From 6e23be652ad90c747aaccf15258bdaa4458185a4 Mon Sep 17 00:00:00 2001
From: "helma@in-silico.ch" <helma@in-silico.ch>
Date: Tue, 13 Nov 2018 14:32:09 +0100
Subject: public dataset download

---
 test/use_cases.rb | 96 ++++---------------------------------------------------
 1 file changed, 7 insertions(+), 89 deletions(-)

(limited to 'test/use_cases.rb')

diff --git a/test/use_cases.rb b/test/use_cases.rb
index ab01269..f39b3e2 100644
--- a/test/use_cases.rb
+++ b/test/use_cases.rb
@@ -49,95 +49,13 @@ class UseCasesTest < MiniTest::Test
     #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
+  def test_download_public_models
+    Download.public_data
+  end
 
+  def test_import_public_models
+    skip
+    Import.public_data
   end
+
 end
-- 
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