obo_parser 0.3.1 → 0.3.2

data/README.rdoc

@@ -1,6 +1,6 @@
 = obo_parser
 
-A simple Ruby gem for parsing OBO formatted ontology files.  Useful for reporting, comparing, and mapping data to other databases.  There is presently no functionality for logical inference across the ontology.
+A simple Ruby gem for parsing OBO 1.2 formatted ontology files.  Useful for reporting, comparing, and mapping data to other databases.  There is presently no functionality for logical inference across the ontology.
 
 == Installation
 
@@ -10,7 +10,7 @@ A simple Ruby gem for parsing OBO formatted ontology files.  Useful for reportin
 
     require 'rubygems'
     require 'obo_parser'
-    foo = parse_obo_file(File.read('my_ontology.obo'))  # => An OboParser instance.  Targets OBO v. 1.4
+    foo = parse_obo_file(File.read('my_ontology.obo'))  # => An OboParser instance  
     first_term = foo.terms.first                        # => An OboParser#Term instance 
     d = first_term.def                                  # => An OboParser#Tag instance
  

data/VERSION

@@ -1 +1 @@
-0.3.1
+0.3.2

data/lib/obo_parser.rb

@@ -69,7 +69,7 @@ module OboParser
         return nil if tag_name.nil?
         result = []
         @other_tags.each do |t|
-          result.push t if t.tag == tag_name
+          result.push(t) if (t.tag == tag_name)
         end
         result
       end
@@ -115,7 +115,7 @@ module OboParser
     end
 
     class Tag
-      attr_accessor :tag, :value, :xrefs, :comment
+      attr_accessor :tag, :value, :xrefs, :comment, :qualifier
     end
 
   end

data/lib/tokens.rb

@@ -18,11 +18,12 @@ module OboParser::Tokens
   end
 
   class TagValuePair < Token
-    attr_reader :tag, :comment, :xrefs
+    attr_reader :tag, :comment, :xrefs, :qualifier
     @regexp = Regexp.new(/\A\s*([^:]+:.+)\s*\n*/i) 
     def initialize(str)
       str.strip!
       tag, value = str.split(':',2)      
+      @tag = tag.strip
 
       value.strip!
 
@@ -43,14 +44,18 @@ module OboParser::Tokens
         @xrefs = xref_list.split(",") 
       end
 
-      @tag = tag.strip
-      @value = value.strip
-
-      @value = @value[1..-2] if @value[0..0] == "\"" # get rid of quote marks
-      @value = @value[1..-2] if @value[0..0] == "'"  # get rid of quote marks
+      if value =~ /\A\"/
+        value =~ /(".*")/
+        @value = $1
+        value.gsub!(@value, '')
+        @qualifier = value.strip
+      else
+        @value = value.strip
+        @qualifier = nil
+      end
 
-      @tag = @tag.strip
-      @value = @value.strip
+      @value = @value[1..-2].strip if @value[0..0] == "\"" # get rid of quote marks
+      @value = @value[1..-2].strip if @value[0..0] == "'"  # get rid of quote marks
     end
   end
 

data/obo_parser.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{obo_parser}
-  s.version = "0.3.1"
+  s.version = "0.3.2"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["mjy"]
-  s.date = %q{2011-04-05}
+  s.date = %q{2011-04-06}
   s.description = %q{Provides all-in-one object containing the contents of an OBO formatted file.  OBO version 1.2 is targeted, though this should work for 1.0. }
   s.email = %q{diapriid@gmail.com}
   s.extra_rdoc_files = [