From 80709f6573a85f2d1195f938006f46044651320b Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 18 May 2020 15:35:29 -0500
Subject: Added warning that 1 is being added when doing log transform on
 traits with sample values between 0 and 1

---
 .../wqflask/static/new/javascript/show_trait.js    | 28 ++++++++++++++++++----
 .../new/javascript/show_trait_mapping_tools.js     |  5 +---
 wqflask/wqflask/templates/show_trait.html          |  3 ++-
 .../templates/show_trait_transform_and_filter.html |  2 +-
 4 files changed, 28 insertions(+), 10 deletions(-)

diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 2f276021..c0b2e6db 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -755,12 +755,12 @@ check_for_zero_to_one_vals = function() {
   $('.trait_value_input').each(function() {
     current_value = $(this).data("value")
     if(isNaN(current_value)) {
-      return;
+      return true;
     } else {
       current_value = parseFloat(current_value)
       if (0 <= current_value && current_value < 1){
         zero_to_one_vals_exist = true
-        return false;
+        return false
       }
     }
   });
@@ -769,7 +769,6 @@ check_for_zero_to_one_vals = function() {
 
 normalize_data = function() {
   if ($('#norm_method option:selected').val() == 'log2' || $('#norm_method option:selected').val() == 'log10'){
-    zero_to_one_vals_exist = check_for_zero_to_one_vals();
     if ($('input[name="transform"]').val() != "log2" && $('#norm_method option:selected').val() == 'log2') {
       log2_normalize_data(zero_to_one_vals_exist)
       $('input[name="transform"]').val("log2")
@@ -810,7 +809,28 @@ normalize_data = function() {
   }
 }
 
-$('#normalize').click(normalize_data);
+zero_to_one_vals_exist = false
+
+show_transform_warning = function() {
+  transform_type = $('#norm_method option:selected').val()
+  zero_to_one_vals_exist = check_for_zero_to_one_vals();
+  if (transform_type == "log2" || transform_type == "log10"){
+    if (zero_to_one_vals_exist){
+      $('#transform_alert').css("display", "block")
+    }
+  } else {
+    $('#transform_alert').css("display", "none")
+  }
+}
+
+$('#norm_method').change(function(){
+  show_transform_warning()
+});
+$('#normalize').hover(function(){
+  show_transform_warning()
+});
+
+$('#normalize').click(normalize_data)
 
 switch_qnorm_data = function() {
   return $('.trait_value_input').each((function(_this) {
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
index 7176a0da..01da3f74 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -131,11 +131,8 @@
   };
 
   outlier_text = "One or more outliers exist in this data set. Please review values before mapping. Including outliers when mapping may lead to misleading results.";
-
-  runtime_warning_text = "This function could take as long as 10-20 minutes to run, so please do not close your browser window until it finishes."
-
   showalert = function(message, alerttype) {
-    return $('#alert_placeholder').append('<div id="alertdiv" class="alert ' + alerttype + '"><a class="close" data-dismiss="alert">�</a><span>' + message + '</span></div>');
+    return $('#outlier_alert_placeholder').append('<div id="mapping_alert" class="alert ' + alerttype + '"><a class="close" data-dismiss="alert">�</a><span>' + message + '</span></div>');
   };
 
   $('#suggestive').hide();
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index d29be30b..7380d198 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -74,6 +74,7 @@
                         <div class="panel-body">
                             {% include 'show_trait_transform_and_filter.html' %}
                         </div>
+                        <div id="transform_alert_placeholder"><div id="transform_alert" style="display: none;"class="alert alert-success outlier-alert"><a class="close" data-dismiss="alert">�</a><span>Because there are some values between 0 and 1, log2 and log10 transforms will add 1 to each value.</span></div></div>
                     </div>
                 </div>
                 <div class="panel panel-default">
@@ -98,7 +99,7 @@
                         <div class="panel-body">
                             {% include 'show_trait_mapping_tools.html' %}
                         </div>
-                        <div id="alert_placeholder"></div>
+                        <div id="outlier_alert_placeholder"></div>
                     </div>
                 </div>                
                 <div class="panel panel-default">
diff --git a/wqflask/wqflask/templates/show_trait_transform_and_filter.html b/wqflask/wqflask/templates/show_trait_transform_and_filter.html
index 4be6d249..b4118b04 100644
--- a/wqflask/wqflask/templates/show_trait_transform_and_filter.html
+++ b/wqflask/wqflask/templates/show_trait_transform_and_filter.html
@@ -70,7 +70,7 @@
 
         <div>
             <p>Outliers highlighted in
-                    <strong style="background-color:yellow;">yellow</strong>
+                    <strong style="background-color:orange;">orange</strong>
                     can be hidden using
                     the <strong>Hide Outliers</strong> button.
             </p>
-- 
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