warnings fixed, cleanup

1 files changed, 27 insertions, 18 deletions

diff --git a/test/use_cases.rb b/test/use_cases.rb
index 4e072d8..4842a18 100644
--- a/test/use_cases.rb
+++ b/test/use_cases.rb
@@ -3,41 +3,50 @@ require_relative "setup.rb"
 class UseCasesTest < MiniTest::Test
 
   def test_PA
-    #kazius = Dataset.from_sdf_file "#{DATA_DIR}/cas_4337.sdf"
-    #hansen = Dataset.from_csv_file "#{DATA_DIR}/hansen.csv"
-    #efsa = Dataset.from_csv_file "#{DATA_DIR}/efsa.csv"
-    #datasets = [kazius,hansen,efsa]
-    #map = {"1" => "mutagen", "0" => "nonmutagen"}
+    # TODO add assertions
+    skip "This test ist very time consuming, enable on demand."
+    kazius = Dataset.from_sdf_file "#{DATA_DIR}/cas_4337.sdf"
+    hansen = Dataset.from_csv_file "#{DATA_DIR}/hansen.csv"
+    efsa = Dataset.from_csv_file "#{DATA_DIR}/efsa.csv"
+    datasets = [kazius,hansen,efsa]
+    map = {"1" => "mutagen", "0" => "nonmutagen"}
     #p "merging"
-    #training_dataset = Dataset.merge datasets: datasets, features: datasets.collect{|d| d.bioactivity_features.first}, value_maps: [nil,map,map], keep_original_features: false, remove_duplicates: true
-    #assert_equal 8281, training_dataset.compounds.size
+    training_dataset = Dataset.merge datasets: datasets, features: datasets.collect{|d| d.bioactivity_features.first}, value_maps: [nil,map,map], keep_original_features: false, remove_duplicates: true
+    assert_equal 8281, training_dataset.compounds.size
     #p training_dataset.features.size
     #p training_dataset.id
     #training_dataset = Dataset.find('5bd8ac8fca62695d767fca6b')
     #training_dataset = Dataset.find('5bd8bbadca62695f69e7a33b')
     #puts training_dataset.to_csv
-    p "create model_validation"
-    #model_validation = Model::Validation.from_dataset training_dataset: training_dataset, prediction_feature: training_dataset.merged_features.first, species: "Salmonella typhimurium", endpoint: "Mutagenicity"
+    #p "create model_validation"
+    model_validation = Model::Validation.from_dataset training_dataset: training_dataset, prediction_feature: training_dataset.merged_features.first, species: "Salmonella typhimurium", endpoint: "Mutagenicity"
     #p model_validation.id
     #model_validation = Model::Validation.find '5bd8df47ca6269604590ab38'
+    #p model_validation.crossvalidations.first.predictions.select{|cid,p| !p["warnings"].empty?}
     #p "predict"
-    #pa = Dataset.from_sdf_file "#{DATA_DIR}/PA.sdf"
-    #prediction_dataset = model_validation.predict pa
+    pa = Dataset.from_sdf_file "#{DATA_DIR}/PA.sdf"
+    prediction_dataset = model_validation.predict pa
     #p prediction_dataset.id
-    prediction_dataset = Dataset.find('5bd98b88ca6269609aab79f4')
-    puts prediction_dataset.to_csv
+    #prediction_dataset = Dataset.find('5bd98b88ca6269609aab79f4')
+    #puts prediction_dataset.to_csv
   end
 
   def test_tox21
+    # TODO add assertions
+    skip "This test ist very time consuming, enable on demand."
     training_dataset = Dataset.from_pubchem_aid 743122
-    p training_dataset.id
+    #p training_dataset.id
     #'5bd9a1dbca626969d97fb421'
-    File.open("AID743122.csv","w+"){|f| f.puts training_dataset.to_csv}
-    model = Model::Lazar.create training_dataset: training_dataset
-    p model.id
+    #File.open("AID743122.csv","w+"){|f| f.puts training_dataset.to_csv}
+    #model = Model::Lazar.create training_dataset: training_dataset
+    #p model.id
     #p Model::Lazar.find('5bd9a70bca626969d97fc9df')
     model_validation = Model::Validation.from_dataset training_dataset: training_dataset, prediction_feature: training_dataset.bioactivity_features.first, species: "Human HG2L7.5c1 cell line", endpoint: "aryl hydrocarbon receptor (AhR) signaling pathway activation"
-    p model_validation.id
+    #model_validation = Model::Validation.find '5bd9b210ca62696be39ab74d'
+    #model_validation.crossvalidations.each do |cv|
+      #p cv
+    #end
+    #p model_validation.crossvalidations.first.predictions.select{|cid,p| !p["warnings"].empty?}
   end
 
   def test_public_models