Merge branch 'testing' into build/python3-migration

6 files changed, 99 insertions, 398 deletions

diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index bc487a59..d1a97310 100644
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -8,7 +8,7 @@
 {% block content %}
 <!-- Start of body -->
 
-    <div class="container" style="min-width: 2050px;">
+    <div class="container">
         <h1>
             <span id="collection_name">{{ uc.name }}</span>
             <input type="text" name="new_collection_name" style="font-size: 20px; display: none; width: 500px;" class="form-control" placeholder="{{ uc.name }}"> 
@@ -85,7 +85,7 @@
             <div style="margin-top: 10px; margin-bottom: 5px;">
                 <b>Show/Hide Columns:</b>
             </div>
-            <div>
+            <div style="min-width: 1500px;">
                 <table class="table-hover table-striped cell-border" id='trait_table' style="float: left;">
                     <thead>
                         <tr>
@@ -97,7 +97,7 @@
                             <th data-export="Description">Description</th>
                             <th data-export="Location">Location</th>
                             <th data-export="Mean">Mean</th>
-                            <th data-export="Max LRS">Max LRS <a href="http://genenetwork.org//glossary.html#L" target="_blank"><sup style="font-size: small; color: #FF0000;"> ?</sup></a></th>
+                            <th data-export="Max LRS">High P <a href="http://genenetwork.org//glossary.html#L" target="_blank"><sup style="font-size: small; color: #FF0000;"> ?</sup></a></th>
                             <th data-export="Peak Location">Peak Location</th>
                             <th data-export="Add. Eff.">Effect Size <a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup style="font-size: small; color: #FF0000;"> ?</sup></a></th>
                         </tr>
@@ -195,11 +195,11 @@
                     { 'type': "natural-minus-na", "width": 120 },
                     { "type": "natural" },
                     { "type": "natural"  },
-                    { "type": "natural", "width": 130 },
-                    { "type": "natural", "width": 35 },
-                    { "type": "natural", "width": 35 },
-                    { "type": "natural", "width": 130 },
-                    { "type": "natural" }
+                    { "type": "natural", "width": 125 },
+                    { "type": "natural", "width": 60 },
+                    { "type": "natural", "width": 60 },
+                    { "type": "natural", "width": 125 },
+                    { "type": "natural", "width": 85 }
                 ],
                 "order": [[1, "asc" ]],
                 buttons: [
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index e2e1aa46..2318bfb8 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -140,7 +140,6 @@
             <b>Show/Hide Columns:</b>
           </div>
           {% endif %}
-          <!--<div id="table_container" style="min-width: {% if dataset.type == 'ProbeSet' or dataset.type == 'Publish' %}2000{% else %}380{% endif %}px;">-->
           <div id="table_container" {% if dataset.type == 'ProbeSet' or dataset.type == 'Publish' %}style="min-width: 1500px;"{% endif %}>
             <table class="table-hover table-striped cell-border" id='trait_table' style="float: left; width: {% if dataset.type == 'Geno' %}380px{% else %}100%{% endif %};">
                 <tbody>
@@ -290,7 +289,6 @@
                     {
                       'title': "Description",
                       'type': "natural",
-                      'width': "500px",
                       'data': null,
                       'render': function(data, type, row, meta) {
                         try {
@@ -303,7 +301,7 @@
                     {
                       'title': "Location",
                       'type': "natural-minus-na",
-                      'width': "120px",
+                      'width': "125px",
                       'data': "location"
                     },
                     {
@@ -314,23 +312,23 @@
                       'orderSequence': [ "desc", "asc"]
                     },
                     {
-                      'title': "Max LRS<a href=\"http://genenetwork.org//glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"><sup style=\"font-size: small; color: #FF0000;\"> ?</sup></a>",
+                      'title': "High P<a href=\"http://genenetwork.org//glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"><sup style=\"font-size: small; color: #FF0000;\"> ?</sup></a>",
                       'type': "natural-minus-na",
                       'data': "lrs_score",
-                      'width': "80px",
+                      'width': "60px",
                       'orderSequence': [ "desc", "asc"]
                     },
                     {
                       'title': "Peak Location",
                       'type': "natural-minus-na",
-                      'width': "120px",
+                      'width': "125px",
                       'data': "lrs_location"
                     },
                     {
                       'title': "Effect Size<a href=\"http://genenetwork.org//glossary.html#A\" target=\"_blank\" style=\"color: white;\"><sup style=\"font-size: small; color: #FF0000;\"> ?</sup></a>",
                       'type': "natural-minus-na",
                       'data': "additive",
-                      'width': "120px",
+                      'width': "85px",
                       'orderSequence': [ "desc", "asc"]
                     }{% elif dataset.type == 'Publish' %},
                     {
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 56df2049..5ed7a90b 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -37,7 +37,7 @@
         <input type="hidden" name="covariates" value="">
         <input type="hidden" name="transform" value="">
 
-        <div class="container" style="min-width: 1450px;">
+        <div class="container" style="min-width: 700px;">
             <div class="panel-group" id="accordion">
                 <div class="panel panel-default">
                     <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseOne" aria-expanded="true">
@@ -143,15 +143,18 @@
     <script type="text/javascript" src="/static/new/javascript/plotly_probability_plot.js"></script>
     <script type="text/javascript" src="/static/new/javascript/compare_traits_scatterplot.js"></script>
 
-    <script type="text/javascript" src="/static/new/javascript/show_trait_mapping_tools.js"></script>
-    <script type="text/javascript" src="/static/new/javascript/show_trait.js"></script>
-    <script type="text/javascript" src="/static/new/javascript/validation.js"></script>
 
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.js') }}"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/scientific.js') }}"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script>
+    <script type="text/javascript" src="https://cdn.datatables.net/scroller/2.0.2/js/dataTables.scroller.min.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/noUiSlider/nouislider.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/javascript/get_covariates_from_collection.js"></script>
+
+    <script type="text/javascript" src="/static/new/javascript/initialize_show_trait_tables.js"></script>
+    <script type="text/javascript" src="/static/new/javascript/show_trait_mapping_tools.js"></script>
+    <script type="text/javascript" src="/static/new/javascript/show_trait.js"></script>
+    <script type="text/javascript" src="/static/new/javascript/validation.js"></script>
+    <script type="text/javascript" src="/static/new/javascript/get_covariates_from_collection.js"></script>
 
     <script type="text/javascript" charset="utf-8">
 
@@ -208,162 +211,6 @@
                    }
                 });
 
-                //ZS: This variable is just created to get the column position of the first case attribute, since it's needed to set the row classes in createdRow for the DataTable
-                {% if sample_groups[0].attributes|length > 0 %}
-                {% if sample_groups[0].se_exists() %}
-                {% if has_num_cases %}
-                attribute_start_pos = 6
-                {% else %}
-                attribute_start_pos = 5
-                {% endif %}
-                {% else %}
-                {% if has_num_cases %}
-                attribute_start_pos = 4
-                {% else %}
-                attribute_start_pos = 3
-                {% endif %}
-                {% endif %}
-                {% endif %}
-
-                var primary_table = $('#samples_primary').DataTable( {
-                  'initComplete': function(settings, json) {
-                    $('.edit_sample_value').change(function() {
-                      edit_data_change();
-                    });
-                  },
-                  'createdRow': function ( row, data, index ) {
-                    $(row).attr('id', "Primary_" + data.this_id)
-                    $(row).addClass("value_se");
-                    if (data.outlier) {
-                      $(row).addClass("outlier");
-                    }
-                    $('td', row).eq(0).attr("align", "center");
-                    $('td', row).eq(0).attr("style", "padding: 2px 0px 0px 2px;");
-                    $('td', row).eq(1).addClass("column_name-Index")
-                    $('td', row).eq(1).attr("align", "right");
-                    $('td', row).eq(1).attr("style", "padding: 2px 4px 0px 2px;");
-                    $('td', row).eq(2).addClass("column_name-Sample")
-                    $('td', row).eq(3).addClass("column_name-Value")
-                    $('td', row).eq(3).attr("style", "text-align: right; padding-top: 2px; padding-bottom: 0px;");
-                    {% if sample_groups[0].se_exists() %}
-                    $('td', row).eq(4).attr("align", "center");
-                    $('td', row).eq(4).attr("style", "padding-left: 2px; padding-right: 2px;");
-                    $('td', row).eq(5).addClass("column_name-SE")
-                    $('td', row).eq(5).attr("style", "text-align: right; padding-top: 2px; padding-bottom: 0px;");
-                    {% if has_num_cases %}
-                    $('td', row).eq(6).addClass("column_name-num_cases")
-                    $('td', row).eq(6).attr("style", "text-align: right; padding-top: 2px; padding-bottom: 0px;");
-                    {% endif %} {% else %} {% if has_num_cases %}
-                    $('td', row).eq(4).addClass("column_name-num_cases")
-                    $('td', row).eq(4).attr("style", "text-align: right; padding-top: 2px; padding-bottom: 0px;");
-                    {% endif %} {% endif %}
-                    {% if sample_groups[0].attributes|length > 0 %}
-                    {% for attribute in sample_groups[0].attributes|sort() %}
-                    $('td', row).eq(attribute_start_pos + {{ loop.index }}).addClass("column_name-{{ sample_groups[0].attributes[attribute].name }}")
-                    $('td', row).eq(attribute_start_pos + {{ loop.index }}).attr("style", "text-align: {{ sample_groups[0].attributes[attribute].alignment }}; padding-top: 2px; padding-bottom: 0px;")
-                    {% endfor %}
-                    {% endif %}
-                  },
-                  'data': js_data['sample_lists'][0],
-                  'columns': [
-                    {
-                      'data': null,
-                      'orderDataType': "dom-checkbox",
-                      'searchable' : false,
-                      'render': function(data, type, row, meta) {
-                        return '<input type="checkbox" name="searchResult" style="min-height: 20px;" class="checkbox edit_sample_checkbox" value="">'
-                      }
-                    },
-                    {
-                      'title': "ID",
-                      'type': "natural",
-                      'searchable' : false,
-                      'data': "this_id"
-                    },
-                    {
-                      'title': "Sample",
-                      'type': "natural",
-                      'data': null,
-                      'render': function(data, type, row, meta) {
-                        return '<span class="edit_sample_sample_name">' + data.name + '</span>'
-                      }
-                    },
-                    {
-                      'title': "<div style='text-align: right;'>Value</div>",
-                      'orderDataType': "dom-input",
-                      'type': "cust-txt",
-                      'data': null,
-                      'render': function(data, type, row, meta) {
-                        if (data.value == null) {
-                          return '<input type="text" data-value="x" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_value" value="x" size=6 maxlength=6>'
-                        } else {
-                          return '<input type="text" data-value="' + data.value.toFixed(3) + '" data-qnorm="' + js_data['qnorm_values'][0][parseInt(data.this_id) - 1] + '" data-zscore="' + js_data['zscore_values'][0][parseInt(data.this_id) - 1] + '" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_value" value="' + data.value.toFixed(3) + '" size=6 maxlength=6>'
-                        }
-                      }
-                    }{% if sample_groups[0].se_exists() %},
-                    {
-                      'bSortable': false,
-                      'type': "natural",
-                      'data': null,
-                      'searchable' : false,
-                      'render': function(data, type, row, meta) {
-                        return '±'
-                      }
-                    },
-                    {
-                      'title': "<div style='text-align: right;'>SE</div>",
-                      'orderDataType': "dom-input",
-                      'type': "cust-txt",
-                      'data': null,
-                      'render': function(data, type, row, meta) {
-                        if (data.variance == null) {
-                          return '<input type="text" data-value="x" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_se" value="x" size=6 maxlength=6>'
-                        } else {
-                          return '<input type="text" data-value="' + data.variance.toFixed(3) + '" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_se" value="' + data.variance.toFixed(3) + '" size=6 maxlength=6>'
-                        }
-                      }
-                    }{% endif %}{% if has_num_cases %},
-                    {
-                      'title': "<div style='text-align: right;'>N</div>",
-                      'orderDataType': "dom-input",
-                      'type': "cust-txt",
-                      'data': null,
-                      'render': function(data, type, row, meta) {
-                        if (data.num_cases == null || data.num_cases == undefined) {
-                          return '<input type="text" data-value="x" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_num_cases" value="x" size=4 maxlength=4>'
-                        } else {
-                          return '<input type="text" data-value="' + data.num_cases + '" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_num_cases" value="' + data.num_cases + '" size=4 maxlength=4>'
-                        }
-                      }
-                    }{% endif %}{% if sample_groups[0].attributes|length > 0 %}{% for attribute in sample_groups[0].attributes|sort() %},
-                    {
-                      'title': "<div style='text-align: {{ sample_groups[0].attributes[attribute].alignment }}'>{{ sample_groups[0].attributes[attribute].name }}</div>",
-                      'type': "natural",
-                      'data': null,
-                      'render': function(data, type, row, meta) {
-                        if (data.extra_attributes['{{ sample_groups[0].attributes[attribute].name }}'] != null && data.extra_attributes['{{ sample_groups[0].attributes[attribute].name }}'] != undefined){
-                          return data.extra_attributes['{{ sample_groups[0].attributes[attribute].name }}']
-                        } else {
-                          return ""
-                        }
-                      }
-                    }{% endfor %}{% endif %}
-                  ],
-                  'order': [[1, "asc"]],
-                  'sDom': "Ztr",
-                  'autoWidth': true,
-                  'deferRender': true,
-                  'paging': false,
-                  'orderClasses': true,
-                  'scrollY': "600px",
-                  'scrollCollapse': false,
-                  'processing': true,
-                  'language': {
-                    'loadingRecords': '&nbsp;',
-                    'processing': 'Loading...'
-                  }
-                } );
-
                 primary_table.on( 'order.dt search.dt draw.dt', function () {
                   primary_table.column(1, {search:'applied', order:'applied'}).nodes().each( function (cell, i) {
                     cell.innerHTML = i+1;
@@ -375,145 +222,6 @@
                 } );
 
                 {% if sample_groups|length != 1 %}
-                var other_table = $('#samples_other').DataTable( {
-                  'initComplete': function(settings, json) {
-                    $('.edit_sample_value').change(function() {
-                      edit_data_change();
-                    });
-                  },
-                  'createdRow': function ( row, data, index ) {
-                    $(row).attr('id', "Other_" + data.this_id)
-                    $(row).addClass("value_se");
-                    if (data.outlier) {
-                      $(row).addClass("outlier");
-                    }
-                    $('td', row).eq(0).attr("align", "center");
-                    $('td', row).eq(0).attr("style", "padding: 2px 0px 0px 2px;");
-                    $('td', row).eq(1).addClass("column_name-Index")
-                    $('td', row).eq(1).attr("align", "right");
-                    $('td', row).eq(1).attr("style", "padding: 2px 4px 0px 2px;");
-                    $('td', row).eq(2).addClass("column_name-Sample")
-                    $('td', row).eq(3).addClass("column_name-Value")
-                    $('td', row).eq(3).attr("style", "text-align: right; padding-top: 2px; padding-bottom: 0px;");
-                    {% if sample_groups[1].se_exists() %}
-                    $('td', row).eq(4).attr("align", "center");
-                    $('td', row).eq(4).attr("style", "padding-left: 2px; padding-right: 2px;");
-                    $('td', row).eq(5).addClass("column_name-SE")
-                    $('td', row).eq(5).attr("style", "text-align: right; padding-top: 2px; padding-bottom: 0px;");
-                    {% if has_num_cases %}
-                    $('td', row).eq(6).addClass("column_name-num_cases")
-                    $('td', row).eq(6).attr("style", "text-align: right; padding-top: 2px; padding-bottom: 0px;");
-                    {% endif %} {% else %} {% if has_num_cases %}
-                    $('td', row).eq(4).addClass("column_name-num_cases")
-                    $('td', row).eq(4).attr("style", "text-align: right; padding-top: 2px; padding-bottom: 0px;");
-                    {% endif %} {% endif %}
-                    {% if sample_groups[1].attributes|length > 0 %}
-                    {% for attribute in sample_groups[1].attributes|sort() %}
-                    $('td', row).eq(attribute_start_pos + {{ loop.index }}).addClass("column_name-{{ sample_groups[1].attributes[attribute].name }}")
-                    $('td', row).eq(attribute_start_pos + {{ loop.index }}).attr("style", "text-align: {{ sample_groups[1].attributes[attribute].alignment }}; padding-top: 2px; padding-bottom: 0px;")
-                    {% endfor %}
-                    {% endif %}
-                  },
-                  'data': js_data['sample_lists'][1],
-                  'columns': [
-                    {
-                      'data': null,
-                      'orderDataType': "dom-checkbox",
-                      'searchable' : false,
-                      'render': function(data, type, row, meta) {
-                        return '<input type="checkbox" name="searchResult" style="min-height: 20px;" class="checkbox edit_sample_checkbox" value="">'
-                      }
-                    },
-                    {
-                      'title': "ID",
-                      'type': "natural",
-                      'data': "this_id",
-                      'searchable' : false
-                    },
-                    {
-                      'title': "Sample",
-                      'type': "natural",
-                      'data': null,
-                      'render': function(data, type, row, meta) {
-                        return '<span class="edit_sample_sample_name">' + data.name + '</span>'
-                      }
-                    },
-                    {
-                      'title': "<div style='text-align: right;'>Value</div>",
-                      'orderDataType': "dom-input",
-                      'type': "cust-txt",
-                      'data': null,
-                      'render': function(data, type, row, meta) {
-                        if (data.value == null) {
-                          return '<input type="text" data-value="x" data-qnorm="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_value" value="x" size=6 maxlength=6>'
-                        } else {
-                          return '<input type="text" data-value="' + data.value.toFixed(3) + '" data-qnorm="' + js_data['qnorm_values'][1][parseInt(data.this_id)] + '" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_value" value="' + data.value.toFixed(3) + '" size=6 maxlength=6>'
-                        }
-                      }
-                    }{% if sample_groups[1].se_exists() %},
-                    {
-                      'bSortable': false,
-                      'type': "natural",
-                      'data': null,
-                      'searchable' : false,
-                      'render': function(data, type, row, meta) {
-                        return '±'
-                      }
-                    },
-                    {
-                      'title': "<div style='text-align: right;'>SE</div>",
-                      'orderDataType': "dom-input",
-                      'type': "cust-txt",
-                      'data': null,
-                      'render': function(data, type, row, meta) {
-                        if (data.variance == null) {
-                          return '<input type="text" data-value="x" data-qnorm="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_se" value="x" size=6 maxlength=6>'
-                        } else {
-                          return '<input type="text" data-value="' + data.variance.toFixed(3) + '" data-qnorm="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_se" value="' + data.variance.toFixed(3) + '" size=6 maxlength=6>'
-                        }
-                      }
-                    }{% endif %}{% if has_num_cases %},
-                    {
-                      'title': "<div style='text-align: right;'>N</div>",
-                      'orderDataType': "dom-input",
-                      'type': "cust-txt",
-                      'data': null,
-                      'render': function(data, type, row, meta) {
-                        if (data.num_cases == null) {
-                          return '<input type="text" data-value="x" data-qnorm="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_num_cases" value="x" size=4 maxlength=4>'
-                        } else {
-                          return '<input type="text" data-value="' + data.num_cases + '" data-qnorm="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_num_cases" value="' + data.num_cases + '" size=4 maxlength=4>'
-                        }
-                      }
-                    }{% endif %}{% if sample_groups[1].attributes|length > 0 %}{% for attribute in sample_groups[1].attributes|sort() %},
-                    {
-                      'title': "<div style='text-align: {{ sample_groups[1].attributes[attribute].alignment }}'>{{ sample_groups[1].attributes[attribute].name }}</div>",
-                      'type': "natural",
-                      'data': null,
-                      'render': function(data, type, row, meta) {
-                        if (data.extra_attributes['{{ sample_groups[1].attributes[attribute].name }}'] != null && data.extra_attributes['{{ sample_groups[1].attributes[attribute].name }}'] != undefined){
-                          return data.extra_attributes['{{ sample_groups[1].attributes[attribute].name }}']
-                        } else {
-                          return ""
-                        }
-                      }
-                    }{% endfor %}{% endif %}
-                  ],
-                  'order': [[1, "asc"]],
-                  'sDom': "Ztr",
-                  'autoWidth': true,
-                  'deferRender': true,
-                  'paging': false,
-                  'orderClasses': true,
-                  'scrollY': "600px",
-                  'scrollCollapse': false,
-                  'processing': true,
-                  'language': {
-                    'loadingRecords': '&nbsp;',
-                    'processing': 'Loading...'
-                  }
-                } );
-
                 $('#other_searchbox').on( 'keyup', function () {
                   other_table.search($(this).val()).draw();
                 } );
diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
index 1378b91b..9420c9c6 100644
--- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html
+++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
@@ -1,5 +1,5 @@
 <div>
-  <div class="col-xs-7">
+  <div class="col-xs-6" style="min-width: 800px;">
     <div style="padding: 20px" class="form-horizontal">
         
         <div class="form-group">
@@ -39,7 +39,7 @@
         
         <div class="form-group">
             <label for="corr_return_results" class="col-xs-2 control-label">Return</label>
-            <div class="col-xs-3 controls">
+            <div class="col-xs-4 controls">
                 <select name="corr_return_results" class="form-control">
                     {% for return_result in corr_tools.return_results_menu %}
                         <option value="{{ return_result }}" 
@@ -55,7 +55,7 @@
         
         <div class="form-group">
             <label for="corr_samples_group" class="col-xs-2 control-label">Samples</label>
-            <div class="col-xs-3 controls">
+            <div class="col-xs-4 controls">
                 <select name="corr_samples_group" class="form-control">
                     {% for group, pretty_group in sample_group_types.items() %}
                         <option value="{{ group }}">{{ pretty_group }}</option>
@@ -66,7 +66,7 @@
             
         <div id="corr_sample_method" class="form-group">
             <label for="corr_sample_method" class="col-xs-2 control-label">Type</label>
-            <div class="col-xs-3 controls">
+            <div class="col-xs-4 controls">
                 <select name="corr_sample_method" class="form-control">
                     <option value="pearson">Pearson</option>
                     <option value="spearman">Spearman Rank</option>
@@ -77,7 +77,7 @@
         {% if dataset.type != "Publish" %}
         <div class="form-group">
             <label class="col-xs-2 control-label">Min Expr</label>
-            <div class="col-xs-3 controls">
+            <div class="col-xs-4 controls">
                 <input name="min_expr" value="" type="text" class="form-control" style="width: 70px;">
             </div>
         </div>
@@ -114,7 +114,7 @@
         </div>
     </div>
   </div>
-  <div class="col-xs-5">
+  <div>
     <span id="sample_r_desc" class="correlation_desc fs12">
         The <a href="http://genenetwork.org/correlationAnnotation.html#genetic_r">Sample Correlation</a>
         is computed
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 27040045..94388b2f 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -397,8 +397,8 @@
             </div>
         </div>
     </div>
-    <div class="col-xs-7">
-        <dl style="width: 500px;">
+    <div>
+        <dl>
              {% for mapping_method in dataset.group.mapping_names %}
              {% if mapping_method == "GEMMA" %}
              <dt style="padding-top: 20px;">GEMMA</dt>
diff --git a/wqflask/wqflask/templates/show_trait_transform_and_filter.html b/wqflask/wqflask/templates/show_trait_transform_and_filter.html
index b4118b04..9fb560a0 100644
--- a/wqflask/wqflask/templates/show_trait_transform_and_filter.html
+++ b/wqflask/wqflask/templates/show_trait_transform_and_filter.html
@@ -1,83 +1,78 @@
 <div>
-    <div class="form-horizontal">
-            <p>Edit or delete values in the Trait Data boxes, and use the
-                <strong>Reset</strong> option as
-                needed.
-            </p>
+  <div class="form-horizontal">
+          <p>Edit or delete values in the Trait Data boxes, and use the
+              <strong>Reset</strong> option as
+              needed.
+          </p>
 
-            <div id="blockMenuSpan" class="input-append" style="margin-bottom: 10px;">
-                <label for="remove_samples_field">Block samples by index:</label>
-                <input type="text" id="remove_samples_field" placeholder="Example: 3, 5-10, 12">
-                <select id="block_group" size="1">
-                  <option value="primary">
-                    {{ sample_group_types['samples_primary'] }}
-                  </option>
-                  <option value="other">
-                    {{ sample_group_types['samples_other'] }}
-                  </option>
-                </select>
-                <input type="button" id="block_by_index" class="btn btn-danger" value="Block">
-            </div>
-            <div id="remove_samples_invalid" class="alert alert-error" style="display:none;">
-                  Please check that your input is formatted correctly, e.g. <strong>3, 5-10, 12</strong>
-            </div>
-            {% if sample_groups[0].attributes %}
-            <div class="input-append" style="margin-top:10px; margin-bottom:10px;">
-                <label for="exclude_menu">Block samples by group:</label>
-                <select id="exclude_menu" size=1>
-                  {% for attribute in sample_groups[0].attributes %}
-                  <option value="{{ sample_groups[0].attributes[attribute].name.replace(' ', '_') }}">
-                      {{ sample_groups[0].attributes[attribute].name }}</option>
-                  {% endfor %}
-                </select>
-                <select id="attribute_values" size=1>
-                </select>
-                <input type="button" id="exclude_group" class="btn" value="Block">
-            </div>
-            {% endif %}
-            <div>
-              <input type="button" id="hide_no_value" class="btn btn-default" value="Hide No Value">
-              <input type="button" id="block_outliers" class="btn btn-default" value="Block Outliers">
-              <input type="button" class="btn btn-success reset" value="Reset">
-              <span class="input-append">
-                <input type="button" class="btn btn-default export" value="Export">
-                <select class="select optional span2 export_format">
-                  <option value="excel">Excel</option>
-                  <option value="csv">CSV</option>
-                </select>
-              </span>
-              <br>
-              <div style="margin-top:10px;">
-              <input type="button" id="normalize" class="btn btn-success" value="Normalize">
-              <select id="norm_method" class="select optional span2">
-                {% if negative_vals_exist == "false" %}
-                <option value="log2">Log2</option>
-                <option value="log10">Log10</option>
-                {% endif %}
-                <option value="zscore">Z-score</option>
-                <option value="qnorm">Quantile</option>
-                <option value="sqrt">Square Root</option>
-                <option value="invert">Invert +/-</option>
+          <div id="blockMenuSpan" class="input-append" style="margin-bottom: 10px;">
+              <label for="remove_samples_field">Block samples by index:</label>
+              <input type="text" id="remove_samples_field" placeholder="Example: 3, 5-10, 12">
+              <select id="block_group" size="1">
+                <option value="primary">
+                  {{ sample_group_types['samples_primary'] }}
+                </option>
+                <option value="other">
+                  {{ sample_group_types['samples_other'] }}
+                </option>
+              </select>
+              <input type="button" id="block_by_index" class="btn btn-danger" value="Block">
+          </div>
+          <div id="remove_samples_invalid" class="alert alert-error" style="display:none;">
+                Please check that your input is formatted correctly, e.g. <strong>3, 5-10, 12</strong>
+          </div>
+          {% if sample_groups[0].attributes %}
+          <div class="input-append" style="margin-top:10px; margin-bottom:10px;">
+              <label for="exclude_menu">Block samples by group:</label>
+              <select id="exclude_menu" size=1>
+                {% for attribute in sample_groups[0].attributes %}
+                <option value="{{ sample_groups[0].attributes[attribute].name.replace(' ', '_') }}">
+                    {{ sample_groups[0].attributes[attribute].name }}</option>
+                {% endfor %}
+              </select>
+              <select id="attribute_values" size=1>
+              </select>
+              <input type="button" id="exclude_group" class="btn" value="Block">
+          </div>
+          {% endif %}
+          <div>
+            <input type="button" id="hide_no_value" class="btn btn-default" value="Hide No Value">
+            <input type="button" id="block_outliers" class="btn btn-default" value="Block Outliers">
+            <input type="button" class="btn btn-success reset" value="Reset">
+            <span class="input-append">
+              <input type="button" class="btn btn-default export" value="Export">
+              <select class="select optional span2 export_format">
+                <option value="excel">Excel</option>
+                <option value="csv">CSV</option>
               </select>
-              </div>
-              <!--
-              {% if sample_groups[0].sample_qnorm is not none %}
-              <input type="button" id="qnorm" class="btn btn-default" value="Quantile Normalize">
+            </span>
+            <br>
+            <div style="margin-top:10px;">
+            <input type="button" id="normalize" class="btn btn-success" value="Normalize">
+            <select id="norm_method" class="select optional span2">
+              {% if negative_vals_exist == "false" %}
+              <option value="log2">Log2</option>
+              <option value="log10">Log10</option>
+              <option value="sqrt">Square Root</option>
               {% endif %}
-              -->
+              <option value="zscore">Z-score</option>
+              <option value="qnorm">Quantile</option>
+              <option value="invert">Invert +/-</option>
+            </select>
             </div>
-        <br>
+          </div>
+      <br>
 
-        <div>
-            <p>Outliers highlighted in
-                    <strong style="background-color:orange;">orange</strong>
-                    can be hidden using
-                    the <strong>Hide Outliers</strong> button.
-            </p>
+      <div>
+          <p>Outliers highlighted in
+                  <strong style="background-color:orange;">orange</strong>
+                  can be hidden using
+                  the <strong>Hide Outliers</strong> button.
+          </p>
 
-            <p>Samples with no value (x) can be hidden by clicking
-                    <strong>Hide No Value</strong> button.
-            </p>
-        </div>
-    </div>
+          <p>Samples with no value (x) can be hidden by clicking
+                  <strong>Hide No Value</strong> button.
+          </p>
+      </div>
+  </div>
 </div>
\ No newline at end of file