From 3935e9bee66fbfff4f35365eb9cff8c79f5fadd8 Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Thu, 29 Oct 2015 10:09:13 +0000
Subject: patch merge

---
 application.rb       | 14 ++++++++------
 views/batch.haml     |  3 +--
 views/neighbors.haml |  4 ++--
 views/predict.haml   |  2 +-
 4 files changed, 12 insertions(+), 11 deletions(-)

diff --git a/application.rb b/application.rb
index 9c9cabb..d77842d 100644
--- a/application.rb
+++ b/application.rb
@@ -259,12 +259,14 @@ post '/predict/?' do
   # validate identifier input
   # transfered input
   if !params[:identifier].blank?
-    @identifier = params[:identifier]
-    begin
-      # get compound from SMILES
-      @compound = Compound.from_smiles @identifier
-    rescue
-      @error_report = "Attention, '#{params[:identifier]}' is not a valid SMILES string."
+    # remove whitespaces they terminate a SMILES string
+    # can result in wrong conversion for compound object
+    @identifier = params[:identifier].gsub(/\s+/, "")
+    $logger.debug "input:#{@identifier}"
+    # get compound from SMILES
+    @compound = Compound.from_smiles @identifier
+    if @compound.blank?
+      @error_report = "Attention, '#{@identifier}' is not a valid SMILES string."
       return haml :error
     end
 
diff --git a/views/batch.haml b/views/batch.haml
index 8389651..ec987c4 100644
--- a/views/batch.haml
+++ b/views/batch.haml
@@ -44,7 +44,7 @@
                 %br
                 %b Prediction:
                 / TODO scientific notation
-                = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} #{model.unit}" : prediction[:value]
+                = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} (#{model.unit})" : prediction[:value]
                 %br
                 / TODO probability
                 %b Confidence:
@@ -53,4 +53,3 @@
               - else
                 %p
                   = "Not enough similar compounds </br>in training dataset."
-              %p
diff --git a/views/neighbors.haml b/views/neighbors.haml
index 21b4b35..a741b45 100644
--- a/views/neighbors.haml
+++ b/views/neighbors.haml
@@ -58,7 +58,7 @@
                     / %td
                 %tbody
                   - type = @model_types[j]
-                - prediction[:neighbors].each_with_index do |neighbor,count|
+                - prediction[:neighbors].uniq.each_with_index do |neighbor,count|
                   %tr
                     / Compound
                     %td{:style =>"vertical-align:middle;padding-left:1em;width:50%;"}
@@ -67,7 +67,7 @@
                       %p= Compound.find(neighbor[0]).smiles
                     / Measured Activity
                     %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;"}
-                      = (type == "Regression") ? neighbor[2].collect{|n| '%.2e' % n + " (#{@models[j].unit})"}.join(", ") : neighbor[2].join(", ")
+                      = (type == "Regression") ? neighbor[2].collect{|n| '%.2e' % n + " (#{@models[j].unit})"}.join("</br>") : neighbor[2].join(", ")
                     / Similarity
                     %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;"}
                       / TODO differentiate between no neighbors found and compound found in dataset, display neighbors for compounds in dataset?
diff --git a/views/predict.haml b/views/predict.haml
index 9863cd9..8ab9ee0 100644
--- a/views/predict.haml
+++ b/views/predict.haml
@@ -24,7 +24,7 @@
   });  
   
   function getInput(){
-    identifier = document.getElementById("identifier").value;
+    identifier = document.getElementById("identifier").value.trim();
     fileselect = document.getElementById("fileselect").value;
     if (fileselect != ""){
       return 1;
-- 
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