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# 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_nil Dataset.find d.id
assert_nil Dataset.find new_dataset.id
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", new_dataset.name
# 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 "c1ccc[nH]1,1,,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
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