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Commiting branch GCAT_6.0 at SVN revision 572

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This commit is contained in:
Yury V Bukhman
2015-06-26 15:51:35 -05:00
parent 2d658405a1
commit c7fb48ce68
14 changed files with 40 additions and 27 deletions
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Rails/app/models/assay.rb
+10 -3
View File
@@ -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
+9 -8
View File
@@ -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 %>