obo 0.1.0

data/test/data/temp

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+SELECT 
+  db."name", 
+  db.description, 
+  db.urlprefix, 
+  db.url, 
+  db.db_id
+FROM 
+  public.cvterm gene, 
+  public.cvterm_relationship is_a_relationship, 
+  public.cvterm biological_region, 
+  public.dbxref, 
+  public.cvterm is_a_cvterm, 
+  public.dbxref is_a_dbxref, 
+  public.db
+WHERE 
+  gene.cvterm_id = is_a_relationship.subject_id AND
+  is_a_relationship.object_id = biological_region.cvterm_id AND
+  is_a_relationship.type_id = is_a_cvterm.cvterm_id AND
+  biological_region.dbxref_id = dbxref.dbxref_id AND
+  is_a_cvterm.dbxref_id = is_a_dbxref.dbxref_id AND
+  is_a_dbxref.db_id = db.db_id AND
+  gene.cv_id = 10 AND 
+  gene."name" = 'gene' AND 
+  biological_region."name" = 'biological_region';

data/test/data/testfile.txt

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+This is line one
+This is line two

data/test/helper.rb

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+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'minitest/unit'
+
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+require 'obo'
+
+class MiniTest::Unit::TestCase
+end
+
+MiniTest::Unit.autorun

data/test/test_obo.rb

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+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')
+  end
+
+  def test_header_parsing
+    header = @obo.elements.first
+    assert_equal Obo::Header, header.class
+    assert_equal '1.2', header['format-version']
+    assert_equal 'cjm', header['saved-by']
+    assert_equal 3, header['remark'].length
+  end
+
+  def test_stanza_parsing
+    first_stanza = @obo.elements.find{|element| element.is_a? Obo::Stanza}
+
+    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_fancy_methods
+    first_stanza = @obo.elements.find{|element| element.is_a? Obo::Stanza}
+    assert_equal 'OBO_REL:is_a', first_stanza.id
+    assert first_stanza.is_reflexive
+    assert first_stanza.is_reflexive?
+
+    assert_raises(NoMethodError){first_stanza.is_a_zebra?}
+  end
+
+  def test_readthrough
+    assert_equal 26, @obo.elements.count
+  end
+
+  def test_rewind
+    # Run through the file to the end
+    @obo.elements.count
+    assert_raises(StopIteration){@obo.elements.count}
+    @obo.rewind
+    assert_equal 26, @obo.elements.count
+  end
+  
+end
+
+

metadata

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+--- !ruby/object:Gem::Specification 
+name: obo
+version: !ruby/object:Gem::Version 
+  prerelease: 
+  version: 0.1.0
+platform: ruby
+authors: 
+- robsyme
+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 
+  name: bundler
+  requirement: &id003 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        version: 1.0.0
+  type: :development
+  prerelease: false
+  version_requirements: *id003
+- !ruby/object:Gem::Dependency 
+  name: jeweler
+  requirement: &id004 !ruby/object:Gem::Requirement 
+    none: false
+    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
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- LICENSE.txt
+- README.rdoc
+files: 
+- .document
+- Gemfile
+- Gemfile.lock
+- LICENSE.txt
+- README.rdoc
+- Rakefile
+- VERSION
+- lib/obo.rb
+- 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: 
+- MIT
+post_install_message: 
+rdoc_options: []
+
+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"
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.5.0
+signing_key: 
+specification_version: 3
+summary: A parser for the OBO flat file format
+test_files: []
+