obo_parser 0.3.7 → 0.4.0

data/test/test_obo_parser.rb

@@ -1,268 +0,0 @@
-require 'test/unit'
-require 'rubygems'
-require 'ruby-debug'
-
-require File.expand_path(File.join(File.dirname(__FILE__), '../lib/obo_parser')) 
-
-class OboParserTest < Test::Unit::TestCase
-  def test_truth
-    assert true
-  end
-end
-
-class Test_OboParserBuilder < Test::Unit::TestCase
-  def test_builder
-    b = OboParser::OboParserBuilder.new
-  end
-end
-
-class Test_Regex < Test::Unit::TestCase
-
-  def test_some_regex
-    assert true 
-  end
-
-end
-
-class Test_Lexer < Test::Unit::TestCase
-
-  def test_term
-    lexer = OboParser::Lexer.new("[Term]")
-    assert lexer.pop(OboParser::Tokens::Term)
-  end
-
-  def test_end_of_file
-    lexer = OboParser::Lexer.new("    \n\n")
-    assert lexer.pop(OboParser::Tokens::EndOfFile)
-
-    lexer = OboParser::Lexer.new("\n")
-    assert lexer.pop(OboParser::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 = OboParser::Lexer.new(input)
-    assert t = lexer.pop(OboParser::Tokens::TagValuePair)
-    assert_equal 'id', t.tag
-    assert_equal 'PATO:0000015', t.value
-
-    assert t = lexer.pop(OboParser::Tokens::TagValuePair)
-    assert_equal 'name', t.tag
-    assert_equal 'color hue', t.value
-
-    assert t = lexer.pop(OboParser::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.', t.value
-    assert_equal(['PATOC:cjm'], t.xrefs) 
-
-    assert t = lexer.pop(OboParser::Tokens::TagValuePair)
-    assert_equal 'subset', t.tag
-    assert_equal 'attribute_slim', t.value
-
-    assert t = lexer.pop(OboParser::Tokens::TagValuePair)
-    assert_equal 'is_a', t.tag
-    assert_equal 'PATO:0001301', t.value
-  end
-
-  def test_typdef
-     input = '[Typedef]
-     id: part_of
-     name: part of
-     is_transitive: true'
-     assert foo = parse_obo_file(input)
-     assert_equal 1, foo.typedefs.size
-     assert_equal 'part_of', foo.typedefs.first.id.value
-  end
-
-  def test_parse_term_stanza2
-    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'
-
-    assert foo = parse_obo_file(input)
-    assert_equal 2, foo.terms.first.tags_named('synonym').size 
-    assert_equal 'xylem initial', foo.terms.first.tags_named('synonym').first.value
-    assert_equal 'xylem mother cell', foo.terms.first.tags_named('synonym')[1].value
-    assert_equal 'CL:0000274', foo.terms.first.tags_named('alt_id').first.value
-
-    assert_equal 2, foo.terms.first.relationships.size 
-    assert_equal(['CL:0000272', 'CL:0000610'], foo.terms.first.relationships.collect{|r| r[1]}.sort)
-    assert_equal(['is_a', 'is_a'], foo.terms.first.relationships.collect{|r| r[0]}.sort)
-  end
-
-  def test_parse_term
-    lexer = OboParser::Lexer.new("[Term]")
-    assert lexer.pop(OboParser::Tokens::Term)
-  end
-
-  def test_xref_list
-    lexer = OboParser::Lexer.new("[foo:bar, stuff:things]") 
-    assert t = lexer.pop(OboParser::Tokens::XrefList)
-    assert_equal( {'foo' => 'bar', 'stuff' => 'things'} , t.value)
-  end
-
-  def test_relationship_tag
-    lexer = OboParser::Lexer.new("relationship: develops_from CL:0000333 ! neural crest cell") 
-    assert t = lexer.pop(OboParser::Tokens::RelationshipTag)
-    assert_equal 'develops_from', t.relation
-    assert_equal 'CL:0000333', t.related_term
-    assert_equal 'relationship', t.tag
-
-    lexer = OboParser::Lexer.new("relationship: develops_from CL:0000333") 
-    assert t = lexer.pop(OboParser::Tokens::RelationshipTag)
-    assert_equal 'develops_from', t.relation
-    assert_equal 'CL:0000333', t.related_term
-    assert_equal 'relationship', t.tag
-  
-    lexer = OboParser::Lexer.new("is_a: CL:0000333 ! Foo") 
-    assert t = lexer.pop(OboParser::Tokens::IsATag)
-    assert_equal 'is_a', t.relation
-    assert_equal 'CL:0000333', t.related_term
-    assert_equal 'Foo', t.comment
-
-    lexer = OboParser::Lexer.new("disjoint_from: CL:0000333") 
-    assert t = lexer.pop(OboParser::Tokens::DisjointFromTag)
-    assert_equal 'disjoint_from', t.relation
-    assert_equal 'CL:0000333', t.related_term
-    assert_equal "", t.comment
-
-    lexer = OboParser::Lexer.new("relationship: part_of CL:0000333 ! Foo") 
-    assert t = lexer.pop(OboParser::Tokens::RelationshipTag)
-    assert_equal 'part_of', t.relation
-    assert_equal 'CL:0000333', t.related_term
-    assert_equal 'Foo', t.comment
-  end
-
-  def test_tagvaluepair
-    lexer = OboParser::Lexer.new("id: PATO:0000179")
-    assert lexer.pop(OboParser::Tokens::TagValuePair)
-  end
-
-  def test_tagvaluepair_with_comments_and_xrefs
-    lexer = OboParser::Lexer.new("def: \"The foo that is bar.\" [PATO:0000179] ! FOO! \n")
-    assert t = lexer.pop(OboParser::Tokens::TagValuePair)
-    assert_equal 'def', t.tag
-    assert_equal 'The foo that is bar.', t.value
-    assert_equal 'FOO!', t.comment
-    assert_equal(['PATO:0000179'], t.xrefs)
-  end
-
-  def test_that_synonyms_parse
-    lexer = OboParser::Lexer.new("synonym: \"Nematoblast\" EXACT []\n")
-    assert t = lexer.pop(OboParser::Tokens::TagValuePair)
-    assert_equal 'synonym', t.tag
-    assert_equal 'Nematoblast', t.value
-    assert_equal 'EXACT', t.qualifier
-    assert_equal nil, t.comment
-    assert_equal([], t.xrefs)
-  end
-
-  def test_that_xref_lists_parse_as_part_of_tagvalue_pair
-    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')
-    assert t = lexer.pop(OboParser::Tokens::TagValuePair)
-    assert_equal 'def', t.tag
-    assert_equal 'Foo and the bar, and stuff, and things.  More stuff, and things!', t.value
-    assert_equal(['GO_REF:0000031', 'GOC:msz', 'GOC:tfm', 'ISBN:9780781765190', 'PMID:16014527'], t.xrefs)
-  end
-
-  def test_crummy_space_filled_xrefs
-    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/ -"]')
-    assert t = lexer.pop(OboParser::Tokens::TagValuePair)
-    assert_equal 'def', t.tag
-    assert_equal 'A quality inhering in a bearer by virtue of emitting light during exposure to radiation from an external source.', t.value
-    assert_equal(['The Free Online dictionary:The Free Online dictionary'], t.xrefs)
-  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.value
-    assert_equal 'quality', foo.terms[1].name.value
-    assert_equal 'part_of', foo.typedefs.last.name.value
-    assert_equal 'OBO_REL:part_of', foo.typedefs.last.id.value
-    assert_equal(['PATOC:GVG'], foo.terms[1].def.xrefs)
-    assert_equal 'is_obsolete', foo.terms.first.tags_named('is_obsolete').first.tag
-    assert_equal 'true', foo.terms.first.tags_named('is_obsolete').first.value
-  end
-
-  def test_complex_file_parsing
-    assert of = File.read(File.expand_path(File.join(File.dirname(__FILE__), '../test/cell.obo')) )
-    foo = parse_obo_file(of)
-    assert_equal 'cell', foo.terms.first.name.value
-    assert_equal 'primary cell line cell', 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
-
-  def test_complex_file_parsing2
-    assert of = File.read(File.expand_path(File.join(File.dirname(__FILE__), '../test/hao.obo')) )
-    foo = parse_obo_file(of)
-    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
-
-  def test_complex_file_parsing3
-    assert of = File.read(File.expand_path(File.join(File.dirname(__FILE__), '../test/tgma.obo')) )
-    foo = parse_obo_file(of)
-   # 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
-
-  def test_complex_file_parsing4
-   assert of = File.read(File.expand_path(File.join(File.dirname(__FILE__), '../test/go.obo')) )
-   foo = parse_obo_file(of)
-   assert_equal 'hemolymph', foo.terms.first.name.value
-   assert_equal 'hemocyte', foo.terms[1].name.value
-   assert_equal 1, foo.terms.first.relationships.size
-  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
-
-  def teardown
-    @of = nil
-  end
-
-end 
-