Added chem. name / value transformation to report.nestle

If mol or mg is given in the feature name the values(actual and
predicted) will be transformed.

3 files changed, 77 insertions, 8 deletions

diff --git a/lib/ot_predictions.rb b/lib/ot_predictions.rb
index 2752fcc..805ffe0 100755
--- a/lib/ot_predictions.rb
+++ b/lib/ot_predictions.rb
@@ -19,7 +19,11 @@ module Lib
     def compound(instance_index)
       @compounds[instance_index]
     end
-    
+
+    def compounds()
+      @compounds
+    end
+
     def compute_stats()
       res = {}
       case feature_type
@@ -36,7 +40,7 @@ module Lib
     end
     
     def self.to_array( predictions, add_pic=false, format=false, validation_uris=nil )
-  
+ 
       confidence_available = false
       predictions.each do |p|
         confidence_available |= p.confidence_values_available?
@@ -44,12 +48,34 @@ module Lib
       res = []
       conf_column = nil
       count = 0
+
       predictions.each do |p|
         v_uris = validation_uris[count] if validation_uris
         count += 1
+        cmpds_mw = {}
+        ds = OpenTox::Dataset.new()
+        ds.save
+       
+        # Get MW of compounds
+        p.compounds.each do |c_uri|
+          ds.add_compound(c_uri)
+          ds.save
+        end 
+        mw_algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"pc/MW")
+        mw_uri = OpenTox::RestClientWrapper.post(mw_algorithm_uri, {:dataset_uri=>ds.uri})
+        mw_ds = OpenTox::Dataset.find(mw_uri)
+        p.compounds.each do |c_uri|
+          cmpds_mw[c_uri] = mw_ds.data_entries[c_uri][mw_uri.to_s + "/feature/MW"].first
+        end
+        mw_ds.delete
+        ds.delete 
+        
+        # Get prediction feature
+        val = OpenTox::Validation.find(v_uris.first)
+        p_feature = val.metadata[OT::predictionFeature].to_s.split("/").last
+
         (0..p.num_instances-1).each do |i|
           a = []
-          
           #PENDING!
           begin
             #a.push( "http://ambit.uni-plovdiv.bg:8080/ambit2/depict/cdk?search="+
@@ -60,9 +86,44 @@ module Lib
             #a.push("Could not add pic: "+ex.message)
             #a.push(p.identifier(i))
           end
-          
-          a << (format ? p.actual_value(i).to_nice_s : p.actual_value(i))
-          a << (format ? p.predicted_value(i).to_nice_s : p.predicted_value(i))
+
+          if cmpds_mw[p.identifier(i)].nil? || (p.feature_type=="classification")
+            a << (format ? p.actual_value(i).to_nice_s : p.actual_value(i))
+            a << (format ? p.predicted_value(i).to_nice_s : p.predicted_value(i))
+          else  # Converting values to mg values if found in prediction feature name
+            if p.actual_value(i).nil?
+              a << (format ? p.actual_value(i).to_nice_s : p.actual_value(i))
+            else
+              if p_feature.downcase.include? "ptd50"
+                td50 = (((10**(-1.0*p.actual_value(i)))*(cmpds_mw[p.identifier(i)].to_f*1000))*1000).round / 1000.0
+                a << (format ? "pTD50: " + p.actual_value(i).to_nice_s + "\n[TD50: " + td50.to_s.chomp + "]" : p.actual_value(i))
+              elsif p_feature.downcase.include? "mol"
+                mg = (((10**(-1.0*p.actual_value(i)))*(cmpds_mw[p.identifier(i)].to_f*1000))*1000).round / 1000.0
+                a << (format ? "log mol/kg bw/day: " + p.actual_value(i).to_nice_s + "\n[mg/kg bw/day: " + mg.to_s.chomp + "]": p.actual_value(i))
+              elsif p_feature.downcase.include? "mg"
+                mg = ((10**p.actual_value(i))*1000).round / 1000.0
+                a << (format ? "log mg/kg bw/day: " + p.actual_value(i).to_nice_s + "\n[mg/kg bw/day: " + mg.to_s.chomp + "]": p.actual_value(i))
+              else
+                a << (format ? p.actual_value(i).to_nice_s : p.actual_value(i))
+              end
+            end
+            if p.predicted_value(i).nil?
+              a << (format ? p.predicted_value(i).to_nice_s : p.predicted_value(i))
+            else
+              if p_feature.downcase.include? "ptd50"
+                td50 = (((10**(-1.0*p.predicted_value(i)))*(cmpds_mw[p.identifier(i)].to_f*1000))*1000).round / 1000.0
+                a << (format ? "pTD50: " + p.predicted_value(i).to_nice_s + "\n[TD50: " + td50.to_s.chomp + "]": p.predicted_value(i))
+              elsif p_feature.downcase.include? "mol"
+                mg = (((10**(-1.0*p.predicted_value(i)))*(cmpds_mw[p.identifier(i)].to_f*1000))*1000).round / 1000.0
+                a << (format ? "log mol/kg bw/day: " + p.predicted_value(i).to_nice_s + "\n[mg/kg bw/day: " + mg.to_s.chomp + "]": p.predicted_value(i))
+              elsif p_feature.downcase.include? "mg"
+                mg = ((10**p.predicted_value(i))*1000).round / 1000.0
+                a << (format ? "log mg/kg bw/day: " + p.predicted_value(i).to_nice_s + "\n[mg/kg bw/day: " + mg.to_s.chomp + "]": p.predicted_value(i))
+              else
+                a << (format ? p.predicted_value(i).to_nice_s : p.predicted_value(i))
+              end
+            end
+          end
           if p.feature_type=="classification"
             if (p.predicted_value(i)!=nil and p.actual_value(i)!=nil)
               if p.classification_miss?(i)
@@ -82,6 +143,12 @@ module Lib
             a << v_uris[i]
           end
           a << p.identifier(i)
+          # Get chemical names and add pubchem_iupac_name
+          c = OpenTox::Compound.new(p.identifier(i))          
+          c_names = c.to_names_hash          
+          a << c_names["pubchem_iupac_name"]
+          a << cmpds_mw[p.identifier(i)] 
+         
           res << a
         end
       end
@@ -103,6 +170,8 @@ module Lib
       header << "Confidence value" if predictions[0].confidence_values_available?
       header << "Validation URI" if validation_uris
       header << "Compound URI"
+      header << "Chemical name (pubchem_iupac_name)"
+      header << "Molecular weight (openbabel)"
       res.insert(0, header)
       
       return res
diff --git a/report/report_content.rb b/report/report_content.rb
index 033b367..0d2c7ec 100755
--- a/report/report_content.rb
+++ b/report/report_content.rb
@@ -412,4 +412,4 @@ class Reports::ReportContent
     @tmp_files.delete(tmp_file_name) if @tmp_files.has_key?(tmp_file_name)
   end
   
-end
\ No newline at end of file
+end
diff --git a/report/report_factory.rb b/report/report_factory.rb
index f73ffd9..c9cab86 100755
--- a/report/report_factory.rb
+++ b/report/report_factory.rb
@@ -124,7 +124,7 @@ module Reports::ReportFactory
     report.end_section
 
     report.add_result(validation_set, Validation::ALL_PROPS, "All Results", "All Results")
-    report.add_predictions( validation_set, false )
+    report.add_predictions( validation_set, true )
     task.progress(100) if task
     report
   end