From 753fcc204d93d86c76860bee6e2f7d0468c3c940 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Thu, 14 Apr 2016 19:43:24 +0200
Subject: features/toxicities fixed

---
 lib/nanoparticle.rb | 30 +++++++++++++++++++-----------
 1 file changed, 19 insertions(+), 11 deletions(-)

(limited to 'lib/nanoparticle.rb')

diff --git a/lib/nanoparticle.rb b/lib/nanoparticle.rb
index 6e9b0ea..0350363 100644
--- a/lib/nanoparticle.rb
+++ b/lib/nanoparticle.rb
@@ -5,12 +5,10 @@ module OpenTox
 
     field :core, type: String
     field :coating, type: Array, default: []
-
-    field :toxicities, type: Hash, default: {}
-    #field :features, type: Hash, default: {}
     field :bundles, type: Array, default: []
 
-    def predict
+    def nanoparticle_neighbors params
+      Dataset.find(params[:training_dataset_id]).nanoparticles
     end
 
     def add_feature feature, value
@@ -21,22 +19,32 @@ module OpenTox
         toxicities[feature.id.to_s] ||= []
         toxicities[feature.id.to_s] << value
       else
-        $logger.warn "Unknown feature type '#{feature.source}'. Value '#{value}' not inserted."
-        warnings << "Unknown feature type '#{feature.source}'. Value '#{value}' not inserted."
+        warn "Unknown feature type '#{feature.source}'. Value '#{value}' not inserted."
       end
     end
 
     def parse_ambit_value feature, v
+      # TODO: units, mmol/log10 conversion
       if v.keys == ["loValue"]
-        add_feature feature, v["loValue"]
+        #if v["loValue"].numeric?
+          add_feature feature, v["loValue"]
+        #else
+          #warn "'#{v["loValue"]}' is not a numeric value, entry ignored."
+        #end
       elsif v.keys.size == 2 and v["loQualifier"] == "mean"
-        add_feature feature, {:mean => v["loValue"]}
+        #add_feature feature, {:mean => v["loValue"]}
+        add_feature feature, v["loValue"]
+        warn "'#{feature.name}' is a mean value. Original data is not available."
       elsif v.keys.size == 2 and v["loQualifier"] #== ">="
-        add_feature feature, {:min => v["loValue"],:max => Float::INFINITY}
+        #add_feature feature, {:min => v["loValue"],:max => Float::INFINITY}
+        warn "Only min value available for '#{feature.name}', entry ignored"
       elsif v.keys.size == 2 and v["upQualifier"] #== ">="
-        add_feature feature, {:max => v["upValue"],:min => -Float::INFINITY}
+        #add_feature feature, {:max => v["upValue"],:min => -Float::INFINITY}
+        warn "Only max value available for '#{feature.name}', entry ignored"
       elsif v.size == 4 and v["loQualifier"] and v["upQualifier"] 
-        add_feature feature, {:min => v["loValue"],:max => v["upValue"]}
+        #add_feature feature, {:min => v["loValue"],:max => v["upValue"]}
+        add_feature feature, [v["loValue"],v["upValue"]].mean
+        warn "Using mean value of range #{v["loValue"]} - #{v["upValue"]} for '#{feature.name}'. Original data is not available."
       elsif v == {} # do nothing
       else
         $logger.warn "Cannot parse Ambit eNanoMapper value '#{v}' for feature '#{feature.name}'."
-- 
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