dimus-biodiversity 0.5.11 → 0.5.13

data/README.rdoc

@@ -31,13 +31,13 @@ You can use it as a library
   parser.all_json
   
   # to clean name up
-  parser.parse("             Plantago       major    ")[:normalized]
+  parser.parse("             Plantago       major    ")[:scientificName][:normalized] 
   
   # to get only cleaned up latin part of the name
-  parser.parse("Pseudocercospora dendrobii (H.C. Burnett) U. Braun & Crous 2003")[:canonical]
+  parser.parse("Pseudocercospora dendrobii (H.C. Burnett) U. Braun & Crous 2003")[:scientificName][:canonical]
   
   # to get detailed information about elements of the name
-  parser.parse("Pseudocercospora dendrobii (H.C. Burnett 1883) U. Braun & Crous 2003")[:details]
+  parser.parse("Pseudocercospora dendrobii (H.C. Burnett 1883) U. Braun & Crous 2003")[:scientificName][:details]
   
   # to resolve lsid and get back RDF file
   LsidResolver.resolve("urn:lsid:ubio.org:classificationbank:2232671")

data/VERSION

@@ -1 +1 @@
-0.5.11
+0.5.13

data/bin/nnparse

@@ -6,6 +6,7 @@ $LOAD_PATH.unshift(File.expand_path(File.dirname(__FILE__) + "/../lib"))
 require 'biodiversity'
 require 'json'
 
+
 if ARGV.empty?
   puts "Usage:\n\nnnparse file_with_scientific_names [output_file]\n\ndefault output_file is parsed.json\n\n"
   exit
@@ -14,16 +15,29 @@ end
 input = ARGV[0]
 output = ARGV[1] || 'parsed.json'
 
+ruby_min_version = RUBY_VERSION.split(".")[0..1].join('').to_i
+
 p = ScientificNameParser.new
 o = open(output, 'w')
-
 count = 0
+puts 'Parsing...'
 IO.foreach(input) do |line|
   count += 1
   puts("%s lines parsed" % count) if count % 10000 == 0
-  name = line.gsub(/^[\d]*\s*/, '').strip 
-  p.parse(name)
-  parsed_data = p.parsed.all_json rescue {'parsed' => false, 'vernacular' => name,  'error' => 'Parser error'}.to_json
+  name = line.gsub(/^[\d]*\s*/, '').strip
+  begin
+    if ruby_min_version < 19
+      old_kcode = $KCODE
+      $KCODE = 'NONE'
+    end
+    p.parse(name) 
+    parsed_data = p.parsed.all_json rescue {'parsed' => false, 'verbatim' => name,  'error' => 'Parser error'}.to_json
+    if ruby_min_version < 19
+      $KCODE = old_kcode
+    end
+  rescue 
+    parsed_data = {'parsed' => false, 'verbatim' => name,  'error' => 'Parser error'}.to_json
+  end
   o.write parsed_data + "\n"
 end
 

data/biodiversity.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{biodiversity}
-  s.version = "0.5.11"
+  s.version = "0.5.13"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Dmitry Mozzherin"]
-  s.date = %q{2009-08-16}
+  s.date = %q{2009-08-17}
   s.default_executable = %q{nnparse}
   s.description = %q{Tools for biodiversity informatics}
   s.email = %q{dmozzherin@gmail.com}

data/lib/biodiversity/parser.rb

@@ -16,6 +16,10 @@ class ScientificNameParser
     @parsed = nil
   end
   
+  def parsed
+    @parsed
+  end
+  
   def parse(a_string)
     @verbatim = a_string
     @parsed = @clean.parse(a_string) || @dirty.parse(a_string) || @canonical.parse(a_string) || {:verbatim => a_string}

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: dimus-biodiversity
 version: !ruby/object:Gem::Version 
-  version: 0.5.11
+  version: 0.5.13
 platform: ruby
 authors: 
 - Dmitry Mozzherin
@@ -9,7 +9,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2009-08-16 00:00:00 -07:00
+date: 2009-08-17 00:00:00 -07:00
 default_executable: nnparse
 dependencies: 
 - !ruby/object:Gem::Dependency