enable csv download

6 files changed, 73 insertions, 65 deletions

diff --git a/application.rb b/application.rb
index 1e9cf35..8168c52 100644
--- a/application.rb
+++ b/application.rb
@@ -189,13 +189,32 @@ get '/prediction/:model_uri/:type/:neighbor/significant_fragments/?' do
   haml :significant_fragments, :layout => false
 end
 
-get '/predict/:dataset/?' do
-  t = Tempfile.new("tempfile.rdf")
-  t << `curl -k -H accept:application/rdf+xml #{params[:dataset]}`
-  send_file t.path,
-    :filename => params[:dataset].split("/").last+".rdf"
-  t.close
-  t.unlink
+get '/predict/?:csv?' do
+  response['Content-Type'] = "text/csv"
+  @csv = "\"Compound\",\"Endpoint\",\"Type\",\"Prediction\",\"Confidence\"\n"
+  @@batch.each do |key, values|
+    values.each do |array|
+      model = array[0]
+      prediction = array[1]
+      compound = key.smiles
+      endpoint = "#{model.endpoint.gsub('_', ' ')} (#{model.species})"
+      if prediction[:confidence] == "measured"
+        type = ""
+        pred = prediction[:value].numeric? ? "#{prediction[:value].round(3)} (#{model.unit})" : prediction[:value]
+        confidence = "measured activity"
+      elsif prediction[:neighbors].size > 0
+        type = model.model.class.to_s.match("Classification") ? "Classification" : "Regression"
+        pred = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} #{model.unit}" : prediction[:value]
+        confidence = prediction[:confidence]
+      else
+        type = ""
+        pred = "Not enough similar compounds in training dataset."
+        confidence = ""
+      end
+      @csv += "\"#{compound}\",\"#{endpoint}\",\"#{type}\",\"#{pred}\",\"#{confidence}\"\n"
+    end
+  end
+  @csv
 end
 
 post '/predict/?' do
@@ -213,6 +232,11 @@ post '/predict/?' do
     input = OpenTox::Dataset.from_csv_file File.join "tmp", params[:fileselect][:filename]
     dataset = OpenTox::Dataset.find input.id 
     @compounds = dataset.compounds
+    if @compounds.size == 0
+      @error_report = "No valid SMILES submitted."
+      dataset.delete
+      return haml :error
+    end
     @batch = {}
     @compounds.each do |compound|
       @batch[compound] = []
@@ -222,7 +246,8 @@ post '/predict/?' do
         @batch[compound] << [model, prediction]
       end
     end
-    input.delete
+    @@batch = @batch
+    dataset.delete
     return haml :batch
   end
 
diff --git a/views/batch.haml b/views/batch.haml
index 7cf1d77..44d22f1 100644
--- a/views/batch.haml
+++ b/views/batch.haml
@@ -1,13 +1,19 @@
 %div.well
-  %a.btn.btn-warning{:href => to('/predict')} Make New Prediction
+  %a.btn.btn-warning{:href => to('/predict')}
+    %span.glyphicon.glyphicon-menu-left{:aria=>{:hidden=>"true"}}
+    Make New Prediction
   / displays all prediction result in first table
   %div.table-responsive
     %table.table.table-bordered{:id=>"batch", :style=>"background-color:white;"}
       %thead
         %tr
-          %h3.col-md-4 Batch Prediction Results: 
+          %h3.col-md-4{:style=>"padding-left:0;"} Batch Prediction Results:
           %h3.col-md-8= @filename
-
+        %tr
+          %span.btn.btn-default
+            %a{:href=>"#{to("/predict/#{@filename}")}", :title=>"download"}
+              %span.glyphicon.glyphicon-download-alt{:aria=>{:hidden=>"true"}}
+                CSV
       %tbody
       / key = compound, values = array of arrays with model, prediction
       - @batch.each do |key, values|
diff --git a/views/error.haml b/views/error.haml
index c1c1f16..555982b 100644
--- a/views/error.haml
+++ b/views/error.haml
@@ -1,5 +1,7 @@
 %div.well
-  %a.btn.btn-warning{:href => to('/predict')} Back
+  %a.btn.btn-warning{:href => to('/predict')}
+    %i.glyphicon.glyphicon-menu-left
+    Back
   %hr
   %div.well{:style=>"width:100%;margin-bottom:2em;"}
     = @error_report
diff --git a/views/layout.haml b/views/layout.haml
index 94a24e9..60f2bb3 100644
--- a/views/layout.haml
+++ b/views/layout.haml
@@ -24,7 +24,7 @@
       %div.row
         %div.col-md-2
           %a{:href=> to("/predict")}
-            %img.media-object{:src=>"/images/ist_logo.png", :alt=>"logo", :style=>"margin:0 3em 1em 2em;"}
+            %img.media-object{:src=>"/images/ist_logo.png", :alt=>"logo", :style=>"margin:0 3em 0 2em;"}
         %div.col-md-8
           %h1.media-heading{:style=>"margin: 0 0 0 1em;"} Lazar Toxicity Predictions
     
diff --git a/views/predict.haml b/views/predict.haml
index 273e567..de92c15 100644
--- a/views/predict.haml
+++ b/views/predict.haml
@@ -103,53 +103,24 @@
 // whole site content needs to be in one form. Input and checkboxes are proofed by js functions. 
 %form{:name => "form", :action => to('/predict'), :method => "post", :enctype => "multipart/form-data", :onsubmit => "return  !!(showcircle())" }
   %fieldset#top.well
-    %div.row
-      %h2.col-md-6 1. Draw a chemical structure
-      %h2.col-md-6 Select csv file
-    %div.row
-      %div.col-md-6
-        #insert
-          %label &nbsp;
-          #appletContainer
-          %br
-          %label{:for => 'identifier'}
-            or enter the
-            %a{:href => "http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification", :rel => "external"} SMILES
-            string:
-          %br
-          %input{:type => 'text', :name => 'identifier', :id => 'identifier', :size => '60'}
-      %div.col-md-6{:style=>"padding-top:3em;"}
-        #batch
-          Browse file (csv) for batch prediction:
-          %br
-          %span.btn.btn-default.btn-file
-            %input{:type=>"file", :name=> "fileselect", :id=>"fileselect", :accept=>".csv"}
-          %p
-          Example structure:
-          %table.table.table-bordered{:style=>"border-bottom:0;"}
-            %thead
-              %tr
-                %th
-                  SMILES
-                %th
-                  notes
-            %tbody
-              %tr
-                %td
-                  compound
-                %td
-              %tr
-                %td
-                  compound
-                %td
-              %tr
-                %td
-                  compound
-                %td
-              %tr
-                %td{:style=>"border-bottom:0;"}
-                  = "...."
-                %td{:style=>"border-bottom:0;"}
+    %h2 1. Draw a chemical structure
+    #insert
+      %label &nbsp;
+      #appletContainer
+      %br
+      %label{:for => 'identifier'}
+        or enter the
+        %a{:href => "http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification", :rel => "external"} SMILES
+        string:
+      %br
+      %input{:type => 'text', :name => 'identifier', :id => 'identifier', :size => '60'}
+      %p
+      %label{:for=>"fileselect"}
+        or upload a CSV file for batch predictions
+      %br
+      %span.btn.btn-default.btn-file
+        -#%input{:type=>"file", :name=> "fileselect", :id=>"fileselect", :accept=>".csv", :disabled=>"disabled"}
+        %input{:type=>"file", :name=> "fileselect", :id=>"fileselect", :accept=>"text/csv"}
 
   %fieldset#middle.well
     %h2 2. Select one or more endpoints
@@ -168,7 +139,10 @@
                   Details | Validation
             %div.panel-collapse.collapse{:id=>"details#{model.id}", :style=>"margin-left:1em;"}
               %b Model:
-              = model.id
+              %br
+              Source:
+              %a{:href=>model.source, :rel=>"external"}
+                = model.source
               %br
               = "Algorithm:\tLAZAR"
               %br
@@ -259,8 +233,8 @@
                       %td
                         =cv.confusion_matrix[0][1]+cv.confusion_matrix[1][1]
                       %td
-                -#= "Confusion Matrix:\t"
-                -#= cv.confusion_matrix
+                        -#= "Confusion Matrix:\t"
+                        -#= cv.confusion_matrix
               - if model.regression? 
                 %br
                 = "Root mean squared error:\t"
diff --git a/views/prediction.haml b/views/prediction.haml
index 87f8511..a03b509 100644
--- a/views/prediction.haml
+++ b/views/prediction.haml
@@ -6,8 +6,9 @@
     });
   });
 %div.well
-  %a.btn.btn-warning{:href => to('/predict')} Make New Prediction
-
+  %a.btn.btn-warning{:href => to('/predict')}
+    %i.glyphicon.glyphicon-menu-left
+    Make New Prediction
   / displays all prediction result in first table
   %div.table-responsive
     %table.table.table-bordered{:id=>"overview", :style=>"background-color:white;"}