From d5bf97c2cb999539c56bf59aa1d7d3286745be84 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Wed, 23 Sep 2015 14:51:41 +0200
Subject: validations fixed (all models were executed with default parameters)

---
 test/experiment.rb | 63 ++++++++++++++++++++++++++++++++++++++++++++++++------
 1 file changed, 57 insertions(+), 6 deletions(-)

(limited to 'test/experiment.rb')

diff --git a/test/experiment.rb b/test/experiment.rb
index 4b54768..76a0498 100644
--- a/test/experiment.rb
+++ b/test/experiment.rb
@@ -63,21 +63,26 @@ class ExperimentTest < MiniTest::Test
   end
 
   def test_regression_fingerprints
+=begin
     datasets = [
-      "LOAEL_mmol_corrected_smiles.csv"
+      "EPAFHM.medi.csv",
+      #"LOAEL_mmol_corrected_smiles.csv"
     ]
     min_sims = [0.3,0.7]
-    types = ["FP2","FP3","FP4","MACCS"]
+    #min_sims = [0.7]
+    #types = ["FP2","FP3","FP4","MACCS","mpd"]
+    types = ["mpd","FP3"]
     experiment = Experiment.create(
-      :name => "Fminer vs fingerprint classification for datasets #{datasets}.",
+      :name => "Fingerprint regression with different types for datasets #{datasets}.",
       :dataset_ids => datasets.collect{|d| Dataset.from_csv_file(File.join(DATA_DIR, d)).id},
     )
     types.each do |type|
       min_sims.each do |min_sim|
         experiment.model_settings << {
-          :algorithm => "OpenTox::Model::LazarRegression",
+          :model_algorithm => "OpenTox::Model::LazarRegression",
+          :prediction_algorithm => "OpenTox::Algorithm::Regression.weighted_average",
           :neighbor_algorithm => "fingerprint_neighbors",
-          :neighbor_algorithm_parameter => {
+          :neighbor_algorithm_parameters => {
             :type => type,
             :min_sim => min_sim,
           }
@@ -85,7 +90,53 @@ class ExperimentTest < MiniTest::Test
       end
     end
     experiment.run
-    p experiment.report
+=end
+#=begin
+    experiment = Experiment.find '56029cb92b72ed673d000000'
+#=end
+    p experiment.id
+    experiment.results.each do |dataset,result|
+      result.each do |r|
+        params = Model::Lazar.find(r["model_id"])[:neighbor_algorithm_parameters]
+        RepeatedCrossValidation.find(r["repeated_crossvalidation_id"]).crossvalidations.each do |cv|
+          cv.validation_ids.each do |vid|
+            model_params = Model::Lazar.find(Validation.find(vid).model_id)[:neighbor_algorithm_parameters]
+            assert_equal params[:type], model_params[:type]
+            assert_equal params[:min_sim], model_params[:min_sim]
+            refute_equal params[:training_dataset_id], model_params[:training_dataset_id]
+          end
+        end
+      end
+    end
+    puts experiment.report.to_yaml
+    p experiment.summary
+  end
 
+  def test_mpd_fingerprints
+=begin
+    datasets = [
+      "EPAFHM.medi.csv",
+    ]
+    types = ["FP2","mpd"]
+    experiment = Experiment.create(
+      :name => "FP2 vs mpd fingerprint regression for datasets #{datasets}.",
+      :dataset_ids => datasets.collect{|d| Dataset.from_csv_file(File.join(DATA_DIR, d)).id},
+    )
+    types.each do |type|
+    experiment.model_settings << {
+      :algorithm => "OpenTox::Model::LazarRegression",
+      :neighbor_algorithm => "fingerprint_neighbors",
+      :neighbor_algorithm_parameter => {
+        :type => type,
+        :min_sim => 0.7,
+      }
+    }
+    end
+    experiment.run
+    p experiment.id
+=end
+    experiment = Experiment.find '55ffd0c02b72ed123c000000'
+    p experiment
+    puts experiment.report.to_yaml
   end
 end
-- 
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