From cdab5069ded9490afe81095059e9a407faf864d9 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Tue, 10 Jan 2017 13:44:43 +0100
Subject: independent_variables stored in GridFS to avoid Mongo database size
 limit problems

---
 lib/compound.rb |  2 --
 lib/model.rb    | 19 +++++++++++++++++--
 test/setup.rb   |  6 +-----
 3 files changed, 18 insertions(+), 9 deletions(-)

diff --git a/lib/compound.rb b/lib/compound.rb
index 8a1143b..1c308d8 100644
--- a/lib/compound.rb
+++ b/lib/compound.rb
@@ -209,7 +209,6 @@ module OpenTox
        update(:svg_id => $gridfs.insert_one(file))
       end
       $gridfs.find_one(_id: self.svg_id).data
-
     end
 
     # Get png image
@@ -223,7 +222,6 @@ module OpenTox
        update(:png_id => $gridfs.insert_one(file))
       end
       Base64.decode64($gridfs.find_one(_id: self.png_id).data)
-
     end
 
     # Get all known compound names. Relies on an external service for name lookups.
diff --git a/lib/model.rb b/lib/model.rb
index 9c4a93f..e5834ae 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -9,6 +9,8 @@ module OpenTox
       include Mongoid::Timestamps
       store_in collection: "models"
 
+      attr_writer :independent_variables # store in GridFS to avoid Mongo database size limit problems
+
       field :name, type: String
       field :creator, type: String, default: __FILE__
       field :algorithms, type: Hash, default:{}
@@ -17,7 +19,7 @@ module OpenTox
       field :prediction_feature_id, type: BSON::ObjectId
       field :dependent_variables, type: Array, default:[]
       field :descriptor_ids, type:Array, default:[]
-      field :independent_variables, type: Array, default:[]
+      field :independent_variables_id, type: BSON::ObjectId
       field :fingerprints, type: Array, default:[]
       field :descriptor_weights, type: Array, default:[]
       field :descriptor_means, type: Array, default:[]
@@ -119,6 +121,7 @@ module OpenTox
         end
 
         descriptor_method = model.algorithms[:descriptors][:method]
+        model.independent_variables = []
         case descriptor_method
         # parse fingerprints
         when "fingerprint"
@@ -179,6 +182,7 @@ module OpenTox
 
       def predict_substance substance
         
+        @independent_variables = Marshal.load $gridfs.find_one(_id: self.independent_variables_id).data
         case algorithms[:similarity][:method]
         when /tanimoto/ # binary features
           similarity_descriptors = substance.fingerprint algorithms[:descriptors][:type]
@@ -234,7 +238,7 @@ module OpenTox
               neighbor_dependent_variables << dependent_variables[i]
               independent_variables.each_with_index do |c,j|
                 neighbor_independent_variables[j] ||= []
-                neighbor_independent_variables[j] << independent_variables[j][i]
+                neighbor_independent_variables[j] << @independent_variables[j][i]
               end
             end
           end
@@ -302,6 +306,17 @@ module OpenTox
 
       end
 
+      def save # store independent_variables in GridFS to avoid Mongo database size limit problems
+        file = Mongo::Grid::File.new(Marshal.dump(@independent_variables), :filename => "#{id}.independent_variables")
+        self.independent_variables_id = $gridfs.insert_one(file)
+        super
+      end
+
+      def independent_variables 
+        @independent_variables ||= Marshal.load $gridfs.find_one(_id: self.independent_variables_id).data
+        @independent_variables
+      end
+
       def training_dataset
         Dataset.find(training_dataset_id)
       end
diff --git a/test/setup.rb b/test/setup.rb
index 63b59fb..40c8ebf 100644
--- a/test/setup.rb
+++ b/test/setup.rb
@@ -6,8 +6,4 @@ include OpenTox
 TEST_DIR ||= File.expand_path(File.dirname(__FILE__))
 DATA_DIR ||= File.join(TEST_DIR,"data")
 training_dataset = Dataset.where(:name => "Protein Corona Fingerprinting Predicts the Cellular Interaction of Gold and Silver Nanoparticles").first
-unless training_dataset
-  Import::Enanomapper.import File.join(File.dirname(__FILE__),"data","enm")
-end
-#$mongo.database.drop
-#$gridfs = $mongo.database.fs
+Import::Enanomapper.import unless training_dataset
-- 
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