value
+        a.value + " " + b.value
+      end
+      
+      def canonical
+        a.canonical + " " + b.canonical
+      end
+      
+      def pos
+        a.pos.merge(b.pos)
+      end
+      
+      def details
+        a_array =  a.details[:infraspecies].class == Array ? a.details[:infraspecies] : [a.details[:infraspecies]] 
+        b_array = b.details[:infraspecies].class == Array ? b.details[:infraspecies] : [b.details[:infraspecies]]
+        a.details.merge({:infraspecies => a_array + b_array})
+      end
+    }
+    /
+    infraspecies {
+      def details
+        {:infraspecies => [super[:infraspecies]]}
+      end
+    }
+  end
+  
+  rule infraspecies
+    a:infraspecies_epitheton space b:authorship {
+      def value
+        a.value + " " + b.value
+      end
+  
+      def canonical
+        a.canonical
+      end
+  
+      def pos
+        a.pos.merge(b.pos)
+      end
+  
+      def details
+        {:infraspecies => a.details[:infraspecies].merge(b.details)}
+      end
+    }
+    /
+    infraspecies_epitheton 
+  end
+  
+  rule infraspecies_epitheton
+    sel:rank space_hard a:species_word {
+      def value 
+        sel.apply(a)
+      end
+      def canonical
+        sel.canonical(a)
+      end
+      
+      def pos
+        {a.interval.begin => ['infraspecies', a.interval.end]}
+      end
+    
+      def details
+        sel.details(a)
+      end
+    }
+    /
+    species_word ![\.] {
+      def value
+        text_value
+      end
+      
+      def canonical
+        value
+      end
+  
+      def pos
+        {interval.begin => ['infraspecies', interval.end]}
+      end
+  
+      def details
+        {:infraspecies => {:epitheton => value, :rank => 'n/a'}}
+      end
+    }
+  end
+  
+  rule taxon_concept_rank
+    ("sec."/"sensu.") {
+      def value
+        "sec."
+      end
+      def apply(a)
+        " " + value + " " + a.value
+      end
+      def details(a = nil)
+        {:taxon_concept => a.details}
+      end    
+    }
+  end
+  
+  rule rank
+    ("morph."/"f.sp."/"B"/"ssp."/"mut."/"nat"/"nothosubsp."/"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)
+        {:infraspecies => {:epitheton => (a.value rescue nil), :rank => text_value}}
+      end
+    }
+    /
+    rank_forma
+  end
+  
+  rule rank_forma
+    ("forma"/"form."/"fo."/"f.")
+    {
+      def value
+        "f."
+      end
+      def apply(a)
+        " " + value + " " + a.value
+      end
+      def canonical(a)
+        " " + a.value
+      end
+      def details(a = nil)
+        {:infraspecies => {:epitheton => (a.value rescue nil), :rank => value}}
+      end
+    }
+  end
+  
+  rule species
+    a:species_epitheton space b:authorship {
+      def value
+        a.value + " " + b.value
+      end
+      
+      def canonical
+        a.canonical
+      end
+      
+      def hybrid
+        a.hybrid rescue false
+      end
+      
+      def pos
+        a.pos.merge(b.pos)
+      end
+      
+      def details
+        {:species => a.details[:species].merge(b.details)}
+      end
+    }
+    /
+    species_epitheton
+  end
+  
+  rule species_epitheton
+    a:species_word &(space_hard author_prefix_word space_hard) {
+      def value 
+        a.value
+      end
+      
+      def canonical
+        a.value
+      end
+      
+      def hybrid
+        a.hybrid rescue false
+      end
+    
+      def pos
+        {a.interval.begin => ['species', a.interval.end]}
+      end
+    
+      def details
+        {:species => {:epitheton => a.value}}
+      end
+    }
+    /
+    species_word {
+      def canonical
+        value
+      end
+      
+      def pos
+        {interval.begin => ['species', interval.end]}
+      end
+      
+      def hybrid
+        false
+      end
+      
+      def details
+        {:species => {:epitheton => value}}
+      end
+    }
+    /
+    species_word_hybrid
+  end
+  
+  rule subgenus
+    left_paren space a:cap_latin_word space right_paren {
+      def value
+        "(" + a.value + ")"
+      end
+      
+      def canonical
+        a.value
+      end
+      
+      def pos
+        {a.interval.begin => ['subgenus', a.interval.end]}
+      end
+      
+      def details
+        {:subgenus => {:epitheton => a.value}}
+      end
+    }
+  end
+  
+  rule genus
+    a:cap_latin_word !(space_hard author_prefix_word space_hard author_word) {
+      def value
+        a.value
+      end
+      
+      def pos
+        {a.interval.begin => ['genus', a.interval.end]}
+      end
+      
+      def canonical
+        a.value
+      end
+          
+      def details
+        {:genus => {:epitheton => a.value}}
+      end
+    }
+  end
+  
+  rule uninomial_name
+    a:uninomial_epitheton space_hard b:authorship {
+      def value
+        a.value + " " + b.value
+      end
+      
+      def canonical
+        a.canonical
+      end
+      
+      def pos
+        a.pos.merge(b.pos)
+      end
+      
+      def hybrid
+        false
+      end
+      
+      def details
+        {:uninomial => a.details[:uninomial].merge(b.details)}
+      end
+    }
+    /
+    uninomial_epitheton
+  end
+
+  rule uninomial_epitheton
+    cap_latin_word {
+      def canonical
+        value
+      end
+      
+      def pos
+        {interval.begin => ['uninomial', interval.end]}
+      end
+      
+      def hybrid
+        false
+      end
+      
+      def details 
+        {:uninomial => {:epitheton => value}}
+      end
+    }
+  end
+  
+  rule authorship
+    a:basionym_authorship_with_parenthesis space b:simple_authorship ","? space c:ex_authorship {
+      def value
+        a.value + " " + b.value + " " + c.value
+      end
+      
+      def pos
+        a.pos.merge(b.pos).merge(c.pos)
+      end
+      
+      def details
+        val = {:authorship => text_value.strip, :combinationAuthorTeam => b.details[:basionymAuthorTeam], :basionymAuthorTeam => a.details[:basionymAuthorTeam]}
+        val[:combinationAuthorTeam].merge!(c.details)
+        val
+      end
+    }
+    /
+    a:basionym_authorship_with_parenthesis space b:simple_authorship {
+      def value
+        a.value + " " + b.value
+      end
+      
+      def pos
+        a.pos.merge(b.pos)
+      end
+      
+      def details
+        {:authorship => text_value.strip, :combinationAuthorTeam => b.details[:basionymAuthorTeam], :basionymAuthorTeam => a.details[:basionymAuthorTeam]}
+      end
+    }
+    /
+    basionym_authorship_with_parenthesis
+    /
+    a:simple_authorship ","? space b:ex_authorship {
+      def value
+        a.value + " " + b.value
+      end
+      
+      def pos
+        a.pos.merge(b.pos)
+      end
+      
+      def details
+        val = a.details
+        val[:authorship] = text_value.strip
+        val[:basionymAuthorTeam].merge!(b.details)
+        val
+      end
+    }
+    /
+    simple_authorship
+  end
+   
+  
+  rule basionym_authorship_with_parenthesis
+    left_paren space a:authors_names space right_paren space [,]? space b:year {
+      def value
+        "(" + a.value + " " + b.value + ")"
+      end
+      
+      def pos
+       a.pos.merge(b.pos)
+      end 
+      
+      def details
+        { :authorship => text_value, 
+          :basionymAuthorTeam => {:author_team => text_value}.merge(a.details).merge(b.details)          
+          }
+      end
+    }
+    /
+    left_paren space a:simple_authorship ","? space b:ex_authorship space right_paren {
+      def value
+        "(" + a.value + " " + b.value + ")"
+      end
+      
+      def pos
+        a.pos.merge(b.pos)
+      end
+      
+      def details
+        val = a.details
+        val[:basionymAuthorTeam].merge!(b.details)
+        val[:authorship] = text_value.strip
+        val
+      end
+    }
+    /
+    left_paren space a:simple_authorship space right_paren {
+      def value
+        "(" + a.value + ")"
+      end
+      
+      def pos
+        a.pos
+      end
+      
+      def details
+        val = a.details
+        val[:authorship] = text_value
+        val      
+      end
+    }
+    /
+    left_paren space a:"?" space right_paren {
+      def value
+        "(?)"
+      end
+      
+      def pos
+        {a.interval.begin => ['unknown_author', a.interval.end]}
+      end
+      
+      def details
+        {:authorship => text_value, :basionymAuthorTeam => {:authorTeam => text_value, :author => ['?']}}
+      end
+    }
+  end
+  
+  rule ex_authorship
+    ex_sep space b:simple_authorship {
+      def value
+        " ex " + b.value
+      end
+      
+      def pos
+        b.pos
+      end
+      
+      def details
+        val = {:exAuthorTeam => {:authorTeam => b.text_value.strip}.merge(b.details[:basionymAuthorTeam])}
+        val
+      end
+    } 
+  end
+  
+
+  rule simple_authorship
+    a:authors_names space [,]? space b:year? [,]? space "non" space authors_names space [,]? space year {
+      def value
+        a.value + " " + b.value
+      end
+      
+      def pos
+        a.pos.merge(b.pos)
+      end
+      
+      def details
+        details_with_arg(:basionymAuthorTeam)
+      end
+      
+      def details_with_arg(authorTeamType = 'basionymAuthorTeam')
+        { :authorship => text_value, 
+          authorTeamType.to_sym => {
+            :authorTeam => a.text_value.strip
+          }.merge(a.details).merge(b.details)
+        }
+      end
+    }
+    /
+    a:authors_names space [,]? space b:year {
+      def value
+        a.value + " " + b.value
+      end
+      
+      def pos
+        a.pos.merge(b.pos)
+      end
+      
+      def details
+        details_with_arg(:basionymAuthorTeam)
+      end
+      
+      def details_with_arg(authorTeamType = 'basionymAuthorTeam')
+        { :authorship => text_value, 
+          authorTeamType.to_sym => {
+            :authorTeam => a.text_value.strip
+          }.merge(a.details).merge(b.details)
+        }
+      end
+    }
+    /
+    authors_names {
+      def details
+        details = details_with_arg(:basionymAuthorTeam)
+        details[:basionymAuthorTeam].merge!(super)
+        details
+      end
+      
+      def details_with_arg(authorTeamType = 'basionymAuthorTeam')
+        { :authorship => text_value, 
+          authorTeamType.to_sym => {
+            :authorTeam => text_value,
+          }
+        }      
+      end
+    }
+  end
+  
+  rule authors_names
+    a:author_name space sep:author_separator space b:authors_names {
+      def value
+        sep.apply(a,b)
+      end
+      
+      def pos
+        sep.pos(a,b)
+      end
+      
+      def details
+        sep.details(a,b)
+      end
+    }
+    /
+    author_name
+    /
+    unknown_auth
+  end
+  
+  
+  rule unknown_auth
+    ("auct."/"hort."/"anon."/"ht.") {
+      def value
+        text_value
+      end
+      
+      def pos
+       {interval.begin => ['unknown_author', interval.end]}
+      end
+      
+      def details
+        {:author => ["unknown"]}
+      end
+    }
+  end
+  
+  rule ex_sep
+    ("ex"/"in") &[\s]
+  end
+  
+  rule author_separator
+    ("&"/","/"and"/"et") {
+      def apply(a,b)
+        sep = text_value.strip
+        sep = " et" if ["&","and","et"].include? sep
+        a.value + sep + " " + b.value
+      end
+      
+      def pos(a,b)
+        a.pos.merge(b.pos)
+      end
+      
+      def details(a,b)
+        {:author => a.details[:author] + b.details[:author]}
+      end
+    }
+  end
+  
+  rule author_name
+    space a:author_prefix_word space b:author_name space {
+      def value
+        a.value + " " + b.value
+      end
+      
+      def pos
+        a.pos.merge(b.pos)
+      end
+      
+      def details
+        {:author => [value]}
+      end
+    }
+    /
+    space a:author_word space b:author_name space {
+      def value
+        a.value + " " + b.value
+      end
+      
+      def pos
+        a.pos.merge(b.pos)
+      end
+      
+      def details
+        {:author => [value]}
+      end
+    }
+    /
+    author_word
+  end
+  
+  rule author_word
+    "A S. Xu" {
+      def value
+        text_value.strip
+      end
+      
+      def pos
+        {interval.begin => ['author_word', 1], (interval.begin + 2) => ['author_word', 2], (interval.begin + 5) => ['author_word', 2]}
+      end
+      
+      def details
+        {:author => [value]}
+      end
+    }
+    /
+    ("arg."/"et al.\{\?\}"/"et al.") {
+      def value
+        text_value.strip
+      end
+      
+      def pos
+        #cheating because there are several words in some of them
+        {interval.begin => ['author_word', interval.end]}
+      end
+      
+      def details
+        {:author => [value]}
+      end
+    }
+    / 
+    ("Å"/"Ö"/"Á"/"Ø"/"Ô"/"Š"/"Ś"/"Č"/"Ķ"/"Ł"/"É"/"Ž"/[A-W]/[Y-Z]) [^0-9\[\]\(\)\s&,]* {
+      def value
+        text_value
+      end
+      
+      def pos
+        {interval.begin => ['author_word', interval.end]}
+      end
+      
+      def details
+        {:author => [value]}
+      end
+    }
+    /
+    "X" [^0-9\[\]\(\)\s&,]+ {
+      def value
+        text_value
+      end
+      
+      def pos
+        {interval.begin => ['author_word', interval.end]}
+      end
+      
+      def details
+        {:author => [value]}
+      end
+    }
+    /
+    author_prefix_word
+  end
+  
+  rule author_prefix_word
+    space ("ab"/"bis"/"da"/"der"/"den"/"della"/"dela"/"de"/"di"/"du"/"la"/"ter"/"van"/"von") &space_hard {
+      def value
+        text_value
+      end
+      
+      def pos
+        #cheating because there are several words in some of them
+        {interval.begin => ['author_word', interval.end]}
+      end
+    }
+  end
+  
+  rule cap_latin_word
+    a:([A-Z]/cap_digraph) b:latin_word "?" {
+      def value
+        (a.value rescue a.text_value) + b.value
+      end
+    }
+    /
+    a:([A-Z]/cap_digraph) b:latin_word {
+      def value
+        (a.value rescue a.text_value) + 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
+      end
+    }
+  end
+
+  rule species_word_hybrid
+    a:multiplication_sign space b:species_word {
+      def value
+        a.value + " " + b.value
+      end
+      
+      def canonical
+        b.value
+      end
+      
+      def hybrid
+        true
+      end
+      
+      def pos
+        {b.interval.begin => ['species', b.interval.end]}
+      end
+      
+      def details
+        {:species => {:epitheton => b.value}}
+      end
+    }
+    /
+    a:"X" space b:species_word {
+      def value
+        "× " + b.value
+      end
+      
+      def canonical
+        b.value
+      end
+      
+      def hybrid
+        true
+      end
+      
+      def pos
+        {b.interval.begin => ['species', b.interval.end]}
+      end
+      
+      def details
+        {:species => {:epitheton => b.value}}
+      end
+    }
+    /
+    a:"x" space_hard b:species_word {
+      def value
+        "× " + b.value
+      end
+      
+      def canonical
+        b.value
+      end
+      
+      def hybrid
+        true
+      end
+      
+      def pos
+        {b.interval.begin => ['species', b.interval.end]}
+      end
+      
+      def details
+        {:species => {:epitheton => b.value}}
+      end
+    }
+  end
+
+  rule species_prefix
+    ("aff."/"corrig."/"?") &space_hard
+  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-zëüäöïéåóç] b:full_name_letters {
+      def value
+        a.text_value + b.value
+      end
+     }
+     /
+     a:digraph b:full_name_letters {
+      def value
+        a.value + 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]+ {
+      def value
+        text_value
+      end
+    }
+  end 
+
+  rule cap_digraph
+    "Æ" {
+      def value
+      'Ae'
+      end
+    }
+    /
+    "Œ" {
+      def value
+      'Oe'
+      end
+    }  
+  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
+        a.value
+      end
+      
+      def pos
+        a.pos
+      end
+      
+      def details
+        a.details
+      end 
+    }
+    /
+    year_number_with_character
+    /
+    year_number
+  end
+
+  rule year_number_with_character
+    a:year_number [a-zA-Z] {
+      def value
+        a.text_value
+      end
+
+      def pos
+        {interval.begin => ['year', interval.end]}
+      end
+
+      def details
+        {:year => value}
+      end
+    }
+  end
+  
+  rule year_number
+    [12] [7890] [0-9] [0-9]? [\?]? {
+      def value
+        text_value
+      end
+      
+      def pos
+        {interval.begin => ['year', interval.end]}
+      end
+      
+      def details
+        {:year => value}
+      end
+    }
+  end
+  
+  rule left_paren
+    "("
+  end
+  
+  rule right_paren
+    ")"
+  end
+  
+  rule hybrid_character
+    ("x"/"X") {
+      def value
+        "×"
+      end
+    }
+    /
+    multiplication_sign
+  end
+  
+  rule multiplication_sign
+    "×" {
+      def value
+        text_value
+      end
+    }
+  end
+  
+  rule space
+    [\s]*
+  end
+
+  rule space_hard
+    [\s]+
+  end
+  
+end