From 8c6c59980bc82dc2177147f2fe34adf8bfbc1539 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Mon, 24 Aug 2015 12:17:07 +0200
Subject: Model::Prediction with tests, initial indexes

---
 lib/compound.rb        |  2 ++
 lib/crossvalidation.rb |  1 +
 lib/feature.rb         |  1 +
 lib/lazar.rb           |  7 +++----
 lib/model.rb           | 13 +++++++++++--
 5 files changed, 18 insertions(+), 6 deletions(-)

(limited to 'lib')

diff --git a/lib/compound.rb b/lib/compound.rb
index c0d6536..fa57aff 100644
--- a/lib/compound.rb
+++ b/lib/compound.rb
@@ -22,6 +22,8 @@ module OpenTox
     field :fp4, type: Array
     field :fp4_size, type: Integer
 
+    index({smiles: 1}, {unique: true})
+
     # Overwrites standard Mongoid method to create fingerprints before database insertion
     def self.find_or_create_by params
       compound = self.find_or_initialize_by params
diff --git a/lib/crossvalidation.rb b/lib/crossvalidation.rb
index d0ad324..5af75bf 100644
--- a/lib/crossvalidation.rb
+++ b/lib/crossvalidation.rb
@@ -8,6 +8,7 @@ module OpenTox
     field :nr_unpredicted, type: Integer
     field :predictions, type: Array
     field :finished_at, type: Time 
+    #belongs_to :prediction
 
     def time
       finished_at - created_at
diff --git a/lib/feature.rb b/lib/feature.rb
index b2bc1f5..22b2846 100644
--- a/lib/feature.rb
+++ b/lib/feature.rb
@@ -29,6 +29,7 @@ module OpenTox
   # Feature for SMARTS fragments
   class Smarts < NominalFeature
     field :smarts, type: String 
+    index "smarts" => 1
     def self.from_smarts smarts
       self.find_or_create_by :smarts => smarts
     end
diff --git a/lib/lazar.rb b/lib/lazar.rb
index 174fb2c..d0128b7 100644
--- a/lib/lazar.rb
+++ b/lib/lazar.rb
@@ -15,20 +15,19 @@ require "base64"
 ENV["MONGOID_ENV"] ||= "development"
 # TODO remove config files, change default via ENV or directly in Mongoid class
 Mongoid.load!("#{File.expand_path(File.join(File.dirname(__FILE__),'..','mongoid.yml'))}")
-# TODO get Mongo::Client from Mongoid
-$mongo = Mongo::Client.new('mongodb://127.0.0.1:27017/opentox')
-# TODO same for GridFS
+$mongo = Mongoid.default_client
+#$mongo = Mongo::Client.new('mongodb://127.0.0.1:27017/opentox')
 $gridfs = $mongo.database.fs
 
 # R setup
 R = Rserve::Connection.new
 
 # Logger setup
+STDOUT.sync = true # for redirection, etc see http://stackoverflow.com/questions/8549443/why-doesnt-logger-output-to-stdout-get-redirected-to-files
 $logger = Logger.new STDOUT # STDERR did not work on my development machine (CH)
 $logger.level = Logger::DEBUG
 Mongo::Logger.logger = $logger
 Mongo::Logger.level = Logger::WARN 
-#Mongoid.logger = $logger
 
 # Require sub-Repositories
 require_relative '../libfminer/libbbrc/bbrc' # include before openbabel
diff --git a/lib/model.rb b/lib/model.rb
index bf8c549..185d70f 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -19,6 +19,8 @@ module OpenTox
       # prediction feature
       field :prediction_feature_id, type: BSON::ObjectId
 
+      #belongs_to :prediction
+
       attr_accessor :prediction_dataset
       attr_accessor :training_dataset
 
@@ -156,11 +158,10 @@ module OpenTox
 
     end
 
-    class PredictionModel
+    class Prediction
       include OpenTox
       include Mongoid::Document
       include Mongoid::Timestamps
-      store_in collection: "models"
 
       # TODO field Validations
       field :endpoint, type: String
@@ -169,6 +170,14 @@ module OpenTox
       field :unit, type: String
       field :model_id, type: BSON::ObjectId
       field :crossvalidation_id, type: BSON::ObjectId
+
+      def predict object
+        Model::Lazar.find(model_id).predict object
+      end
+
+      def crossvalidation
+        CrossValidation.find crossvalidation_id
+      end
     end
 
   end
-- 
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