obo_parser 0.1.0

data/test/test_obo_parser.rb

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+require 'test/unit'
+require 'rubygems'
+require 'ruby-debug'
+
+require File.expand_path(File.join(File.dirname(__FILE__), '../lib/obo_file'))
+
+class OboParserTest < Test::Unit::TestCase
+  def test_truth
+    assert true
+  end
+end
+
+class Test_OboFileBuilder < Test::Unit::TestCase
+  def test_builder
+    b = OboFile::OboFileBuilder.new
+  end
+end
+
+
+class Test_Regex < Test::Unit::TestCase
+
+  def test_comment_stripping
+    # hackish, likely will fail with complex combinations of "!"
+    txt = "line without note\nBegin taxa; ! comment\n! not this line\n'this ok!'\n\"this too!!\""
+    r2 = Regexp.new(/(\s*?![^!'"]*?\n)/i)
+    assert_equal "line without note\nBegin taxa;\n\n'this ok!'\n\"this too!!\"" , txt.gsub(r2, "\n")    
+  end
+end
+
+class Test_Lexer < Test::Unit::TestCase
+  
+  def test_term
+     lexer = OboFile::Lexer.new("[Term]")
+     assert lexer.pop(OboFile::Tokens::Term)
+  end
+  
+  def test_end_of_file
+     lexer = OboFile::Lexer.new("    \n\n")
+     assert lexer.pop(OboFile::Tokens::EndOfFile)
+  
+     lexer = OboFile::Lexer.new("\n")
+     assert lexer.pop(OboFile::Tokens::EndOfFile)
+  end
+
+  def test_parse_term_stanza
+    input = '
+      id: PATO:0000015
+      name: color hue
+      def: "A chromatic scalar-circular quality inhering in an object that manifests in an observer by virtue of the dominant wavelength of the visible light; may be subject to fiat divisions, typically into 7 or 8 spectra." [PATOC:cjm]
+      subset: attribute_slim
+      is_a: PATO:0001301'
+    lexer = OboFile::Lexer.new(input)
+    assert t = lexer.pop(OboFile::Tokens::TagValuePair)
+    assert_equal 'id', t.tag
+    assert_equal 'PATO:0000015', t.value
+
+    assert t = lexer.pop(OboFile::Tokens::TagValuePair)
+    assert_equal 'name', t.tag
+    assert_equal 'color hue', t.value
+
+    assert t = lexer.pop(OboFile::Tokens::TagValuePair)
+    assert_equal 'def', t.tag
+    assert_equal '"A chromatic scalar-circular quality inhering in an object that manifests in an observer by virtue of the dominant wavelength of the visible light; may be subject to fiat divisions, typically into 7 or 8 spectra." [PATOC:cjm]', t.value
+
+    assert t = lexer.pop(OboFile::Tokens::TagValuePair)
+    assert_equal 'subset', t.tag
+    assert_equal 'attribute_slim', t.value
+
+    assert t = lexer.pop(OboFile::Tokens::TagValuePair)
+    assert_equal 'is_a', t.tag
+    assert_equal 'PATO:0001301', t.value
+  end
+
+
+  def test_parse_term
+     lexer = OboFile::Lexer.new("[Term]")
+     assert lexer.pop(OboFile::Tokens::Term)
+  end
+
+  def test_tagvaluepair
+     lexer = OboFile::Lexer.new("id: PATO:0000179")
+     assert lexer.pop(OboFile::Tokens::TagValuePair)
+  end
+end
+
+class Test_Parser < Test::Unit::TestCase
+  def setup
+    @of = File.read(File.expand_path(File.join(File.dirname(__FILE__), '../test/obo_1.0_test.txt')) )
+  end
+
+  def test_file_parsing
+    foo = parse_obo_file(@of)
+    assert_equal 'pato', foo.terms[0].name
+    assert_equal 'quality', foo.terms[1].name
+    assert_equal 'part_of', foo.typedefs.last.name
+    assert_equal 'OBO_REL:part_of', foo.typedefs.last.id
+  end
+
+  def teardown
+    @of = nil
+  end
+
+  def test_file_completes_without_typedefs
+    @of2 = File.read(File.expand_path(File.join(File.dirname(__FILE__), '../test/obo_1.0_test_wo_typedefs.txt')) )
+    assert foo = parse_obo_file(@of2)
+  end
+
+end 
+

data/uninstall.rb

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+# Uninstall hook code here

metadata

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+--- !ruby/object:Gem::Specification 
+name: obo_parser
+version: !ruby/object:Gem::Version 
+  prerelease: false
+  segments: 
+  - 0
+  - 1
+  - 0
+  version: 0.1.0
+platform: ruby
+authors: 
+- mjy
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2010-03-17 00:00:00 -04:00
+default_executable: 
+dependencies: []
+
+description: "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. "
+email: diapriid@gmail.com
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- LICENSE
+- README
+- README.rdoc
+files: 
+- .document
+- .gitignore
+- LICENSE
+- README
+- README.rdoc
+- Rakefile
+- VERSION
+- init.rb
+- install.rb
+- lib/lexer.rb
+- lib/obo_file.rb
+- lib/parser.rb
+- lib/tokens.rb
+- obo_parser.gemspec
+- tasks/obo_parser_tasks.rake
+- test/cell.obo
+- test/obo_1.0_test.txt
+- test/obo_1.0_test_wo_typedefs.txt
+- test/test_obo_parser.rb
+- uninstall.rb
+has_rdoc: true
+homepage: http://github.com/mjy/obo_parser
+licenses: []
+
+post_install_message: 
+rdoc_options: 
+- --charset=UTF-8
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      segments: 
+      - 0
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      segments: 
+      - 0
+      version: "0"
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.3.6
+signing_key: 
+specification_version: 3
+summary: A simple OBO file handler.
+test_files: 
+- test/test_obo_parser.rb