rbbt-util 5.28.6 → 5.28.11

data/test/rbbt/knowledge_base/test_registry.rb

@@ -45,7 +45,7 @@ TP53 NFKB1|GLI1 activation|activation true|true
 
   def test_index_flat
     require 'rbbt/sources/tfacts'
-    file = TFacts.regulators
+    file = TFactS.regulators
     KNOWLEDGE_BASE.register :tfacts, file,  :type => :flat, :source => "Transcription Factor Associated Gene Name=~Associated Gene Name", :merge => true
     assert KNOWLEDGE_BASE.subset(:tfacts, :source => ["TP53"], :target => :all).length > 10
   end

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

@@ -4,19 +4,12 @@ require 'rbbt/annotations'
 require 'rbbt/util/tmpfile'
 require 'test/unit'
 
-module TestAnnotation
-  extend Annotation
-
-  self.annotation :test_annotation
-end
-
 class TestPersistTSVCDB < Test::Unit::TestCase
 
   if Persist.respond_to? :open_cbd
     def test_organism
       require 'rbbt/sources/organism'
       TmpFile.with_file nil do |tmp_file|
-        file = CMD.cmd("head -n 1000000", :in => Organism.identifiers("Hsa").open, :pipe => true)
         tsv = Organism.identifiers("Hsa").tsv(:key_field => "Associated Gene Name", :fields => ["Ensembl Gene ID"], :type => :single, :persist => true, :persist_engine => "CDB", :persist_dir => tmp_file)
         assert_equal "ENSG00000141510", tsv["TP53"]
       end

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

@@ -5,15 +5,9 @@ require 'rbbt/annotations'
 require 'rbbt/util/tmpfile'
 require 'test/unit'
 
-module TestAnnotation
-  extend Annotation
-
-  self.annotation :test_annotation
-end
-
 class TestPersistTSVKC < Test::Unit::TestCase
   if Persist.respond_to? :open_kyotocabinet
-    def _test_organism_kch
+    def test_organism_kch
       require 'rbbt/sources/organism'
       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 => "kch", :persist_dir => tmp_file
@@ -22,7 +16,7 @@ class TestPersistTSVKC < Test::Unit::TestCase
     end
 
 
-    def _test_organism_kct
+    def test_organism_kct
       require 'rbbt/sources/organism'
       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 => "kct", :persist_dir => tmp_file

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

@@ -4,12 +4,6 @@ require 'rbbt/annotations'
 require 'rbbt/util/tmpfile'
 require 'test/unit'
 
-module TestAnnotation
-  extend Annotation
-
-  self.annotation :test_annotation
-end
-
 class TestPersistTSVLevelDB < Test::Unit::TestCase
 
   if Persist.respond_to? :open_leveldb

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

@@ -4,12 +4,6 @@ require 'rbbt/annotations'
 require 'rbbt/util/tmpfile'
 require 'test/unit'
 
-module TestAnnotation
-  extend Annotation
-
-  self.annotation :test_annotation
-end
-
 class TestPersistTSVLMDB < Test::Unit::TestCase
 
   def test_organism

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

@@ -4,7 +4,8 @@ require 'rbbt/annotations'
 require 'rbbt/util/tmpfile'
 require 'test/unit'
 
-module TestAnnotation
+
+module TestAnnotationModule
   extend Annotation
 
   self.annotation :test_annotation
@@ -25,8 +26,8 @@ class TestPersistTSVTC < Test::Unit::TestCase
       entity1 = "Entity 1"
       entity2 = "Entity 2"
 
-      TestAnnotation.setup(entity1, :test_annotation => "1")
-      TestAnnotation.setup(entity2, :test_annotation => "2")
+      TestAnnotationModule.setup(entity1, :test_annotation => "1")
+      TestAnnotationModule.setup(entity2, :test_annotation => "2")
 
       annotations = [entity1, entity2]
 
@@ -56,9 +57,9 @@ class TestPersistTSVTC < Test::Unit::TestCase
       entity2 = "Entity 2"
       entity2bis = "Entity 2"
 
-      TestAnnotation.setup(entity1, :test_annotation => "1")
-      TestAnnotation.setup(entity2, :test_annotation => "2")
-      TestAnnotation.setup(entity2bis, :test_annotation => "2")
+      TestAnnotationModule.setup(entity1, :test_annotation => "1")
+      TestAnnotationModule.setup(entity2, :test_annotation => "2")
+      TestAnnotationModule.setup(entity2bis, :test_annotation => "2")
 
       annotations = [entity1, entity2, entity2bis]
 
@@ -105,8 +106,8 @@ class TestPersistTSVTC < Test::Unit::TestCase
       entity1 = "Entity 1"
       entity2 = "Entity 2"
 
-      TestAnnotation.setup(entity1, :test_annotation => "1")
-      TestAnnotation.setup(entity2, :test_annotation => "2")
+      TestAnnotationModule.setup(entity1, :test_annotation => "1")
+      TestAnnotationModule.setup(entity2, :test_annotation => "2")
 
       annotations = [entity1, entity2]
 
@@ -138,7 +139,7 @@ class TestPersistTSVTC < Test::Unit::TestCase
       entity2 = "Entity 2"
 
       annotations = [entity1, entity2]
-      TestAnnotation.setup(annotations, :test_annotation => "1")
+      TestAnnotationModule.setup(annotations, :test_annotation => "1")
       annotations.extend AnnotatedArray
 
       persisted_annotations = Persist.persist("Test", :annotations, :annotation_repo => repo) do
@@ -171,11 +172,11 @@ class TestPersistTSVTC < Test::Unit::TestCase
       entity2 = "Entity 2"
 
       annotations = [entity1, entity2]
-      TestAnnotation.setup(annotations, :test_annotation => "1")
+      TestAnnotationModule.setup(annotations, :test_annotation => "1")
       annotations.extend AnnotatedArray
 
       annotations_ary = [annotations]
-      TestAnnotation.setup(annotations_ary, :test_annotation => "1")
+      TestAnnotationModule.setup(annotations_ary, :test_annotation => "1")
       annotations_ary.extend AnnotatedArray
 
       persisted_annotations = Persist.persist("Test", :annotations, :annotation_repo => repo) do
@@ -210,9 +211,9 @@ class TestPersistTSVTC < Test::Unit::TestCase
       entity2 = "Entity 2"
       entity2bis = "Entity 2"
 
-      TestAnnotation.setup(entity1, :test_annotation => "1")
-      TestAnnotation.setup(entity2, :test_annotation => "2")
-      TestAnnotation.setup(entity2bis, :test_annotation => "2")
+      TestAnnotationModule.setup(entity1, :test_annotation => "1")
+      TestAnnotationModule.setup(entity2, :test_annotation => "2")
+      TestAnnotationModule.setup(entity2bis, :test_annotation => "2")
 
       annotations = [entity1, entity2, entity2bis]
 

data/test/rbbt/test_entity.rb

@@ -199,7 +199,6 @@ class TestEntity < Test::Unit::TestCase
 
 
     $processed_multiple = []
-    Log.severity = 0
 
     array = ReversableString.setup([string1, string2])
     assert_equal [string1, string2].collect{|s| s.chars}, array.multiple_annotation_list

data/test/rbbt/test_knowledge_base.rb

@@ -62,7 +62,7 @@ class TestKnowledgeBase < Test::Unit::TestCase
       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 :tfacts, TFactS.regulators, :source =>"=~Associated Gene Name"
 
       kb.get_index(:tfacts).reverse
     end
@@ -74,7 +74,7 @@ class TestKnowledgeBase < Test::Unit::TestCase
       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 :tfacts, TFactS.regulators, :source =>"=~Associated Gene Name"
 
       assert_equal "Ensembl Gene ID", kb.get_database(:tfacts).key_field
 
@@ -113,10 +113,9 @@ class TestKnowledgeBase < Test::Unit::TestCase
 
   def test_knowledge_base_reuse
     organism = Organism.default_code("Hsa")
-    Log.severity = 0
     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"))
+      Association.index(TFactS.regulators, :persist_file => tmpdir.tfacts, :format => {"Gene" => "Ensembl Gene ID"}, :namespace => Organism.default_code("Hsa"))
 
       kb = KnowledgeBase.load(tmpdir)
       assert kb.identify_source('tfacts', "TP53") =~ /ENSG/

data/test/rbbt/test_persist.rb

@@ -4,12 +4,6 @@ require 'rbbt/annotations'
 require 'rbbt/util/tmpfile'
 require 'test/unit'
 
-module TestAnnotation
-  extend Annotation
-
-  self.annotation :test_annotation
-end
-
 class TestPersist < Test::Unit::TestCase
 
   def test_array_persist
@@ -78,4 +72,14 @@ class TestPersist < Test::Unit::TestCase
       stream.join
     end
   end
+
+  def test_newer
+    TmpFile.with_file("Test1") do |tmp1|
+      sleep 1
+      TmpFile.with_file("Test1") do |tmp2|
+        assert Persist.newer?(tmp1, tmp2)
+        assert ! Persist.newer?(tmp2, tmp1)
+      end
+    end
+  end
 end

data/test/rbbt/test_workflow.rb

@@ -204,7 +204,6 @@ class TestWorkflow < Test::Unit::TestCase
 
   def test_update_on_input_dependency_update
     Open.repository_dirs << File.join(ENV["HOME"],".rbbt/tmp/test/workflow")
-    Log.severity = 0
     Misc.with_env "RBBT_UPDATE", "true" do
       send_input_dep_to_reverse_job = TestWF.job(:send_input_dep_to_reverse, nil, :name => "Miguel")
       send_input_dep_to_reverse_job.clean
@@ -376,21 +375,23 @@ class TestWorkflow < Test::Unit::TestCase
   def test_delete_dep
     job = TestWF.job(:t3).recursive_clean
     job.run
-    assert job.checks.select{|d| d.task_name.to_s == "t1" }.any?
-    job = TestWF.job(:t3)
-    job.step(:t1).clean
-    assert job.checks.select{|d| d.task_name.to_s == "t1" }.empty?
-    job = TestWF.job(:t3).recursive_clean
-    job.run
-    assert job.checks.select{|d| d.task_name.to_s == "t1" }.any?
-    job = TestWF.job(:t3)
-    sleep 1
-    Open.touch job.step(:t1).path
-    Misc.with_env "RBBT_UPDATE", "false" do
-      assert job.updated?
-    end
-    Misc.with_env "RBBT_UPDATE", "true" do
-      assert ! job.updated?
+    Misc.with_env "RBBT_UPDATE", 'true' do
+      assert job.checks.select{|d| d.task_name.to_s == "t1" }.any?
+      job = TestWF.job(:t3)
+      job.step(:t1).clean
+      assert job.checks.select{|d| d.task_name.to_s == "t1" }.empty?
+      job = TestWF.job(:t3).recursive_clean
+      job.run
+      assert job.checks.select{|d| d.task_name.to_s == "t1" }.any?
+      job = TestWF.job(:t3)
+      sleep 1
+      Open.touch job.step(:t1).path
+      Misc.with_env "RBBT_UPDATE", "false" do
+        assert job.updated?
+      end
+      Misc.with_env "RBBT_UPDATE", "true" do
+        assert ! job.updated?
+      end
     end
   end
 

data/test/rbbt/tsv/parallel/test_traverse.rb

@@ -392,6 +392,20 @@ class TestTSVParallelThrough < Test::Unit::TestCase
     assert_equal size, stream.read.split("\n").length
   end
 
+  def test_traverse_into_path
+    size = 100
+    array = (1..size).to_a.collect{|n| n.to_s}
+    TmpFile.with_file do |tmpfile|
+      Path.setup(tmpfile)
+      io = TSV.traverse array, :into => tmpfile do |e|
+        e
+      end
+      io.join
+      assert_equal size, Open.read(tmpfile).split("\n").length
+    end
+  end
+
+
   def test_traverse_progress
     size = 1000
     array = (1..size).to_a.collect{|n| n.to_s}

data/test/rbbt/tsv/test_accessor.rb

@@ -222,6 +222,17 @@ row2    aa|aa|AA|AA    b1|b2|B1|B2    Id1|Id1|Id2|Id2
     end
   end
 
+  def test_to_s_no_fields
+    file1 =<<-EOF
+row6 dd dd ee
+row1 a b c
+row2 A B C
+row3 1 2 3
+   EOF
+    tsv1 = TSV.open StringIO.new(file1), :sep => " "
+    assert tsv1.to_s(:sort, true).include?('dd')
+  end
+
   def test_to_s_unmerge_expand
     content =<<-EOF
 #Id    ValueA    ValueB    OtherID

data/test/rbbt/tsv/test_attach.rb

@@ -630,10 +630,8 @@ E    B
     tsv1 = Rbbt.tmp.test.test1.data.tsv :double,  :sep => /\s+/
     tsv2 = Rbbt.tmp.test.test2.data.tsv :double,  :sep => /\s+/
 
-    Log.severity = 0
     tsv1.attach tsv2, :fields => ["ValueE"] #, :persist_input => true
     Log.tsv tsv1
-    ppp tsv1
     
   end
 end

data/test/rbbt/tsv/test_index.rb

@@ -29,7 +29,7 @@ row2    A    B    Id3
 
     TmpFile.with_file(content) do |filename|
       tsv = TSV.open(File.open(filename), :sep => /\s+/, :key_field => "OtherID", :persistence => false)
-      index = tsv.index(:case_insensitive => true, :persistence => true)
+      index = tsv.index(:persistence => true)
       assert index["row1"].include? "Id1"
       assert_equal "OtherID", index.fields.first
     end
@@ -45,9 +45,8 @@ row2    A    B    Id3
 
     TmpFile.with_file(content) do |filename|
       tsv = TSV.open(File.open(filename), :sep => /\s+/, :key_field => "OtherID", :persistence => false)
-      Log.tsv tsv
-      index = tsv.index(:case_insensitive => true, :persistence => false, :fields => ["Id"], :target => "ValueA")
-      Log.tsv index
+      index = tsv.index(:persistence => false, :fields => ["Id"], :target => "ValueA")
+      assert_equal "A", index["row2"] 
     end
 
   end
@@ -243,7 +242,7 @@ g:         ____
     EOF
     TmpFile.with_file(data) do |datafile|
       load_segment_data(datafile)
-      TmpFile.with_file(load_segment_data(datafile)) do |tsvfile|
+      TmpFile.with_file(load_segment_data(datafile).to_s) do |tsvfile|
         f = TSV.range_index(tsvfile, "Start", "End", :persistence => true)
 
         #assert_equal %w(), f[0].sort
@@ -286,8 +285,8 @@ f:             ___
 g:         ____
     EOF
     TmpFile.with_file(data) do |datafile|
-      TmpFile.with_file(load_segment_data(datafile)) do |tsvfile|
-        f = TSV.range_index(tsvfile, "Start", "End", :filters => [["field:Start", "3"]])
+      TmpFile.with_file(load_segment_data(datafile).to_s) do |tsvfile|
+        f = TSV.range_index(tsvfile, "Start", "End", :filters => [["field:Start", "3"]], :persist_update => true)
 
         assert_equal %w(), f[0].sort
         assert_equal %w(), f[1].sort

data/test/rbbt/tsv/test_manipulate.rb

@@ -117,6 +117,26 @@ row2 A B C
     end
   end
 
+  def test_slice_empty
+    content =<<-EOF
+#ID ValueA ValueB Comment
+row1 a b c
+row2 A B C
+    EOF
+
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.open(File.open(filename), :type => :list, :sep => /\s/)
+      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?
+      end
+    end
+  end
+
   def test_select
      content =<<-EOF
 #Id    ValueA    ValueB    OtherID
@@ -264,7 +284,7 @@ row3    a    C    Id4
 
   def test_reorder_flat
     content =<<-EOF
-#Id    ValueA    
+#Id    ValueA
 row1    a aa aaa
 row2    A
 row3    a
@@ -272,9 +292,8 @@ row3    a
 
     TmpFile.with_file(content) do |filename|
       tsv = TSV.open(File.open(filename), :sep => /\s+/, :type => :flat)
-      
-      assert_equal ["row1", "row3"].sort, tsv.reorder("ValueA")["a"]
 
+      assert_equal ["row1", "row3"].sort, tsv.reorder("ValueA")["a"]
     end
   end
 

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

@@ -1,4 +1,5 @@
 require File.join(File.expand_path(File.dirname(__FILE__)), '../../..', 'test_helper.rb')
+require 'rbbt/util/R'
 require 'rbbt/util/R/model'
 
 class TestRModel < Test::Unit::TestCase
@@ -49,7 +50,7 @@ data = rbbt.model.inpute(data, CI ~ Dose, method=drm, classes='numeric', fct=LL.
     assert_equal result.size, result.column("CI").values.flatten.reject{|p| p.nil? or p.empty? or p == "NA"}.length
   end
 
-  def test_ab_surv_corr
+  def __test_ab_surv_corr
     require 'rbbt/workflow'
     Workflow.require_workflow "Miller"
 

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

@@ -5,7 +5,6 @@ require 'rbbt/util/R/plot'
 class TestRPlot < Test::Unit::TestCase
   def __test_ggplotgif
 
-    Log.severity = 0
     x = R.eval_a 'rnorm(100, 0, 1)'
     data = TSV.setup(x, "Num~#:type=:single#:cast=:to_f")
 
@@ -22,7 +21,6 @@ ggplot(data) + geom_density(bw=frame.value, aes(x=Val))
 
   def test_gif
 
-    Log.severity = 0
     x = R.eval_a 'rnorm(100, 0, 1)'
     data = TSV.setup(x, "Num~#:type=:single#:cast=:to_f")
 

data/test/rbbt/util/concurrency/test_processes.rb

@@ -7,7 +7,7 @@ require 'rbbt/util/concurrency/processes'
 class TestConcurrencyProcess < Test::Unit::TestCase
 
   def setup
-    Log.severity = 0
+    #Log.severity = 0
   end
 
   def test_process_throttle