rbbt-util 5.14.33 → 5.14.34

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

@@ -11,14 +11,14 @@ class TestTSVParallelThrough < Test::Unit::TestCase
 
     head = 100
 
-    tsv = Organism.identifiers("Hsa").tsv :head => head
+    tsv = datafile_test('identifiers').tsv :head => head
     res = {}
     TSV.traverse tsv do |k,v|
        res[k] = v
     end
     assert_equal head, res.keys.compact.sort.length
 
-    tsv = Organism.identifiers("Hsa").tsv :head => head
+    tsv = datafile_test('identifiers').tsv :head => head
     TSV.traverse tsv, :into => res do |k,v|
       [k,v]
     end
@@ -30,7 +30,7 @@ class TestTSVParallelThrough < Test::Unit::TestCase
 
     head = 100
 
-    tsv = Organism.identifiers("Hsa").tsv :head => head
+    tsv = datafile_test('identifiers').tsv :head => head
     res = {}
     TSV.traverse tsv do |k,v|
        res[k] = v
@@ -38,7 +38,7 @@ class TestTSVParallelThrough < Test::Unit::TestCase
     assert_equal head, res.keys.compact.sort.length
     assert res.values.compact.flatten.uniq.length > 0
 
-    tsv = Organism.identifiers("Hsa").tsv :head => head
+    tsv = datafile_test('identifiers').tsv :head => head
     TSV.traverse tsv, :into => res, :cpus => 5 do |k,v|
       [k,v]
     end
@@ -52,7 +52,7 @@ class TestTSVParallelThrough < Test::Unit::TestCase
 
     head = 1000
 
-    tsv = Organism.identifiers("Hsa").open
+    tsv = datafile_test('identifiers').open
     res = {}
     TSV.traverse tsv, :head => head, :into => res do |k,v|
       [k,v]
@@ -66,7 +66,7 @@ class TestTSVParallelThrough < Test::Unit::TestCase
 
     head = 1000
 
-    tsv = Organism.identifiers("Hsa")
+    tsv = datafile_test('identifiers')
     res = {}
     TSV.traverse tsv, :head => head, :cpus => 5, :into => res do |k,v|
       [k,v]
@@ -80,23 +80,23 @@ class TestTSVParallelThrough < Test::Unit::TestCase
 
     head = 1000
 
-    tsv = Organism.identifiers("Hsa").open
+    tsv = datafile_test('identifiers').open
     res = []
 
     TSV.traverse tsv, :head => head, :type => :keys do |v|
        res << v
     end
 
-    assert_equal res, Organism.identifiers("Hsa").tsv(:head => head).keys
+    assert_equal res, datafile_test('identifiers').tsv(:head => head).keys
 
-    tsv = Organism.identifiers("Hsa").open
+    tsv = datafile_test('identifiers').open
     res = []
 
     TSV.traverse tsv, :head => head, :type => :keys, :into => res do |v|
       v
     end
 
-    assert_equal res.sort, Organism.identifiers("Hsa").tsv(:head => head).keys.sort
+    assert_equal res.sort, datafile_test('identifiers').tsv(:head => head).keys.sort
   end
   
   def test_traverse_array
@@ -160,9 +160,9 @@ class TestTSVParallelThrough < Test::Unit::TestCase
   def test_traverse_benchmark
     require 'rbbt/sources/organism'
 
-    head = 2_000
+    head = 5_000
 
-    tsv = Organism.identifiers("Hsa").open
+    tsv = datafile_test('identifiers').open
     Misc.benchmark do
       res = {}
       TSV.traverse tsv, :head => head do |k,v|
@@ -170,7 +170,7 @@ class TestTSVParallelThrough < Test::Unit::TestCase
       end
     end
 
-    tsv = Organism.identifiers("Hsa").open
+    tsv = datafile_test('identifiers').open
     Misc.benchmark do
       res = {}
       TSV.traverse tsv, :head => head, :cpus => 5, :into => res do |k,v|
@@ -184,8 +184,8 @@ class TestTSVParallelThrough < Test::Unit::TestCase
 
     head = 2_000
 
-    stream = Organism.identifiers("Hsa").open 
-    dumper = TSV::Dumper.new Organism.identifiers("Hsa").tsv_options
+    stream = datafile_test('identifiers').open 
+    dumper = TSV::Dumper.new datafile_test('identifiers').tsv_options
     dumper.init
     TSV.traverse stream, :head => head, :into => dumper do |k,v|
       k = k.first
@@ -203,8 +203,8 @@ class TestTSVParallelThrough < Test::Unit::TestCase
     head = 2_000
     threads = 10
 
-    stream = Organism.identifiers("Hsa").open 
-    dumper = TSV::Dumper.new Organism.identifiers("Hsa").tsv_options
+    stream = datafile_test('identifiers').open 
+    dumper = TSV::Dumper.new datafile_test('identifiers').tsv_options
     dumper.init
 
     TSV.traverse stream, :threads => threads, :head => head, :into => dumper do |k,v|
@@ -223,8 +223,8 @@ class TestTSVParallelThrough < Test::Unit::TestCase
     head = 2_000
     cpus = 10
 
-    stream = Organism.identifiers("Hsa").open 
-    dumper = TSV::Dumper.new Organism.identifiers("Hsa").tsv_options
+    stream = datafile_test('identifiers').open 
+    dumper = TSV::Dumper.new datafile_test('identifiers').tsv_options
     dumper.init
     TSV.traverse stream, :cpus => cpus, :head => head, :into => dumper do |k,v|
       k = k.first
@@ -243,7 +243,7 @@ class TestTSVParallelThrough < Test::Unit::TestCase
 
     head = 2_000
 
-    tsv = TSV::Parser.new Organism.identifiers("Hsa").open, :head => head
+    tsv = TSV::Parser.new datafile_test('identifiers').open, :head => head
     dumper = TSV::Dumper.new tsv.options
 
     TSV.traverse tsv, :head => head, :into => dumper do |k,v|
@@ -265,7 +265,7 @@ class TestTSVParallelThrough < Test::Unit::TestCase
     head = 2_000
     threads = 3
 
-    tsv = TSV::Parser.new Organism.identifiers("Hsa").open, :head => head
+    tsv = TSV::Parser.new datafile_test('identifiers').open, :head => head
 
     dumper = TSV::Dumper.new tsv.options
     dumper.init
@@ -286,11 +286,12 @@ class TestTSVParallelThrough < Test::Unit::TestCase
   def test_traverse_dumper_cpus
     require 'rbbt/sources/organism'
 
-    head = 10_000
+    head = 5_000
     cpus = 4
 
-    stream = Organism.identifiers("Hsa").open 
-    dumper = TSV::Dumper.new Organism.identifiers("Hsa").tsv_options
+    stream = datafile_test('identifiers').open 
+    dumper = TSV::Dumper.new datafile_test('identifiers').tsv_options
+    dumper.init
 
     TSV.traverse stream, :head => head, :cpus => cpus, :into => dumper do |k,v|
       k = k.first
@@ -302,6 +303,7 @@ class TestTSVParallelThrough < Test::Unit::TestCase
       [k, v.length]
     end
 
+    
     assert_equal head, res.size
   end
 
@@ -311,8 +313,8 @@ class TestTSVParallelThrough < Test::Unit::TestCase
     head = 2_000
 
     Log.info Log.color :red, "TRAVERSE EXCEPTION"
-    stream = Organism.identifiers(Organism.default_code("Hsa")).open 
-    dumper = TSV::Dumper.new Organism.identifiers(Organism.default_code("Hsa")).tsv_options
+    stream = datafile_test('identifiers').open
+    dumper = TSV::Dumper.new datafile_test('identifiers').tsv_options
     dumper.init
 
     assert_raise StopException do
@@ -332,8 +334,8 @@ class TestTSVParallelThrough < Test::Unit::TestCase
     cpus = 2
 
     Log.info Log.color :red, "TRAVERSE EXCEPTION"
-    stream = Organism.identifiers(Organism.default_code("Hsa")).open 
-    dumper = TSV::Dumper.new Organism.identifiers(Organism.default_code("Hsa")).tsv_options
+    stream = datafile_test('identifiers').open 
+    dumper = TSV::Dumper.new datafile_test('identifiers').tsv_options
     dumper.init
 
     assert_raise ProcessFailed do

data/test/rbbt/tsv/test_change_id.rb

@@ -47,4 +47,14 @@ aa xx
     @f1.identifiers = @id
     assert @f1.change_key("X").include? "x"
   end
+
+  def test_translate_key
+    @f1.identifiers = @id
+    assert TSV.translate(@f1, @f1.key_field, "X", :persist => false).include? "x"
+  end
+
+  def test_translate_key_persist
+    @f1.identifiers = @id
+    assert TSV.translate(@f1, @f1.key_field, "X", :persist => true).include? "x"
+  end
 end

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

@@ -5,7 +5,7 @@ class TestRModel < Test::Unit::TestCase
   def model
   end
 
-  def _test_fit
+  def test_fit
     data = TSV.setup({}, :key_field => "Dose", :fields => ["Response"], :type => :single)
     10.times do 
       x = rand(10)
@@ -20,29 +20,28 @@ class TestRModel < Test::Unit::TestCase
     x = 5
     y = 10 + 3 * x 
     input = TSV.setup({"new 1" => [x]}, :key_field => "Code", :fields => ["Dose"], :type => :single)
-    puts model.predict(input).to_s
     pred = model.predict(input)["new 1"]["Prediction"].to_f
     assert pred > y and pred < y + 4
   end
 
-  def _test_add_fit
+  def test_add_fit
     tsv = TSV.open datafile_test('dose_response'), :type => :list
     tsv = tsv.slice(["Dose", "Response"])
 
-    result = tsv.R <<-EOF, :R_debug => true
+    result = tsv.R <<-EOF, :R_method => :shell
 library(drc, quietly=T)
 library(txtplot)
 data = rbbt.model.add_fit(data, Response ~ Dose, method=drm, classes='numeric', fct=LL.4(),na.action=na.omit)
 txtplot(data$Dose, data$Response)
 txtplot(data$Dose, data$Prediction)
     EOF
-    ppp result
+    assert result.fields.include? "Prediction"
   end
 
-  def _test_add_inpute
+  def test_add_inpute
     tsv = TSV.open datafile_test('dose_response'), :type => :list
 
-    result = tsv.R <<-EOF, :R_debug => true
+    result = tsv.R <<-EOF, :R_method => :eval
 library(drc, quietly=T)
 data = rbbt.model.inpute(data, CI ~ Dose, method=drm, classes='numeric', fct=LL.4(), na.action=na.exclude)
     EOF
@@ -76,14 +75,14 @@ data = rbbt.model.inpute(data, CI ~ Dose, method=drm, classes='numeric', fct=LL.
     rppa = rppa.slice([antibody,"Compound", "Dose"])
     rppa.rename_field antibody, "RPPA"
 
-    model = R::Model.new "viability", "Effect ~ Dose * Compound", "Compound" => :factor
+    model = R::Model.new "viability", "Effect ~ Dose", "Compound" => :factor
 
-    model.fit(viability.select("Compound"){|c| ! c.include? "-"}, 'drm', :fct => ":LL.4()")
+    model.fit(viability.select("Compound"){|c| ! c.include? "-"}, 'lm')
 
     rppa = model.predict(rppa, "Prediction")
 
     plot_script = "plot<-ggplot(data=data) + geom_point(aes(x=RPPA, y=Prediction, color=Compound));"
 
-    puts R::SVG.ggplotSVG rppa, plot_script, 7, 7, :R_method => :eval 
+    R::SVG.ggplotSVG rppa, plot_script, 7, 7, :R_method => :eval 
   end
 end

data/test/rbbt/util/test_misc.rb

@@ -265,7 +265,7 @@ eum fugiat quo voluptas nulla pariatur?"
     time_spent = Time.new - time
 
     assert time_spent >= t * sleep_time
-    assert time_spent <= t * 1.2 * sleep_time
+    assert time_spent <= t * 1.5 * sleep_time
     assert_equal (0..t-1).to_a.collect{|i| "LINE #{ i }".reverse}, lines1
     assert_equal (0..t-1).to_a.collect{|i| "LINE #{ i }".downcase}, lines2
   end

data/test/test_helper.rb

@@ -27,7 +27,10 @@ class Test::Unit::TestCase
     #end
   end
 
-  def datafile_test(file)
+  def self.datafile_test(file)
     Path.setup(File.join(File.dirname(__FILE__), 'data', file.to_s))
   end
+  def datafile_test(file)
+    Test::Unit::TestCase.datafile_test(file)
+  end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.14.33
+  version: 5.14.34
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-10-07 00:00:00.000000000 Z
+date: 2014-10-13 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -142,11 +142,19 @@ files:
 - lib/rbbt/annotations/annotated_array.rb
 - lib/rbbt/annotations/util.rb
 - lib/rbbt/association.rb
+- lib/rbbt/association/database.rb
 - lib/rbbt/association/index.rb
 - lib/rbbt/association/item.rb
+- lib/rbbt/association/open.rb
+- lib/rbbt/association/util.rb
 - lib/rbbt/entity.rb
+- lib/rbbt/entity/identifiers.rb
 - lib/rbbt/fix_width_table.rb
 - lib/rbbt/knowledge_base.rb
+- lib/rbbt/knowledge_base/entity.rb
+- lib/rbbt/knowledge_base/query.rb
+- lib/rbbt/knowledge_base/registry.rb
+- lib/rbbt/knowledge_base/syndicate.rb
 - lib/rbbt/monitor.rb
 - lib/rbbt/packed_index.rb
 - lib/rbbt/persist.rb
@@ -306,8 +314,15 @@ files:
 - share/rbbt_commands/workflow/task
 - share/unicorn.rb
 - test/rbbt/annotations/test_util.rb
+- test/rbbt/association/test_database.rb
 - test/rbbt/association/test_index.rb
 - test/rbbt/association/test_item.rb
+- test/rbbt/association/test_open.rb
+- test/rbbt/association/test_util.rb
+- test/rbbt/entity/test_identifiers.rb
+- test/rbbt/knowledge_base/test_entity.rb
+- test/rbbt/knowledge_base/test_query.rb
+- test/rbbt/knowledge_base/test_registry.rb
 - test/rbbt/persist/test_tsv.rb
 - test/rbbt/persist/tsv/test_cdb.rb
 - test/rbbt/persist/tsv/test_kyotocabinet.rb
@@ -425,13 +440,20 @@ test_files:
 - test/rbbt/util/R/test_model.rb
 - test/rbbt/util/R/test_eval.rb
 - test/rbbt/test_packed_index.rb
+- test/rbbt/entity/test_identifiers.rb
 - test/rbbt/test_association.rb
+- test/rbbt/knowledge_base/test_registry.rb
+- test/rbbt/knowledge_base/test_entity.rb
+- test/rbbt/knowledge_base/test_query.rb
 - test/rbbt/test_resource.rb
 - test/rbbt/test_entity.rb
 - test/rbbt/test_knowledge_base.rb
 - test/rbbt/annotations/test_util.rb
 - test/rbbt/association/test_index.rb
 - test/rbbt/association/test_item.rb
+- test/rbbt/association/test_open.rb
+- test/rbbt/association/test_util.rb
+- test/rbbt/association/test_database.rb
 - test/rbbt/test_tsv.rb
 - test/rbbt/workflow/test_task.rb
 - test/rbbt/workflow/test_step.rb