require_relative "setup.rb"

class UseCasesTest < MiniTest::Test

  def test_PA
    # 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
    #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 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
    #p prediction_dataset.id
    #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
    #'5bd9a1dbca626969d97fb421'
    #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"
    #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
    Download.mutagenicity
    exit
    #skip
    # TODO clean mongo
    # PubChem Classification
    [
      {
        :aid => 1205,
        :species => "Rodents",
        :endpoint => "Carcinogenicity",
        :qmrf => {:group => "QMRF 4.12. Carcinogenicity", :name => "OECD 451 Carcinogenicity Studies"}
      },{
        :aid => 1208,
        :species => "Rat",
        :endpoint => "Carcinogenicity",
        :qmrf => {:group => "QMRF 4.12. Carcinogenicity", :name => "OECD 451 Carcinogenicity Studies"}
      },{
        :aid => 1199,
        :species => "Mouse",
        :endpoint => "Carcinogenicity",
        :qmrf => {:group => "QMRF 4.12. Carcinogenicity", :name => "OECD 451 Carcinogenicity Studies"}
      }
    ].each do |assay|
      Download.pubchem_classification aid: assay[:aid], species: assay[:species], endpoint: assay[:endpoint], active: "carcinogen", inactive: "non-carcinogen", qmrf: assay[:qmrf]
    end
    

=begin
    # Mutagenicity
    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"}
    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
    # rename merged feature
    training_dataset.merged_features.first.name = "Mutagenicity"
    training_dataset.merged_features.first.save
    Model::Validation.from_dataset training_dataset: training_dataset, prediction_feature: training_dataset.merged_features.first, species: "Salmonella typhimurium", endpoint: "Mutagenicity"
    
    # Blood Brain Barrier Penetration
    bbb = Dataset.from_csv_file "#{DATA_DIR}/bbb.csv"
    Model::Validation.from_dataset training_dataset: bbb, prediction_feature: bbb.bioactivity_features.first, species: "Human", endpoint: "Blood Brain Barrier Penetration"

    # PubChem Regression
    # TODO transformations
    [
      {
        :aid => 1195,
        :species => "Human",
        :endpoint => "Maximum Recommended Daily Dose"
      },{
        :aid => 1208,
        :species => "Rat (TD50)",
        :endpoint => "Carcinogenicity"
      },{
        :aid => 1199,
        :species => "Mouse (TD50)",
        :endpoint => "Carcinogenicity"
      },{
        :aid => 1188,
        :species => "Fathead minnow",
        :endpoint => "Acute Toxicity"
      }
    ].each do |assay|
      Model::Validation.from_pubchem_aid aid: assay[:aid], species: assay[;species], endpoint: assay[:endpoint], regression:true
    end

    # daphnia
    daphnia = Dataset.from_csv_file "#{DATA_DIR}/daphnia.csv"
    Model::Validation.from_dataset training_dataset: daphnia, prediction_feature: daphnia.bioactivity_features.first, species: "Daphnia magna", endpoint: "Acute toxicity"

    # LOAEL
    loael = Dataset.from_csv_file "#{DATA_DIR}/loael.csv"
    Model::Validation.from_dataset training_dataset: loael, prediction_feature: loael.bioactivity_features.first, species: "Rat", endpoint: "Lowest observed adverse effect level (LOAEL)"
=end

=begin
      # 1204  estrogen receptor
      # 1259408, # GENE-TOX
      # 1159563 HepG2 cytotoxicity assay
      # 588209 hepatotoxicity
      # 1259333 cytotoxicity
      # 1159569 HepG2 cytotoxicity counterscreen Measured in Cell-Based System Using Plate Reader - 2153-03_Inhibitor_Dose_DryPowder_Activity
      # 2122 HTS Counterscreen for Detection of Compound Cytotoxicity in MIN6 Cells
      # 116724 Acute toxicity determined after intravenal administration in mice
      # 1148549 Toxicity in po dosed mouse assessed as mortality after 7 days
=end

  end
end