From 43b257c759ae3b83ae68b0448e2e4cff67f951be Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Tue, 24 Apr 2018 10:58:01 +0000
Subject: always show sa prediction in batch mode

---
 application.rb | 11 +++++++++--
 helper.rb      | 13 +++++++++++--
 2 files changed, 20 insertions(+), 4 deletions(-)

diff --git a/application.rb b/application.rb
index edff1c9..ca1f2ee 100644
--- a/application.rb
+++ b/application.rb
@@ -100,7 +100,14 @@ get '/task/?' do
         sorter << {"Lazar mutagenicity (Salmonella typhimurium)" => ""}
         sorter << {"Prediction" => prediction[:value]}
         sorter << {"Probability" => prediction[:probabilities].collect{|k,v| "#{k}: #{v.signif(3)}"}.join("</br>")}
-      else
+      elsif !prediction[:value] && type == "Classification"
+        sorter << {"Consensus prediction" => prediction["Consensus prediction"]}
+        sorter << {"Consensus confidence" => prediction["Consensus confidence"]}
+        sorter << {"Structural alerts for mutagenicity" => prediction["Structural alerts for mutagenicity"]}
+        sorter << {"Lazar mutagenicity (Salmonella typhimurium)" => ""}
+        sorter << {"Prediction" => ""}
+        sorter << {"Probability" => ""}
+      #else
         sorter << {"Warnings" => prediction[:warnings].join("</br>")}
       end
       sorter.each_with_index do |hash,idx|
@@ -337,7 +344,7 @@ post '/predict/?' do
                 end
                 prediction["Consensus prediction"] = sa_prediction[:prediction] == false ? "non-mutagenic" : "mutagenic"
                 prediction["Consensus confidence"] = confidence.signif(3)
-                prediction["Structural alerts for mutagenicity"] = sa_prediction[:matches].blank? ? "none" : sa_prediction[:matches].collect{|a| a.first}.join("; ")
+                prediction["Structural alerts for mutagenicity"] = sa_prediction[:matches].blank? ? "none" : sa_prediction[:matches].collect{|a| a.first}.join("; ").gsub(/,/," ")
               end
               # add additionally fields for html representation
               unless prediction[:value].blank? || type == "Classification"
diff --git a/helper.rb b/helper.rb
index ca20def..06b1517 100644
--- a/helper.rb
+++ b/helper.rb
@@ -109,8 +109,17 @@ helpers do
         line += "#{output['model_name']},#{compound.smiles},#{prediction[:info] ? prediction[:info] : "no"},"\
           "#{prediction[:measurements].collect{|m| m.delog10.signif(3)}.join("; ") if prediction[:info]},,,,,,,"+ [inApp,note].join(",")+"\n"
       else
-        line += "Consensus mutagenicity,#{compound.smiles},#{prediction[:info] ? prediction[:info] : "no"},"\
-          "#{prediction[:measurements].join("; ") if prediction[:info]},,,,,,,"+ [inApp,note].join(",")+"\n"
+        #line += "Consensus mutagenicity,#{compound.smiles},#{prediction[:info] ? prediction[:info] : "no"},"\
+        #  "#{prediction[:measurements].join("; ") if prediction[:info]},,,,,,,"+ [inApp,note].join(",")+"\n"
+        line += "Consensus mutagenicity,#{compound.smiles},"\
+          "\"#{prediction[:info] ? prediction[:info] : "no"}\",\"#{output['measurements'].join("; ") if prediction[:info]}\","\
+          "#{prediction['Consensus prediction']},"\
+          "#{prediction['Consensus confidence']},"\
+          "#{prediction['Structural alerts for mutagenicity']},"\
+          "#{output['prediction_value']},"\
+          "#{!prediction[:probabilities].blank? ? output['probabilities'].first : ""},"\
+          "#{!prediction[:probabilities].blank? ? output['probabilities'].last : ""},"\
+          "#{inApp},#{note.nil? ? "" : note}\n"
       end
 
     end
-- 
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