rbbt-util 5.28.8 → 5.28.14

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

@@ -156,6 +156,15 @@ for this dependency
     Open.read(file).reverse
   end
 
+  task :create_file => :text do |file|
+    Open.write(file('a'), "A")
+    Open.write(file('b'), "B")
+    "DONE"
+  end
+
+  dep_task :reverse_step_file, TestWF, :reverse_file do |jobname, options, dependencies|
+    dep = dependencies.flatten.first
+  end
 
 end
 
@@ -204,7 +213,6 @@ 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 +384,23 @@ 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
 
@@ -439,4 +449,27 @@ class TestWorkflow < Test::Unit::TestCase
       end
     end
   end
+
+  def test_input_step_file_check
+    job = TestWF.job(:t3).recursive_clean
+    job.run
+    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
 end

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

@@ -566,7 +566,7 @@ row2,CC
       tsv3.keys.each{|k| tsv3[k] = nil if tsv3[k] == ""}
     end
 
-    assert_equal tsv1.attach(tsv2, :complete => true).attach(tsv3, :complete => true)["row1"], [nil, "B", nil]
+    assert_equal [nil, "B", nil], tsv1.attach(tsv2, :complete => true).attach(tsv3, :complete => true)["row1"]
   end
 
   def test_attach_index_both_non_key
@@ -597,10 +597,10 @@ A    Id3
 
     tsv1 = tsv2 = nil
 
-    tsv1 = Rbbt.tmp.test.test1.data.tsv :double,  :sep => /\s+/
-    tsv2 = Rbbt.tmp.test.test2.data.tsv :double,  :sep => /\s+/
+    tsv1 = Rbbt.tmp.test.test1.data.produce(true).tsv :double,  :sep => /\s+/
+    tsv2 = Rbbt.tmp.test.test2.data.produce(true).tsv :double,  :sep => /\s+/
 
-    tsv2.identifiers = Rbbt.tmp.test.test2.identifiers.produce.find #.to_s
+    tsv2.identifiers = Rbbt.tmp.test.test2.identifiers.produce(true).produce.find #.to_s
 
     tsv1.attach tsv2, :fields => ["ValueE"] #, :persist_input => true
     Log.tsv tsv1
@@ -627,14 +627,92 @@ E    B
 
     tsv1 = tsv2 = nil
 
-    tsv1 = Rbbt.tmp.test.test1.data.tsv :double,  :sep => /\s+/
-    tsv2 = Rbbt.tmp.test.test2.data.tsv :double,  :sep => /\s+/
+    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.severity = 0
     tsv1.attach tsv2, :fields => ["ValueE"] #, :persist_input => true
     Log.tsv tsv1
-    ppp tsv1
     
   end
+
+  def test_attach_complete
+    content1 =<<-EOF
+#: :sep=/\\s+/
+#Id    ValueA
+row1    a|aa|aaa
+row2    A
+    EOF
+
+    content2 =<<-EOF
+#: :sep=/\\s+/
+#Id    ValueB
+row1    b
+row3    C
+    EOF
+    Rbbt.claim Rbbt.tmp.test.test1.data, :string, content1
+    Rbbt.claim Rbbt.tmp.test.test2.data, :string, content2
+
+    tsv1 = tsv2 = nil
+
+    tsv1 = Rbbt.tmp.test.test1.data.produce(true).tsv :double,  :sep => /\s+/
+    tsv2 = Rbbt.tmp.test.test2.data.produce(true).tsv :double,  :sep => /\s+/
+
+    tsv1.attach tsv2, :complete => true
+    assert_equal [[], ["C"]], tsv1["row3"]
+
+    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
+
+  def test_attach_complete_identifiers
+    content1 =<<-EOF
+#: :sep=/\\s+/
+#Id    ValueA
+row1    a|aa|aaa
+row2    A
+    EOF
+
+    content2 =<<-EOF
+#: :sep=/\\s+/
+#Id2    ValueB
+ROW_1    b
+ROW_2    C
+    EOF
+
+    identifiers =<<-EOF
+#: :sep=/\\s+/
+#Id    Id2
+row1    ROW_1
+row2    ROW_2
+row3    ROW_3
+    EOF
+    Rbbt.claim Rbbt.tmp.test.test1.data, :string, content1
+    Rbbt.claim Rbbt.tmp.test.test2.data, :string, content2
+    Rbbt.claim Rbbt.tmp.test.identifiers.data, :string, identifiers
+
+    tsv1 = tsv2 = nil
+
+    tsv1 = Rbbt.tmp.test.test1.data.produce(true).tsv :double,  :sep => /\s+/
+    tsv2 = Rbbt.tmp.test.test2.data.produce(true).tsv :double,  :sep => /\s+/
+    ids = Rbbt.tmp.test.identifiers.data.produce(true).tsv :double,  :sep => /\s+/
+
+    tsv1.identifiers = ids
+
+    tsv1.attach tsv2
+    assert_equal [["A"], ["C"]], tsv1["row2"]
+
+    tsv1 = Rbbt.tmp.test.test1.data.produce(true).tsv :double,  :sep => /\s+/
+    tsv2 = Rbbt.tmp.test.test2.data.produce(true).tsv :double,  :sep => /\s+/
+    ids = Rbbt.tmp.test.identifiers.data.produce(true).tsv :double,  :sep => /\s+/
+
+    tsv1.identifiers = ids
+
+    tsv1.attach tsv2, :complete => true
+    assert_equal [["A"], ["C"]], tsv1["row2"]
+  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

@@ -284,7 +284,7 @@ row3    a    C    Id4
 
   def test_reorder_flat
     content =<<-EOF
-#Id    ValueA    
+#Id    ValueA
 row1    a aa aaa
 row2    A
 row3    a
@@ -292,9 +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

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

@@ -2,12 +2,14 @@ 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)
+      assert_equal "1234", stream.read(4)
+      assert_equal "56", stream.read(2)
       stream.seek 500003
       assert_equal "4567", stream.read(4)
       assert_equal "89", stream.read(2)
@@ -20,23 +22,25 @@ class TestBgzf < Test::Unit::TestCase
       Misc.benchmark do
         tsv = TSV.open(Open.open(file))
       end
-      compressed = file + '.bgz'
 
-      `bgzip #{file} -c > #{compressed}`
-      stream = Bgzf.setup File.open(compressed)
+      `gzip #{file}`
+      stream = Open.open(file + '.gz')
       Misc.benchmark do
         tsv = TSV.open(stream)
       end
 
-      `gzip #{file}`
-      stream = Open.open(file + '.gz')
+      `gunzip #{file}.gz`
+      compressed = file + '.bgz'
+      `bgzip #{file} -c > #{compressed}`
+      stream = Bgzf.setup File.open(compressed)
       Misc.benchmark do
         tsv = TSV.open(stream)
       end
+
     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_lock.rb

@@ -48,7 +48,6 @@ if __FILE__ == $0
   TmpFile.with_file do |dir|
     Structure.workdir = dir
     Path.setup dir
-    Log.severity = 4
     TSV.traverse (0..size).to_a, :cpus => cpus, :type => :array, :bar => true do |i|
       begin
         v = rand(num).to_s