From 23ecfc6fa5ae4913e5cd17b7d58432d1f88d780c Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Mon, 10 Aug 2015 09:48:57 +0200
Subject: transfer to new git project started

---
 test/dataset-long.rb | 116 +++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 116 insertions(+)
 create mode 100644 test/dataset-long.rb

(limited to 'test/dataset-long.rb')

diff --git a/test/dataset-long.rb b/test/dataset-long.rb
new file mode 100644
index 0000000..50ae8fc
--- /dev/null
+++ b/test/dataset-long.rb
@@ -0,0 +1,116 @@
+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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