- Improved Interval Analyst table appearance in mapping results

- Made the text on the "Forgot Password" page more simple and less cluttered

- Added line to index page about RANGE search function

- Fixed bar chart on trait page so that it sets the bottom margin depending upon the longest sample name length

6 files changed, 79 insertions, 53 deletions

diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 11231032..1ce0e725 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -2155,8 +2155,8 @@ class DisplayMappingResults(object):
                         humanStartString = humanChr = humanStartDisplay = "--"
 
                     geneDescription = theGO["GeneDescription"]
-                    if len(geneDescription) > 26:
-                        geneDescription = geneDescription[:26]+"..."
+                    if len(geneDescription) > 70:
+                        geneDescription = geneDescription[:70]+"..."
 
                     if theGO["snpDensity"] < 0.000001:
                         snpDensityStr = "0"
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 56f62090..31f59a13 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -829,6 +829,23 @@ get_sample_names = function(sample_list) {
   })();
 };
 
+get_bar_bottom_margin = function(sample_list){
+  bottom_margin = 80
+  max_length = 0
+  sample_names = get_sample_names(sample_list)
+  for (i=0; i < sample_names.length; i++){
+    if (sample_names[i].length > max_length) {
+      max_length = sample_names[i].length
+    }
+  }
+
+  if (max_length > 6){
+    bottom_margin += 9*(max_length - 6)
+  }
+
+  return bottom_margin;
+}
+
 root.stats_group = 'samples_primary';
 
 if (Object.keys(js_data.sample_group_types).length > 1) {
@@ -906,6 +923,49 @@ get_bar_range = function(sample_list){
 
 root.chart_range = get_bar_range(sample_lists[0])
 
+if (js_data.num_values < 256) {
+  bar_chart_width = 25 * get_sample_vals(sample_lists[0]).length
+
+  //ZS: Set bottom margin dependent on longest sample name length, since those can get long
+  bottom_margin = get_bar_bottom_margin(sample_lists[0])
+
+  root.bar_layout = {
+    xaxis: {
+        titlefont: {
+          size: 16
+        },
+        showline: true,
+        ticklen: 4,
+        tickfont: {
+          size: 16
+        }
+    },
+    yaxis: {
+        range: root.chart_range,
+        titlefont: {
+          size: 16
+        },
+        showline: true,
+        ticklen: 4,
+        tickfont: {
+          size: 16
+        }
+    },
+    width: bar_chart_width,
+    height: 600,
+    margin: {
+        l: 50,
+        r: 30,
+        t: 30,
+        b: bottom_margin
+    }
+  };
+
+  $('.bar_chart_tab').click(function() {
+    update_bar_chart();
+  });
+}
+
 total_sample_count = 0
 for (i = 0, i < sample_lists.length; i++;) {
   total_sample_count += get_sample_vals(sample_lists[i]).length
@@ -964,46 +1024,6 @@ $('.histogram_samples_group').change(function() {
   return update_histogram();
 });
 
-if (js_data.num_values < 256) {
-  bar_chart_width = 25 * get_sample_vals(sample_lists[0]).length
-
-  root.bar_layout = {
-    xaxis: {
-        titlefont: {
-          size: 16
-        },
-        showline: true,
-        ticklen: 4,
-        tickfont: {
-          size: 16
-        }
-    },
-    yaxis: {
-        range: root.chart_range,
-        titlefont: {
-          size: 16
-        },
-        showline: true,
-        ticklen: 4,
-        tickfont: {
-          size: 16
-        }
-    },
-    width: bar_chart_width,
-    height: 600,
-    margin: {
-        l: 50,
-        r: 30,
-        t: 30,
-        b: 80
-    }
-  };
-
-  $('.bar_chart_tab').click(function() {
-    update_bar_chart();
-  });
-}
-
 root.box_layout = {
     xaxis: {
         showline: true,
diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html
index a22708ab..0116245d 100644
--- a/wqflask/wqflask/templates/index_page.html
+++ b/wqflask/wqflask/templates/index_page.html
@@ -143,6 +143,9 @@
                         highly expressed genes (15 to 16 log2 units) AND with peak <a href="http://www.genenetwork.org/glossary.html#L">LRS</a>
                         linkage between 23 and 46.</li>
 
+                        <li><b>RANGE=(1.5 2.5)</b> in the <b>Any</b> field finds traits with values with a specified fold-range (minimum = 1). 
+                        Useful for finding "housekeeping genes" <b>(1.0 1.2)</b> or highly variable molecular assays <b>(10 100)</b>.</li>
+
                         <li><b>RIF=mitochondrial</b> searches RNA databases for <a href="https://en.wikipedia.org/wiki/GeneRIF">
                         GeneRIF</a> links.</li>
 
diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html
index 926b9840..e32b1c82 100755
--- a/wqflask/wqflask/templates/index_page_orig.html
+++ b/wqflask/wqflask/templates/index_page_orig.html
@@ -148,6 +148,9 @@
                         highly expressed genes (15 to 16 log2 units) AND with peak <a href="http://www.genenetwork.org/glossary.html#L">LRS</a>
                         linkage between 23 and 46.</li>
 
+                        <li><b>RANGE=(1.5 2.5)</b> in the <b>Any</b> field finds traits with values with a specified fold-range (minimum = 1). 
+                        Useful for finding "housekeeping genes" <b>(1.0 1.2)</b> or highly variable molecular assays <b>(10 100)</b>.</li>
+
                         <li><b>RIF=mitochondrial</b> searches RNA databases for <a href="https://en.wikipedia.org/wiki/GeneRIF">
                         GeneRIF</a> links.</li>
 
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index 317747c1..f31c5fe5 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -347,6 +347,16 @@
             } );
 
             $('#interval_analyst').dataTable( {
+                "createdRow": function ( row, data, index ) {
+                  $('td', row).eq(1).attr("align", "right");
+                  $('td', row).eq(3).attr("align", "right");
+                  $('td', row).eq(4).attr("align", "right");
+                  $('td', row).eq(5).attr("align", "right");
+                  $('td', row).eq(6).attr("align", "right");
+                  $('td', row).eq(7).attr("align", "right");
+                  $('td', row).eq(8).attr("align", "center");
+                  $('td', row).eq(9).attr("align", "right");
+                },
                 "columns": [
                     { "bSortable": false},
                     { "type": "natural" },
diff --git a/wqflask/wqflask/templates/new_security/forgot_password.html b/wqflask/wqflask/templates/new_security/forgot_password.html
index 09ae2c1c..a981b6bd 100644
--- a/wqflask/wqflask/templates/new_security/forgot_password.html
+++ b/wqflask/wqflask/templates/new_security/forgot_password.html
@@ -2,29 +2,19 @@
 {% block title %}Forgot Password{% endblock %}
 {% block content %}
 
-    {{ header("Forgot Password", "Easily reset your password.") }}
-
     <div class="container">
         <div class="page-header">
             <h1>Password Reset</h1>
         </div>
 
-
         <div class="security_box">
 
-            <h4>Enter your email address</h4>
-
-            <h5>And we'll send you a link to reset your password</h5>
-
-
+            <h4>Enter your email address and we'll send you a link to reset your password</h4>
 
             <form class="form-horizontal" action="/n/forgot_password_submit"
                   method="POST" name="login_user_form">
                 <fieldset>
-
-
                     <div class="control-group">
-                        <label class="control-label" for="email_address">Email Address</label>
                         <div class="controls">
                             <input id="email_address" class="focused" name="email_address" type="text" value="">
                         </div>