obo 0.1.4 → 0.1.5

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: e16927a494bf3379df6023df94df5c6edf87918d
+  data.tar.gz: 4c191ef4175dd9e59302b1aea6c5f150d4fa1394
+SHA512:
+  metadata.gz: 68359ab9cc3ba6989e1dc74d2847309b4a2066b23646e52811bd6898b5501c763e80540a76211607b1fdff487134fbc56db3e44db17b91c683ce7b4697ab085f
+  data.tar.gz: 7e842778b3b1aac99ceebc06e527db3285de94fd14f2875510108dab9c087608dc7aa043114d1320271c919450d6418a6e36d55ed1e4ea7fe7320baa8ba6c424

data/VERSION

@@ -1 +1 @@
-0.1.2
+0.1.5

data/lib/obo/parser.rb

@@ -4,7 +4,7 @@ require_relative 'stanza'
 module Obo
   class Parser
     STANZA_START = /^\[(.*?)\]/
-    TAG_VALUE    = /^(.*?):\s*([^!]*)\n/
+    TAG_VALUE    = /^(.*?):\s*([^!]*)\s*(.*?)\n/
 
     def initialize(filename)
       @io = File.open(filename)
@@ -25,7 +25,7 @@ module Obo
         while io.gets
           case $_
           when TAG_VALUE
-            stanza.add($1, $2)
+            stanza.add($1, $2.strip)
           when STANZA_START
             yielder << stanza
             stanza = Stanza.new($1.strip)

data/lib/obo/version.rb

@@ -1,3 +1,3 @@
 module Obo
-  VERSION = "0.1.4"
+  VERSION = "0.1.5"
 end

data/test/test_obo.rb

@@ -20,9 +20,32 @@ class TestObo < MiniTest::Unit::TestCase
     assert_equal 'Typedef', first_stanza.name
     assert_equal 'OBO_REL:is_a', first_stanza['id']
     assert_equal 'is_a', first_stanza['name']
+      
     assert first_stanza['is_reflexive']
   end
 
+  def test_stanza_fields_and_values
+    @obo = Obo::Parser.new('test/data/so_2_4_3.obo')
+    terms = []
+
+    @obo.elements.each do |elm|
+      terms << elm
+    end
+
+    sofa = terms[1]
+    assert_equal "SO:0000000", sofa["id"] 
+    assert_equal "Sequence_Ontology", sofa["name"]
+    assert_equal "SOFA", sofa["subset"]
+    assert_equal true, sofa.is_obsolete
+
+    region = terms[2]
+    assert_equal "SO:0000001", region["id"]
+    #tests stripping of comments
+    assert_equal "SO:0000110", region["is_a"]    
+    assert_equal %{"sequence" EXACT []}, region["synonym"] 
+      
+  end
+  
   def test_fancy_methods
     first_stanza = @obo.elements.find{|element| element.is_a? Obo::Stanza}
     assert_equal 'OBO_REL:is_a', first_stanza.id
@@ -51,6 +74,8 @@ class TestObo < MiniTest::Unit::TestCase
     @obo.elements.count
     assert_equal 27, @obo.elements.count
   end
+  
 end
 
 
+

metadata

@@ -1,8 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: obo
 version: !ruby/object:Gem::Version
-  version: 0.1.4
-  prerelease: 
+  version: 0.1.5
 platform: ruby
 authors:
 - Robert Syme
@@ -10,12 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-06-25 00:00:00.000000000 Z
+date: 2014-04-22 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -23,12 +21,11 @@ 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:
@@ -60,33 +57,26 @@ 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: 1.8.24
+rubygems_version: 2.0.3
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: A parser for the OBO flat file format
 test_files:
 - test/data/ro.obo