Commiting branch GCAT_6.0 at SVN revision 572

Rails/app/models/assay.rb

@@ -139,7 +139,7 @@ class Assay
     # (4) start index (A Positive Integer Number)
     if 
       start_index == ''
-      self.start_index = 2
+      self.start_index = 1
     else  
       self.start_index.gsub(/\s+/, "")  # remove white spaces
       self.start_index = self.start_index.to_i
@@ -276,6 +276,7 @@ class Assay
     # (2) transformation. N value (A Real Number)
     R.assign "add.constant", self.transformation
     # R.assign "add.constant", 0
+
     # (3) blank value (A Real Number)
     if (self.blank_value == nil)
       R.eval "blank.value <- NULL"
@@ -284,8 +285,14 @@ class Assay
     else
       R.assign "blank.value", self.blank_value
     end
-    # (4) start index (A Positive Integer Number)
-    R.assign "start.index", self.start_index
+
+    # (4) start index (A Positive Integer Number).  Cannot be 1 if blank value is nil.
+    if(self.blank_value == nil && self.start_index == 1)
+      return {:error_message => "Error: inoculation timepoint cannot be 1 if using first OD reading as blank", :path => inputfile}
+    else 
+      R.assign "start.index", self.start_index
+    end
+    
     # (5) remove points [a space-separated list of points. Example: 2,3,4,5 (Positive Integer Number)]
     R.assign "points.to.remove", self.remove_points
     

Rails/app/views/assays/_form.html.erb

@@ -45,16 +45,17 @@
           </div>
         </li>
         <li>
-          <h3><span data-tooltip="OD value for blank well read. As the default option <NULL>, GCAT will automatically take the first OD reading of each well to be the blank.">Media background</span></h3>
-          <%= f.radio_button(:blank_value, "zero", {:class => "user_enter3 user_enter3_no"}) %>
-          <%= f.label(:blank_value_zero, "0" ) %> <br/>
-          <%= f.radio_button(:blank_value, "default", {:class => "user_enter3 user_enter3_no"}) %>
-          <%= f.label(:blank_value_default, "Take the first OD reading of each well to be the blank") %><br>
+          <h3><span data-tooltip="OD value for blank well read">Media background</span></h3>
           <%= f.radio_button(:blank_value, "user", {:checked => true, :class => "user_enter3 user_enter3_yes"}) %>
           <%= f.label(:blank_value_user, "User Input.") %>
           <div class="field optional_input3" style="display:none">
             <%= f.text_field :blank_value_input, :placeholder => 'Enter your OD blank value here' %>
           </div>
+          <br>
+          <%= f.radio_button(:blank_value, "default", {:class => "user_enter3 user_enter3_no"}) %>
+          <%= f.label(:blank_value_default, "Take the first OD reading of each well to be the blank") %><br>
+          <%= f.radio_button(:blank_value, "zero", {:class => "user_enter3 user_enter3_no"}) %>
+          <%= f.label(:blank_value_zero, "Set to 0" ) %>
         </li>
         <li>
           <h3><span data-tooltip="GCAT transforms optical density (OD) to log(x+δ). x = OD – Media background. Specify a value for n or choose from the defaults. Note: 0 is not recommended unless all wells contain many repeated measurements for initial density that can be used to accurately estimate the baseline density. See the user manual for more details.">OD Transform</span></h3>
@@ -84,8 +85,8 @@
           <h3><span data-tooltip="Enter the index of the timepoint at which the wells were inoculated with the culture. 
             " >Inoculation timepoint</span></h3>
           <div class="field">
-              <%= f.label :start_index, "Enter the timepoint index (positive integer only).  The default value is 2. "  %><br />
-              <%= f.text_field(:start_index, :type => 'number', :min =>'1', :size => '3', :value => '2') %>
+              <%= f.label :start_index, "Enter the timepoint index (positive integer only).  The default value is 1. "  %><br />
+              <%= f.text_field(:start_index, :type => 'number', :min =>'1', :size => '3', :value => '1') %>
           </div>
         </li>
         <li>
@@ -156,4 +157,4 @@
   </div>
   </ul>
 </section>
-<% end %>
+<% end %>