diff options
-rw-r--r-- | all.rb | 1 | ||||
-rw-r--r-- | dataset.rb | 34 | ||||
-rw-r--r-- | r-util.rb | 179 | ||||
-rw-r--r-- | test-util.rb | 36 |
4 files changed, 218 insertions, 32 deletions
@@ -13,3 +13,4 @@ require './lazar.rb' require './validation.rb' require './toxcreate.rb' require './transform.rb' +require './r-util.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 |