From f8faf510b4574df1a00fa61a9f0a1681fc2f4857 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Tue, 25 Aug 2015 17:20:55 +0200
Subject: Experiments added

---
 lib/model.rb | 27 +++++++++++++++++----------
 1 file changed, 17 insertions(+), 10 deletions(-)

(limited to 'lib/model.rb')

diff --git a/lib/model.rb b/lib/model.rb
index 185d70f..418ec18 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -2,24 +2,27 @@ module OpenTox
 
   module Model
 
-    class Lazar 
+    class Model
       include OpenTox
       include Mongoid::Document
       include Mongoid::Timestamps
       store_in collection: "models"
 
-      field :title, as: :name, type: String
+      field :name, type: String
       field :creator, type: String, default: __FILE__
       # datasets
       field :training_dataset_id, type: BSON::ObjectId
       # algorithms
       field :prediction_algorithm, type: String
-      field :neighbor_algorithm, type: String
-      field :neighbor_algorithm_parameters, type: Hash
       # prediction feature
       field :prediction_feature_id, type: BSON::ObjectId
+    end
 
-      #belongs_to :prediction
+    class Lazar < Model
+
+      # algorithms
+      field :neighbor_algorithm, type: String
+      field :neighbor_algorithm_parameters, type: Hash
 
       attr_accessor :prediction_dataset
       attr_accessor :training_dataset
@@ -36,7 +39,7 @@ module OpenTox
         prediction_feature.nominal ?  lazar = OpenTox::Model::LazarClassification.new : lazar = OpenTox::Model::LazarRegression.new
         lazar.training_dataset_id = training_dataset.id
         lazar.prediction_feature_id = prediction_feature.id
-        lazar.title = prediction_feature.title 
+        lazar.name = "#{training_dataset.name} #{prediction_feature.name}" 
 
         lazar.save
         lazar
@@ -83,7 +86,7 @@ module OpenTox
             acts.empty? ? nil : n << acts
           end
           neighbors.compact! # remove neighbors without training activities
-          predictions << Algorithm.run(prediction_algorithm, neighbors)
+          predictions << Algorithm.run(prediction_algorithm, compound, neighbors)
         end 
 
         # serialize result
@@ -97,14 +100,14 @@ module OpenTox
         when "OpenTox::Dataset"
           # prepare prediction dataset
           prediction_dataset = LazarPrediction.new(
-            :title => "Lazar prediction for #{prediction_feature.title}",
+            :name => "Lazar prediction for #{prediction_feature.name}",
             :creator =>  __FILE__,
             :prediction_feature_id => prediction_feature.id
 
           )
-          confidence_feature = OpenTox::NumericFeature.find_or_create_by( "title" => "Prediction confidence" )
+          confidence_feature = OpenTox::NumericFeature.find_or_create_by( "name" => "Prediction confidence" )
           # TODO move into warnings field
-          warning_feature = OpenTox::NominalFeature.find_or_create_by("title" => "Warnings")
+          warning_feature = OpenTox::NominalFeature.find_or_create_by("name" => "Warnings")
           prediction_dataset.features = [ prediction_feature, confidence_feature, warning_feature ]
           prediction_dataset.compounds = compounds
           prediction_dataset.data_entries = predictions.collect{|p| [p[:value], p[:confidence], p[:warning]]}
@@ -112,6 +115,10 @@ module OpenTox
           return prediction_dataset
         end
 
+        def training_dataset
+          return Dataset.find(training_dataset_id)
+        end
+
       end
       
       def training_activities
-- 
cgit v1.2.3