obo 0.1.0 → 0.1.3

checksums.yaml

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

data/.gitignore

@@ -0,0 +1,51 @@
+# rcov generated
+coverage
+
+# rdoc generated
+rdoc
+
+# yard generated
+doc
+.yardoc
+
+# bundler
+.bundle
+
+# jeweler generated
+pkg
+
+# Have editor/IDE/OS specific files you need to ignore? Consider using a global gitignore: 
+#
+# * Create a file at ~/.gitignore
+# * Include files you want ignored
+# * Run: git config --global core.excludesfile ~/.gitignore
+#
+# After doing this, these files will be ignored in all your git projects,
+# saving you from having to 'pollute' every project you touch with them
+#
+# Not sure what to needs to be ignored for particular editors/OSes? Here's some ideas to get you started. (Remember, remove the leading # of the line)
+#
+# For MacOS:
+#
+#.DS_Store
+
+# For TextMate
+#*.tmproj
+#tmtags
+
+# For emacs:
+*~
+\#*
+.\#*
+
+# For vim:
+#*.swp
+
+# For redcar:
+#.redcar
+
+# For rubinius:
+#*.rbc
+
+# Don't need lock file for gem
+Gemfile.lock

data/Gemfile

@@ -1,14 +1,9 @@
 source "http://rubygems.org"
-# Add dependencies required to use your gem here.
-# Example:
-#   gem "activesupport", ">= 2.3.5"
 
-# Add dependencies to develop your gem here.
-# Include everything needed to run rake, tests, features, etc.
+gemspec
+
 group :development do
-  gem "minitest", ">= 0"
-  gem "yard", "~> 0.6.0"
-  gem "bundler", "~> 1.0.0"
-  gem "jeweler", "~> 1.6.0"
-  gem "rcov", ">= 0"
+  gem "rake"
+  gem "yard"
+  gem "simplecov", :require => false
 end

data/README.rdoc

@@ -1,6 +1,8 @@
 = obo
 
-Description goes here.
+The OBO format is used to describe ontologies, commonly used in biology. The format is defined at {geneontology.org}[http://www.geneontology.org/GO.format.obo-1_2.shtml]. At the moment, the parser is pretty bare-bones and is enough for me to easily get ontologies into a db. 
+
+The parser (over)uses Enumerators to ensure that you can parse arbitrarily large files. I'm very happy to have feedback about the merits (or lack of merit) of this approach.
 
 == Contributing to obo
  

data/Rakefile

@@ -1,7 +1,9 @@
 # encoding: utf-8
 
-require 'rubygems'
+#require 'rubygems'
+require 'bundler/gem_tasks'
 require 'bundler'
+
 begin
   Bundler.setup(:default, :development)
 rescue Bundler::BundlerError => e
@@ -9,37 +11,16 @@ rescue Bundler::BundlerError => e
   $stderr.puts "Run `bundle install` to install missing gems"
   exit e.status_code
 end
-require 'rake'
-
-require 'jeweler'
-Jeweler::Tasks.new do |gem|
-  # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
-  gem.name = "obo"
-  gem.homepage = "http://github.com/robsyme/obo"
-  gem.license = "MIT"
-  gem.summary = %Q{A parser for the OBO flat file format}
-  gem.description = %Q{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}
-  gem.email = "rob.syme@gmail.com"
-  gem.authors = ["robsyme"]
-  # dependencies defined in Gemfile
-end
-Jeweler::RubygemsDotOrgTasks.new
 
+require 'rake'
 require 'rake/testtask'
+
 Rake::TestTask.new(:test) do |test|
   test.libs << 'lib' << 'test'
   test.pattern = 'test/**/test_*.rb'
   test.verbose = true
 end
 
-require 'rcov/rcovtask'
-Rcov::RcovTask.new do |test|
-  test.libs << 'test'
-  test.pattern = 'test/**/test_*.rb'
-  test.verbose = true
-  test.rcov_opts << '--exclude "gems/*"'
-end
-
 task :default => :test
 
 require 'yard'

data/VERSION

@@ -1 +1 @@
-0.1.0
+0.1.2

data/lib/obo.rb

@@ -1,133 +1,7 @@
-
-
 module Obo
-
-  class Header
-    attr_reader :tagvalues
-
-    def initialize
-      @tagvalues = Hash.new{|h,k| h[k] = []}
-    end
-
-    def [](tag)
-      values = @tagvalues[tag]
-      values.length == 1 ? values.first : values
-    end
-    
-    def add(tag,value)
-      @tagvalues[tag] << value
-    end
-  end
-
-  class Stanza
-    attr_reader :name
-    attr_reader :tagvalues
-
-    def initialize(name)
-      @name = name
-      @tagvalues = Hash.new{|h,k| h[k] = []}
-    end
-
-    def [](tag)
-      values = @tagvalues[tag]
-      case values.length
-      when 0
-        nil
-      when 1
-        values.first
-      else values
-      end
-    end
-
-    def add(tag,value)
-      @tagvalues[tag] << case value
-                         when 'true'
-                           true
-                         when 'false'
-                           false
-                         else value  
-                         end
-    end
-
-    def method_missing(method, *args, &block)
-      values = self[method.to_s]
-
-      if values
-        return values
-      elsif method =~ /\?$/
-        self.send(method[0..-2])
-      else
-        raise NoMethodError, "No method #{method} on #{self.class}"
-      end
-      
-    end
-  end
-  
-  
-  class Parser
-
-    STANZA_START = /^\[(.*?)\]/
-    TAG_VALUE = /^(.*?):([^!]*)/
-
-    def initialize(filename)
-      @header = nil
-      @io = File.open(filename)
-    end
-
-    def elements(io = @io)
-      Enumerator.new do |yielder|
-        header = Header.new
-        previous_line_position = io.pos
-        line = lines.next
-        until line.is_a? Stanza
-          header.add(*line)
-          previous_line_position = io.pos
-          line = lines.next
-        end
-        yielder << header
-        io.pos = previous_line_position
-
-        stanzas.each{|stanza| yielder << stanza}
-      end
-    end
-
-    def stanzas
-      Enumerator.new do |yielder|
-        stanza = lines.first{|line| line.is_a? Stanza}
-
-        lines.each do |line|
-          case line
-          when Array
-            stanza.add(*line)
-          when Stanza
-            yielder << stanza
-            stanza = line
-          end
-        end
-        
-      end
-    end
-
-    def rewind(io = @io)
-      io.pos = 0
-    end
-
-    private
-
-    # 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
-    end
-
-  end
 end
 
+require_relative 'obo/header'
+require_relative 'obo/stanza'
+require_relative 'obo/parser'
+

data/lib/obo/header.rb

@@ -0,0 +1,19 @@
+module Obo
+  class Header
+    attr_reader :tagvalues
+
+    def initialize
+      @tagvalues = Hash.new{|h,k| h[k] = []}
+    end
+
+    def [](tag)
+      values = @tagvalues[tag]
+      values.length == 1 ? values.first : values
+    end
+
+    def add(tag,value)
+      @tagvalues[tag] << value
+    end
+  end
+end
+

data/lib/obo/parser.rb

@@ -0,0 +1,75 @@
+require_relative 'header'
+require_relative 'stanza'
+
+module Obo
+  class Parser
+    STANZA_START = /^\[(.*?)\]/
+    TAG_VALUE    = /^(.*?):([^!]*)/
+
+    def initialize(filename)
+      @header = nil
+      @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
+        end
+
+        yielder << header
+        io.pos = prev_line_position
+
+        stanzas.each { |stanza| yielder << stanza }
+      end
+    end
+
+    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
+          end
+        rescue StopIteration
+          yielder << stanza
+        end
+
+      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
+    end
+  end
+end
+

data/lib/obo/stanza.rb

@@ -0,0 +1,46 @@
+module Obo
+  class Stanza
+    attr_reader :name
+    attr_reader :tagvalues
+
+    def initialize(name)
+      @name = name
+      @tagvalues = Hash.new{|h,k| h[k] = []}
+    end
+
+    def [](tag)
+      values = @tagvalues[tag]
+      case values.length
+      when 0
+        nil
+      when 1
+        values.first
+      else values
+      end
+    end
+
+    def add(tag,value)
+      @tagvalues[tag] << case value
+                         when 'true'
+                           true
+                         when 'false'
+                           false
+                         else value
+                         end
+    end
+
+    def method_missing(method, *args, &block)
+      values = self[method.to_s]
+
+      if values
+        return values
+      elsif method =~ /\?$/
+        self.send(method[0..-2])
+      else
+        raise NoMethodError, "No method #{method} on #{self.class}"
+      end
+
+    end
+  end
+end
+

data/lib/obo/version.rb

@@ -0,0 +1,3 @@
+module Obo
+  VERSION = "0.1.3"
+end

data/obo.gemspec

@@ -0,0 +1,23 @@
+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'obo/version'
+
+Gem::Specification.new do |s|
+  s.name = "obo"
+  s.version = Obo::VERSION
+  s.authors = ["Robert Syme", "Darren Oakley"]
+  s.email = ["rob.syme@gmail.com", "daz.oakley@gmail.com"]
+  s.description = "The OBO format is the text file format used by OBO-Edit, the open-source, platform-independent application for viewing and editing ontologies. The format is described here: http://www.geneontology.org/GO.format.obo-1_2.shtml"
+  s.summary = "A parser for the OBO flat file format"
+  s.homepage = "http://github.com/robsyme/obo"
+  s.licenses = ["MIT"]
+
+  s.files         = `git ls-files`.split($/)
+  s.executables   = s.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  s.test_files    = s.files.grep(%r{^(test|spec|features)/})
+  s.require_paths = ["lib"]
+
+  s.add_development_dependency "bundler", "~> 1.3"
+end
+

data/test/helper.rb

@@ -1,5 +1,6 @@
 require 'rubygems'
 require 'bundler'
+
 begin
   Bundler.setup(:default, :development)
 rescue Bundler::BundlerError => e
@@ -7,8 +8,12 @@ rescue Bundler::BundlerError => e
   $stderr.puts "Run `bundle install` to install missing gems"
   exit e.status_code
 end
+
 require 'minitest/unit'
 
+require 'simplecov'
+SimpleCov.start
+
 $LOAD_PATH.unshift(File.dirname(__FILE__))
 $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
 require 'obo'

data/test/test_obo.rb

@@ -2,7 +2,6 @@ require 'helper'
 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')
@@ -35,7 +34,17 @@ class TestObo < MiniTest::Unit::TestCase
   end
 
   def test_readthrough
-    assert_equal 26, @obo.elements.count
+    assert_equal 27, @obo.elements.count
+  end
+
+  def test_term_extraction
+    typedefs = []
+
+    @obo.elements.each do |elm|
+      typedefs << elm
+    end
+
+    assert_equal 26, typedefs.select { |e| e.class == Obo::Stanza && e.name == "Typedef" }.size
   end
 
   def test_rewind
@@ -43,9 +52,8 @@ class TestObo < MiniTest::Unit::TestCase
     @obo.elements.count
     assert_raises(StopIteration){@obo.elements.count}
     @obo.rewind
-    assert_equal 26, @obo.elements.count
+    assert_equal 27, @obo.elements.count
   end
-  
 end
 
 

metadata

@@ -1,127 +1,88 @@
---- !ruby/object:Gem::Specification 
+--- !ruby/object:Gem::Specification
 name: obo
-version: !ruby/object:Gem::Version 
-  prerelease: 
-  version: 0.1.0
+version: !ruby/object:Gem::Version
+  version: 0.1.3
 platform: ruby
-authors: 
-- robsyme
+authors:
+- Robert Syme
+- Darren Oakley
 autorequire: 
 bindir: bin
 cert_chain: []
-
-date: 2011-05-24 00:00:00 +08:00
-default_executable: 
-dependencies: 
-- !ruby/object:Gem::Dependency 
-  name: minitest
-  requirement: &id001 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        version: "0"
-  type: :development
-  prerelease: false
-  version_requirements: *id001
-- !ruby/object:Gem::Dependency 
-  name: yard
-  requirement: &id002 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ~>
-      - !ruby/object:Gem::Version 
-        version: 0.6.0
-  type: :development
-  prerelease: false
-  version_requirements: *id002
-- !ruby/object:Gem::Dependency 
+date: 2013-05-03 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &id003 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        version: 1.0.0
+      - !ruby/object:Gem::Version
+        version: '1.3'
   type: :development
   prerelease: false
-  version_requirements: *id003
-- !ruby/object:Gem::Dependency 
-  name: jeweler
-  requirement: &id004 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        version: 1.6.0
-  type: :development
-  prerelease: false
-  version_requirements: *id004
-- !ruby/object:Gem::Dependency 
-  name: rcov
-  requirement: &id005 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        version: "0"
-  type: :development
-  prerelease: false
-  version_requirements: *id005
-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: rob.syme@gmail.com
+      - !ruby/object:Gem::Version
+        version: '1.3'
+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:
+- rob.syme@gmail.com
+- daz.oakley@gmail.com
 executables: []
-
 extensions: []
-
-extra_rdoc_files: 
-- LICENSE.txt
-- README.rdoc
-files: 
+extra_rdoc_files: []
+files:
 - .document
+- .gitignore
 - Gemfile
-- Gemfile.lock
 - LICENSE.txt
 - README.rdoc
 - Rakefile
 - VERSION
 - lib/obo.rb
+- lib/obo/header.rb
+- lib/obo/parser.rb
+- lib/obo/stanza.rb
+- lib/obo/version.rb
+- obo.gemspec
 - test/data/ro.obo
 - test/data/so_2_4_3.obo
 - test/data/temp
 - test/data/testfile.txt
 - test/helper.rb
 - test/test_obo.rb
-has_rdoc: true
 homepage: http://github.com/robsyme/obo
-licenses: 
+licenses:
 - MIT
+metadata: {}
 post_install_message: 
 rdoc_options: []
-
-require_paths: 
+require_paths:
 - lib
-required_ruby_version: !ruby/object:Gem::Requirement 
-  none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      hash: -3947284209714185762
-      segments: 
-      - 0
-      version: "0"
-required_rubygems_version: !ruby/object:Gem::Requirement 
-  none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      version: "0"
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - '>='
+    - !ruby/object:Gem::Version
+      version: '0'
 requirements: []
-
 rubyforge_project: 
-rubygems_version: 1.5.0
+rubygems_version: 2.0.0.rc.2
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: A parser for the OBO flat file format
-test_files: []
-
+test_files:
+- test/data/ro.obo
+- test/data/so_2_4_3.obo
+- test/data/temp
+- test/data/testfile.txt
+- test/helper.rb
+- test/test_obo.rb
+has_rdoc: 

data/Gemfile.lock

@@ -1,22 +0,0 @@
-GEM
-  remote: http://rubygems.org/
-  specs:
-    git (1.2.5)
-    jeweler (1.6.0)
-      bundler (~> 1.0.0)
-      git (>= 1.2.5)
-      rake
-    minitest (2.1.0)
-    rake (0.8.7)
-    rcov (0.9.9)
-    yard (0.6.8)
-
-PLATFORMS
-  ruby
-
-DEPENDENCIES
-  bundler (~> 1.0.0)
-  jeweler (~> 1.6.0)
-  minitest
-  rcov
-  yard (~> 0.6.0)