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# TODO: check json specification at https://github.com/opentox-api/api-specification/issues/2
require_relative "setup.rb"
class DatasetTest < MiniTest::Test
def test_all
d1 = OpenTox::Dataset.new
d1.save
datasets = OpenTox::Dataset.all
assert_equal OpenTox::Dataset, datasets.first.class
d1.delete
end
def test_create_empty
d = OpenTox::Dataset.new
assert_equal OpenTox::Dataset, d.class
refute_nil d.id
assert_kind_of BSON::ObjectId, d.id
end
def test_client_create
d = OpenTox::Dataset.new
assert_equal OpenTox::Dataset, d.class
d[:title] = "Create dataset test"
# features not set
assert_raises OpenTox::BadRequestError do
d << [OpenTox::Compound.from_smiles("c1ccccc1NN"), 1,2]
end
# add data entries
d.features = ["test1", "test2"].collect do |title|
f = OpenTox::Feature.new
f[:title] = title
f.numeric = true
f.save
f
end
# wrong feature size
assert_raises OpenTox::BadRequestError do
d << [OpenTox::Compound.from_smiles("c1ccccc1NN"), 1,2,3]
end
d << [OpenTox::Compound.from_smiles("c1ccccc1NN"), 1,2]
d << [OpenTox::Compound.from_smiles("CC(C)N"), 4,5]
d << [OpenTox::Compound.from_smiles("C1C(C)CCCC1"), 6,7]
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
# check if dataset has been saved correctly
new_dataset = OpenTox::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
OpenTox::Dataset.find d.id
end
assert_raises Mongoid::Errors::DocumentNotFound do
OpenTox::Dataset.find new_dataset.id
end
end
def test_dataset_accessors
d = OpenTox::Dataset.new
d.upload "#{DATA_DIR}/multicolumn.csv"
# create empty dataset
new_dataset = OpenTox::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 = OpenTox::Dataset.new
d.upload File.join(DATA_DIR,"EPAFHM.mini.csv")
assert_equal OpenTox::Dataset, d.class
refute_nil d["warnings"]
assert_match "EPAFHM.mini.csv", d["source"]
assert_equal "EPAFHM.mini.csv", d.title
d.delete
#assert_equal false, URI.accessible?(d.uri)
end
def test_create_from_file_with_wrong_smiles_compound_entries
d = OpenTox::Dataset.new
d.upload 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 = OpenTox::Dataset.new
d.upload "#{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 = OpenTox::Compound.from_smiles row.shift
original_compound = OpenTox::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 = OpenTox::Dataset.from_csv_file "#{DATA_DIR}/hamster_carcinogenicity.csv"
assert_equal OpenTox::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 = OpenTox::Dataset.new
d.upload "#{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 = OpenTox::Dataset.new
dataset.upload "#{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 = OpenTox::Feature.find f.id; feature.delete}
dataset.delete
end
def test_compound_index_mapping
e = :error
n = nil
c1 = ["F","C","N","O","S","S","S","C"]
c2 = ["F","N","C","O","O","P","C","S"]
res = [ 0 , 2 , 1 , 3 , 3 , n , 7, e ]
# compound_index() assings each compound in c2 to a single compound in c1 (required by validation)
# explanation for each index of the expected mapping result 'res':
# 0: "F" in c2 occurs only once in c1 at the same pos -> 0
# 1: "N" in c2 occurs once in c1 at position 2 -> 2
# 2: "C" in c2 occurs twice in c1 (1,7), assume that ordering is equal -> 1
# 3: "O" in c2 occurs only once in c1 at position 3 (n to 1 mapping possible in direction c2->c1) -> 3
# 4: "O" in c2 occurs only once in c1 at position 3 (n to 1 mapping possible in direction c2->c1) -> 3
# 5: "P" in c2 does not occur in c1 -> nil
# 6: "C" in c2 occurs twice in c1 (1,7), assume that ordering is equal -> 7
# 7: "S" in c2 occurs more than once in c1 (n to 1 mapping not possible in direction c1->c2) -> error
assert_equal c1.size,c2.size
f1 = "/tmp/c1.csv"
f2 = "/tmp/c2.csv"
File.open(f1, "w") { |file| file.write((["SMILES"]+c1).join("\n")) }
File.open(f2, "w") { |file| file.write((["SMILES"]+c2).join("\n")) }
d1 = OpenTox::Dataset.new
d1.upload f1
d2 = OpenTox::Dataset.new
d2.upload f2
assert_equal d1.compounds.size,c1.size
assert_equal d2.compounds.size,c2.size
c1.size.times do |i|
begin
m = d1.compound_index(d2,i)
rescue
m = e
end
assert_equal m,res[i]
end
end
def test_same_feature
datasets = []
features = []
2.times do |i|
d = OpenTox::Dataset.new
d.upload "#{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
end
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