diff options
Diffstat (limited to 'dataset.rb')
| -rw-r--r-- | dataset.rb | 81 |
1 files changed, 48 insertions, 33 deletions
@@ -2,9 +2,11 @@ require 'rubygems' require 'opentox-ruby' require 'test/unit' require 'validate-owl' +require 'test-util' class DatasetTest < Test::Unit::TestCase - + include TestUtil + def setup @datasets = { @@regression_training_dataset.uri => nil, @@ -27,8 +29,13 @@ class DatasetTest < Test::Unit::TestCase #@new_dataset.delete end -=begin -=end +# def test_get_pc +# ds_uri = OpenTox::RestClientWrapper.post(CONFIG[:services]["opentox-dataset"], {:file => File.new("data/EPAFHM.csv")} ,{:accept => "text/uri-list", :subjectid => @@subjectid}).to_s.chomp +# puts "DS: #{ds_uri}" +# fds_uri = OpenTox::Algorithm.pc_descriptors( { :dataset_uri => ds_uri, :pc_type => "constitutional" } ) +# puts "FDS: #{fds_uri}" +# end + def test_save_external @dataset = OpenTox::Dataset.find "http://apps.ideaconsult.net:8080/ambit2/dataset/2698" @@ -158,7 +165,7 @@ class DatasetTest < Test::Unit::TestCase @dataset.load_all @@subjectid csv = @dataset.to_csv.split("\n") assert_equal csv.size, data[:nr_compounds]+1 if data - assert_equal csv.first.split(", ").size, data[:nr_dataset_features]+1 if data + assert_equal csv.first.split(",").size, data[:nr_dataset_features]+1 if data end end @@ -219,39 +226,47 @@ class DatasetTest < Test::Unit::TestCase end end -=begin -=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] + + def test_merge() + #upload + dataset1 = OpenTox::Dataset.create_from_csv_file(File.new("data/hamster_carcinogenicity.csv").path, @@subjectid) + dataset2 = OpenTox::Dataset.create_from_csv_file(File.new("data/multi_cell_call.csv").path, @@subjectid) + #merge1 + title = "test merge" + dataset_merge1 = OpenTox::Dataset.merge(dataset1, dataset2, { DC.title => title,DC.creator => "testsuite"}, @@subjectid ) + dataset_reloaded1 = OpenTox::Dataset.find(dataset_merge1.uri, @@subjectid) + #test1 + [dataset_merge1, dataset_reloaded1].each do |d| + assert_equal d.metadata[DC.title],title + assert_equal d.features.size,(dataset1.features.size+dataset2.features.size) + assert_equal d.compounds.size,(dataset1.compounds+dataset2.compounds).uniq.size + [dataset1, dataset2].each do |d_i| + d_i.compounds.each{|c| assert d.compounds.include?(c)} + d_i.features.keys.each{|f| assert d.features.keys.include?(f)} + d_i.features.keys.each do |f| + assert_equal d_i.features[f],d.features[f] + d_i.compounds do |c| + assert_equal d_i.data_entries[c][f],d.data_entries[c][f] + end + end 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 + #merge2 + compounds1 = dataset1.compounds[0..dataset1.compounds.size/2] + features1 = [] + dataset_merge2 = OpenTox::Dataset.merge(dataset1, dataset2, {}, @@subjectid, features1, nil, compounds1 ) + dataset_reloaded2 = OpenTox::Dataset.find(dataset_merge2.uri, @@subjectid) + #test2 + [dataset_merge2, dataset_reloaded2].each do |d| + assert_equal d.features.size,dataset2.features.size + assert_equal d.compounds.size,(compounds1+dataset2.compounds).uniq.size + end + #cleanup + [dataset_merge1, dataset_merge2, dataset1, dataset2].each do |d| + OpenTox::RestClientWrapper.delete(d.uri,{:subjectid => @@subjectid}) end end - + def validate(data) assert_kind_of OpenTox::Dataset, @dataset assert_equal @dataset.data_entries.size, data[:nr_data_entries] if data |