diff options
Diffstat (limited to 'r-util.rb')
| -rw-r--r-- | r-util.rb | 222 |
1 files changed, 222 insertions, 0 deletions
diff --git a/r-util.rb b/r-util.rb new file mode 100644 index 0000000..77f68fa --- /dev/null +++ b/r-util.rb @@ -0,0 +1,222 @@ +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) + pred_feature = @@hamster.features.keys[0] + fminer = File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc") + hamster_features_uri = OpenTox::RestClientWrapper.post(fminer, + {:dataset_uri=>@@hamster.uri,:prediction_feature=>pred_feature,:subjectid=>@@subjectid}).to_s + @@hamster_features = OpenTox::Dataset.find(hamster_features_uri,@@subjectid) + @@resources = [@@hamster.uri, hamster_features_uri] + end + + def global_teardown + @@rutil.quit_r + if DELETE + @@resources.each do |uri| + OpenTox::RestClientWrapper.delete(uri,{:subjectid=>@@subjectid}) + end + else + puts "Resources "+@@resources.to_yaml + end + OpenTox::Authorization.logout(@@subjectid) if defined?(@@signout) + 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" + dataframe = @@rutil.dataset_to_dataframe(@@hamster,"NA",@@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(@@hamster,dataset_conv) + dataset_equal(@@hamster,dataset_conv_reloaded) + + feats = @@hamster_features.features.keys[0..(@@hamster_features.features.keys.size/2)] + dataframe = @@rutil.dataset_to_dataframe(@@hamster_features,"NA",@@subjectid,feats) + dataset_conv = @@rutil.dataframe_to_dataset(dataframe,@@subjectid) + dataset_conv_reloaded = OpenTox::Dataset.find(dataset_conv.uri,@@subjectid) + @@resources << dataset_conv.uri + [dataset_conv, dataset_conv_reloaded].each do |d| + assert_equal d.compounds.sort,@@hamster_features.compounds.sort + assert_equal d.features.keys.sort,feats.sort + d.compounds.each do |c| + d.features.keys.each do |f| + if @@hamster_features.data_entries[c]==nil || @@hamster_features.data_entries[c][f]==nil + assert d.data_entries[c]==nil || d.data_entries[c][f]==nil + else + assert_not_nil d.data_entries[c] + assert_equal @@hamster_features.data_entries[c][f],d.data_entries[c][f] + end + end + end + end + + dataframe = @@rutil.dataset_to_dataframe(@@hamster_features,"NA",@@subjectid) + @@rutil.r.eval "#{dataframe} <- #{dataframe}[2:10,10:20]" + dataset_conv = @@rutil.dataframe_to_dataset(dataframe,@@subjectid) + dataset_conv_reloaded = OpenTox::Dataset.find(dataset_conv.uri,@@subjectid) + @@resources << dataset_conv.uri + [dataset_conv,dataset_conv_reloaded].each do |d| + assert_equal d.compounds.size,9 + d.compounds.size.times do |i| + assert_equal d.compounds[i],@@hamster_features.compounds[i+1] + end + assert_equal d.features.size,11 + d.compounds.each do |c| + d.features.keys.each do |f| + if @@hamster_features.data_entries[c]==nil || @@hamster_features.data_entries[c][f]==nil + assert d.data_entries[c]==nil || d.data_entries[c][f]==nil + else + assert_not_nil d.data_entries[c] + assert_equal @@hamster_features.data_entries[c][f],d.data_entries[c][f] + end + end + end + end + 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] } + data_combined = OpenTox::Dataset.merge(@@hamster,@@hamster_features,{},@@subjectid) + res = @@rutil.stratified_split(data_combined,0,@@split_ratio,@@subjectid,1) + @@resources += [ 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| + next if fast_embedding==false and !@@rutil.package_installed?("smacof") + 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", nil, fast_embedding, @@subjectid) + @@rutil.feature_value_plot([stratified_file], split[:split1].uri, split[:split2].uri, + "five percent stratified", "rest", nil, 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 |