biodiversity19 0.5.15 → 0.5.16

data/.gitignore

@@ -11,3 +11,4 @@ biodiversity*.gem
 tmp
 .DS_Store
 spec/parser/test_data_new.txt
+t

data/Rakefile

@@ -19,7 +19,7 @@ begin
   Jeweler::Tasks.new do |gem|
     gem.name = "biodiversity19"
     gem.summary = 'Parser of scientific names'
-    gem.description = 'Tools for biodiversity informatics for ruby 1.9'
+    gem.description = 'Tools for biodiversity informatics'
     gem.email = "dmozzherin@gmail.com"
     gem.homepage = "http://github.com/dimus/biodiversity"
     gem.authors = ["Dmitry Mozzherin"]
@@ -36,8 +36,24 @@ rescue LoadError
 end
 
 task :tt do
-  system("tt #{dir}/lib/biodiversity/parser/scientific_name_clean.treetop")
-  system("tt #{dir}/lib/biodiversity/parser/scientific_name_dirty.treetop")
-  system("tt #{dir}/lib/biodiversity/parser/scientific_name_canonical.treetop")
+  ['scientific_name_clean', 'scientific_name_dirty', 'scientific_name_canonical'].each do |f|
+    system("tt #{dir}/lib/biodiversity/parser/#{f}.treetop")
+    rf = "#{dir}/lib/biodiversity/parser/#{f}.rb"
+    rfn = open(rf + ".tmp", 'w')
+    skip_head = false
+    f = open(rf)
+    f.each_with_index do |l, i|
+      skip_head = l.match(/^# Autogenerated/) if i == 0
+      if skip_head && (l.strip == '' || l.match(/^# Autogenerated/))
+        next  
+      else
+        skip_head = false
+        rfn.write(l)
+      end
+    end
+    rfn.close
+    f.close
+    `mv #{rf}.tmp #{rf}`
+  end
 end
 

data/VERSION

@@ -1 +1 @@
-0.5.15
+0.5.16

data/bin/nnparse

@@ -1,6 +1,6 @@
 #!/usr/bin/env ruby
 require 'rubygems'
-gem 'dimus-biodiversity' rescue gem 'biodiversity' rescue nil
+gem 'biodiversity' rescue nil
 
 $LOAD_PATH.unshift(File.expand_path(File.dirname(__FILE__) + "/../lib"))
 require 'biodiversity'
@@ -31,7 +31,7 @@ IO.foreach(input) do |line|
       $KCODE = 'NONE'
     end
     p.parse(name) 
-    parsed_data = p.parsed.all_json rescue {'parsed' => false, 'verbatim' => name,  'error' => 'Parser error'}.to_json
+    parsed_data = p.parsed.all_json rescue {'scientificName' => {'parsed' => false, 'verbatim' => name,  'error' => 'Parser error'}}.to_json
     if ruby_min_version < 19
       $KCODE = old_kcode
     end

data/{biodiversity.gemspec → biodiversity19.gemspec}

@@ -4,12 +4,12 @@
 # -*- encoding: utf-8 -*-
 
 Gem::Specification.new do |s|
-  s.name = %q{biodiversity}
-  s.version = "0.5.15"
+  s.name = %q{biodiversity19}
+  s.version = "0.5.16"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Dmitry Mozzherin"]
-  s.date = %q{2010-03-25}
+  s.date = %q{2010-04-08}
   s.default_executable = %q{nnparse}
   s.description = %q{Tools for biodiversity informatics}
   s.email = %q{dmozzherin@gmail.com}
@@ -27,7 +27,7 @@ Gem::Specification.new do |s|
      "VERSION",
      "bin/nnparse",
      "bin/parserver",
-     "biodiversity.gemspec",
+     "biodiversity19.gemspec",
      "conf/environment.rb",
      "lib/biodiversity.rb",
      "lib/biodiversity/guid.rb",
@@ -56,13 +56,13 @@ Gem::Specification.new do |s|
   s.rubygems_version = %q{1.3.6}
   s.summary = %q{Parser of scientific names}
   s.test_files = [
-    "spec/parser/scientific_name_dirty.spec.rb",
+    "spec/biodiversity_spec.rb",
+     "spec/guid/lsid.spec.rb",
+     "spec/parser/scientific_name.spec.rb",
      "spec/parser/scientific_name_canonical.spec.rb",
      "spec/parser/scientific_name_clean.spec.rb",
+     "spec/parser/scientific_name_dirty.spec.rb",
      "spec/parser/spec_helper.rb",
-     "spec/parser/scientific_name.spec.rb",
-     "spec/biodiversity_spec.rb",
-     "spec/guid/lsid.spec.rb",
      "spec/spec_helper.rb"
   ]
 
@@ -72,13 +72,16 @@ Gem::Specification.new do |s|
 
     if Gem::Version.new(Gem::RubyGemsVersion) >= Gem::Version.new('1.2.0') then
       s.add_runtime_dependency(%q<treetop>, [">= 0"])
+      s.add_runtime_dependency(%q<json>, [">= 0"])
       s.add_development_dependency(%q<rspec>, [">= 0"])
     else
       s.add_dependency(%q<treetop>, [">= 0"])
+      s.add_dependency(%q<json>, [">= 0"])
       s.add_dependency(%q<rspec>, [">= 0"])
     end
   else
     s.add_dependency(%q<treetop>, [">= 0"])
+    s.add_dependency(%q<json>, [">= 0"])
     s.add_dependency(%q<rspec>, [">= 0"])
   end
 end

data/lib/biodiversity/parser/scientific_name_canonical.rb

@@ -3,11 +3,9 @@ module ScientificNameCanonical
   include Treetop::Runtime
 
   def root
-    @root || :root
+    @root ||= :root
   end
 
-  include ScientificNameClean
-
   include ScientificNameDirty
 
   module Root0
@@ -18,6 +16,10 @@ module ScientificNameCanonical
     def details
       [super]
     end
+
+    def parser_run
+      3
+    end
   end
 
   module Root1
@@ -28,6 +30,10 @@ module ScientificNameCanonical
     def details
       [super]
     end
+
+    def parser_run
+      3
+    end
   end
 
   def _nt_root

data/lib/biodiversity/parser/scientific_name_canonical.treetop

@@ -1,6 +1,5 @@
 # encoding: UTF-8
 grammar ScientificNameCanonical
-  include ScientificNameClean
   include ScientificNameDirty
 
   rule root
@@ -12,6 +11,10 @@ grammar ScientificNameCanonical
       def details
         [super]
       end
+
+      def parser_run
+        3
+      end
     }
     /
     uninomial_with_garbage {
@@ -22,6 +25,10 @@ grammar ScientificNameCanonical
       def details
         [super]
       end
+
+      def parser_run
+        3
+      end
     }
   end