descriptor tests working

2 files changed, 26 insertions, 27 deletions

diff --git a/test/compound.rb b/test/compound.rb
index 70271fc..86930b6 100644
--- a/test/compound.rb
+++ b/test/compound.rb
@@ -68,4 +68,10 @@ class CompoundTest < MiniTest::Test
     assert_equal "CHEMBL581676", c.chemblid
   end
 
+  def test_sdf_storage
+    c = OpenTox::Compound.from_smiles "CC(=O)CC(C)C#N"
+    c.sdf
+    assert !c.sdf_id.nil?
+  end
+
 end
diff --git a/test/descriptor.rb b/test/descriptor.rb
index 7ed0abd..e5b64e0 100644
--- a/test/descriptor.rb
+++ b/test/descriptor.rb
@@ -21,11 +21,11 @@ class DescriptorTest < MiniTest::Test
   def test_smarts
     c = OpenTox::Compound.from_smiles "N=C=C1CCC(=F=FO)C1"
     result = OpenTox::Algorithm::Descriptor.smarts_match c, "FF"
-    assert_equal [[1]], result
+    assert_equal [1], result
     smarts = ["CC", "C", "C=C", "CO", "FF", "C1CCCC1", "NN"]
     result = OpenTox::Algorithm::Descriptor.smarts_match c, smarts
-    assert_equal [[1, 1, 1, 0, 1, 1, 0]], result
-    smarts_count = [[10, 6, 2, 0, 2, 10, 0]]
+    assert_equal [1, 1, 1, 0, 1, 1, 0], result
+    smarts_count = [10, 6, 2, 0, 2, 10, 0]
     result = OpenTox::Algorithm::Descriptor.smarts_count c, smarts
     assert_equal smarts_count, result
   end
@@ -33,57 +33,50 @@ class DescriptorTest < MiniTest::Test
   def test_compound_openbabel_single
     c = OpenTox::Compound.from_smiles "CC(=O)CC(C)C#N"
     result = OpenTox::Algorithm::Descriptor.physchem c, ["Openbabel.logP"]
-    assert_equal 1, result[0].size
-    assert_equal 1.12518, result[0][0]
+    assert_equal [1.12518], result
   end
 
   def test_compound_cdk_single
     c = OpenTox::Compound.from_smiles "c1ccccc1"
     result = OpenTox::Algorithm::Descriptor.physchem c, ["Cdk.AtomCount"]
-    assert_equal 12, result[c]["Cdk.AtomCount.nAtom"]
+    assert_equal [12], result
     c = OpenTox::Compound.from_smiles "CC(=O)CC(C)C#N"
     result = OpenTox::Algorithm::Descriptor.physchem c, ["Cdk.AtomCount"]
-    assert_equal 17, result[c]["Cdk.AtomCount.nAtom"]
+    assert_equal [17], result
     result = OpenTox::Algorithm::Descriptor.physchem c, ["Cdk.CarbonTypes"]
     c_types = {"Cdk.CarbonTypes.C1SP1"=>1, "Cdk.CarbonTypes.C2SP1"=>0, "Cdk.CarbonTypes.C1SP2"=>0, "Cdk.CarbonTypes.C2SP2"=>1, "Cdk.CarbonTypes.C3SP2"=>0, "Cdk.CarbonTypes.C1SP3"=>2, "Cdk.CarbonTypes.C2SP3"=>1, "Cdk.CarbonTypes.C3SP3"=>1, "Cdk.CarbonTypes.C4SP3"=>0}
-    assert_equal c_types, result[c]
+    assert_equal [1, 0, 0, 1, 0, 2, 1, 1, 0], result
   end
 
   def test_compound_joelib_single
     c = OpenTox::Compound.from_smiles "CC(=O)CC(C)C#N"
     result = OpenTox::Algorithm::Descriptor.physchem c, ["Joelib.LogP"]
-    assert_equal 2.65908, result[c]["Joelib.LogP"]
+    assert_equal [2.65908], result
   end
 
   def test_compound_all
     c = OpenTox::Compound.from_smiles "CC(=O)CC(C)C#N"
     result = OpenTox::Algorithm::Descriptor.physchem c
-    assert_equal 332, result[c].size
-    {
-      "Cdk.LongestAliphaticChain.nAtomLAC"=>5,
-      "Joelib.count.HeavyBonds"=>7,
-      "Openbabel.MR"=>30.905,
-      #"Cdk.LengthOverBreadthDescriptor.LOBMAX"=>1.5379006098352144,
-      #"Joelib.GeometricalShapeCoefficient"=>5.210533887682899,
-    }.each do |d,v|
-      assert_equal v, result[c][d]
-    end
+    assert_equal 332, result.size
+    assert_equal 30.8723, result[2]
+    assert_equal 1.12518, result[328]
   end
 
   def test_compound_descriptor_parameters
     c = OpenTox::Compound.from_smiles "CC(=O)CC(C)C#N"
-    result = OpenTox::Algorithm::Descriptor.physchem c, [ "Openbabel.logP", "Cdk.AtomCount", "Cdk.CarbonTypes", "Joelib.LogP" ]
-    assert_equal 12, result[c].size
-    expect = {"Openbabel.logP"=>1.12518, "Cdk.AtomCount.nAtom"=>17, "Cdk.CarbonTypes.C1SP1"=>1, "Cdk.CarbonTypes.C2SP1"=>0, "Cdk.CarbonTypes.C1SP2"=>0, "Cdk.CarbonTypes.C2SP2"=>1, "Cdk.CarbonTypes.C3SP2"=>0, "Cdk.CarbonTypes.C1SP3"=>2, "Cdk.CarbonTypes.C2SP3"=>1, "Cdk.CarbonTypes.C3SP3"=>1, "Cdk.CarbonTypes.C4SP3"=>0, "Joelib.LogP"=>2.65908}
-    assert_equal expect, result[c]
+    result = OpenTox::Algorithm::Descriptor.physchem c, [ "Openbabel.logP", "Cdk.AtomCount", "Cdk.CarbonTypes", "Joelib.LogP" ], true
+    assert_equal 12, result.last.size
+    assert_equal ["Openbabel.logP", "Cdk.AtomCount.nAtom", "Cdk.CarbonTypes.C1SP1", "Cdk.CarbonTypes.C2SP1", "Cdk.CarbonTypes.C1SP2", "Cdk.CarbonTypes.C2SP2", "Cdk.CarbonTypes.C3SP2", "Cdk.CarbonTypes.C1SP3", "Cdk.CarbonTypes.C2SP3", "Cdk.CarbonTypes.C3SP3", "Cdk.CarbonTypes.C4SP3", "Joelib.LogP"], result.first
+    assert_equal [1.12518, 17, 1, 0, 0, 1, 0, 2, 1, 1, 0, 2.65908], result.last
   end
 
   def test_dataset_descriptor_parameters
-    dataset = OpenTox::Dataset.new 
-    dataset.upload File.join(DATA_DIR,"hamster_carcinogenicity.mini.csv")
+    dataset = OpenTox::Dataset.from_csv_file File.join(DATA_DIR,"hamster_carcinogenicity.mini.csv")
     d = OpenTox::Algorithm::Descriptor.physchem dataset, [ "Openbabel.logP", "Cdk.AtomCount", "Cdk.CarbonTypes", "Joelib.LogP" ]
-    assert_equal dataset.compounds.size, d.keys.size
-    assert_equal 12, d.first.last.size
+    assert_kind_of Dataset, d
+    assert_equal dataset.compounds, d.compounds
+    assert_equal dataset.compounds.size, d.data_entries.size
+    assert_equal 12, d.data_entries.first.size
   end
 
 end