obo 0.1.3 → 0.1.4

data/lib/obo/parser.rb

@@ -4,72 +4,43 @@ require_relative 'stanza'
 module Obo
   class Parser
     STANZA_START = /^\[(.*?)\]/
-    TAG_VALUE    = /^(.*?):([^!]*)/
+    TAG_VALUE    = /^(.*?):\s*([^!]*)\n/
 
     def initialize(filename)
-      @header = nil
-      @io     = File.open(filename)
+      @io = File.open(filename)
     end
 
     def elements(io = @io)
       Enumerator.new do |yielder|
-        header             = Header.new
-        prev_line_position = io.pos
-        line               = lines.next
-
-        until line.is_a? Stanza
-          header.add(*line)
-          prev_line_position = io.pos
-          line               = lines.next
+        header = Header.new
+        while io.gets.match TAG_VALUE
+          header.add($1, $2)
         end
 
         yielder << header
-        io.pos = prev_line_position
 
-        stanzas.each { |stanza| yielder << stanza }
-      end
-    end
+        io.gets until $_.match(STANZA_START)
+        stanza = Stanza.new($1.strip)
 
-    def rewind(io = @io)
-      io.pos = 0
-    end
-
-    private
-
-    def stanzas
-      Enumerator.new do |yielder|
-        stanza = lines.first { |line| line.is_a? Stanza }
-
-        begin
-          while line = lines.next
-            case line
-            when Array
-              stanza.add(*line)
-            when Stanza
-              yielder << stanza
-              stanza = line
-            end
+        while io.gets
+          case $_
+          when TAG_VALUE
+            stanza.add($1, $2)
+          when STANZA_START
+            yielder << stanza
+            stanza = Stanza.new($1.strip)
           end
-        rescue StopIteration
-          yielder << stanza
         end
 
+        yielder << stanza
+        rewind
       end
     end
 
-    # Yields lines that are either Stanza name or tag-value pairs
-    def lines(io = @io)
-      Enumerator.new do |yielder|
-        while line = io.gets
-          case line.strip
-          when STANZA_START
-            yielder << Stanza.new($1.strip)
-          when TAG_VALUE
-            yielder << [$1.strip,$2.strip]
-          end
-        end
-      end
+    def rewind(io = @io)
+      io.pos = 0
     end
+
   end
 end
 

data/lib/obo/version.rb

@@ -1,3 +1,3 @@
 module Obo
-  VERSION = "0.1.3"
+  VERSION = "0.1.4"
 end

data/test/test_obo.rb

@@ -4,7 +4,6 @@ require "pp"
 class TestObo < MiniTest::Unit::TestCase
   def setup
     @obo = Obo::Parser.new('test/data/ro.obo')
-#    @obo = Obo::Parser.new('test/data/so_2_4_3.obo')
   end
 
   def test_header_parsing
@@ -50,8 +49,6 @@ class TestObo < MiniTest::Unit::TestCase
   def test_rewind
     # Run through the file to the end
     @obo.elements.count
-    assert_raises(StopIteration){@obo.elements.count}
-    @obo.rewind
     assert_equal 27, @obo.elements.count
   end
 end

metadata

@@ -1,7 +1,8 @@
 --- !ruby/object:Gem::Specification
 name: obo
 version: !ruby/object:Gem::Version
-  version: 0.1.3
+  version: 0.1.4
+  prerelease: 
 platform: ruby
 authors:
 - Robert Syme
@@ -9,11 +10,12 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-05-03 00:00:00.000000000 Z
+date: 2013-06-25 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -21,11 +23,12 @@ dependencies:
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
         version: '1.3'
-description: 'The OBO format is the text file format used by OBO-Edit, the open-source,
+description: ! 'The OBO format is the text file format used by OBO-Edit, the open-source,
   platform-independent application for viewing and editing ontologies. The format
   is described here: http://www.geneontology.org/GO.format.obo-1_2.shtml'
 email:
@@ -57,26 +60,33 @@ files:
 homepage: http://github.com/robsyme/obo
 licenses:
 - MIT
-metadata: {}
 post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
   requirements:
-  - - '>='
+  - - ! '>='
     - !ruby/object:Gem::Version
       version: '0'
+      segments:
+      - 0
+      hash: 2033594933957096070
 required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
   requirements:
-  - - '>='
+  - - ! '>='
     - !ruby/object:Gem::Version
       version: '0'
+      segments:
+      - 0
+      hash: 2033594933957096070
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.0.0.rc.2
+rubygems_version: 1.8.24
 signing_key: 
-specification_version: 4
+specification_version: 3
 summary: A parser for the OBO flat file format
 test_files:
 - test/data/ro.obo

checksums.yaml

@@ -1,7 +0,0 @@
----
-SHA1:
-  metadata.gz: 179add8eb74e998aa0db59d8aa58520648d56995
-  data.tar.gz: 94d64cb521380eeb3fb394bb42f8dba46c81497a
-SHA512:
-  metadata.gz: f7495d695a3c85947b3504a12965ec58b8fb8d4307aefa02263129b8580611d7f3f914d62a478e7d4185a2543fe16ff09061464e018783ea305e781e2c9eb714
-  data.tar.gz: ab6ec0e629f33b10df673301eb721502be9857dc99362a7551a742819fa4d69874cc794eabe354d00682b237c88c5082652c1e20c7256856b019961275b28c08