various small fixes

2 files changed, 20 insertions, 23 deletions

diff --git a/application.rb b/application.rb
index 0957d71..13df650 100644
--- a/application.rb
+++ b/application.rb
@@ -3,12 +3,7 @@ require_relative 'prediction.rb'
 require_relative 'helper.rb'
 include OpenTox
 
-configure :production do
-  $logger = Logger.new(STDOUT)
-  enable :reloader
-end
-
-configure :development do
+configure :production, :development do
   $logger = Logger.new(STDOUT)
   enable :reloader
 end
@@ -31,9 +26,10 @@ get '/?' do
 end
 
 get '/predict/?' do
-  if params[:tpid] && !params[:tpid].blank?
-    pid = params[:tpid].to_i
-    Process.kill(9,pid) #if (Process.getpgid(pid) rescue nil).present?
+  begin
+    Process.kill(9,params[:tpid].to_i) if !params[:tpid].blank? #if (Process.getpgid(pid) rescue nil).present?
+  rescue
+    nil
   end
   @models = Model::Validation.all
   @models = @models.delete_if{|m| m.model.name =~ /\b(Net cell association)\b/}
@@ -134,10 +130,12 @@ end
 get '/predict/csv/:task/:model/:filename/?' do
   response['Content-Type'] = "text/csv"
   task = Task.find params[:task].to_s
+  m = Model::Validation.find params[:model].to_s
+  endpoint = (params[:model] == "Cramer") ? "Oral_toxicity_(Cramer_rules)" : (m.endpoint =~ /Mutagenicity/i ? "Consensus_mutagenicity" : "#{m.endpoint}_(#{m.species})")
   tempfile = Tempfile.new
   tempfile.write(task.csv)
   tempfile.rewind
-  send_file tempfile, :filename => "#{Time.now.strftime("%Y-%m-%d")}_lazar_batch_prediction_#{params[:model]}_#{params[:filename]}", :type => "text/csv", :disposition => "attachment"
+  send_file tempfile, :filename => "#{Time.now.strftime("%Y-%m-%d")}_lazar_batch_prediction_#{endpoint}_#{params[:filename]}", :type => "text/csv", :disposition => "attachment"
 end
 
 post '/predict/?' do
@@ -186,7 +184,7 @@ post '/predict/?' do
           if type == "Regression"
             unit = (type == "Regression") ? "(#{m.unit})" : ""
             converted_unit = (type == "Regression") ? "#{m.unit =~ /\b(mmol\/L)\b/ ? "(mg/L)" : "(mg/kg_bw/day)"}" : ""
-            header = "ID,Endpoint,Unique SMILES,inTrainingSet,Measurements,Prediction #{unit},Prediction #{converted_unit},"\
+            header = "ID,Endpoint,Unique SMILES,inTrainingSet,Measurements #{unit},Prediction #{unit},Prediction #{converted_unit},"\
               "Prediction Interval Low #{unit},Prediction Interval High #{unit},"\
               "Prediction Interval Low #{converted_unit},Prediction Interval High #{converted_unit},"\
               "inApplicabilityDomain,Note\n"
@@ -204,7 +202,6 @@ post '/predict/?' do
           predictions = []
           @compounds.each do |compound|
             if Prediction.where(compound: compound.id, model: m.id).exists?
-              $logger.debug "prediction already exists !"
               prediction = Prediction.find_by(compound: compound.id, model: m.id).prediction
             else
               prediction = m.predict(compound)
@@ -297,8 +294,8 @@ post '/predict/?' do
 
     end#main task
     @pid = task.pid
-    $logger.debug "application pid: #{@pid}"
 
+    #@dataset.delete
     File.delete File.join("tmp", params[:fileselect][:filename])
     return haml :batch
   end
diff --git a/helper.rb b/helper.rb
index 12a6ce2..3bd1755 100644
--- a/helper.rb
+++ b/helper.rb
@@ -59,7 +59,7 @@ helpers do
           if prediction[:info] =~ /\b(identical)\b/i
             prediction[:info] = "This compound was part of the training dataset. All information "\
               "from this compound was removed from the training data before the "\
-              "prediction, to obtain unbiased results."
+              "prediction to obtain unbiased results."
           end
           note = "\"#{prediction[:warnings].uniq.join(" ")}\""
 
@@ -69,11 +69,11 @@ helpers do
           output["db_hit"] = prediction[:info] if prediction[:info]
           
           if prediction[:measurements].is_a?(Array)
-            output["measurements"] = (type == "Regression") ? prediction[:measurements].collect{|value| "#{value.delog10.signif(3)} (#{model.unit})"} : prediction[:measurements].collect{|value| "#{value}"}
-            output["converted_measurements"] = (type == "Regression") ? prediction[:measurements].collect{|value| "#{compound.mmol_to_mg(value.delog10).signif(3)} #{model.unit =~ /mmol\/L/ ? "(mg/L)" : "(mg/kg_bw/day)"}"} : false
+            output["measurements"] = (type == "Regression") ? prediction[:measurements].collect{|value| "#{value.delog10.signif(3)}"} : prediction[:measurements].collect{|value| "#{value}"}
+            output["converted_measurements"] = (type == "Regression") ? prediction[:measurements].collect{|value| "#{compound.mmol_to_mg(value.delog10).signif(3)}"} : false
           else
-            output["measurements"] = (type == "Regression") ? "#{prediction[:measurements].delog10.signif(3)} (#{model.unit})}" : "#{prediction[:measurements]}"
-            output["converted_measurements"] = (type == "Regression") ? "#{compound.mmol_to_mg(prediction[:measurements].delog10).signif(3)} #{(model.unit =~ /\b(mmol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : false
+            output["measurements"] = (type == "Regression") ? "#{prediction[:measurements].delog10.signif(3)}" : "#{prediction[:measurements]}"
+            output["converted_measurements"] = (type == "Regression") ? "#{compound.mmol_to_mg(prediction[:measurements].delog10).signif(3)}" : false
 
           end #db_hit
 
@@ -86,7 +86,7 @@ helpers do
             end #prediction interval
 
             line += "#{idx+1},#{output['model_name']},#{compound.smiles},"\
-              "\"#{prediction[:info] ? prediction[:info] : "no"}\",\"#{prediction[:measurements].join("; ") if prediction[:info]}\","\
+              "\"#{prediction[:info] ? prediction[:info] : "no"}\",\"#{output['measurements'].join("; ") if prediction[:info]}\","\
               "#{output['prediction_value'] != false ? output['prediction_value'] : ""},"\
               "#{output['converted_value'] != false ? output['converted_value'] : ""},"\
               "#{output['interval'].split(" - ").first.strip unless output['interval'] == false},"\
@@ -117,7 +117,7 @@ helpers do
             output['probability'] = prediction[:probabilities] ? prediction[:probabilities].collect{|k,v| "#{k}: #{v.signif(3)}"} : false
 
             line += "#{idx+1},Consensus mutagenicity,#{compound.smiles},"\
-              "\"#{prediction[:info] ? prediction[:info] : "no"}\",\"#{prediction[:measurements].join("; ") if prediction[:info]}\","\
+              "\"#{prediction[:info] ? prediction[:info] : "no"}\",\"#{output['measurements'].join("; ") if prediction[:info]}\","\
               "#{sa_prediction[:prediction] == false ? "non-mutagenic" : "mutagenic"},"\
               "#{output['confidence']},#{output['sa_matches'] != false ? "\"#{output['sa_matches']}\"" : "none"},"\
               "#{output['prediction_value']},"\
@@ -134,7 +134,7 @@ helpers do
           if prediction[:info] =~ /\b(identical)\b/i
             prediction[:info] = "This compound was part of the training dataset. All information "\
               "from this compound was removed from the training data before the "\
-              "prediction, to obtain unbiased results."
+              "prediction to obtain unbiased results."
           end
           note = "\"#{prediction[:warnings].join(" ")}\""
 
@@ -143,10 +143,10 @@ helpers do
 
           if type == "Regression"
             line += "#{idx+1},#{output['model_name']},#{compound.smiles},#{prediction[:info] ? prediction[:info] : "no"},"\
-              "#{prediction[:measurements] if prediction[:info]},,,,,,,"+ [inApp,note].join(",")+"\n"
+              "#{prediction[:measurements].collect{|m| m.delog10.signif(3)}.join("; ") if prediction[:info]},,,,,,,"+ [inApp,note].join(",")+"\n"
           else
             line += "#{idx+1},Consensus mutagenicity,#{compound.smiles},#{prediction[:info] ? prediction[:info] : "no"},"\
-              "#{prediction[:measurements] if prediction[:info]},,,,,,,"+ [inApp,note].join(",")+"\n"
+              "#{prediction[:measurements].join("; ") if prediction[:info]},,,,,,,"+ [inApp,note].join(",")+"\n"
           end
 
         end