50 times faster bbrc setup by eliminating @fminer.add_fminer_data

3 files changed, 39 insertions, 36 deletions

diff --git a/standalone.rb b/standalone.rb
index 907fa2c..5c0897f 100644
--- a/standalone.rb
+++ b/standalone.rb
@@ -1,5 +1,6 @@
 require 'minitest/autorun'
 [
+  "feature",
   "algorithm",
   "compound",
   "dataset-long",
@@ -7,13 +8,13 @@ require 'minitest/autorun'
   "descriptor-long",
   "descriptor",
   "edit_objects",
-  #"error",
+  "error",
   "fminer",
   "lazar-fminer",
   "lazar-long",
 #"lazar-models",
-  #"lazar-physchem-long",
-  #"lazar-physchem-short",
+  "lazar-physchem-long",
+  "lazar-physchem-short",
 #"lazarweb",
   #"task",
   #"validation-long",
diff --git a/test/lazar-fminer.rb b/test/lazar-fminer.rb
index 6c0ee41..04d1704 100644
--- a/test/lazar-fminer.rb
+++ b/test/lazar-fminer.rb
@@ -6,7 +6,6 @@ class LazarFminerTest < MiniTest::Test
     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
     assert_equal training_dataset.compounds.size, feature_dataset.compounds.size
     assert_equal 54, feature_dataset.features.size
     feature_dataset.data_entries.each do |e|
@@ -17,25 +16,33 @@ class LazarFminerTest < MiniTest::Test
     [ {
       :compound => OpenTox::Compound.from_inchi("InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H"),
       :prediction => "false",
-      :confidence => 0.25281385281385277
+      :confidence => 0.25281385281385277,
+      :nr_neighbors => 11
     },{
       :compound => OpenTox::Compound.from_smiles("c1ccccc1NN"),
       :prediction => "false",
-      :confidence => 0.3639589577089577
-    } ].each do |example|
-      prediction_dataset = model.predict :compound => example[:compound]
+      :confidence => 0.3639589577089577,
+      :nr_neighbors => 14
+    }, {
+      :compound => Compound.from_smiles('OCCCCCCCC\C=C/CCCCCCCC'),
+      :prediction => "false",
+      :confidence => 0.5555555555555556,
+      :nr_neighbors => 1
+    }].each do |example|
+      prediction = model.predict example[:compound]
 
-      prediction = prediction_dataset.data_entries.first.first
-      confidence = prediction_dataset.data_entries.first.last
-      assert_equal example[:prediction], prediction
-      assert_equal example[:confidence], confidence
+      assert_equal example[:prediction], prediction[:value]
+      assert_equal example[:confidence], prediction[:confidence]
+      assert_equal example[:nr_neighbors], prediction[:neighbors].size
     end
 
     # make a dataset prediction
     compound_dataset = OpenTox::Dataset.from_csv_file File.join(DATA_DIR,"EPAFHM.mini.csv")
-    prediction = model.predict :dataset => compound_dataset
+    prediction = model.predict compound_dataset
     assert_equal compound_dataset.compounds, prediction.compounds
 
+    assert_match /No neighbors/, prediction.data_entries[7][2]
+    assert_equal "measured", prediction.data_entries[14][1]
     # cleanup
     [training_dataset,model,feature_dataset,compound_dataset].each{|o| o.delete}
   end
diff --git a/test/lazar-long.rb b/test/lazar-long.rb
index 487a015..b69adfa 100644
--- a/test/lazar-long.rb
+++ b/test/lazar-long.rb
@@ -3,30 +3,27 @@ require_relative "setup.rb"
 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, :min_frequency => 5)
-    feature_dataset = OpenTox::CalculatedDataset.find model.feature_dataset_id
+    dataset = OpenTox::Dataset.from_csv_file File.join(DATA_DIR,"hamster_carcinogenicity.csv")
+    model = OpenTox::Model::Lazar.create dataset, OpenTox::Algorithm::Fminer.bbrc(dataset, :min_frequency => 5)
+    feature_dataset = OpenTox::Dataset.find model.feature_dataset_id
     assert_equal dataset.compounds.size, feature_dataset.compounds.size
     assert_equal 41, feature_dataset.features.size
-    assert_equal '[#7&A]-[#6&A]=[#7&A]', feature_dataset.features.first.title
+    assert_equal 'N-C=N', feature_dataset.features.first.smarts
     compound = OpenTox::Compound.from_inchi("InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H")
-    prediction_dataset = model.predict :compound => compound
-    prediction = prediction_dataset.data_entries.first
-    assert_equal "false", prediction.first
-    assert_equal 0.12380952380952381, prediction.last
+    prediction = model.predict compound
+    assert_equal "false", prediction[:value]
+    assert_equal 0.12380952380952381, prediction[:confidence]
     dataset.delete
     model.delete
     feature_dataset.delete
-    prediction_dataset.delete
   end
 
   def test_lazar_bbrc_large_ds
     # TODO fminer crashes with these settings
-    dataset = OpenTox::MeasuredDataset.new 
-    dataset.upload File.join(DATA_DIR,"multi_cell_call_no_dup.csv")
-    feature_dataset = OpenTox::Algorithm::Fminer.bbrc(:dataset => dataset)#, :min_frequency => 15)
-    model = OpenTox::Model::Lazar.create feature_dataset
+    skip "it seems that fminer aborts without further notice"
+    dataset = OpenTox::Dataset.from_csv_file File.join(DATA_DIR,"multi_cell_call_no_dup.csv")
+    feature_dataset = OpenTox::Algorithm::Fminer.bbrc dataset#, :min_frequency => 15)
+    model = OpenTox::Model::Lazar.create dataset, feature_dataset
     model.save
     p model.id
     feature_dataset = OpenTox::CalculatedDataset.find model.feature_dataset_id
@@ -34,7 +31,7 @@ class LazarExtendedTest < MiniTest::Test
     assert_equal 52, feature_dataset.features.size
     assert_equal '[#17&A]-[#6&A]', feature_dataset.features.first.title
     compound = OpenTox::Compound.from_inchi("InChI=1S/C10H9NO2S/c1-8-2-4-9(5-3-8)13-6-10(12)11-7-14/h2-5H,6H2,1H3")
-    prediction_dataset = model.predict :compound => compound
+    prediction_dataset = model.predict compound
     prediction = prediction_dataset.data_entries.first
     assert_in_delta 0.025, prediction[:confidence], 0.001
     #assert_equal 0.025885845574483608, prediction[:confidence]
@@ -56,15 +53,13 @@ class LazarExtendedTest < MiniTest::Test
     p model.id
     #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
+      compound = Compound.from_smiles("Clc1ccccc1NN")
+      prediction = model.predict compound
+      assert_equal "1", prediction[:value]
+      assert_in_delta 0.019858401199860445, prediction[:confidence], 0.001
     end
-
-    #dataset.delete
-    #feature_dataset.delete
+    dataset.delete
+    feature_dataset.delete
   end
 
 end