rbbt 1.2.5 → 2.0.0

data/test/rbbt/sources/test_go.rb

@@ -1,24 +0,0 @@
-require File.dirname(__FILE__) + '/../../test_helper'
-
-require 'rbbt/sources/go'
-require 'test/unit'
-
-class TestGo < Test::Unit::TestCase
-
-  def test_go
-    assert_match('vacuole inheritance',GO::id2name('GO:0000011'))
-    assert_equal(['vacuole inheritance','alpha-glucoside transport'], GO::id2name(['GO:0000011','GO:0000017']))
-  end
-
-  def test_ancestors
-    assert GO.id2ancestors('GO:0000001').include? 'GO:0048308'
-  end
-
-  def test_namespace
-    assert_equal 'biological_process', GO.id2namespace('GO:0000001')
-  end
-
-
-end
-
-

data/test/rbbt/sources/test_organism.rb

@@ -1,59 +0,0 @@
-require File.dirname(__FILE__) + '/../../test_helper'
-require 'rbbt/sources/organism'
-require 'test/unit'
-
-class TestOrganism < Test::Unit::TestCase
-
-  def test_all
-    assert Organism.all.include? 'Sce'
-  end
-
-  def test_ner
-    assert(Organism.ner(:Sce, :abner).is_a? Abner)
-  end
-
-  def test_norm
-    assert_equal(["S000003008"], Organism.norm(:Sce).select(['S000029454','S000003008'],'SLU1', 'SLU1 has been used in the literature to refer to both HEM2/YGL040C, which encodes a porphobilinogen synthase and SLU1, which is essential for splicing.'))
-
-  end
-
-  def test_supported_ids
-
-    ids = Organism.supported_ids('Sce', :examples => true)
-    assert(ids.first[0] == 'SGD DB Id' && ids.first[1] =~ /^S00/)
-    
-    ids = Organism.supported_ids('Sce')
-    assert(ids.first == 'SGD DB Id')
-  end
-
-  def test_index
-    index = Organism.id_index('Sce')
-    assert_equal("S000004431", index['851160'])
-  end
-
-  def test_index_partial
-    index = Organism.id_index('Sce',:other => ['Ensembl Gene ID', 'Protein ID'])
-    assert_nil(index['851160'])
-    assert_equal("S000000838", index['YER036C'])
-    
-    index = Organism.id_index('Sce',:other => ['Ensembl Gene ID', 'Protein ID'], :native => "Entrez Gene ID")
-    assert_equal("856758", index['YER036C'])
-
-  end
-
-  def test_go_terms
-
-    begin
-      goterms = Organism.goterms('Sce')
-      assert(goterms["S000000838"].include? "GO:0016887")
-    rescue
-      puts $!
-      puts "No goterms produced, see if it is all installed"
-    end
-
-  end
-
-
-end
-
-

data/test/rbbt/sources/test_polysearch.rb

@@ -1,27 +0,0 @@
-require File.dirname(__FILE__) + '/../../test_helper'
-require 'rbbt'
-require 'rbbt/util/tmpfile'
-require 'rbbt/sources/polysearch'
-require 'test/unit'
-
-class TestPolysearch < Test::Unit::TestCase
-
-  def test_match
-    text =<<-EOT
-
-    Analysis of sorted peripheral blood lymphocytes (CD8 T cells, CD4 T cells,
-    B cells, NK cells) from patients with melanoma. These subpopulations are
-    involved in antitumor responses and negatively impacted by cancer. Results
-    provide insight into molecular mechanisms of immune dysfunction in cancer.
-
-    EOT
-
-    assert_equal(["B cells", "T cells", "blood", "lymphocytes",  "peripheral blood", "peripheral blood lymphocytes"].sort, Polysearch.match(text,nil).values.flatten.uniq.sort) 
-  end
-
-  def test_name
-    assert_equal('ligament', Polysearch.name('organ','OR00039'))
-  end
-end
-
-

data/test/rbbt/sources/test_pubmed.rb

@@ -1,39 +0,0 @@
-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_full_text
-    pmid = '16438716'
-    assert(PubMed.get_article(pmid).full_text =~ /Discovering/)
-  end
- 
-  def test_query
-    assert(PubMed.query('chagoyen[All Fields] AND ("loattrfull text"[sb] AND hasabstract[text])').include? '16438716')
-  end
-
-  def test_bibentry
-    assert("vazquez2008sent", PubMed::Article.make_bibentry('vazquez', 2008, "SENT: Semantic features in text"))
-    assert("vazquez2008aes", PubMed::Article.make_bibentry('vazquez', 2008, "An Example System"))
-  end
-
-end
-
-

data/test/rbbt/util/test_arrayHash.rb

@@ -1,257 +0,0 @@
-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

@@ -1,37 +0,0 @@
-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