obo_parser 0.3.4 → 0.3.5
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/README.rdoc +12 -3
- data/VERSION +1 -1
- data/lib/tokens.rb +3 -2
- data/lib/utilities.rb +193 -53
- data/obo_parser.gemspec +26 -28
- data/test/cell.obo +1 -1
- data/test/go.obo +18523 -0
- data/test/hao.obo +14175 -0
- data/test/test_obo_parser.rb +38 -4
- data/test/tgma.obo +18522 -0
- metadata +12 -12
- data/.gitignore +0 -21
data/test/test_obo_parser.rb
CHANGED
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@@ -99,7 +99,6 @@ class Test_Lexer < Test::Unit::TestCase
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99
99
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assert_equal 2, foo.terms.first.relationships.size
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100
100
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assert_equal(['CL:0000272', 'CL:0000610'], foo.terms.first.relationships.collect{|r| r[1]}.sort)
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101
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assert_equal(['is_a', 'is_a'], foo.terms.first.relationships.collect{|r| r[0]}.sort)
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102
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-
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103
102
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end
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103
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104
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def test_parse_term
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@@ -143,11 +142,8 @@ class Test_Lexer < Test::Unit::TestCase
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142
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assert_equal 'part_of', t.relation
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assert_equal 'CL:0000333', t.related_term
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assert_equal 'Foo', t.comment
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146
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-
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145
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end
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148
146
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149
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-
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150
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-
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151
147
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def test_tagvaluepair
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lexer = OboParser::Lexer.new("id: PATO:0000179")
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assert lexer.pop(OboParser::Tokens::TagValuePair)
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@@ -221,6 +217,44 @@ class Test_Parser < Test::Unit::TestCase
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assert_equal 2, foo.terms[9].relationships.size
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end
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220
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+
def test_complex_file_parsing2
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221
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assert of = File.read(File.expand_path(File.join(File.dirname(__FILE__), '../test/hao.obo')) )
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222
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foo = parse_obo_file(of)
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223
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assert_equal 'anatomical entity', foo.terms.first.name.value
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224
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assert_equal 'ventral mesofurco-profurcal muscle', foo.terms[1].name.value
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225
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+
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#tmp = foo.terms[9].tags_named('synonym')
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227
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#assert_equal 2, tmp.size
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228
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#assert_equal 'xylem initial', tmp.first.value
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#assert_equal 'xylem mother cell', tmp[1].value
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#assert_equal([], tmp[1].xrefs)
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+
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#assert_equal 2, foo.terms[9].relationships.size
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end
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+
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def test_complex_file_parsing3
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assert of = File.read(File.expand_path(File.join(File.dirname(__FILE__), '../test/tgma.obo')) )
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foo = parse_obo_file(of)
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# assert_equal 'anatomical entity', foo.terms.first.name.value
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# assert_equal 'ventral mesofurco-profurcal muscle', foo.terms[1].name.value
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#tmp = foo.terms[9].tags_named('synonym')
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#assert_equal 2, tmp.size
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#assert_equal 'xylem initial', tmp.first.value
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#assert_equal 'xylem mother cell', tmp[1].value
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#assert_equal([], tmp[1].xrefs)
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#assert_equal 2, foo.terms[9].relationships.size
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end
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+
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def test_complex_file_parsing4
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assert of = File.read(File.expand_path(File.join(File.dirname(__FILE__), '../test/go.obo')) )
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252
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foo = parse_obo_file(of)
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assert_equal 'hemolymph', foo.terms.first.name.value
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assert_equal 'hemocyte', foo.terms[1].name.value
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255
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assert_equal 1, foo.terms.first.relationships.size
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256
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end
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257
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+
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def test_file_completes_without_typedefs
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@of2 = File.read(File.expand_path(File.join(File.dirname(__FILE__), '../test/obo_1.0_test_wo_typedefs.txt')) )
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assert foo = parse_obo_file(@of2)
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