obo_parser 0.3.7 → 0.4.0

data/spec/lib/obo_parser_spec.rb

@@ -0,0 +1,272 @@
+require 'spec_helper'
+
+describe OboParser do
+
+  context 'test builder' do
+    specify 'can be #new' do
+      expect( OboParser::OboParserBuilder.new).to be_truthy
+    end
+  end
+
+  context 'lexer' do
+    specify 'term' do
+      lexer = OboParser::Lexer.new('[Term]')
+      expect(lexer.pop(OboParser::Tokens::Term)).to be_truthy
+    end
+
+    context 'end_of_file' do
+      specify 'one' do
+        lexer = OboParser::Lexer.new("    \n\n")
+        expect(lexer.pop(OboParser::Tokens::EndOfFile)).to be_truthy
+      end
+
+      specify 'two' do
+        lexer = OboParser::Lexer.new("\n")
+        expect(lexer.pop(OboParser::Tokens::EndOfFile)).to be_truthy
+      end
+    end
+
+    context 'parse_term_stanza' do
+      let(: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'
+      }
+      let(:lexer) { OboParser::Lexer.new(input) } 
+
+      specify 'pop a number of values off' do
+        expect(t = lexer.pop(OboParser::Tokens::TagValuePair)).to be_truthy
+        expect(t.tag).to eq('id')
+        expect(t.value).to eq('PATO:0000015')
+      
+        expect(t = lexer.pop(OboParser::Tokens::TagValuePair)).to be_truthy
+        expect(t.tag).to eq('name')
+        expect(t.value).to eq('color hue')
+
+        expect(t = lexer.pop(OboParser::Tokens::TagValuePair)).to be_truthy
+        expect(t.tag).to eq('def')
+        expect(t.value).to eq('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.')
+        expect(t.xrefs).to eq(['PATOC:cjm']) 
+
+        expect(t = lexer.pop(OboParser::Tokens::TagValuePair)).to be_truthy
+        expect(t.tag).to eq('subset')
+        expect(t.value).to eq('attribute_slim')
+
+        expect(t = lexer.pop(OboParser::Tokens::TagValuePair)).to be_truthy
+        expect(t.tag).to eq('is_a')
+        expect(t.value).to eq('PATO:0001301')
+      end
+    end
+
+    context 'typdef' do
+      let(:input) {'[Typedef]
+       id: part_of
+       name: part of
+       is_transitive: true'
+      }
+
+      specify 'parses' do
+        expect(foo = parse_obo_file(input)).to be_truthy
+        expect(foo.typedefs.size).to eq(1)
+        expect(foo.typedefs.first.id.value).to eq('part_of')
+      end
+    end
+
+    context 'parse_term_stanza2' do
+      let(:input) {'[Term]
+      id: CL:0000009
+      name: fusiform initial
+      alt_id: CL:0000274
+      def: "An elongated cell with approximately wedge-shaped ends, found in the vascular cambium, which gives rise to the elements of the axial system in the secondary vascular tissues." [ISBN:0471245208]
+      synonym: "xylem initial" RELATED []
+      synonym: "xylem mother cell" RELATED []
+      is_a: CL:0000272 ! cambial initial
+      is_a: CL:0000610 ! plant cell'
+      }
+
+      specify 'parsing' do
+        expect( t = parse_obo_file(input)).to be_truthy
+        expect( t.terms.first.tags_named('synonym').size).to eq(2) 
+        expect( t.terms.first.tags_named('synonym').first.value).to eq('xylem initial') 
+        expect( t.terms.first.tags_named('synonym')[1].value ).to eq('xylem mother cell')
+        expect( t.terms.first.tags_named('alt_id').first.value).to eq('CL:0000274')
+
+        expect( t.terms.first.relationships.size ).to eq(2)
+        expect( t.terms.first.relationships.collect{|r| r[1]}.sort).to contain_exactly('CL:0000272', 'CL:0000610')
+        expect( t.terms.first.relationships.collect{|r| r[0]}.sort).to contain_exactly( 'is_a', 'is_a')
+      end
+
+      specify 'parse_term' do
+        lexer = OboParser::Lexer.new("[Term]")
+        expect(lexer.pop(OboParser::Tokens::Term)).to be_truthy
+      end
+
+      specify 'xref_list' do
+        lexer = OboParser::Lexer.new("[foo:bar, stuff:things]") 
+        expect(t = lexer.pop(OboParser::Tokens::XrefList)).to be_truthy
+        expect(t.value).to eq({'foo' => 'bar', 'stuff' => 'things'})
+      end
+    end
+
+    context 'relationship_tag' do
+      specify '1' do
+        lexer = OboParser::Lexer.new("relationship: develops_from CL:0000333 ! neural crest cell") 
+        expect(t = lexer.pop(OboParser::Tokens::RelationshipTag)).to be_truthy
+        expect(t.relation).to eq('develops_from')
+        expect(t.related_term).to eq( 'CL:0000333') 
+        expect(t.tag).to eq('relationship')
+      end
+
+      specify '2' do
+        lexer = OboParser::Lexer.new("relationship: develops_from CL:0000333") 
+        expect(t = lexer.pop(OboParser::Tokens::RelationshipTag)).to be_truthy
+        expect(t.relation).to eq('develops_from')
+        expect(t.related_term).to eq( 'CL:0000333') 
+        expect(t.tag).to eq('relationship')
+      end
+
+      specify '3 IsATag' do
+        lexer = OboParser::Lexer.new("is_a: CL:0000333 ! Foo") 
+        expect(t = lexer.pop(OboParser::Tokens::IsATag)).to be_truthy
+        expect(t.relation).to eq('is_a')
+        expect(t.related_term).to eq( 'CL:0000333') 
+        expect(t.comment).to eq('Foo')
+      end
+
+      specify '4 DisjointFromTag' do
+        lexer = OboParser::Lexer.new("disjoint_from: CL:0000333") 
+        expect(t = lexer.pop(OboParser::Tokens::DisjointFromTag)).to be_truthy
+        expect(t.relation).to eq('disjoint_from')
+        expect(t.related_term).to eq( 'CL:0000333') 
+        expect(t.comment).to eq('')
+      end
+
+      specify '4 RelationshipTag' do
+        lexer = OboParser::Lexer.new("relationship: part_of CL:0000333 ! Foo") 
+        expect(t = lexer.pop(OboParser::Tokens::RelationshipTag)).to be_truthy
+        expect(t.relation).to eq('part_of')
+        expect(t.related_term).to eq( 'CL:0000333') 
+        expect(t.comment).to eq('Foo')
+      end
+
+      specify 'tagvaluepair' do
+        lexer = OboParser::Lexer.new("id: PATO:0000179")
+        expect( lexer.pop(OboParser::Tokens::TagValuePair)).to be_truthy
+      end
+
+      specify 'tagvaluepair_with_comments_and_xrefs' do
+        lexer = OboParser::Lexer.new("def: \"The foo that is bar.\" [PATO:0000179] ! FOO! \n")
+        expect( t = lexer.pop(OboParser::Tokens::TagValuePair) ).to be_truthy
+        expect( t.tag).to eq( 'def' )
+        expect( t.value).to eq( 'The foo that is bar.')
+        expect( t.comment).to eq( 'FOO!' )
+        expect( t.xrefs).to eq( ['PATO:0000179'] ) 
+      end
+
+      specify 'tagvaluepair_with_comments_and_xrefs' do
+        lexer = OboParser::Lexer.new("def: \"The foo that is bar.\" [PATO:0000179] ! FOO! \n")
+        expect( t = lexer.pop(OboParser::Tokens::TagValuePair) ).to be_truthy 
+        expect( t.tag).to eq('def')
+        expect( t.value).to eq( 'The foo that is bar.' )
+        expect( t.comment).to eq( 'FOO!' )
+        expect( t.xrefs).to eq( ['PATO:0000179'] )
+      end
+
+      specify 'that_synonyms_parse' do
+        lexer = OboParser::Lexer.new("synonym: \"Nematoblast\" EXACT []\n")
+        expect(t = lexer.pop(OboParser::Tokens::TagValuePair)).to be_truthy
+        expect(t.tag).to eq('synonym')
+        expect(t.value).to eq('Nematoblast')
+        expect(t.qualifier).to eq('EXACT')
+        expect(t.comment).to eq(nil)
+        expect(t.xrefs).to eq([])
+      end
+
+      specify 'that_xref_lists_parse_as_part_of_tagvalue_pair' do
+        lexer = OboParser::Lexer.new('def: "Foo and the bar, and stuff, and things.  More stuff, and things!" [GO_REF:0000031 "Foo!" , GOC:msz {some=trailingmodifier}, GOC:tfm, ISBN:9780781765190 "Fundamental Immunology!, 6ed (Paul,ed), 2003", PMID:16014527] {qualifier=foo} ! and a comment')
+        expect( t = lexer.pop(OboParser::Tokens::TagValuePair) ).to be_truthy
+        expect(t.tag).to eq('def')
+        expect(t.value).to eq('Foo and the bar, and stuff, and things.  More stuff, and things!')
+        expect(t.xrefs).to eq(['GO_REF:0000031', 'GOC:msz', 'GOC:tfm', 'ISBN:9780781765190', 'PMID:16014527'])
+      end
+
+      specify 'crummy_space_filled_xrefs' do
+        lexer = OboParser::Lexer.new('def: "A quality inhering in a bearer by virtue of emitting light during exposure to radiation from an external source." [The Free Online dictionary:The Free Online dictionary "www.thefreedictionary.com/ -"]')
+        expect(t = lexer.pop(OboParser::Tokens::TagValuePair)).to be_truthy
+        expect(t.tag).to eq('def')
+        expect(t.value).to eq( 'A quality inhering in a bearer by virtue of emitting light during exposure to radiation from an external source.')
+        expect(t.xrefs).to eq(['The Free Online dictionary:The Free Online dictionary'])
+      end
+    end
+  end
+
+  context 'Test_Parse' do
+    let(:of) { File.read(File.expand_path(File.join(File.dirname(__FILE__), '../files/obo_1.0_test.txt')) ) }
+    let(:foo) { parse_obo_file(of) }
+
+    specify 'file_parsing' do
+      expect(foo.terms[0].name.value).to eq( 'pato') 
+      expect(foo.terms[1].name.value).to eq('quality') 
+      expect(foo.typedefs.last.name.value).to eq('part_of') 
+      expect( foo.typedefs.last.id.value).to eq(  'OBO_REL:part_of')
+      expect( foo.terms[1].def.xrefs).to eq(['PATOC:GVG'])
+      expect( foo.terms.first.tags_named('is_obsolete').first.tag).to eq('is_obsolete') 
+      expect( foo.terms.first.tags_named('is_obsolete').first.value).to eq('true') 
+    end
+  end
+
+  context 'complex_file_parsing' do
+    let(:of) { File.read(File.expand_path(File.join(File.dirname(__FILE__), '../files/cell.obo')) ) }
+    let(:foo) { parse_obo_file(of) } 
+
+    specify 'complex_file_parsing' do
+      expect(foo.terms.first.name.value).to eq( 'cell' ) 
+      expect(foo.terms[1].name.value).to eq('primary cell line cell')
+      tmp = foo.terms[9].tags_named('synonym')
+      expect(tmp.size).to eq(2)
+      expect(tmp.first.value).to eq('xylem initial')
+      expect(tmp[1].value).to eq( 'xylem mother cell' )
+      expect(tmp[1].xrefs).to eq([])
+      expect(foo.terms[9].relationships.size).to eq(2)
+    end
+  end
+
+  specify 'complex_file_parsing_2' do
+    expect(of = File.read(File.expand_path(File.join(File.dirname(__FILE__), '../files/hao.obo')) )).to be_truthy
+    foo = parse_obo_file(of)
+    expect(foo.terms.first.name.value).to eq('anatomical entity')
+    expect(foo.terms[1].name.value).to eq('ventral mesofurco-profurcal muscle')
+  end
+
+  specify 'complex_file_parsing_3' do
+    expect(of = File.read(File.expand_path(File.join(File.dirname(__FILE__), '../files/tgma.obo')) ) ).to be_truthy
+    expect(foo = parse_obo_file(of)).to be_truthy
+
+    # assert_equal 'anatomical entity', foo.terms.first.name.value
+    # assert_equal 'ventral mesofurco-profurcal muscle', foo.terms[1].name.value
+
+    #tmp = foo.terms[9].tags_named('synonym')
+    #assert_equal 2, tmp.size
+    #assert_equal 'xylem initial', tmp.first.value
+    #assert_equal 'xylem mother cell', tmp[1].value
+    #assert_equal([], tmp[1].xrefs)
+
+    #assert_equal 2, foo.terms[9].relationships.size
+  end
+
+  specify 'complex_file_parsing4' do
+    expect(of = File.read(File.expand_path(File.join(File.dirname(__FILE__), '../files/go.obo')) )).to be_truthy
+    expect(foo = parse_obo_file(of)).to be_truthy
+    expect(foo.terms.first.name.value).to eq( 'hemolymph')
+    expect( foo.terms[1].name.value).to eq('hemocyte')
+    expect( foo.terms.first.relationships.size).to eq(1)
+  end
+
+  specify 'file_completes_without_typedefs' do
+    expect(of2 = File.read(File.expand_path(File.join(File.dirname(__FILE__), '../files/obo_1.0_test_wo_typedefs.txt')) )).to be_truthy
+    expect(foo = parse_obo_file(of2)).to be_truthy
+  end
+
+end

data/spec/spec_helper.rb

@@ -0,0 +1,32 @@
+require 'rubygems'
+require 'bundler/setup'
+Bundler.setup
+
+require 'obo_parser'
+require 'byebug'
+require 'awesome_print'
+require 'fileutils'
+
+# FileUtils::mkdir_p 'tmp'
+
+RSpec.configure do |config|
+
+  config.raise_errors_for_deprecations!
+
+   config.run_all_when_everything_filtered = false 
+   # config.filter_run :focus
+
+  # Run specs in random order to surface order dependencies. If you find an
+  # order dependency and want to debug it, you can fix the order by providing
+  # the seed, which is printed after each run.
+  #     --seed 1234
+  # config.order = 'random'
+
+end
+
+# def in_range(value, percentage, midpoint)  #order of second and third params to be consistent with be_within
+#   # value is a scalar for testing against the range, percentage is a float less than 1, midpoint is the nominal center of the range
+#   return (value <= midpoint*(1.0 + percentage)) & (value >= midpoint*(1.0 - percentage))
+# end
+
+

metadata

@@ -1,87 +1,164 @@
---- !ruby/object:Gem::Specification 
+--- !ruby/object:Gem::Specification
 name: obo_parser
-version: !ruby/object:Gem::Version 
-  hash: 29
-  prerelease: 
-  segments: 
-  - 0
-  - 3
-  - 7
-  version: 0.3.7
+version: !ruby/object:Gem::Version
+  version: 0.4.0
 platform: ruby
-authors: 
-- mjy
+authors:
+- Matt Yoder
 autorequire: 
 bindir: bin
 cert_chain: []
-
-date: 2011-08-25 00:00:00 Z
-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
+date: 2011-08-25 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 11.1.2
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 11.1.2
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.4'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.4'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.5'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.5'
+- !ruby/object:Gem::Dependency
+  name: guard-rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: byebug
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: awesome_print
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.6'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.6'
+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: 
+extra_rdoc_files: []
+files:
+- ".document"
+- ".gitignore"
+- Gemfile
+- Gemfile.lock
+- Guardfile
 - LICENSE
-- README.rdoc
-files: 
-- .document
-- LICENSE
-- README.rdoc
+- README.md
 - Rakefile
 - VERSION
 - init.rb
 - install.rb
 - lib/lexer.rb
 - lib/obo_parser.rb
+- lib/obo_parser/version.rb
 - lib/parser.rb
 - lib/tokens.rb
 - lib/utilities.rb
 - obo_parser.gemspec
+- obo_parser/version.rb
+- spec/files/cell.obo
+- spec/files/go.obo
+- spec/files/hao.obo
+- spec/files/obo_1.0_test.txt
+- spec/files/obo_1.0_test_wo_typedefs.txt
+- spec/files/tgma.obo
+- spec/lib/obo_parser_spec.rb
+- spec/spec_helper.rb
 - tasks/obo_parser_tasks.rake
 - test/cell.obo
 - test/go.obo
 - test/hao.obo
 - test/obo_1.0_test.txt
 - test/obo_1.0_test_wo_typedefs.txt
-- test/test_obo_parser.rb
 - test/tgma.obo
 - uninstall.rb
 homepage: http://github.com/mjy/obo_parser
-licenses: []
-
+licenses:
+- MIT
+metadata: {}
 post_install_message: 
 rdoc_options: []
-
-require_paths: 
+require_paths:
 - lib
-required_ruby_version: !ruby/object:Gem::Requirement 
-  none: false
-  requirements: 
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
   - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 3
-      segments: 
-      - 0
-      version: "0"
-required_rubygems_version: !ruby/object:Gem::Requirement 
-  none: false
-  requirements: 
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
   - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 3
-      segments: 
-      - 0
-      version: "0"
+    - !ruby/object:Gem::Version
+      version: '0'
 requirements: []
-
 rubyforge_project: 
-rubygems_version: 1.7.2
+rubygems_version: 2.6.4
 signing_key: 
-specification_version: 3
-summary: A simple OBO file handler.
+specification_version: 4
+summary: Ruby parsering for OBO files.
 test_files: []
-