kazius lazar predictions working

6 files changed, 44 insertions, 58 deletions

diff --git a/test/data_entry.rb b/test/data_entry.rb
index 7c9e49e..c956352 100644
--- a/test/data_entry.rb
+++ b/test/data_entry.rb
@@ -43,10 +43,12 @@ class DataEntryTest < MiniTest::Test
     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 0.0113, d[d.compounds.first, feature]
-    assert_equal 0.00323, DataEntry[d.compounds[5], feature]
     assert_equal 0.00323, d[d.compounds[5], feature]
+    d2 = Dataset.find d.id
+    p d2.data_entries
+    assert_equal 0.0113, d2[d.compounds.first, feature]
+    assert_equal 0.00323, d2[d.compounds[5], feature]
   end
 
   def test_upload_kazius
diff --git a/test/dataset-long.rb b/test/dataset-long.rb
index cba84dd..fbdeeb9 100644
--- a/test/dataset-long.rb
+++ b/test/dataset-long.rb
@@ -12,8 +12,7 @@ class DatasetLongTest < MiniTest::Test
 
   def test_01_upload_epafhm
     f = File.join DATA_DIR, "EPAFHM.csv"
-    d = OpenTox::Dataset.new 
-    d.upload f
+    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
@@ -33,8 +32,7 @@ class DatasetLongTest < MiniTest::Test
     ]
     errors = ['O=P(H)(OC)OC', 'C=CCNN.HCl' ]
     f = File.join DATA_DIR, "multi_cell_call.csv"
-    d = OpenTox::Dataset.new 
-    d.upload f
+    d = OpenTox::Dataset.from_csv_file f 
     csv = CSV.read f
     assert_equal true, d.features.first.nominal
     assert_nil d["index"]
@@ -49,8 +47,7 @@ class DatasetLongTest < MiniTest::Test
 
   def test_03_upload_isscan
     f = File.join DATA_DIR, "ISSCAN-multi.csv"
-    d = OpenTox::Dataset.new 
-    d.upload f
+    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
@@ -63,8 +60,7 @@ class DatasetLongTest < MiniTest::Test
     threads = []
     3.times do |t|
       threads << Thread.new(t) do |up|
-        d = OpenTox::Dataset.new 
-        d.upload "#{DATA_DIR}/hamster_carcinogenicity.csv"
+        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
@@ -81,8 +77,7 @@ class DatasetLongTest < MiniTest::Test
 
   def test_05_upload_kazius
     f = File.join DATA_DIR, "kazius.csv"
-    d = OpenTox::Dataset.new 
-    d.upload f
+    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
@@ -93,8 +88,7 @@ class DatasetLongTest < MiniTest::Test
   def test_06_upload_feature_dataset
     t1 = Time.now
     f = File.join DATA_DIR, "rat_feature_dataset.csv"
-    d = OpenTox::Dataset.new 
-    d.upload f
+    d = OpenTox::Dataset.from_csv_file f 
     t2 = Time.now
     p "Upload: #{t2-t1}"
     d2 = OpenTox::Dataset.find d.id
diff --git a/test/fminer-long.rb b/test/fminer-long.rb
index 187b344..a5027d6 100644
--- a/test/fminer-long.rb
+++ b/test/fminer-long.rb
@@ -7,14 +7,14 @@ class FminerTest < MiniTest::Test
     dataset = OpenTox::Dataset.new 
     #multi_cell_call.csv
     dataset.upload File.join(DATA_DIR,"multi_cell_call.csv")
-    feature_dataset = OpenTox::Algorithm::Fminer.bbrc(:dataset => dataset)#, :min_frequency => 15)
+    feature_dataset = OpenTox::Algorithm::Fminer.bbrc(dataset)#, :min_frequency => 15)
     dataset.delete
     feature_dataset.delete
   end
 
   def test_fminer_isscan
     dataset = OpenTox::Dataset.from_csv_file File.join(DATA_DIR,"ISSCAN-multi.csv")
-    feature_dataset = OpenTox::Algorithm::Fminer.bbrc(:dataset => dataset)#, :min_frequency => 15)
+    feature_dataset = OpenTox::Algorithm::Fminer.bbrc(dataset)#, :min_frequency => 15)
     assert_equal feature_dataset.compounds.size, dataset.compounds.size
     p feature_dataset
     dataset.delete
@@ -23,12 +23,11 @@ class FminerTest < MiniTest::Test
 
   def test_fminer_kazius
     dataset = OpenTox::Dataset.from_csv_file File.join(DATA_DIR,"kazius.csv")
-    feature_dataset = OpenTox::Algorithm::Fminer.bbrc(:dataset => dataset)#, :min_frequency => 50)
-    #feature_dataset = OpenTox::Algorithm::Fminer.bbrc(:dataset => dataset, :min_frequency => 200)
-    #feature_dataset = OpenTox::Algorithm::Fminer.bbrc(:dataset => dataset)#, :min_frequency => 15)
+    # TODO reactivate default settings
+    feature_dataset = OpenTox::Algorithm::Fminer.bbrc(dataset, :min_frequency => 20)
     assert_equal feature_dataset.compounds.size, dataset.compounds.size
-    p feature_dataset.compounds.size
-    p feature_dataset.features.size
+    feature_dataset = Dataset.find feature_dataset.id
+    assert feature_dataset.data_entries.size, dataset.compounds.size
     dataset.delete
     feature_dataset.delete
   end
diff --git a/test/fminer.rb b/test/fminer.rb
index e319b5e..649a78e 100644
--- a/test/fminer.rb
+++ b/test/fminer.rb
@@ -5,29 +5,16 @@ class FminerTest < MiniTest::Test
   def test_fminer_bbrc
     dataset = OpenTox::Dataset.from_csv_file File.join(DATA_DIR,"hamster_carcinogenicity.csv")
     refute_nil dataset.id
-    feature_dataset = OpenTox::Algorithm::Fminer.bbrc :dataset => dataset
+    feature_dataset = OpenTox::Algorithm::Fminer.bbrc dataset
+    feature_dataset = Dataset.find feature_dataset.id
     assert_equal dataset.compounds.size, feature_dataset.compounds.size
     assert_equal 54, feature_dataset.features.size
     assert_equal "C-C-C=C", feature_dataset.features.first.smarts
     compounds = feature_dataset.compounds
     smarts = feature_dataset.features.collect{|f| f.smarts}
     match = OpenTox::Algorithm::Descriptor.smarts_count compounds, smarts
-    p smarts
-    compounds.each_with_index do |c,i|
-      p c.smiles
-      p match[i]
-      p feature_dataset.feature_values(c)
-      smarts.each_with_index do |s,j|
-        #unless match[i][j] == DataEntry.where(:dataset_id => feature_dataset.id, :compound_id => c.id, :feature_id => feature_dataset.features[j]).distinct(:value).first
-          #p c
-          #p s
-          #p feature_dataset.features[j]
-          #p match[i][j]
-          #p DataEntry.where(:dataset_id => feature_dataset.id, :compound_id => c.id, :feature_id => feature_dataset.features[j]).distinct(:value)
-        #end
-
-        #assert_equal match[i][j], feature_dataset[c,feature_dataset.features[j]]
-      end
+    feature_dataset.data_entries.each_with_index do |fingerprint,i|
+      assert_equal match[i], fingerprint
     end
 
     dataset.delete
diff --git a/test/lazar-fminer.rb b/test/lazar-fminer.rb
index 11fef72..6c0ee41 100644
--- a/test/lazar-fminer.rb
+++ b/test/lazar-fminer.rb
@@ -3,18 +3,16 @@ require_relative "setup.rb"
 class LazarFminerTest < MiniTest::Test
 
   def test_lazar_fminer
-    training_dataset = OpenTox::Dataset.from_csv_file File.join(DATA_DIR,"hamster_carcinogenicity.csv")
-    feature_dataset = OpenTox::Algorithm::Fminer.bbrc(:dataset => training_dataset)
-    #p feature_dataset
-    model = OpenTox::Model::Lazar.create training_dataset, feature_dataset
+    training_dataset = Dataset.from_csv_file File.join(DATA_DIR,"hamster_carcinogenicity.csv")
+    feature_dataset = Algorithm::Fminer.bbrc(training_dataset)
+    model = Model::Lazar.create training_dataset, feature_dataset
     #feature_dataset = OpenTox::Dataset.find model.feature_dataset_id
-    p model
     assert_equal training_dataset.compounds.size, feature_dataset.compounds.size
     assert_equal 54, feature_dataset.features.size
-    #feature_dataset.data_entries.each do |e|
-      #assert_equal e.size, feature_dataset.features.size
-    #end
-    assert_equal '[#6&A]-[#6&A]-[#6&A]=[#6&A]', feature_dataset.features.first.smarts
+    feature_dataset.data_entries.each do |e|
+      assert_equal e.size, feature_dataset.features.size
+    end
+    assert_equal 'C-C-C=C', feature_dataset.features.first.smarts
 
     [ {
       :compound => OpenTox::Compound.from_inchi("InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H"),
@@ -34,14 +32,11 @@ class LazarFminerTest < MiniTest::Test
     end
 
     # make a dataset prediction
-    compound_dataset = OpenTox::Dataset.from_sdf File.join(DATA_DIR,"EPAFHM.mini.csv")
-    #assert_equal compound_dataset.uri.uri?, true
+    compound_dataset = OpenTox::Dataset.from_csv_file File.join(DATA_DIR,"EPAFHM.mini.csv")
     prediction = model.predict :dataset => compound_dataset
     assert_equal compound_dataset.compounds, prediction.compounds
-    #prediction = OpenTox::Dataset.new prediction_uri
-    #assert_equal prediction.uri.uri?, true
 
     # cleanup
-    [dataset,model,feature_dataset,compound_dataset].each{|o| o.delete}
+    [training_dataset,model,feature_dataset,compound_dataset].each{|o| o.delete}
   end
 end
diff --git a/test/lazar-long.rb b/test/lazar-long.rb
index 8f59ec3..487a015 100644
--- a/test/lazar-long.rb
+++ b/test/lazar-long.rb
@@ -5,7 +5,7 @@ class LazarExtendedTest < MiniTest::Test
   def test_lazar_bbrc_ham_minfreq
     dataset = OpenTox::MeasuredDataset.new 
     dataset.upload File.join(DATA_DIR,"hamster_carcinogenicity.csv")
-    model = OpenTox::Model::Lazar.create OpenTox::Algorithm::Fminer.bbrc(:dataset => dataset, :min_frequency => 5)
+    model = OpenTox::Model::Lazar.create OpenTox::Algorithm::Fminer.bbrc(dataset, :min_frequency => 5)
     feature_dataset = OpenTox::CalculatedDataset.find model.feature_dataset_id
     assert_equal dataset.compounds.size, feature_dataset.compounds.size
     assert_equal 41, feature_dataset.features.size
@@ -48,13 +48,22 @@ class LazarExtendedTest < MiniTest::Test
   end
 
   def test_lazar_kazius
-    # TODO find a solution for feature datasets > 16M (size limit in mongodb)
-    dataset = OpenTox::MeasuredDataset.from_csv_file File.join(DATA_DIR,"kazius.csv")
-    feature_dataset = OpenTox::Algorithm::Fminer.bbrc(:dataset => dataset, :min_frequency => 100)
+    dataset = Dataset.from_csv_file File.join(DATA_DIR,"kazius.csv")
+    feature_dataset = Algorithm::Fminer.bbrc(dataset, :min_frequency => 100)
     assert_equal feature_dataset.compounds.size, dataset.compounds.size
-    model = OpenTox::Model::Lazar.create feature_dataset
+    model = Model::Lazar.create dataset, feature_dataset
+    #model = Model::Lazar.find('55b8e9c07a78383f6700017e')
     p model.id
-    dataset.delete
+    #prediction_times = []
+    2.times do
+    compound = Compound.from_smiles("Clc1ccccc1NN")
+    prediction = model.predict :compound => compound
+    p prediction.data_entries
+    assert_equal "1", prediction.data_entries.first.first
+    assert_in_delta 0.019858401199860445, prediction.data_entries.first.last, 0.001
+    end
+
+    #dataset.delete
     #feature_dataset.delete
   end