rbbt-util 5.42.0 → 5.43.0

data/test/rbbt/persist/tsv/test_lmdb.rb

@@ -7,11 +7,13 @@ require 'test/unit'
 class TestPersistTSVLMDB < Test::Unit::TestCase
 
   def test_organism
-    require 'rbbt/sources/organism'
-    if Persist.respond_to? :open_lmdb
-      TmpFile.with_file do |tmp_file|
-        tsv = Organism.identifiers("Hsa").tsv :key_field => "Associated Gene Name", :fields => ["Ensembl Gene ID"], :type => :single, :persist => true, :persist_engine => "LMDB", :persist_dir => tmp_file
-        assert_equal "ENSG00000141510", tsv["TP53"]
+    keyword_test :lmdb do
+      require 'rbbt/sources/organism'
+      if Persist.respond_to? :open_lmdb
+        TmpFile.with_file do |tmp_file|
+          tsv = Organism.identifiers("Hsa").tsv :key_field => "Associated Gene Name", :fields => ["Ensembl Gene ID"], :type => :single, :persist => true, :persist_engine => "LMDB", :persist_dir => tmp_file
+          assert_equal "ENSG00000141510", tsv["TP53"]
+        end
       end
     end
   end

data/test/rbbt/test_entity.rb

@@ -54,7 +54,7 @@ module ReversableString
   end
 
   persist :reverse_text_ary_p, :marshal
-  persist :reverse_text_single_p, :memory
+  #persist :reverse_text_single_p, :memory
 
   persist :reverse_text_ary_p_array, :array, :dir => TmpFile.tmp_file
 
@@ -133,12 +133,15 @@ class TestEntity < Test::Unit::TestCase
 
     assert_equal 2, $count
 
+    a = ["String1", "String2"]
+    ReversableString.setup a
+
     $count = 0
 
     assert_equal "2gnirtS", a.reverse_text_single_p.last
-    assert_equal 0, $count
+    assert_equal 2, $count
     assert_equal "2gnirtS", a[1].reverse_text_single_p
-    assert_equal 1, $count
+    assert_equal 3, $count
   end
 
   def test_property_ary_p_array
@@ -168,7 +171,7 @@ class TestEntity < Test::Unit::TestCase
 
     # After persist
     ReversableString.persist :random
-    assert(ReversableString.persisted?(:random))
+    assert ReversableString.persisted?(:random)
 
     r1 = a.random
     r2 = a.random
@@ -176,7 +179,7 @@ class TestEntity < Test::Unit::TestCase
 
     # After unpersist
     ReversableString.unpersist :random
-    assert(! ReversableString.persisted?(:random))
+    refute ReversableString.persisted?(:random)
 
     r1 = a.random
     r2 = a.random

data/test/rbbt/test_knowledge_base.rb

@@ -50,77 +50,154 @@ end
 class TestKnowledgeBase < Test::Unit::TestCase
   def setup
     require 'rbbt/sources/organism'
-    require 'rbbt/sources/tfacts'
-    require 'rbbt/sources/kegg'
 
     Gene.add_identifiers Organism.identifiers("NAMESPACE"), "Ensembl Gene ID", "Associated Gene Name"
-    Gene.add_identifiers KEGG.identifiers
+  end
+
+  def test_knowledge_base_simple
+    organism = Organism.default_code("Hsa")
+    TmpFile.with_file do |tmpdir|
+      kb = KnowledgeBase.new tmpdir, Organism.default_code("Hsa")
+      kb.format = {"Gene" => "Ensembl Gene ID"}
+
+      kb.register :gene_ages, datadir_test.gene_ages
+
+      i = kb.get_index(:gene_ages)
+
+      assert_include i.match("ENSG00000000003"), "ENSG00000000003~Bilateria"
+    end
+  end
+
+  def test_knowledge_base_translate
+    organism = Organism.default_code("Hsa")
+    TmpFile.with_file do |tmpdir|
+      kb = KnowledgeBase.new tmpdir, Organism.default_code("Hsa")
+      kb.format = {"Gene" => "Ensembl Gene ID"}
+
+      kb.register :gene_ages, datadir_test.gene_ages, :source => "FamilyAge", :target => "=>Associated Gene Name"
 
+      i = kb.get_index(:gene_ages)
+
+      assert_include i.match("Bilateria"), "Bilateria~SMAD4"
+    end
   end
 
+
   def test_knowledge_base_reverse
     organism = Organism.default_code("Hsa")
     TmpFile.with_file do |tmpdir|
       kb = KnowledgeBase.new tmpdir, Organism.default_code("Hsa")
       kb.format = {"Gene" => "Ensembl Gene ID"}
 
-      kb.register :tfacts, TFactS.regulators, :source =>"=~Associated Gene Name"
+      kb.register :gene_ages, datadir_test.gene_ages
 
-      kb.get_index(:tfacts).reverse
+      ri = kb.get_index(:gene_ages).reverse
+
+      assert_include ri.match("Bilateria"), "Bilateria~ENSG00000000003"
     end
   end
 
-  def test_knowledge_base
+  def test_entity
     organism = Organism.default_code("Hsa")
     TmpFile.with_file do |tmpdir|
       kb = KnowledgeBase.new tmpdir, Organism.default_code("Hsa")
       kb.format = {"Gene" => "Ensembl Gene ID"}
 
-      kb.register :tfacts, TFactS.regulators, :source =>"=~Associated Gene Name"
+      kb.register :gene_ages, datadir_test.gene_ages, :source => "=>Associated Gene Name"
 
-      assert_equal "Ensembl Gene ID", kb.get_database(:tfacts).key_field
+      kb.register :CollecTRI, datadir_test.CollecTRI, 
+        :source => "Transcription Factor", :target => "Target Gene",
+        :fields => ["[ExTRI] Confidence", "[ExTRI] PMID"]
 
-      kb.register :kegg, KEGG.gene_pathway, :source_format => "Ensembl Gene ID"
-      assert_match "Ensembl Gene ID", kb.get_database(:kegg).key_field
+      smad4 = Gene.setup("SMAD4", "Associated Gene Name", kb.namespace)
+      smad7 = Gene.setup("SMAD7", "Associated Gene Name", kb.namespace)
 
-      gene = Gene.setup("TP53", "Associated Gene Name", organism).ensembl
-      assert_equal "TP53", gene.name
-      assert_equal "ENSG00000141510", gene.ensembl
 
-      downstream = gene.follow kb, :tfacts
-      upstream = gene.backtrack kb, :tfacts
-      close = gene.expand kb, :tfacts
+      assert_include smad4.follow(kb, :CollecTRI), smad7
+      assert_include smad7.backtrack(kb, :CollecTRI), smad4
+      refute smad7.follow(kb, :CollecTRI).include?(smad4)
+      assert_include smad7.expand(kb, :CollecTRI), smad4
+      assert_include smad4.expand(kb, :CollecTRI), smad7
 
-      assert downstream.length < downstream.follow(kb, :tfacts,false).flatten.length
+    end
+  end
 
-      Misc.benchmark(50) do
-        downstream.follow(kb, :tfacts, false)
-        downstream.backtrack(kb, :tfacts, false)
-        downstream.expand(kb, :tfacts, false)
-      end
+  def __test_benchmark
+    organism = Organism.default_code("Hsa")
+    TmpFile.with_file do |tmpdir|
+      kb = KnowledgeBase.new tmpdir, Organism.default_code("Hsa")
+      kb.format = {"Gene" => "Ensembl Gene ID"}
+
+      kb.register :gene_ages, datadir_test.gene_ages, :source => "=>Associated Gene Name"
+
+      kb.register :CollecTRI, datadir_test.CollecTRI, 
+        :source => "Transcription Factor", :target => "Target Gene (Associated Gene Name)",
+        :fields => ["[ExTRI] Confidence", "[ExTRI] PMID"]
+
+
+      smad4 = Gene.setup("SMAD4", "Associated Gene Name", kb.namespace)
+      downstream = smad4.follow(kb, :CollecTRI, true)
+      Gene.setup(downstream)
+
+      downstream.follow(kb, :CollecTRI)
+      downstream.backtrack(kb, :CollecTRI)
+      downstream.expand(kb, :CollecTRI)
 
       Misc.benchmark(50) do
-        downstream.follow(kb, :tfacts)
-        downstream.backtrack(kb, :tfacts)
-        downstream.expand(kb, :tfacts)
+        downstream.follow(kb, :CollecTRI)
+        downstream.backtrack(kb, :CollecTRI)
+        downstream.expand(kb, :CollecTRI)
       end
       
       Misc.benchmark(50) do
-        downstream.follow(kb, :tfacts, true)
-        downstream.backtrack(kb, :tfacts, true)
-        downstream.expand(kb, :tfacts, true)
+        downstream.follow(kb, :CollecTRI, true)
+        downstream.backtrack(kb, :CollecTRI, true)
+        downstream.expand(kb, :CollecTRI, true)
       end
     end
   end
 
+  def test_identifier_files
+    organism = Organism.default_code("Hsa")
+    TmpFile.with_file do |tmpdir|
+      Path.setup(tmpdir)
+      kb = KnowledgeBase.new tmpdir, Organism.default_code("Hsa")
+
+      kb.register :gene_ages, datadir_test.gene_ages
+
+      assert_include kb.get_database(:gene_ages).identifier_files.first, "test/data"
+      assert_include kb.get_index(:gene_ages).identifier_files.first, "test/data"
+
+    end
+  end
+
   def test_knowledge_base_reuse
     organism = Organism.default_code("Hsa")
     TmpFile.with_file do |tmpdir|
       Path.setup(tmpdir)
-      Association.index(TFactS.regulators, :persist_file => tmpdir.tfacts, :format => {"Gene" => "Ensembl Gene ID"}, :namespace => Organism.default_code("Hsa"))
+      kb = KnowledgeBase.new tmpdir, Organism.default_code("Hsa")
+      kb.register :CollecTRI, datadir_test.CollecTRI,
+        :source => "Transcription Factor=~Associated Gene Name=>Ensembl Gene ID", :target => "Target Gene",
+        :fields => ["[ExTRI] Confidence", "[ExTRI] PMID"]
+
+      assert kb.get_database(:CollecTRI).identifier_files.any?
+
+      i = Association.index(datadir_test.CollecTRI, :persist_file => tmpdir.CollecTRI, 
+                        :source => "Transcription Factor=~Associated Gene Name=>Ensembl Gene ID", :target => "Target Gene",
+                        :fields => ["[ExTRI] Confidence", "[ExTRI] PMID"],
+                        :format => {"Gene" => "Ensembl Gene ID"},
+                        :namespace => Organism.default_code("Hsa"))
+
+      assert i.identifier_files.any?
 
       kb = KnowledgeBase.load(tmpdir)
-      assert kb.identify_source('tfacts', "TP53") =~ /ENSG/
+
+      assert kb.get_database(:CollecTRI).identifier_files.any?
+
+      i =  kb.get_index(:CollecTRI)
+
+      assert i.identifier_files.any?
+      assert kb.identify_source('CollecTRI', "SMAD4") =~ /ENSG/
     end
   end
 

data/test/rbbt/test_packed_index.rb

@@ -2,7 +2,7 @@ require File.join(File.expand_path(File.dirname(__FILE__)), '..', 'test_helper.r
 require 'rbbt/packed_index'
 
 class TestPackedIndex < Test::Unit::TestCase
-  def _test_packed_index
+  def test_packed_index
 
     TmpFile.with_file do |tmpfile|
       pi = PackedIndex.new tmpfile, true, %w(i i 23s f f f f f)
@@ -14,10 +14,10 @@ class TestPackedIndex < Test::Unit::TestCase
       pi.close
       pi = PackedIndex.new(tmpfile, false)
       Misc.benchmark(1000) do
-      100.times do |i|
-        assert_equal i, pi[i][0] 
-        assert_equal i+2, pi[i][1] 
-      end
+        100.times do |i|
+          assert_equal i, pi[i][0] 
+          assert_equal i+2, pi[i][1] 
+        end
       end
       assert_equal nil, pi[100]
       assert_equal nil, pi[101]

data/test/rbbt/test_tsv.rb

@@ -651,7 +651,7 @@ row3    AA    BB|BBB    Id3|Id2
     end
   end
 
-  def test_benchmark
+  def __test_benchmark
     num = 10_000
     txt = num.times.inject(nil) do |acc,i|
       (acc.nil? ? "" : acc << "\n") << (0..10).collect{|v| v == 0 ? i : [v,v] * "|" } * "\t"

data/test/rbbt/test_workflow.rb

@@ -174,21 +174,26 @@ for this dependency
     "alt"
   end
 
+  task :overr_alt2 => :string do
+    "alt"
+  end
+
+
   dep :overr_orig
   task :overr_target => :string do
     step(:overr_orig).load.reverse
   end
 
   dep :overr_alt, :not_overriden => true
-  dep :overr_target, "TestWF#overr_orig" => :overr_alt, :not_overriden => true
+  dep :overr_target, "TestWF#overr_orig" => :overr_alt
   task :overr_action => :string do
     step(:overr_target).load.upcase
   end
 
 
-  dep :overr_alt, :not_overriden => true
-  dep :overr_target, "TestWF#overr_orig" => :overr_alt
-  task :overr_action2 => :string do
+  dep :overr_alt2, :not_overriden => true
+  dep :overr_target, "TestWF#overr_orig" => :overr_alt2, :not_overriden => true
+  task :not_overr_action => :string do
     step(:overr_target).load.upcase
   end
 
@@ -354,12 +359,10 @@ class TestWorkflow < Test::Unit::TestCase
 
   def test_stream_order
 
-    Log.with_severity 0 do
-      job = TestWF.job(:stream2)
-      job.recursive_clean
-      job.produce
+    job = TestWF.job(:stream2)
+    job.recursive_clean
+    job.produce
 
-    end
   end
 
   def test_rec_input_use
@@ -450,13 +453,16 @@ class TestWorkflow < Test::Unit::TestCase
       end
     end
 
-    job = TestWF.job(:reverse_file, nil, :file => "code")
-    TmpFile.with_file do |dir|
-      Path.setup(dir)
-      Step.save_job_inputs(job, dir)
-      assert_equal Dir.glob(dir + "/*"), [dir.file.find + '.as_path']
-      inputs  = Workflow.load_inputs(dir, [:file], :file => :file)
-      assert_equal inputs, {:file => 'code'}
+    TmpFile.with_file("code") do |tmpfile|
+      job_orig = TestWF.job(:reverse_file, nil, :file => tmpfile)
+      TmpFile.with_file do |dir|
+        Path.setup(dir)
+        Step.save_job_inputs(job_orig, dir)
+        assert_equal [dir.file.find + '.as_path'], Dir.glob(dir + "/*")
+        inputs  = Workflow.load_inputs(dir, [:file], :file => :file)
+        job = TestWF.job(:reverse_file, nil, inputs)
+        assert job_orig.path, job.path
+      end
     end
 
   end
@@ -507,11 +513,12 @@ class TestWorkflow < Test::Unit::TestCase
 
     assert Symbol === job.step(:overr_orig).overriden
     assert TrueClass === job.step(:overr_target).overriden
-    assert ! job.overriden
+    assert job.overriden
 
-    job = TestWF.job(:overr_action2)
+    job = TestWF.job(:not_overr_action)
+    assert ! job.overriden
     assert_equal "TLA", job.run
-    assert job.overriden
+    assert ! job.step(:overr_target).overriden
   end
 
   def test_anonymous_workflow
@@ -539,65 +546,63 @@ class TestWorkflow < Test::Unit::TestCase
   end
 
   def test_low_level_step
-    Log.with_severity 0 do
-      TmpFile.with_file do |tmpdir|
-        Path.setup tmpdir
-
-        s1 = Step.new tmpdir.s1 do "s1" end 
-        s1.task_name = "s1"
-
-        # run clean run
-        assert_equal "s1", s1.run
-        s1.clean
-        assert_equal "s1", s1.run
-        assert_equal "s1", s1.run
-
-        # is persisted because it raises RbbtException
-        s1.task = proc do raise RbbtException end
-        assert_equal "s1", s1.run
-        s1.clean
-        assert_raises RbbtException do s1.run end
-        assert RbbtException === s1.get_exception
-        assert s1.error?
-
-        s1.recursive_clean
-        s1.task = proc do "s1" end
-
-        # add dependencies
-        s2 = Step.new tmpdir.s2 do 
-          step(:s1).load + " -> s2"  
-        end 
-        s2.task_name = "s2"
-        s2.dependencies << s1
-
-        s3 = Step.new tmpdir.s3 do 
-          step(:s2).load + " -> s3"  
-        end 
-        s3.task_name = "s3"
-        s3.dependencies << s2
-
-        assert_equal "s1 -> s2", s2.run
-        assert_equal "s1 -> s2 -> s3", s3.run
-        
-        # Test recusive behaviour
-        s1.task = proc do raise RbbtException end
-        ComputeDependency.setup(s1, :produce)
-        s1.clean
-        s3.clean
-        s3.run
-        assert_equal "s1 -> s2 -> s3", s3.run
-
-        s1.task = proc do raise RbbtException end
-        ComputeDependency.setup(s1, :produce)
-        s3.recursive_clean
-        assert_raises RbbtException do s3.run end
-
-        s1.task = proc{|v| v }
-        s1.inputs = ["test"]
-        assert_equal "test", s1.run
-        s3.recursive_clean
-        assert_equal "test -> s2 -> s3", s3.run
-      end
+    TmpFile.with_file do |tmpdir|
+      Path.setup tmpdir
+
+      s1 = Step.new tmpdir.s1 do "s1" end 
+      s1.task_name = "s1"
+
+      # run clean run
+      assert_equal "s1", s1.run
+      s1.clean
+      assert_equal "s1", s1.run
+      assert_equal "s1", s1.run
+
+      # is persisted because it raises RbbtException
+      s1.task = proc do raise RbbtException end
+      assert_equal "s1", s1.run
+      s1.clean
+      assert_raises RbbtException do s1.run end
+      assert RbbtException === s1.get_exception
+      assert s1.error?
+
+      s1.recursive_clean
+      s1.task = proc do "s1" end
+
+      # add dependencies
+      s2 = Step.new tmpdir.s2 do 
+        step(:s1).load + " -> s2"  
+      end 
+      s2.task_name = "s2"
+      s2.dependencies << s1
+
+      s3 = Step.new tmpdir.s3 do 
+        step(:s2).load + " -> s3"  
+      end 
+      s3.task_name = "s3"
+      s3.dependencies << s2
+
+      assert_equal "s1 -> s2", s2.run
+      assert_equal "s1 -> s2 -> s3", s3.run
+
+      # Test recusive behaviour
+      s1.task = proc do raise RbbtException end
+      ComputeDependency.setup(s1, :produce)
+      s1.clean
+      s3.clean
+      s3.run
+      assert_equal "s1 -> s2 -> s3", s3.run
+
+      s1.task = proc do raise RbbtException end
+      ComputeDependency.setup(s1, :produce)
+      s3.recursive_clean
+      assert_raises RbbtException do s3.run end
+
+      s1.task = proc{|v| v }
+      s1.inputs = ["test"]
+      assert_equal "test", s1.run
+      s3.recursive_clean
+      assert_equal "test -> s2 -> s3", s3.run
     end
   end
 

data/test/rbbt/tsv/test_accessor.rb

@@ -312,4 +312,8 @@ row2    aa|aa|AA|AA    b1|b2|B1|B2    Id1|Id1|Id2|Id2
     end
 
   end
+
+  def test_identifier_files
+    assert_include datadir_test.CollecTRI.identifier_files.first, "test/data"
+  end
 end

data/test/rbbt/tsv/test_attach.rb

@@ -215,7 +215,6 @@ row2    E
 
     tsv1 = Rbbt.tmp.test.test1.data.produce(true).tsv :double,  :sep => /\s+/
     tsv2 = Rbbt.tmp.test.test2.data.produce(true).tsv :double,  :sep => /\s+/
-    Log.tsv tsv2
 
     tsv2.identifiers = Rbbt.tmp.test.test2.identifiers.produce.find #.to_s
 
@@ -603,8 +602,7 @@ A    Id3
     tsv2.identifiers = Rbbt.tmp.test.test2.identifiers.produce(true).produce.find #.to_s
 
     tsv1.attach tsv2, :fields => ["ValueE"] #, :persist_input => true
-    Log.tsv tsv1
-    ppp tsv1
+    assert_equal [["a", "aa", "aaa"], ["b"], ["e"]], tsv1["row1"]
     
   end
 
@@ -631,7 +629,7 @@ E    B
     tsv2 = Rbbt.tmp.test.test2.data.produce(true).tsv :double,  :sep => /\s+/
 
     tsv1.attach tsv2, :fields => ["ValueE"] #, :persist_input => true
-    Log.tsv tsv1
+    assert_equal [["a", "aa", "aaa"], ["b"], ["e"]], tsv1["row1"]
     
   end
 
@@ -663,7 +661,6 @@ row3    C
     tsv1 = Rbbt.tmp.test.test1.data.produce(true).tsv :double,  :sep => /\s+/
     tsv2 = Rbbt.tmp.test.test2.data.produce(true).tsv :double,  :sep => /\s+/
 
-    ppp tsv1.attach tsv2, :complete => ["AA"]
     tsv1.attach tsv2, :complete => ["AA"]
     assert_equal [["AA"], ["C"]], tsv1["row3"]
   end

data/test/rbbt/tsv/test_index.rb

@@ -111,16 +111,22 @@ row3    A    a|B    Id4
       assert_equal "Id1", index['a']
       assert_equal "Id3", index['A']
       assert_equal "OtherID", index.fields.first
+      assert_equal "Id1", index['a']
+
+      index = tsv.index(:order => true, :persist => false)
+      assert_equal "Id1", index['a']
 
       tsv.delete "Id1"
 
+      index = tsv.index(:order => true, :persist => false)
+      assert_equal "Id3", index['a']
+
       index = tsv.index(:order => true, :persist => true)
       assert_equal "Id1", index['a']
       assert_equal "Id3", index['A']
       assert_equal "OtherID", index.fields.first
-
-      index = tsv.index(:order => true, :persist => false)
       assert_equal "Id1", index['a']
+
     end
   end
 

data/test/rbbt/tsv/test_manipulate.rb

@@ -13,8 +13,6 @@ rowa    a|aa    b|BB  C|CC
 
     TmpFile.with_file(content) do |filename|
       tsv = TSV.open(File.open(filename), :sep => /\s+/, :type => :double)
-      Log.tsv tsv
-      Log.tsv tsv.reorder("ValueA", nil, :zipped => true)
       assert_equal ["A", "AA", "a", "aa"].sort, tsv.reorder("ValueA", nil, :zipped => true).keys.sort
     end
   end
@@ -129,7 +127,6 @@ row2 A B C
       tsv = tsv.slice []
       assert tsv.fields.empty?
       TmpFile.with_file do |tmpfile|
-        iii tsv.to_s
         Open.write(tmpfile, tsv.to_s)
         tsv = TSV.open tmpfile
         assert tsv.fields.empty?

data/test/rbbt/util/R/test_model.rb

@@ -3,8 +3,6 @@ require 'rbbt/util/R'
 require 'rbbt/util/R/model'
 
 class TestRModel < Test::Unit::TestCase
-  def model
-  end
 
   def test_fit
     data = TSV.setup({}, :key_field => "Dose", :fields => ["Response"], :type => :single)

data/test/rbbt/util/misc/test_bgzf.rb

@@ -2,12 +2,12 @@ require File.join(File.expand_path(File.dirname(__FILE__)), '../../..', 'test_he
 require 'rbbt/util/misc/bgzf'
 
 class TestBgzf < Test::Unit::TestCase
-  def _test_Bgzf
+  def test_Bgzf
     content = "1234567890" * 1000000
     TmpFile.with_file(content) do |file|
       compressed = file + '.gz'
       `bgzip #{file} -c > #{compressed}`
-      stream = Bgzf.setup File.open(compressed)
+      stream = Bgzf.setup Open.open(compressed, :noz => true)
       assert_equal "1234", stream.read(4)
       assert_equal "56", stream.read(2)
       stream.seek 500003
@@ -40,7 +40,7 @@ class TestBgzf < Test::Unit::TestCase
     end
   end
 
-  def _test_bgzip
+  def test_bgzip
     assert File.exist?(Bgzf.bgzip_cmd)
     assert 'bgzip', File.basename(Bgzf.bgzip_cmd)
   end

data/test/rbbt/util/misc/test_communication.rb

@@ -3,9 +3,11 @@ require 'rbbt/util/misc/communication'
 
 class TestCommunication < Test::Unit::TestCase
   def test_send_email
-    to = from = 'mvazque2@localhost'
-    subject = message = "Test"
-    iii Misc.send_email(to, from, subject, message)
+    keyword_test :mail do
+      to = from = 'mvazque2@localhost'
+      subject = message = "Test"
+      Misc.send_email(to, from, subject, message)
+    end
   end
 end
 

data/test/rbbt/util/test_migrate.rb

@@ -14,9 +14,7 @@ class TestMigrate < Test::Unit::TestCase
     Open.write(test_file, "TEST")
     TmpFile.with_file do |tmpdir|
       Misc.in_dir tmpdir do
-        Log.with_severity 0 do
-          Rbbt.migrate('tmp/test/migration_test/migration_test_file', :current)
-        end
+        Rbbt.migrate('tmp/test/migration_test/migration_test_file', :current)
       end
       assert_equal "TEST", Open.read(File.join(tmpdir, 'tmp/test/migration_test/migration_test_file'))
     end