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require_relative "setup.rb"
class DatasetLongTest < MiniTest::Test
def test_01_upload_epafhm
f = File.join DATA_DIR, "EPAFHM.csv"
d = OpenTox::Dataset.from_csv_file f
csv = CSV.read f
assert_equal csv.size-1, d.compounds.size
assert_equal csv.first.size-1, d.features.size
assert_equal csv.size-1, d.data_entries.size
d.delete
end
=begin
# TODO catch OpenBabel segfaults and identify/remove cause
def test_02_upload_multicell
duplicates = [
"http://localhost:8082/compound/InChI=1S/C6HCl5O/c7-1-2(8)4(10)6(12)5(11)3(1)9/h12H",
"http://localhost:8082/compound/InChI=1S/C12H8Cl6O/c13-8-9(14)11(16)5-3-1-2(6-7(3)19-6)4(5)10(8,15)12(11,17)18/h2-7H,1H2",
"http://localhost:8082/compound/InChI=1S/C2HCl3/c3-1-2(4)5/h1H",
"http://localhost:8082/compound/InChI=1S/C4H5Cl/c1-3-4(2)5/h3H,1-2H2",
"http://localhost:8082/compound/InChI=1S/C4H7Cl/c1-4(2)3-5/h1,3H2,2H3",
"http://localhost:8082/compound/InChI=1S/C8H14O4/c1-5-4-8(11-6(2)9)12-7(3)10-5/h5,7-8H,4H2,1-3H3",
"http://localhost:8082/compound/InChI=1S/C19H30O5/c1-3-5-7-20-8-9-21-10-11-22-14-17-13-19-18(23-15-24-19)12-16(17)6-4-2/h12-13H,3-11,14-15H2,1-2H3",
]
errors = ['O=P(H)(OC)OC', 'C=CCNN.HCl' ]
f = File.join DATA_DIR, "multi_cell_call.csv"
d = OpenTox::Dataset.from_csv_file f
csv = CSV.read f
assert_equal true, d.features.first.nominal
assert_nil d["index"]
assert_equal csv.size-1-errors.size, d.compounds.size
assert_equal csv.first.size-1, d.features.size
assert_equal csv.size-1-errors.size, d.data_entries.size
p d.warnings
(duplicates+errors).each do |uri|
assert d.warnings.grep %r{#{uri}}
end
d.delete
end
=end
def test_03_upload_isscan
f = File.join DATA_DIR, "ISSCAN-multi.csv"
d = OpenTox::Dataset.from_csv_file f
csv = CSV.read f
assert_equal csv.size-1, d.compounds.size
assert_equal csv.first.size-1, d.features.size
assert_equal csv.size-1, d.data_entries.size
d.delete
#assert_equal false, URI.accessible?(d.uri)
end
def test_04_simultanous_upload
threads = []
3.times do |t|
threads << Thread.new(t) do |up|
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
end
end
threads.each {|aThread| aThread.join}
end
def test_05_upload_kazius
f = File.join DATA_DIR, "kazius.csv"
d = OpenTox::Dataset.from_csv_file f
csv = CSV.read f
assert_equal csv.size-1, d.compounds.size
assert_equal csv.first.size-1, d.features.size
assert_equal csv.size-1, d.data_entries.size
# TODO: check if warning is correct:
# Duplicate compound InChI=1S/C5H4N4S/c10-5-3-4(7-1-6-3)8-2-9-5/h1-2H,(H2,6,7,8,9,10) at rows 1357, 2235
#assert_empty d.warnings
# 493 COC1=C(C=C(C(=C1)Cl)OC)Cl,1
c = d.compounds[491]
assert_equal c.smiles, "COc1cc(c(cc1Cl)OC)Cl"
assert_equal d[c.id,d.features.first.id], 1
d.delete
end
def test_upload_feature_dataset
t = Time.now
f = File.join DATA_DIR, "rat_feature_dataset.csv"
d = Dataset.from_csv_file f
assert_equal 458, d.features.size
d.save
p "Upload: #{Time.now-t}"
d2 = Dataset.find d.id
t = Time.now
assert_equal d.features.size, d2.features.size
csv = CSV.read f
csv.shift # remove header
assert_equal csv.size, d2.compounds.size
assert_equal csv.first.size-1, d2.features.size
d2.compounds.each_with_index do |compound,i|
row = csv[i]
row.shift # remove compound
assert_equal row, d2.data_entries[i]
end
p "Dowload: #{Time.now-t}"
d2.delete
assert_raises Mongoid::Errors::DocumentNotFound do
Dataset.find d.id
end
end
end
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