rbbt 1.2.5 → 2.0.0

data/test/rbbt/util/test_index.rb

@@ -1,31 +0,0 @@
-require File.dirname(__FILE__) + '/../../test_helper'
-require 'rbbt/util/index'
-require 'test/unit'
-
-class TestIndex < Test::Unit::TestCase
-
-   
-  def test_index
-    require 'rbbt/util/tmpfile'
-    require 'rbbt/util/open'
-
-    tmp = TmpFile.tmp_file('test_open-')
-    data =<<-EOD
-S000006236 856144 YPR032W YPR032W NP_015357 SNI1_YEAST Q12038|Q12038 CAA95028|CAA89286 SRO7
-S000001262 856629 YHR219W YHR219W NP_012091 YH19_YEAST P38900 AAB69742 YHR219W
-    EOD
-    Open.write(tmp,data)
-
-    index = Index.index(tmp,:sep => " |\\|")
-    assert(index['AAB69742'] == 'S000001262' )
-    assert(index['Q12038'] == 'S000006236' )
-
-    FileUtils.rm tmp
-    
- end
-
-
-
-end
-
-

data/test/rbbt/util/test_misc.rb

@@ -1,20 +0,0 @@
-require File.dirname(__FILE__) + '/../../test_helper'
-require 'rbbt/util/misc'
-require 'test/unit'
-
-class TestIndex < Test::Unit::TestCase
-
-   
-  def test_chunk
-    a = %w(a b c d e f g h i j k l m)
-    assert_equal([["a", "d", "g", "j", "m"], ["b", "e", "h", "k"], ["c", "f", "i", "l"]], a.chunk(3))
-  end
-
-  def test_special
-    assert "BRC".is_special?
-    assert !"bindings".is_special?
-  end
-
-end
-
-

data/test/rbbt/util/test_open.rb

@@ -1,110 +0,0 @@
-require File.dirname(__FILE__) + '/../../test_helper'
-require File.dirname(__FILE__) + '/../../test_helper'
-require 'rbbt/util/open'
-require 'test/unit'
-
-class TestOpen < Test::Unit::TestCase
-
-  def test_remote
-
-    assert(  Open.remote("http://localhost:20002/asdf.html"))
-    assert(! Open.remote("/tmp/foo.xml"))
-
-  end
-
-  def test_gziped
-    assert(Open.gziped("/tmp/foo.xml.gz"))
-    assert(Open.gziped("http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/gene-associations/gene_association.goa_human.gz?rev=HEAD"))
-    assert(Open.gziped("http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/gene-associations/gene_association.goa_human.gz"))
-  end
-
-  def test_read_write
-    require 'rbbt/util/tmpfile'
-    require 'fileutils'
-
-    tmp     = TmpFile.tmp_file('test-')
-
-    content = "test content"
-    
-    Open.write(tmp, content)    
-    assert(Open.read(tmp) == content)
-
-    assert_equal("tast contant", Open.read(IO::popen("cat #{ tmp }|tr 'e' 'a'")))
-
-    FileUtils.rm(tmp)
-  end
-
-  def test_append
-    require 'rbbt/util/tmpfile'
-    require 'fileutils'
-
-    tmp      = TmpFile.tmp_file('test-')
-    content1 = "test content1"
-    content2 = "test content2"
-
-    Open.write(tmp, content1)
-    Open.append(tmp, content2)
-    assert(Open.read(tmp) == content1 + content2)
-    FileUtils.rm(tmp)
-  end
-
-
-  def test_read_remote
-    url ="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&retmode=xml&id=16438716" 
-
-    assert(Open.read(url, :quiet =>true) =~ /Discovering semantic features in the literature: a foundation for building functional associations./)
-  end
-    
-  def test_to_hash
-    require 'rbbt/util/tmpfile'
-
-    tmp = TmpFile.tmp_file('test_open-')
-    data =<<-EOD
-row1 a b 3
-row1 aa bb 33
-row2 a d e r
-    EOD
-    Open.write(tmp,data)
-
-    data = Open.to_hash(tmp, :native => 1,:extra => [2,3],:sep => " ")
-    assert(data['a'][0].include?('b')) 
-    assert(data['a'][0].include?('d'))
-    
-    data = Open.to_hash(tmp,:native => 1, :sep => " ")
-    assert(data['a'][1].include?('b') && data['a'][1].include?('d'))
-
-    data = Open.to_hash(tmp,:native => 1, :sep => " ", :flatten => true)
-    assert(["row1", "bb", "33"].sort, data["aa"].sort)
-    assert(["row1", "row2", "b", "d", "3", "e", "r"].sort, data["a"].sort)
-    
-    data = Open.to_hash(tmp,:native => 1, :sep => " ", :single => true)
-    assert_equal({"aa"=>"row1", "a"=>"row1"}, data)
-    
-    FileUtils.rm tmp
-  end
-
-  def test_fields
-    assert_equal(["1","2"] , Open.fields("1\t2") )
-    assert_equal(["1","2",""] , Open.fields("1\t2\t") )
-    assert_equal(["","",""] , Open.fields("\t\t") )
-  end
-
-  def test_select_field
-    data =<<-EOD
-row1 a b 3
-row1 aa bb 33
-row2 a d e r
-    EOD
- 
-    TmpFile.with_file(data) do |file|
-      data = Open.to_hash(file, :select => Open.func_match_field(%w(row1), :sep => " "), :sep => " ")
-      assert ! data.include?('row2')
-      assert data.include?('row1')
-    end
-  end
-
-
-
-end
-
-

data/test/rbbt/util/test_simpleDSL.rb

@@ -1,57 +0,0 @@
-require File.dirname(__FILE__) + '/../../test_helper'
-require 'rbbt/util/simpleDSL'
-require 'test/unit'
-
-class TestDSL < Test::Unit::TestCase
-  class Test < SimpleDSL
-
-    def action(name, *args, &block)
-      @actions[name] = args.first
-    end
-
-    def initialize(file=nil,&block)
-      @actions = {}
-      super(:action, file, &block)
-    end
-
-    def actions
-      @actions
-    end
-
-  end
-
-  def setup 
-    
-    @parser = Test.new do
-      action1 "Hello"
-      action2 "Good bye"
-    end
-  end
-
-  def test_config
-    config = <<-EOC
-  action1("Hello")
-  action2("Good bye")
-    EOC
-
-    assert_equal(@parser.config(:action),config)
-  end
-
-  def test_actions
-    assert_equal({:action1=>"Hello", :action2=>"Good bye"}, @parser.actions)
-  end
-
-  def test_method_missing
-    assert_raise(NoMethodError){@parser.cues}
-  end
-
-  def test_parse
-    @parser.parse :action do
-      action3 "Back again"
-    end
-
-     assert_equal({:action1 =>"Hello", :action2 =>"Good bye", :action3 =>"Back again"}, @parser.actions)
-
-  end
-
-end

data/test/rbbt/util/test_tmpfile.rb

@@ -1,21 +0,0 @@
-require File.dirname(__FILE__) + '/../../test_helper'
-require 'rbbt/util/tmpfile'
-require 'test/unit'
-
-class TestTmpFile < Test::Unit::TestCase
-
-  def test_tmp_file
-    assert(TmpFile.tmp_file("test") =~ /tmp\/test\d+$/)
-  end
-
-  def test_do_tmp_file
-    content = "Hello World!"
-    TmpFile.with_file(content) do |file|
-      assert_equal content, File.open(file).read
-    end
-  end
-
-
-end
-
-

data/test/test_helper.rb

@@ -1,4 +0,0 @@
-require 'test/unit'
-$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
-$LOAD_PATH.unshift(File.dirname(__FILE__))
-

data/test/test_rbbt.rb

@@ -1,11 +0,0 @@
-require File.dirname(__FILE__) + '/test_helper.rb'
-
-class TestRbbt < Test::Unit::TestCase
-
-  def setup
-  end
-  
-  def test_truth
-    assert true
-  end
-end