Added transformation for measured acts.

3 files changed, 72 insertions, 31 deletions

diff --git a/application.rb b/application.rb
index 34a11e3..57503db 100644
--- a/application.rb
+++ b/application.rb
@@ -527,12 +527,35 @@ post '/predict/?' do # post chemical name to model
     else
       @value_map = nil
     end
+
     prediction_dataset = OpenTox::LazarPrediction.find(prediction_dataset_uri, @subjectid)
     if prediction_dataset.metadata[OT.hasSource].match(/dataset/)
-      @predictions << {
-        :title => model.name,
-        :measured_activities => prediction_dataset.measured_activities(@compound)
-      }
+      if model.name.downcase.include? "ptd50"
+        mw = calc_mw(@compound.uri)
+	td50 = ptd50_to_td50(prediction_dataset.measured_activities(@compound).first.to_f, mw)
+	prediction_trans = "TD50: #{td50}"
+      elsif model.name.downcase.include? "loael"
+        if model.name.downcase.include? "mol"
+          mw = calc_mw(@compound.uri)
+          mg = logmmol_to_mg(prediction_dataset.measured_activities(@compound).first.to_f, mw)
+          prediction_trans = "mg/kg bw/day: #{mg}"
+        elsif model.name.downcase.include? "mg"
+          mg = logmg_to_mg(prediction_dataset.measured_activities(@compound).first.to_f)
+          prediction_trans = "mg/kg bw/day: #{mg}"
+        end
+      end
+      if prediction_trans.nil?
+        @predictions << {
+          :title => model.name,
+          :measured_activities => prediction_dataset.measured_activities(@compound)
+      	}
+      else
+        @predictions << {
+          :title => model.name,
+          :measured_activities => prediction_dataset.measured_activities(@compound),
+          :prediction_transformed => prediction_trans
+        }
+      end
     else
       predicted_feature = prediction_dataset.metadata[OT.dependentVariables]
       prediction = OpenTox::Feature.find(predicted_feature, @subjectid)
@@ -540,42 +563,24 @@ post '/predict/?' do # post chemical name to model
         @predictions << {
           :title => model.name,
           :error => prediction.metadata[OT.error]
-          }
+        }
       elsif prediction_dataset.value(@compound).nil?
         @predictions << {
           :title => model.name,
           :error => "Not enough similar compounds in training dataset."
-          }
+        }
       else
         if model.name.downcase.include? "ptd50"
-          ds = OpenTox::Dataset.new()
-          ds.save(@subjectid)
-          ds.add_compound(@compound.uri)
-          ds.save(@subjectid)
-          mw_algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"pc/MW")
-          mw_uri = OpenTox::RestClientWrapper.post(mw_algorithm_uri, {:dataset_uri=>ds.uri})
-          ds.delete(@subjectid)
-          mw_ds = OpenTox::Dataset.find(mw_uri, @subjectid)
-          mw = mw_ds.data_entries[@compound.uri][mw_uri.to_s + "/feature/MW"].first
-          mw_ds.delete(@subjectid)
-          td50 = (((10**(-1.0*prediction_dataset.value(@compound)))*(mw.to_f*1000))*1000).round / 1000.0
+          mw = calc_mw(@compound.uri)
+          td50 = ptd50_to_td50(prediction_dataset.value(@compound), mw)
           prediction_trans = "TD50: #{td50}"
         elsif model.name.downcase.include? "loael"
           if model.name.downcase.include? "mol"
-            ds = OpenTox::Dataset.new()
-            ds.save(@subjectid)
-            ds.add_compound(@compound.uri)
-            ds.save(@subjectid)
-            mw_algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"pc/MW")
-            mw_uri = OpenTox::RestClientWrapper.post(mw_algorithm_uri, {:dataset_uri=>ds.uri})
-            ds.delete(@subjectid)
-            mw_ds = OpenTox::Dataset.find(mw_uri, @subjectid)
-            mw = mw_ds.data_entries[@compound.uri][mw_uri.to_s + "/feature/MW"].first
-            mw_ds.delete(@subjectid)
-            mg = (((10**(-1.0*prediction_dataset.value(@compound)))*(mw.to_f*1000))*1000).round / 1000.0
+            mw = calc_mw(@compound.uri)
+            mg = logmmol_to_mg(prediction_dataset.value(@compound), mw)
             prediction_trans = "mg/kg bw/day: #{mg}"
           elsif model.name.downcase.include? "mg" 
-            mg = ((10**prediction_dataset.value(@compound))*1000).round / 1000.0
+            mg = logmg_to_mg(prediction_dataset.value(@compound))
             prediction_trans = "mg/kg bw/day: #{mg}"
           end
         end
@@ -585,7 +590,7 @@ post '/predict/?' do # post chemical name to model
             :model_uri => model.uri,
             :prediction => prediction_dataset.value(@compound),
             :confidence => prediction_dataset.confidence(@compound)
-            }
+          }
         else
           @predictions << {
             :title => model.name,
@@ -593,7 +598,7 @@ post '/predict/?' do # post chemical name to model
             :prediction => prediction_dataset.value(@compound),
             :confidence => prediction_dataset.confidence(@compound),
             :prediction_transformed => prediction_trans
-            }
+          }
         end
       end
     end
diff --git a/helper.rb b/helper.rb
index c38d2f4..b7943a1 100644
--- a/helper.rb
+++ b/helper.rb
@@ -158,4 +158,38 @@ helpers do
     return out
   end
 
+  def logmmol_to_mg(value ,mw)
+    mg = round_to((10**(-1.0*round_to(value.to_f, 2))*(mw.to_f*1000)),4)
+    return mg
+  end
+
+  def logmg_to_mg(value)
+    mg = round_to(10**round_to(value.to_f, 2),4)
+    return mg
+  end
+
+  def ptd50_to_td50(value ,mw)
+    td50 = round_to((10**(-1.0*round_to(value.to_f, 2))*(mw.to_f*1000)),4)
+    return td50   
+  end
+
+  def round_to(value, deci)
+    rounded = (value.to_f*(10**deci)).round / (10**deci).to_f
+    return rounded
+  end
+
+  def calc_mw(compound_uri)
+    ds = OpenTox::Dataset.new()
+    ds.save(@subjectid)
+    ds.add_compound(compound_uri)
+    ds.save(@subjectid)
+    mw_algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"pc/MW")
+    mw_uri = OpenTox::RestClientWrapper.post(mw_algorithm_uri, {:dataset_uri=>ds.uri})
+    ds.delete(@subjectid)
+    mw_ds = OpenTox::Dataset.find(mw_uri, @subjectid)
+    mw = mw_ds.data_entries[compound_uri][mw_uri.to_s + "/feature/MW"].first.to_f
+    mw_ds.delete(@subjectid)
+    return mw 
+  end
+
 end
diff --git a/views/prediction.haml b/views/prediction.haml
index efa5a84..f44eec1 100644
--- a/views/prediction.haml
+++ b/views/prediction.haml
@@ -17,6 +17,8 @@
             %br
             - p[:measured_activities].each do |a|
               = activity_markup(a, @value_map)
+            - if p[:prediction_transformed]
+              = p[:prediction_transformed]
             %br
               (
               %a{:href => "#", :id => "linkTrainingData#{p.object_id}"} Measured activity