1 files changed, 92 insertions, 0 deletions
diff --git a/test/data_entry.rb b/test/data_entry.rb
new file mode 100644
index 0000000..13a2884
--- /dev/null
+++ b/test/data_entry.rb
@@ -0,0 +1,92 @@
+require_relative "setup.rb"
+
+class DataEntryTest < MiniTest::Test
+
+  def test_create
+
+    # add features
+    features = ["test1", "test2"].collect do |title|
+      NumericBioAssay.find_or_create_by( :title => title, :numeric => true)
+    end
+
+    compounds = []
+    input = [
+      ["c1ccccc1NN",1,2],
+      ["CC(C)N",4,5],
+      ["C1C(C)CCCC1",6,7],
+    ]
+    input.each do |row|
+      smi = row.shift
+      compound = Compound.find_or_create_by(:smiles => smi)
+      compounds << compound
+      row.each_with_index do |value,i|
+        DataEntry.find_or_create compound, features[i], value
+      end
+    end
+    
+    assert_equal 3, compounds.size
+    assert_equal 2, features.size
+    input.each_with_index do |row,i|
+      row.each_with_index do |v,j|
+        assert_equal DataEntry[compounds[i],features[j]], input[i][j]
+      end
+    end
+  end
+
+  def test_create_from_file
+    d = OpenTox::Dataset.from_csv_file File.join(DATA_DIR,"EPAFHM.mini.csv")
+    assert_equal OpenTox::Dataset, d.class
+    refute_nil d.warnings
+    assert_match /row 13/, d.warnings.join
+    assert_match "EPAFHM.mini.csv",  d.source
+    assert_equal 1, d.features.size
+    feature = d.features.first
+    assert_kind_of NumericBioAssay, feature
+    assert_match "EPAFHM.mini.csv",  feature.source
+    assert_equal 0.0113, DataEntry[d.compounds.first, feature]
+    assert_equal 0.00323, DataEntry[d.compounds[5], feature]
+  end
+
+  def test_upload_kazius
+    d = OpenTox::Dataset.from_csv_file File.join DATA_DIR, "kazius.csv"
+    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 DataEntry[c,d.features.first], 1
+  end
+
+  def test_upload_feature_dataset
+    t1 = Time.now
+    f = File.join DATA_DIR, "rat_feature_dataset.csv"
+    d = OpenTox::Dataset.from_csv_file f
+    assert_equal 458, d.features.size
+    d.save
+    t2 = Time.now
+    p "Upload: #{t2-t1}"
+    d2 = OpenTox::Dataset.find d.id
+    t3 = Time.now
+    p "Dowload: #{t3-t2}"
+    assert_equal d.features.size, d2.features.size
+    csv = CSV.read f
+    assert_equal csv.size-1, d2.compounds.size
+    assert_equal csv.first.size-1, d2.features.size
+    # asserting complete ds
+    3.times do
+      cid = rand(d.compounds.size)
+      3.times do
+        fid = rand(d.features.size)
+        # TODO data access is slow
+        assert_equal csv[cid+1][fid+1].to_i, DataEntry[d2.compounds[cid],d2.features[fid]]
+      end
+    end
+    #assert_equal csv.size-1, d.data_entries.size
+    d2.delete
+    assert_raises Mongoid::Errors::DocumentNotFound do
+      Dataset.find d.id
+    end
+  end
+
+
+end
+