dimus-biodiversity 0.0.7 → 0.0.8

data/README.rdoc

@@ -33,4 +33,6 @@ You can use it as a library
   # to get detailed information about elements of the name
   parser.parse("Pseudocercospora dendrobii (H.C. Burnett 1883) U. Braun & Crous 2003").details
   
-  
+  # to resolve lsid and get back RDF file
+  LsidResolver.resolve("urn:lsid:ubio.org:classificationbank:2232671")
+

data/bin/nnparse

@@ -34,6 +34,7 @@ IO.foreach(ARGV[0]) do |n|
   unless parsed
     name_dict[:details] = {:parsed => false}
     last_result = JSON.generate name_dict
+    puts n
     count += 1
   else
     name_dict[:output] = parsed.value

data/lib/biodiversity.rb

@@ -4,6 +4,8 @@ require 'treetop'
 dir = File.dirname(__FILE__)
 
 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/scientific_name.rb

@@ -295,7 +295,7 @@ module ScientificName
     end
 
     i0 = index
-    r1 = _nt_name_authors_part
+    r1 = _nt_name_part_authors_mix
     if r1
       r0 = r1
     else
@@ -544,7 +544,7 @@ module ScientificName
     return r0
   end
 
-  module NameAuthorsPart0
+  module NamePartAuthorsMix0
     def a
       elements[0]
     end
@@ -564,9 +564,51 @@ module ScientificName
     def c
       elements[4]
     end
+
+    def space
+      elements[5]
+    end
+
+    def d
+      elements[6]
+    end
   end
 
-  module NameAuthorsPart1
+  module NamePartAuthorsMix1
+    def value
+      a.value + " " + b.value + " " + c.value + " " + d.value
+    end
+    def canonical
+      a.canonical + " " + c.canonical
+    end
+    def details
+      a.details.merge(c.details).merge({:species_authors=>b.details, :subspecies_authors => d.details})
+    end
+  end
+
+  module NamePartAuthorsMix2
+    def a
+      elements[0]
+    end
+
+    def space
+      elements[1]
+    end
+
+    def b
+      elements[2]
+    end
+
+    def space
+      elements[3]
+    end
+
+    def c
+      elements[4]
+    end
+  end
+
+  module NamePartAuthorsMix3
     def value 
       a.value + " " + b.value + " " + c.value
     end
@@ -578,43 +620,89 @@ module ScientificName
     end
   end
 
-  def _nt_name_authors_part
+  def _nt_name_part_authors_mix
     start_index = index
-    if node_cache[:name_authors_part].has_key?(index)
-      cached = node_cache[:name_authors_part][index]
+    if node_cache[:name_part_authors_mix].has_key?(index)
+      cached = node_cache[:name_part_authors_mix][index]
       @index = cached.interval.end if cached
       return cached
     end
 
-    i0, s0 = index, []
-    r1 = _nt_species_name
-    s0 << r1
-    if r1
-      r2 = _nt_space
-      s0 << r2
-      if r2
-        r3 = _nt_authors_part
-        s0 << r3
-        if r3
-          r4 = _nt_space
-          s0 << r4
-          if r4
-            r5 = _nt_subspecies_name
-            s0 << r5
+    i0 = index
+    i1, s1 = index, []
+    r2 = _nt_species_name
+    s1 << r2
+    if r2
+      r3 = _nt_space
+      s1 << r3
+      if r3
+        r4 = _nt_authors_part
+        s1 << r4
+        if r4
+          r5 = _nt_space
+          s1 << r5
+          if r5
+            r6 = _nt_subspecies_name
+            s1 << r6
+            if r6
+              r7 = _nt_space
+              s1 << r7
+              if r7
+                r8 = _nt_authors_part
+                s1 << r8
+              end
+            end
           end
         end
       end
     end
-    if s0.last
-      r0 = (SyntaxNode).new(input, i0...index, s0)
-      r0.extend(NameAuthorsPart0)
-      r0.extend(NameAuthorsPart1)
+    if s1.last
+      r1 = (SyntaxNode).new(input, i1...index, s1)
+      r1.extend(NamePartAuthorsMix0)
+      r1.extend(NamePartAuthorsMix1)
     else
-      self.index = i0
-      r0 = nil
+      self.index = i1
+      r1 = nil
+    end
+    if r1
+      r0 = r1
+    else
+      i9, s9 = index, []
+      r10 = _nt_species_name
+      s9 << r10
+      if r10
+        r11 = _nt_space
+        s9 << r11
+        if r11
+          r12 = _nt_authors_part
+          s9 << r12
+          if r12
+            r13 = _nt_space
+            s9 << r13
+            if r13
+              r14 = _nt_subspecies_name
+              s9 << r14
+            end
+          end
+        end
+      end
+      if s9.last
+        r9 = (SyntaxNode).new(input, i9...index, s9)
+        r9.extend(NamePartAuthorsMix2)
+        r9.extend(NamePartAuthorsMix3)
+      else
+        self.index = i9
+        r9 = nil
+      end
+      if r9
+        r0 = r9
+      else
+        self.index = i0
+        r0 = nil
+      end
     end
 
-    node_cache[:name_authors_part][start_index] = r0
+    node_cache[:name_part_authors_mix][start_index] = r0
 
     return r0
   end

data/lib/biodiversity/parser/scientific_name.treetop

@@ -31,7 +31,7 @@ grammar ScientificName
   end
   
   rule scientific_name
-    name_authors_part
+    name_part_authors_mix
     /
     space a:name_part space b:authors_part space c:status_part space {
       def value
@@ -100,7 +100,19 @@ grammar ScientificName
     latin_word
   end
   
-  rule name_authors_part 
+  rule name_part_authors_mix
+    a:species_name space b:authors_part space c:subspecies_name space d:authors_part {
+      def value
+        a.value + " " + b.value + " " + c.value + " " + d.value
+      end
+      def canonical
+        a.canonical + " " + c.canonical
+      end
+      def details
+        a.details.merge(c.details).merge({:species_authors=>b.details, :subspecies_authors => d.details})
+      end
+    }
+    /
     a:species_name space b:authors_part space c:subspecies_name {
       def value 
         a.value + " " + b.value + " " + c.value

data/spec/parser/scientific_name.spec.rb

@@ -2,7 +2,7 @@ dir = File.dirname("__FILE__")
 require 'rubygems'
 require 'spec'
 require 'treetop'
-require 'biodiversity'
+
 Treetop.load(File.expand_path(dir + '../../lib/biodiversity/parser/scientific_name'))
 
 describe ScientificName do
@@ -53,7 +53,8 @@ describe ScientificName do
   it 'should parse species autonym for complex subspecies authorships' do
     parse("Aus bus Linn. var. bus").should_not be_nil
     details("Aus bus Linn. var. bus").should == {:species=>"bus", :species_authors=>{:authors=>{:names=>["Linn."]}}, :genus=>"Aus", :subspecies=>[{:rank=>"var.", :value=>"bus"}]}
-    # aus genus, bus species, Linn. author, var. rank, bus infraspecific epithet 
+    parse("Agalinis purpurea (L.) Briton var. borealis (Berg.) Peterson 1987").should_not be_nil
+    details("Agalinis purpurea (L.) Briton var. borealis (Berg.) Peterson 1987").should == {:species=>"purpurea", :genus=>"Agalinis", :species_authors=>{:orig_authors=>{:names=>["L."]}, :authors=>{:names=>["Briton"]}}, :subspecies_authors=>{:orig_authors=>{:names=>["Berg."]}, :authors=>{:year=>"1987", :names=>["Peterson"]}}, :subspecies=>[{:value=>"borealis", :rank=>"var."}]}
   end
   
   it 'should parse several authors' do

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: dimus-biodiversity
 version: !ruby/object:Gem::Version 
-  version: 0.0.7
+  version: 0.0.8
 platform: ruby
 authors: 
 - Dmitry Mozzherin