add r-util tests

4 files changed, 218 insertions, 32 deletions

diff --git a/all.rb b/all.rb
index c3ded9a..b209f57 100644
--- a/all.rb
+++ b/all.rb
@@ -13,3 +13,4 @@ require './lazar.rb'
 require './validation.rb'
 require './toxcreate.rb'
 require './transform.rb'
+require './r-util.rb'
diff --git a/dataset.rb b/dataset.rb
index 5483ee4..30d59e6 100644
--- a/dataset.rb
+++ b/dataset.rb
@@ -4,7 +4,8 @@ require 'test/unit'
 require 'validate-owl'
 
 class DatasetTest < Test::Unit::TestCase
-
+  include TestUtil
+  
   def setup
     @datasets = {
       @@regression_training_dataset.uri => nil,
@@ -261,38 +262,7 @@ class DatasetTest < Test::Unit::TestCase
       OpenTox::RestClientWrapper.delete(d.uri,{:subjectid => @@subjectid})
     end
   end
-
   
-  def dataset_equal(d,d2)
-    assert d.compounds.sort==d2.compounds.sort,
-      d.compounds.sort.to_yaml+"\n!=\n"+d2.compounds.sort.to_yaml
-    assert d.features.keys.size==d2.features.keys.size,
-      d.features.keys.to_yaml+"\n!=\n"+d2.features.keys.to_yaml
-    assert d.features.keys.sort==d2.features.keys.sort,
-      d.features.keys.sort.to_yaml+"\n!=\n"+d2.features.keys.sort.to_yaml
-    d.compounds.each do |c|
-      d.features.keys.each do |f|
-        assert_array_about_equal d.data_entries[c][f],d2.data_entries[c][f]
-      end
-    end
-  end
-  
-  def assert_array_about_equal(a,a2)
-    if (a!=nil || a2!=nil)
-      raise "no arrays #{a.class} #{a2.class}" unless a.is_a?(Array) and a2.is_a?(Array)
-      assert a.size==a2.size
-      a.sort! 
-      a2.sort!
-      a.size.times do |i|
-        if (a[i].is_a?(Float) and a2[i].is_a?(Float))
-          assert (a[i]-a2[i]).abs<0.0000001,"#{a[i]}(#{a[i].class}) != #{a2[i]}(#{a2[i].class})"
-        else
-          assert a[i]==a2[i],"#{a[i]}(#{a[i].class}) != #{a2[i]}(#{a2[i].class})"
-        end
-      end
-    end
-  end
-
   def validate(data)
     assert_kind_of OpenTox::Dataset, @dataset
     assert_equal @dataset.data_entries.size, data[:nr_data_entries] if data
diff --git a/r-util.rb b/r-util.rb
new file mode 100644
index 0000000..713d0b1
--- /dev/null
+++ b/r-util.rb
@@ -0,0 +1,179 @@
+require 'rubygems'
+require 'opentox-ruby'
+require 'test/unit'
+require 'validate-owl'
+require 'test-util'
+
+DELETE = true
+
+class RUtilTest < Test::Unit::TestCase
+  include TestUtil
+
+  def global_setup
+    unless defined?(@@subjectid) 
+      @@subjectid = OpenTox::Authorization.authenticate("guest","guest")
+      @@signout = true
+    end 
+    @@rutil = OpenTox::RUtil.new
+    @@hamster = OpenTox::Dataset.create_from_csv_file(File.new("data/hamster_carcinogenicity.csv").path, @@subjectid)
+    @@resources = [@@hamster.uri]
+  end
+
+  def global_teardown
+    OpenTox::Authorization.logout(@@subjectid) if defined?(@@signout)
+    @@rutil.quit_r
+    if DELETE
+      @@resources.each do |uri|
+        OpenTox::RestClientWrapper.delete(uri,{:subjectid=>@@subjectid})
+      end
+    else
+      puts "Resources "+@@resources.to_yaml
+    end
+  end
+  
+  def pre_files(files)
+    files.each{|f| File.delete(f) if File.exist?(f)}
+  end
+  
+  def post_files(files)
+    files.each{|f| assert File.exist?(f)}
+    if DELETE
+      files.each{|f| File.delete(f) if File.exist?(f)}
+    else
+      puts "Plotted to "+files.to_yaml
+    end
+  end
+
+  def test_paired_ttest
+    puts "ttest"
+    x = Array.new(1000,0).collect{|e| rand()}
+    y = Array.new(1000,0).collect{|e| rand()}
+    res = @@rutil.paired_ttest(x,y)
+    puts "x >> y ? #{res}"
+    assert_equal res,0
+    y = Array.new(1000,0).collect{|e| rand()-0.1}
+    res = @@rutil.paired_ttest(x,y)
+    puts "x >> y ? #{res}"
+    assert res>0
+  end
+  
+  def test_boxplot
+    puts "boxplot"
+    files = ["/tmp/box.svg","/tmp/box.png"]
+    pre_files(files)
+    data = [ 
+      [ :method, [4,4,5,5,4,3,2] ],
+      [ :method2, [1,2,3,4,5,4,6] ], 
+      [ :asdf, [9,1,8,0,7,1,6] ] ]
+    @@rutil.boxplot(files, data, "comparison1" )
+    post_files(files)
+  end
+  
+  def test_double_hist_plot
+    puts "double_hist_plot"
+    hist_num_log = "/tmp/hist_num_log.svg"
+    hist_num = "/tmp/hist_num.svg"
+    hist_cat = "/tmp/hist_cat.svg"
+    pre_files [hist_num_log,hist_num,hist_cat]
+    data1 = Array.new(1000,0).collect{|x| rand()*rand()}
+    data2 = Array.new(1000,0).collect{|x| rand()*rand()*rand()}
+    @@rutil.double_hist_plot([hist_num_log], data1, data2, true, true )
+    @@rutil.double_hist_plot([hist_num], data1, data2, true, false )
+    data1 = "a,a,a,a,b,b,b,b,b,b,b,b,b,b,c,c,c".split(",")
+    data2 = "a,a,a,a,a,a,b,b,b,b,b,b,c,c,c,c,c,d,d,d,d,d".split(",")
+    @@rutil.double_hist_plot([hist_cat], data1, data2, false )
+    post_files [hist_num_log,hist_num,hist_cat]
+  end
+
+  def test_dataset_to_dataframe
+    puts "dataset_to_dataframe"
+    dataset = @@hamster
+    dataframe = @@rutil.dataset_to_dataframe(dataset,0,@@subjectid)
+    dataset_conv = @@rutil.dataframe_to_dataset(dataframe,@@subjectid)
+    dataset_conv_reloaded = OpenTox::Dataset.find(dataset_conv.uri,@@subjectid)
+    @@resources << dataset_conv.uri
+    dataset_equal(dataset,dataset_conv)
+    dataset_equal(dataset,dataset_conv_reloaded)
+  end
+
+  def stratified_split
+    unless defined?@@strat
+      @@split_ratio = 0.05
+      @@split_has_duplicates = false #hamster has no duplicates
+#     res = @@rutil.stratified_split(@@hamster,0,@@split_ratio,1)
+#     @@resources += [ res[0].uri, res[1].uri ]
+#     @@strat = { :data => @@hamster, :split1 => res[0], :split2 => res[1] }
+      pred_feature = @@hamster.features.keys[0]
+      fminer = File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc")
+      feature_dataset_uri = OpenTox::RestClientWrapper.post(fminer,
+        {:dataset_uri=>@@hamster.uri,:prediction_feature=>pred_feature,:subjectid=>@@subjectid}).to_s
+      feature_dataset = OpenTox::Dataset.find(feature_dataset_uri,@@subjectid)
+      data_combined = OpenTox::Dataset.merge(@@hamster,feature_dataset,{},@@subjectid)
+      res = @@rutil.stratified_split(data_combined,0,@@split_ratio,@@subjectid,1)
+      @@resources += [ feature_dataset_uri, data_combined.uri, res[0].uri, res[1].uri ]
+      @@strat = {:data => data_combined, :split1 => res[0], :split2 => res[1] }
+    end
+    @@strat
+  end
+       
+  def test_stratified_split
+    puts "test_stratified_split"
+    split = stratified_split
+    size = split[:data].compounds.size
+    size1 = split[:split1].compounds.size
+    size2 = split[:split2].compounds.size
+    assert_equal size,(split[:split1].compounds+split[:split2].compounds).uniq.size
+    unless @@split_has_duplicates
+      assert_equal (@@split_ratio*size).round,size1,
+        "Dataset #{size} should be split into #{(@@split_ratio*size).round}/#{size-(@@split_ratio*size).round}"+
+        " (exact: #{@@split_ratio*size}), instead: #{size1}/#{size2}"
+    end
+    split[:data].compounds.each do |c|
+      include1 = split[:split1].compounds.include?(c)
+      include2 = split[:split2].compounds.include?(c)
+      unless @@split_has_duplicates
+        assert(((include1 and !include2) or (!include1 and include2)))
+      else
+        assert((include1 or include2))
+      end
+    end
+  end
+
+  def test_feature_value_plot
+    puts "feature_value_plot"
+    split = stratified_split
+    data = split[:data]
+    dataset1 = data.split( data.compounds[0..4], data.features.keys, {}, @@subjectid)
+    dataset2 = data.split( data.compounds[5..-1], data.features.keys, {}, @@subjectid)
+    @@resources += [dataset1.uri, dataset2.uri]
+    files = []
+    #plot
+    [true,false].each do |fast_embedding|
+      random_file = "/tmp/feature_value_plot_random_fast#{fast_embedding}.svg"
+      stratified_file = "/tmp/feature_value_plot_stratified_fast#{fast_embedding}.svg"
+      pre_files [random_file, stratified_file]
+      @@rutil.feature_value_plot([random_file], dataset1.uri, dataset2.uri,
+         "first five", "rest", fast_embedding, @@subjectid)
+      @@rutil.feature_value_plot([stratified_file], split[:split1].uri, split[:split2].uri,
+          "five percent stratified", "rest", fast_embedding, @@subjectid)
+      files += [random_file, stratified_file]
+    end
+    #cleanup
+    post_files files
+  end  
+
+  # hack to have a global_setup and global_teardown 
+  def teardown
+    if((@@expected_test_count-=1) == 0)
+      global_teardown
+    end
+  end
+  
+  def setup
+    unless defined?@@expected_test_count
+      @@expected_test_count = (self.class.instance_methods.reject{|method| method[0..3] != 'test'}).length
+      global_setup
+    end
+  end
+  
+end
diff --git a/test-util.rb b/test-util.rb
new file mode 100644
index 0000000..2620656
--- /dev/null
+++ b/test-util.rb
@@ -0,0 +1,36 @@
+require 'rubygems'
+require 'test/unit'
+
+module TestUtil
+  
+  def dataset_equal(d,d2)
+    assert d.compounds.sort==d2.compounds.sort,
+      d.compounds.sort.to_yaml+"\n!=\n"+d2.compounds.sort.to_yaml
+    assert d.features.keys.size==d2.features.keys.size,
+      d.features.keys.to_yaml+"\n!=\n"+d2.features.keys.to_yaml
+    assert d.features.keys.sort==d2.features.keys.sort,
+      d.features.keys.sort.to_yaml+"\n!=\n"+d2.features.keys.sort.to_yaml
+    d.compounds.each do |c|
+      d.features.keys.each do |f|
+        assert_array_about_equal d.data_entries[c][f],d2.data_entries[c][f]
+      end
+    end
+  end
+  
+  def assert_array_about_equal(a,a2)
+    if (a!=nil || a2!=nil)
+      raise "no arrays #{a.class} #{a2.class}" unless a.is_a?(Array) and a2.is_a?(Array)
+      assert a.size==a2.size
+      a.sort! 
+      a2.sort!
+      a.size.times do |i|
+        if (a[i].is_a?(Float) and a2[i].is_a?(Float))
+          assert (a[i]-a2[i]).abs<0.0000001,"#{a[i]}(#{a[i].class}) != #{a2[i]}(#{a2[i].class})"
+        else
+          assert a[i]==a2[i],"#{a[i]}(#{a[i].class}) != #{a2[i]}(#{a2[i].class})"
+        end
+      end
+    end
+  end
+  
+end
\ No newline at end of file