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Diffstat (limited to 'test/dataset.rb')
| -rw-r--r-- | test/dataset.rb | 199 |
1 files changed, 199 insertions, 0 deletions
diff --git a/test/dataset.rb b/test/dataset.rb new file mode 100644 index 0000000..b3e1403 --- /dev/null +++ b/test/dataset.rb @@ -0,0 +1,199 @@ +# TODO; check compound/data_entry sequences with missing and duplicated values + +require_relative "setup.rb" + +class DatasetTest < MiniTest::Test + + def test_all + d1 = Dataset.new + d1.save + datasets = Dataset.all + assert_equal Dataset, datasets.first.class + d1.delete + end + + def test_create_empty + d = Dataset.new + assert_equal Dataset, d.class + refute_nil d.id + assert_kind_of BSON::ObjectId, d.id + end + + def test_client_create + d = Dataset.new + assert_equal Dataset, d.class + d.name = "Create dataset test" + + # features not set + # << operator was removed for efficiency reasons (CH) + #assert_raises BadRequestError do + # d << [Compound.from_smiles("c1ccccc1NN"), 1,2] + #end + + # add data entries + d.features = ["test1", "test2"].collect do |title| + f = Feature.new + f.name = title + f.numeric = true + f.save + f + end + + # wrong feature size + # << operator was removed for efficiency reasons (CH) + #assert_raises BadRequestError do + # d << [Compound.from_smiles("c1ccccc1NN"), 1,2,3] + #end + + # manual low-level insertions without consistency checks for runtime efficiency + data_entries = [] + d.compound_ids << Compound.from_smiles("c1ccccc1NN").id + data_entries << [1,2] + d.compound_ids << Compound.from_smiles("CC(C)N").id + data_entries << [4,5] + d.compound_ids << Compound.from_smiles("C1C(C)CCCC1").id + data_entries << [6,7] + d.data_entries = data_entries + assert_equal 3, d.compounds.size + assert_equal 2, d.features.size + assert_equal [[1,2],[4,5],[6,7]], d.data_entries + d.save_all + # check if dataset has been saved correctly + new_dataset = Dataset.find d.id + assert_equal 3, new_dataset.compounds.size + assert_equal 2, new_dataset.features.size + assert_equal [[1,2],[4,5],[6,7]], new_dataset.data_entries + d.delete + assert_raises Mongoid::Errors::DocumentNotFound do + Dataset.find d.id + end + assert_raises Mongoid::Errors::DocumentNotFound do + Dataset.find new_dataset.id + end + end + + def test_dataset_accessors + d = Dataset.from_csv_file "#{DATA_DIR}/multicolumn.csv" + # create empty dataset + new_dataset = Dataset.find d.id + # get metadata + assert_match "multicolumn.csv", new_dataset.source + assert_equal "multicolumn.csv", new_dataset.title + # get features + assert_equal 6, new_dataset.features.size + assert_equal 7, new_dataset.compounds.size + assert_equal ["1", nil, "false", nil, nil, 1.0], new_dataset.data_entries.last + d.delete + end + + def test_create_from_file + d = Dataset.from_csv_file File.join(DATA_DIR,"EPAFHM.mini.csv") + assert_equal Dataset, d.class + refute_nil d.warnings + assert_match "EPAFHM.mini.csv", d.source + assert_equal "EPAFHM.mini.csv", d.name + d.delete + #assert_equal false, URI.accessible?(d.uri) + end + + def test_create_from_file_with_wrong_smiles_compound_entries + d = Dataset.from_csv_file File.join(DATA_DIR,"wrong_dataset.csv") + refute_nil d.warnings + assert_match /2|3|4|5|6|7|8/, d.warnings.join + d.delete + end + + def test_multicolumn_csv + d = Dataset.from_csv_file "#{DATA_DIR}/multicolumn.csv" + refute_nil d.warnings + assert d.warnings.grep(/Duplicate compound/) + assert d.warnings.grep(/3, 5/) + assert_equal 6, d.features.size + assert_equal 7, d.compounds.size + assert_equal 5, d.compounds.collect{|c| c.inchi}.uniq.size + assert_equal [["1", "1", "true", "true", "test", 1.1], ["1", "2", "false", "7.5", "test", 0.24], ["1", "3", "true", "5", "test", 3578.239], ["0", "4", "false", "false", "test", -2.35], ["1", "2", "true", "4", "test_2", 1], ["1", "2", "false", "false", "test", -1.5], ["1", nil, "false", nil, nil, 1.0]], d.data_entries + assert_equal "c1cc[nH]c1,1,,false,,,1.0", d.to_csv.split("\n")[7] + csv = CSV.parse(d.to_csv) + original_csv = CSV.read("#{DATA_DIR}/multicolumn.csv") + csv.shift + original_csv.shift + csv.each_with_index do |row,i| + compound = Compound.from_smiles row.shift + original_compound = Compound.from_smiles original_csv[i].shift + assert_equal original_compound.inchi, compound.inchi + row.each_with_index do |v,j| + if v.numeric? + assert_equal original_csv[i][j].strip.to_f, row[j].to_f + else + assert_equal original_csv[i][j].strip, row[j].to_s + end + end + end + d.delete + end + + def test_from_csv + d = Dataset.from_csv_file "#{DATA_DIR}/hamster_carcinogenicity.csv" + assert_equal Dataset, d.class + assert_equal 1, d.features.size + assert_equal 85, d.compounds.size + assert_equal 85, d.data_entries.size + csv = CSV.read("#{DATA_DIR}/hamster_carcinogenicity.csv") + csv.shift + assert_equal csv.collect{|r| r[1]}, d.data_entries.flatten + d.delete + #assert_equal false, URI.accessible?(d.uri) + end + + def test_from_csv_classification + ["int", "float", "string"].each do |mode| + d = Dataset.from_csv_file "#{DATA_DIR}/hamster_carcinogenicity.mini.bool_#{mode}.csv" + csv = CSV.read("#{DATA_DIR}/hamster_carcinogenicity.mini.bool_#{mode}.csv") + csv.shift + entries = d.data_entries.flatten + csv.each_with_index do |r, i| + assert_equal r[1].to_s, entries[i] + end + d.delete + end + end + + def test_from_csv2 + File.open("#{DATA_DIR}/temp_test.csv", "w+") { |file| file.write("SMILES,Hamster\nCC=O,true\n ,true\nO=C(N),true") } + dataset = Dataset.from_csv_file "#{DATA_DIR}/temp_test.csv" + assert_equal "Cannot parse SMILES compound ' ' at position 3, all entries are ignored.", dataset.warnings.join + File.delete "#{DATA_DIR}/temp_test.csv" + dataset.features.each{|f| feature = Feature.find f.id; feature.delete} + dataset.delete + end + + def test_same_feature + datasets = [] + features = [] + 2.times do |i| + d = Dataset.from_csv_file "#{DATA_DIR}/hamster_carcinogenicity.mini.csv" + features << d.features.first + assert features[0].id==features[-1].id,"re-upload should find old feature, but created new one" + datasets << d + end + datasets.each{|d| d.delete} + end + + def test_create_from_file + d = Dataset.from_csv_file File.join(DATA_DIR,"EPAFHM.mini.csv") + assert_equal Dataset, d.class + refute_nil d.warnings + assert_match /row 13/, d.warnings.join + assert_match "EPAFHM.mini.csv", d.source + assert_equal 1, d.features.size + feature = d.features.first + assert_kind_of NumericBioAssay, feature + assert_equal 0.0113, d.data_entries[0][0] + assert_equal 0.00323, d.data_entries[5][0] + d2 = Dataset.find d.id + assert_equal 0.0113, d2.data_entries[0][0] + assert_equal 0.00323, d2.data_entries[5][0] + end + +end + |