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Diffstat (limited to 'test/dataset-long.rb')
| -rw-r--r-- | test/dataset-long.rb | 114 |
1 files changed, 0 insertions, 114 deletions
diff --git a/test/dataset-long.rb b/test/dataset-long.rb deleted file mode 100644 index 49b61df..0000000 --- a/test/dataset-long.rb +++ /dev/null @@ -1,114 +0,0 @@ -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 - assert_empty d.warnings - # 493 COC1=C(C=C(C(=C1)Cl)OC)Cl,1 - c = d.compounds[491] - assert_equal c.smiles, "COc1cc(Cl)c(cc1Cl)OC" - assert_equal d.data_entries[491][0], "1" - d.delete - end - - def test_upload_feature_dataset - skip - 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_empty d2.warnings - 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_nil Dataset.find d.id - end - -end |