rbbt 1.1.8 → 1.2.1

data/test/rbbt/sources/test_pubmed.rb

@@ -0,0 +1,29 @@
+require File.dirname(__FILE__) + '/../../test_helper'
+require 'rbbt/sources/pubmed'
+require 'test/unit'
+
+class TestPubMed < Test::Unit::TestCase
+
+  def test_get_online
+    pmid = '16438716'
+    assert(PubMed.get_online(pmid) =~ /Discovering semantic features in the literature: a foundation for building functional associations./)
+
+    pmids = ['16438716', 17204154]
+    assert(PubMed.get_online(pmids)[pmid] =~ /Discovering semantic features in the literature: a foundation for building functional associations./)
+  end
+
+  def test_get_article
+    pmid = '16438716'
+    assert(PubMed.get_article(pmid).title == "Discovering semantic features in the literature: a foundation for building functional associations.")
+    
+    pmids = ['16438716', 17204154]
+    assert(PubMed.get_article(pmids)[pmid].title == "Discovering semantic features in the literature: a foundation for building functional associations.")
+  end
+
+  def test_query
+    assert(PubMed.query('chagoyen[All Fields] AND ("loattrfull text"[sb] AND hasabstract[text])').include? '16438716')
+  end
+
+end
+
+

data/test/rbbt/util/test_arrayHash.rb

@@ -0,0 +1,257 @@
+require File.dirname(__FILE__) + '/../../test_helper'
+require 'rbbt/util/arrayHash'
+require 'test/unit'
+
+class TestArrayHash < Test::Unit::TestCase
+
+  def test_merge_values
+    list1 = ["A|B","C"]
+    list2 = ["a|b","c"]
+    list3 = ["a|b",""]
+    list4 = nil
+
+    assert_equal(["A|B|a|b","C|c"], ArrayHash.merge_values(list1,list2))
+
+    assert_equal(["A|B|a|b","C"], ArrayHash.merge_values(list1,list3))
+
+    assert_equal(["a|b|A|B","C"], ArrayHash.merge_values(list3,list1))
+    
+    assert_equal(["A|B","C"], ArrayHash.merge_values(list4,list1))
+  end
+
+  def test_pullout
+    data_in = {
+      "1" => ['A|B','C'],
+      "2" => ['a|b','c']
+    }
+
+    data_out0 = {
+      'A' => ["1",'C'],
+      'B' => ["1",'C'],
+      'a' => ["2",'c'],
+      'b' => ["2",'c'],
+    }
+
+    data_out0_ci = {
+      'a' => ["1|2",'C|c'],
+      'b' => ["1|2",'C|c'],
+    }
+
+
+
+    data_out1 = {
+      'C' => ["1",'A|B'],
+      'c' => ["2",'a|b'],
+    }
+
+
+    assert_equal(data_out0, ArrayHash.pullout(data_in,0, :case_insensitive => false))
+    assert_equal(data_out1, ArrayHash.pullout(data_in,1, :case_insensitive => false))
+    assert_equal(data_out0_ci, ArrayHash.pullout(data_in,0,:case_insensitive => true))
+
+    assert_equal("1|2", ArrayHash.pullout(data_in,0,:case_insensitive => true, :index => true)['A'])
+    assert_equal("1|2", ArrayHash.pullout(data_in,0,:case_insensitive => true, :index => true)['a'])
+   
+  end
+
+  def test_merge
+    hash1 = {
+      '1' => ['A','B'],
+      '2' => ['a','b'],
+    }
+
+    hash2 = {
+      '1' => ['C']
+    }
+    
+    hash_merged1 = {
+      '1' => ['A','B','C'],
+      '2' => ['a','b','']
+    }
+
+    hash3 = {
+      'A' => ['D']
+    }
+
+    hash_merged2 = {
+      '1' => ['A','B','D'],
+      '2' => ['a','b','']
+    }
+
+    hash4 = {
+      'D' => ['1']
+    }
+
+
+    assert_equal(hash_merged1, ArrayHash.merge(hash1, hash2, 'main', 'main', :case_insensitive => false))
+    assert_equal(hash_merged2, ArrayHash.merge(hash1, hash3, 0, 'main', :case_insensitive => false))
+    assert_equal(hash_merged2, ArrayHash.merge(hash1, hash4, 'main', 0, :case_insensitive => false))
+  end
+
+  def test_case_insensitive
+     hash1 = {
+      'c' => ['A','B'],
+      'd' => ['a','b'],
+    }
+
+    hash2 = {
+      'C' => ['D']
+    }
+
+    hash_merged1 = {
+      'c' => ['A','B',''],
+      'd' => ['a','b',''],
+      'C' => ['','','D']
+    }
+ 
+    hash_merged2 = {
+      'c' => ['A','B','D'],
+      'd' => ['a','b',''],
+    }
+   
+    assert_equal(hash_merged1, ArrayHash.merge(hash1, hash2, 'main', 'main', :case_insensitive => false))
+    assert_equal(hash_merged2, ArrayHash.merge(hash1, hash2, 'main', 'main', :case_insensitive => true))
+  
+  end
+
+  def test_clean
+     data = {
+      '1' => ['A','B'],
+      '2' => ['a','A'],
+     }
+     data_clean = {
+      '1' => ['A','B'],
+      '2' => ['a',''],
+     }
+     assert_equal(data_clean, ArrayHash.clean(data))
+
+     data = {
+      '1' => ['A','B'],
+      '2' => ['a','A|b'],
+     }
+     data_clean = {
+      '1' => ['A','B'],
+      '2' => ['a','b'],
+     }
+     assert_equal(data_clean, ArrayHash.clean(data))
+
+     data = {
+      '1' => ['A','B'],
+      '2' => ['A|a','b'],
+     }
+     data_clean = {
+      '1' => ['A','B'],
+      '2' => ['a','b'],
+     }
+     assert_equal(data_clean, ArrayHash.clean(data))
+
+
+     data = {
+      '1' => ['a1','a2'],
+      '2' => ['a3','a4|A1'],
+     }
+     data_clean = {
+      '1' => ['a1','a2'],
+      '2' => ['a3','a4'],
+     }
+     assert_equal(data, ArrayHash.clean(data))
+     assert_equal(data_clean, ArrayHash.clean(data, :case_sensitive => true))
+
+
+  end
+  
+  
+  def test_field_pos
+    data = {
+      '1' => ['A','B'],
+      '2' => ['a','b'],
+    }
+
+    table = ArrayHash.new(table, 'Entrez', ['FA', 'FB'])
+
+    assert_equal(0, table.field_pos('FA'))
+    assert_equal(:main, table.field_pos('Entrez'))
+    assert_equal(:main, table.field_pos('entrez'))
+
+  end
+
+  def test_object_merge
+    data1 = {
+      '1' => ['A','B'],
+      '2' => ['a','b'],
+    }
+    table1 = ArrayHash.new(data1, 'Entrez', ['FA', 'FB'])
+
+    data2 = {
+      '1' => ['C']
+    }
+    table2 = ArrayHash.new(data2, 'Entrez', ['FC'])
+
+    hash_merged1 = {
+      '1' => ['A','B','C'],
+      '2' => ['a','b','']
+    }
+    names1 = %w(FA FB FC)
+
+    table1.merge(table2, 'Entrez', :case_insensitive => false)
+    assert_equal(hash_merged1, table1.data)
+    assert_equal(names1, table1.fields)
+
+
+ 
+    data3 = {
+      'b' => ['d']
+    }
+    table3 = ArrayHash.new(data3, 'FB', ['FD'])
+ 
+    hash_merged2 = {
+      '1' => ['A','B','C',''],
+      '2' => ['a','b','','d']
+    }
+    names2 = %w(FA FB FC FD)
+
+   
+    table1.merge(table3, 'FB', :case_insensitive => false)
+    assert_equal(hash_merged2, table1.data)
+    assert_equal(names2, table1.fields)
+  end
+
+  def test_remove
+    data = {
+      '1' => ['A','B'],
+      '2' => ['a','b'],
+    }
+    data2 = {
+      '1' => ['B'],
+      '2' => ['b'],
+    }
+
+
+    table = ArrayHash.new(data, 'Entrez', ['FA', 'FB'])
+    table.remove('FA')
+
+    assert_equal(nil, table.field_pos('FA'))
+    assert_equal(['FB'], table.fields)
+    assert_equal(data2, table.data)
+  end
+
+  def test_process
+    data_in = {
+      '1' => ['A','B'],
+      '2' => ['a','b'],
+    }
+    data_out = {
+      '1' => ['FA(A)','B'],
+      '2' => ['FA(a)','b'],
+    }
+
+    table = ArrayHash.new(data_in, 'Entrez', ['FA', 'FB'])
+
+    table.process('FA'){|n| "FA(#{n})"}
+
+    assert_equal(data_out, table.data)
+  end
+
+end
+
+

data/test/rbbt/util/test_filecache.rb

@@ -0,0 +1,37 @@
+require File.dirname(__FILE__) + '/../../test_helper'
+require 'rbbt'
+require 'rbbt/util/filecache'
+require 'test/unit'
+
+class TestFileCache < Test::Unit::TestCase
+
+  def setup
+    @cachedir = Rbbt.cachedir
+  end
+  
+  def test_escape
+    path = '/etc/password'
+    assert_equal('_SLASH_etc_SLASH_password',FileCache.clean_path(path))
+  end
+
+  def test_path
+    assert_equal(File.expand_path(FileCache.path('123456789.xml')), File.expand_path(File.join(@cachedir, '/5/6/7/8/9/123456789.xml')))
+    assert_equal(File.expand_path(FileCache.path('12.xml')), File.expand_path(File.join(@cachedir, '/1/2/12.xml')))
+
+    assert_raise(FileCache::BadPathError){FileCache.path('/etc/passwd')}
+  end
+
+  def test_add_read
+    filename = 'test_file_cache.txt'
+    content  = 'hello'
+
+    FileCache.del_file(filename)
+    FileCache.add_file(filename, content)
+    assert_raise(FileCache::FileExistsError){FileCache.add_file(filename,'')}
+    assert_nothing_raised{FileCache.add_file(filename,'',:force => true)}
+    FileCache.del_file(filename)
+    
+  end
+
+
+end

data/test/rbbt/util/test_index.rb

@@ -0,0 +1,31 @@
+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

@@ -0,0 +1,20 @@
+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

@@ -0,0 +1,97 @@
+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
+
+
+
+
+end
+
+