From 3dae9e9580ea535c22d862ca1c65f25378b69926 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 27 Feb 2019 16:43:33 -0600
Subject: Added loading page for correlation

Added a better error page for mapping if no results are returned (which generally implied an error occurred during the running of GEMMA)

Fixed some issues with tables, like them sorting incorrectly or showing the wrong number of digits
---
 wqflask/wqflask/marker_regression/run_mapping.py   | 188 +++++++++++----------
 wqflask/wqflask/show_trait/show_trait.py           |   2 +-
 .../wqflask/static/new/javascript/show_trait.js    |   4 +-
 wqflask/wqflask/templates/correlation_page.html    |  29 +---
 wqflask/wqflask/templates/loading_correlation.html |  24 +++
 wqflask/wqflask/templates/mapping_error.html       |  14 ++
 wqflask/wqflask/templates/search_result_page.html  |   4 +-
 wqflask/wqflask/templates/show_trait.html          |  50 +++++-
 wqflask/wqflask/views.py                           |  95 +++++++----
 9 files changed, 252 insertions(+), 158 deletions(-)
 create mode 100644 wqflask/wqflask/templates/loading_correlation.html
 create mode 100644 wqflask/wqflask/templates/mapping_error.html

diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 73d985b8..7ee3ac01 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -242,99 +242,103 @@ class RunMapping(object):
         else:
             logger.debug("RUNNING NOTHING")
 
-        if self.pair_scan == True:
-            self.qtl_results = []
-            highest_chr = 1 #This is needed in order to convert the highest chr to X/Y
-            for marker in results:
-                if marker['chr1'] > 0 or marker['chr1'] == "X" or marker['chr1'] == "X/Y":
-                    if marker['chr1'] > highest_chr or marker['chr1'] == "X" or marker['chr1'] == "X/Y":
-                        highest_chr = marker['chr1']
-                    if 'lod_score' in marker.keys():
-                        self.qtl_results.append(marker)
-
-            self.trimmed_markers = results
-
-            for qtl in enumerate(self.qtl_results):
-                self.json_data['chr1'].append(str(qtl['chr1']))
-                self.json_data['chr2'].append(str(qtl['chr2']))
-                self.json_data['Mb'].append(qtl['Mb'])
-                self.json_data['markernames'].append(qtl['name'])
-
-            self.js_data = dict(
-                json_data = self.json_data,
-                this_trait = self.this_trait.name,
-                data_set = self.dataset.name,
-                maf = self.maf,
-                manhattan_plot = self.manhattan_plot,
-                mapping_scale = self.mapping_scale,
-                qtl_results = self.qtl_results
-            )
-
+        self.no_results = False
+        if len(results) == 0:
+          self.no_results = True
         else:
-            self.qtl_results = []
-            highest_chr = 1 #This is needed in order to convert the highest chr to X/Y
-            for marker in results:
-                if marker['chr'] > 0 or marker['chr'] == "X" or marker['chr'] == "X/Y":
-                    if marker['chr'] > highest_chr or marker['chr'] == "X" or marker['chr'] == "X/Y":
-                        highest_chr = marker['chr']
-                    if ('lod_score' in marker.keys()) or ('lrs_value' in marker.keys()):
-                        self.qtl_results.append(marker)
-
-            with Bench("Exporting Results"):
-                export_mapping_results(self.dataset, self.this_trait, self.qtl_results, self.mapping_results_path, self.mapping_scale, self.score_type)
-
-            with Bench("Trimming Markers for Figure"):
-                if len(self.qtl_results) > 30000:
-                    self.qtl_results = trim_markers_for_figure(self.qtl_results)
-
-            with Bench("Trimming Markers for Table"):
-                self.trimmed_markers = trim_markers_for_table(results)
-
-            if self.mapping_method != "gemma":
-                self.json_data['chr'] = []
-                self.json_data['pos'] = []
-                self.json_data['lod.hk'] = []
-                self.json_data['markernames'] = []
-
-                self.json_data['suggestive'] = self.suggestive
-                self.json_data['significant'] = self.significant
-
-                #Need to convert the QTL objects that qtl reaper returns into a json serializable dictionary
-                for index, qtl in enumerate(self.qtl_results):
-                    #if index<40:
-                    #    logger.debug("lod score is:", qtl['lod_score'])
-                    if qtl['chr'] == highest_chr and highest_chr != "X" and highest_chr != "X/Y":
-                        #logger.debug("changing to X")
-                        self.json_data['chr'].append("X")
-                    else:
-                        self.json_data['chr'].append(str(qtl['chr']))
-                    self.json_data['pos'].append(qtl['Mb'])
-                    if 'lrs_value' in qtl.keys():
-                        self.json_data['lod.hk'].append(str(qtl['lrs_value']))
-                    else:
-                        self.json_data['lod.hk'].append(str(qtl['lod_score']))
-                    self.json_data['markernames'].append(qtl['name'])
-
-                #Get chromosome lengths for drawing the interval map plot
-                chromosome_mb_lengths = {}
-                self.json_data['chrnames'] = []
-                for key in self.species.chromosomes.chromosomes.keys():
-                    self.json_data['chrnames'].append([self.species.chromosomes.chromosomes[key].name, self.species.chromosomes.chromosomes[key].mb_length])
-                    chromosome_mb_lengths[key] = self.species.chromosomes.chromosomes[key].mb_length
-
-                self.js_data = dict(
-                    result_score_type = self.score_type,
-                    json_data = self.json_data,
-                    this_trait = self.this_trait.name,
-                    data_set = self.dataset.name,
-                    maf = self.maf,
-                    manhattan_plot = self.manhattan_plot,
-                    mapping_scale = self.mapping_scale,
-                    chromosomes = chromosome_mb_lengths,
-                    qtl_results = self.qtl_results,
-                    num_perm = self.num_perm,
-                    perm_results = self.perm_output,
-                )
+          if self.pair_scan == True:
+              self.qtl_results = []
+              highest_chr = 1 #This is needed in order to convert the highest chr to X/Y
+              for marker in results:
+                  if marker['chr1'] > 0 or marker['chr1'] == "X" or marker['chr1'] == "X/Y":
+                      if marker['chr1'] > highest_chr or marker['chr1'] == "X" or marker['chr1'] == "X/Y":
+                          highest_chr = marker['chr1']
+                      if 'lod_score' in marker.keys():
+                          self.qtl_results.append(marker)
+
+              self.trimmed_markers = results
+
+              for qtl in enumerate(self.qtl_results):
+                  self.json_data['chr1'].append(str(qtl['chr1']))
+                  self.json_data['chr2'].append(str(qtl['chr2']))
+                  self.json_data['Mb'].append(qtl['Mb'])
+                  self.json_data['markernames'].append(qtl['name'])
+
+              self.js_data = dict(
+                  json_data = self.json_data,
+                  this_trait = self.this_trait.name,
+                  data_set = self.dataset.name,
+                  maf = self.maf,
+                  manhattan_plot = self.manhattan_plot,
+                  mapping_scale = self.mapping_scale,
+                  qtl_results = self.qtl_results
+              )
+
+          else:
+              self.qtl_results = []
+              highest_chr = 1 #This is needed in order to convert the highest chr to X/Y
+              for marker in results:
+                  if marker['chr'] > 0 or marker['chr'] == "X" or marker['chr'] == "X/Y":
+                      if marker['chr'] > highest_chr or marker['chr'] == "X" or marker['chr'] == "X/Y":
+                          highest_chr = marker['chr']
+                      if ('lod_score' in marker.keys()) or ('lrs_value' in marker.keys()):
+                          self.qtl_results.append(marker)
+
+              with Bench("Exporting Results"):
+                  export_mapping_results(self.dataset, self.this_trait, self.qtl_results, self.mapping_results_path, self.mapping_scale, self.score_type)
+
+              with Bench("Trimming Markers for Figure"):
+                  if len(self.qtl_results) > 30000:
+                      self.qtl_results = trim_markers_for_figure(self.qtl_results)
+
+              with Bench("Trimming Markers for Table"):
+                  self.trimmed_markers = trim_markers_for_table(results)
+
+              if self.mapping_method != "gemma":
+                  self.json_data['chr'] = []
+                  self.json_data['pos'] = []
+                  self.json_data['lod.hk'] = []
+                  self.json_data['markernames'] = []
+
+                  self.json_data['suggestive'] = self.suggestive
+                  self.json_data['significant'] = self.significant
+
+                  #Need to convert the QTL objects that qtl reaper returns into a json serializable dictionary
+                  for index, qtl in enumerate(self.qtl_results):
+                      #if index<40:
+                      #    logger.debug("lod score is:", qtl['lod_score'])
+                      if qtl['chr'] == highest_chr and highest_chr != "X" and highest_chr != "X/Y":
+                          #logger.debug("changing to X")
+                          self.json_data['chr'].append("X")
+                      else:
+                          self.json_data['chr'].append(str(qtl['chr']))
+                      self.json_data['pos'].append(qtl['Mb'])
+                      if 'lrs_value' in qtl.keys():
+                          self.json_data['lod.hk'].append(str(qtl['lrs_value']))
+                      else:
+                          self.json_data['lod.hk'].append(str(qtl['lod_score']))
+                      self.json_data['markernames'].append(qtl['name'])
+
+                  #Get chromosome lengths for drawing the interval map plot
+                  chromosome_mb_lengths = {}
+                  self.json_data['chrnames'] = []
+                  for key in self.species.chromosomes.chromosomes.keys():
+                      self.json_data['chrnames'].append([self.species.chromosomes.chromosomes[key].name, self.species.chromosomes.chromosomes[key].mb_length])
+                      chromosome_mb_lengths[key] = self.species.chromosomes.chromosomes[key].mb_length
+
+                  self.js_data = dict(
+                      result_score_type = self.score_type,
+                      json_data = self.json_data,
+                      this_trait = self.this_trait.name,
+                      data_set = self.dataset.name,
+                      maf = self.maf,
+                      manhattan_plot = self.manhattan_plot,
+                      mapping_scale = self.mapping_scale,
+                      chromosomes = chromosome_mb_lengths,
+                      qtl_results = self.qtl_results,
+                      num_perm = self.num_perm,
+                      perm_results = self.perm_output,
+                  )
 
     def run_rqtl_plink(self):
         # os.chdir("") never do this inside a webserver!!
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 9b4470fe..4e4c7705 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -414,7 +414,7 @@ def get_table_widths(sample_groups, has_num_cases=False):
         trait_table_width += 70
     if has_num_cases:
         trait_table_width += 30
-    trait_table_width += len(sample_groups[0].attributes)*40
+    trait_table_width += len(sample_groups[0].attributes)*70
 
     trait_table_width = str(trait_table_width) + "px"
 
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index bcb67527..f278b840 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -447,14 +447,14 @@ submit_special = function(url) {
 
 submit_corr = function(){
     var url;
-    url = "/corr_compute";
+    url = "/corr_loading";
     return submit_special(url);
 };
 
 $(".corr_compute").on("click", (function(_this) {
   return function() {
     var url;
-    url = "/corr_compute";
+    url = "/corr_loading";
     return submit_special(url);
   };
 })(this));
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 76aa8d2d..76513c82 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -229,22 +229,6 @@
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
 
     <script type="text/javascript" charset="utf-8">
-        function getValue(x) {
-            if (x.indexOf('input') >= 0) {
-                if ($(x).val() == 'x') {
-                    return 0;
-                }
-                else {
-                   return parseFloat($(x).val());
-                }
-            }
-            else if (isNaN(x)) {
-                return x;
-            }
-            return parseFloat(x);
-        }
-
-
         jQuery.fn.dataTableExt.oSort['numeric-html-asc']  = function(a,b) {
             a = Math.abs(parseFloat($(a).text()));
             b = Math.abs(parseFloat($(b).text()));
@@ -258,24 +242,19 @@
         };
 
         jQuery.fn.dataTableExt.oSort['cust-txt-asc'] = function (a, b) {
-            var x = getValue(a);
-            var y = getValue(b); 
-            
-            if (x == 'N/A' || x == '') {
+            if (a == 'N/A' || a == '') {
                 return 1;
             }
-            else if (y == 'N/A' || y == '') {
+            else if (b == 'N/A' || b == '') {
                 return -1;
             }
             else {
-                return ((x < y) ? -1 : ((x > y) ? 1 : 0));
+                return ((a < b) ? -1 : ((a > b) ? 1 : 0));
             }
         };
             
         jQuery.fn.dataTableExt.oSort['cust-txt-desc'] = function (a, b) {
-            var x = getValue(a);
-            var y = getValue(b);
-            return ((x < y) ? 1 : ((x > y) ? -1 : 0));
+            return ((a < b) ? 1 : ((a > b) ? -1 : 0));
         };
 
 
diff --git a/wqflask/wqflask/templates/loading_correlation.html b/wqflask/wqflask/templates/loading_correlation.html
new file mode 100644
index 00000000..2017c3de
--- /dev/null
+++ b/wqflask/wqflask/templates/loading_correlation.html
@@ -0,0 +1,24 @@
+<title>Loading Correlation Results</title>
+<link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/bootstrap.css" />
+<form method="post" action="/corr_compute" name="loading_form" id="loading_form" class="form-horizontal">
+  {% for key, value in start_vars.iteritems() %}
+  <input type="hidden" name="{{ key }}" value="{{ value }}">
+  {% endfor %}
+  <div class="container">
+    <div>
+      <div style="min-height: 80vh; display: flex; align-items: center;">
+        <div style="margin-bottom: 10px; left: 50%; margin-right: -50%; transform: translate(-50%, -50%); position: absolute;">
+        <h1>Loading&nbsp;Correlation&nbsp;Results...</h1>
+        </div>
+        <div class="progress center-block" style="margin-top: 5px; margin-left: 25%; margin-right: 25%; position: absolute; height:50px; width:50%; top:50%;">
+          <div class="progress-bar progress-bar-striped active" role="progressbar" aria-valuenow="100" aria-valuemin="0" aria-valuemax="100" style="width:100%;"></div>
+        </div>
+      </div>
+    </div>
+  </div>
+</form>
+<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.10.2/jquery.min.js"></script>
+<script src="/static/packages/bootstrap/js/bootstrap.min.js"></script>
+<script  type="text/javascript">
+$("#loading_form").submit();
+</script>
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/mapping_error.html b/wqflask/wqflask/templates/mapping_error.html
new file mode 100644
index 00000000..b73a2c31
--- /dev/null
+++ b/wqflask/wqflask/templates/mapping_error.html
@@ -0,0 +1,14 @@
+{% extends "base.html" %}
+{% block title %}Error{% endblock %}
+{% block content %}
+<!-- Start of body -->
+    {{ header("An error occurred during mapping") }}
+
+    <div class="container">
+        <p>There is likely an issue with the genotype file associated with this group/RISet. Please contact Zach Sloan (zachary.a.sloan@gmail.com) or Arthur Centeno (acenteno@gmail.com) about the data set in question.</p>
+    </div>
+
+
+<!-- End of body -->
+
+{% endblock %}
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 31a5b94e..5f529edb 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -224,7 +224,7 @@
                     }
                     $('td', row).eq(4).attr('title', $('td', row).eq(4).text());
                     $('td', row).eq(4).attr('data-export', $('td', row).eq(4).text());
-                    $('td', row).slice(6,10).attr("align", "right");
+                    $('td', row).slice(5,10).attr("align", "right");
                     $('td', row).eq(5).attr('data-export', $('td', row).eq(5).text());
                     $('td', row).eq(6).attr('data-export', $('td', row).eq(6).text());
                     $('td', row).eq(7).attr('data-export', $('td', row).eq(7).text());
@@ -282,6 +282,7 @@
                     {
                       'title': "Location",
                       'type': "natural",
+                      'width': "140px",
                       'data': "location"
                     },
                     {
@@ -299,6 +300,7 @@
                     {
                       'title': "Max LRS Location",
                       'type': "natural",
+                      'width': "140px",
                       'data': "lrs_location"
                     },
                     {
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 9d2cb7ed..d7d85741 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -161,12 +161,42 @@
               } );
             };
             
+            function getValue(x) {
+                if (x == 'x') {
+                    return "x";
+                }
+                else {
+                   return parseFloat(x);
+                }
+            }
+
             $.fn.dataTable.ext.order['dom-input'] = function (settings, col) {
               return this.api().column(col, { order: 'index' }).nodes().map(function (td, i) {
                 return $('input', td).val();
               });
             }
 
+            $.fn.dataTableExt.oSort['cust-txt-asc'] = function (a, b) {
+                var x = getValue(a);
+                var y = getValue(b);
+
+                if (x == 'x' || x == '') {
+                    return 1;
+                }
+                else if (y == 'x' || y == '') {
+                    return -1;
+                }
+                else {
+                    return ((x < y) ? -1 : ((x > y) ? 1 : 0));
+                }
+            };
+
+            $.fn.dataTableExt.oSort['cust-txt-desc'] = function (a, b) {
+                var x = getValue(a);
+                var y = getValue(b);
+                return ((x < y) ? 1 : ((x > y) ? -1 : 0));
+            };
+
             $(document).ready( function () {
                 $('.panel-heading').click(function () {
                    if ($(this).hasClass('collapsed')){
@@ -257,12 +287,13 @@
                     {
                       'title': "Value",
                       '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 + '" data-qnorm="' + js_data['qnorm_values'][0][parseInt(data.this_id)] + '" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_value" value="' + data.value + '" size=6 maxlength=6>'
+                          return '<input type="text" data-value="' + data.value.toFixed(3) + '" data-qnorm="' + js_data['qnorm_values'][0][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[0].se_exists() %},
@@ -277,20 +308,21 @@
                     {
                       'title': "SE",
                       '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 + '" data-qnorm="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_se" value="' + data.variance + '" size=6 maxlength=6>'
+                          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': "N",
-                      'type': "natural",
+                      'orderDataType': "dom-input",
+                      'type': "cust-txt",
                       'data': null,
-                      'orderDataType': "cust-txt",
                       '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>'
@@ -387,12 +419,13 @@
                     {
                       'title': "Value",
                       '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 + '" 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 + '" size=6 maxlength=6>'
+                          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() %},
@@ -407,20 +440,21 @@
                     {
                       'title': "SE",
                       '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 + '" data-qnorm="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_se" value="' + data.variance + '" size=6 maxlength=6>'
+                          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': "N",
-                      'type': "natural",
+                      'orderDataType': "dom-input",
+                      'type': "cust-txt",
                       'data': null,
-                      'orderDataType': "cust-txt",
                       '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>'
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index cd2e047b..0b0871b1 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -684,36 +684,39 @@ def mapping_results_page():
         with Bench("Total time in RunMapping"):
             template_vars = run_mapping.RunMapping(start_vars, temp_uuid)
 
-        if template_vars.mapping_method != "gemma" and template_vars.mapping_method != "plink":
-            template_vars.js_data = json.dumps(template_vars.js_data,
-                                               default=json_default_handler,
-                                               indent="   ")
-
-        result = template_vars.__dict__
-
-        if result['pair_scan']:
-            with Bench("Rendering template"):
-                img_path = result['pair_scan_filename']
-                logger.info("img_path:", img_path)
-                initial_start_vars = request.form
-                logger.info("initial_start_vars:", initial_start_vars)
-                imgfile = open(TEMPDIR + img_path, 'rb')
-                imgdata = imgfile.read()
-                imgB64 = imgdata.encode("base64")
-                bytesarray = array.array('B', imgB64)
-                result['pair_scan_array'] = bytesarray
-                rendered_template = render_template("pair_scan_results.html", **result)
+        if template_vars.no_results:
+            rendered_template = render_template("mapping_error.html")
         else:
-            gn1_template_vars = display_mapping_results.DisplayMappingResults(result).__dict__
-            #pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL)
-            #logger.info("pickled result length:", len(pickled_result))
-            #Redis.set(key, pickled_result)
-            #Redis.expire(key, 1*60)
-
-            with Bench("Rendering template"):
-                if (gn1_template_vars['mapping_method'] == "gemma") or (gn1_template_vars['mapping_method'] == "plink"):
-                    gn1_template_vars.pop('qtlresults', None)
-                rendered_template = render_template("mapping_results.html", **gn1_template_vars)
+          if template_vars.mapping_method != "gemma" and template_vars.mapping_method != "plink":
+              template_vars.js_data = json.dumps(template_vars.js_data,
+                                                 default=json_default_handler,
+                                                 indent="   ")
+
+          result = template_vars.__dict__
+
+          if result['pair_scan']:
+              with Bench("Rendering template"):
+                  img_path = result['pair_scan_filename']
+                  logger.info("img_path:", img_path)
+                  initial_start_vars = request.form
+                  logger.info("initial_start_vars:", initial_start_vars)
+                  imgfile = open(TEMPDIR + img_path, 'rb')
+                  imgdata = imgfile.read()
+                  imgB64 = imgdata.encode("base64")
+                  bytesarray = array.array('B', imgB64)
+                  result['pair_scan_array'] = bytesarray
+                  rendered_template = render_template("pair_scan_results.html", **result)
+          else:
+              gn1_template_vars = display_mapping_results.DisplayMappingResults(result).__dict__
+              #pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL)
+              #logger.info("pickled result length:", len(pickled_result))
+              #Redis.set(key, pickled_result)
+              #Redis.expire(key, 1*60)
+
+              with Bench("Rendering template"):
+                  if (gn1_template_vars['mapping_method'] == "gemma") or (gn1_template_vars['mapping_method'] == "plink"):
+                      gn1_template_vars.pop('qtlresults', None)
+                  rendered_template = render_template("mapping_results.html", **gn1_template_vars)
 
     return rendered_template
 
@@ -769,6 +772,40 @@ def network_graph_page():
     else:
         return render_template("empty_collection.html", **{'tool':'Network Graph'})
 
+@app.route("/corr_loading", methods=('POST',))
+def corr_loading_page():
+    logger.info(request.url)
+    initial_start_vars = request.form
+    logger.debug("Marker regression called with initial_start_vars:", initial_start_vars.items())
+    #temp_uuid = initial_start_vars['temp_uuid']
+    wanted = (
+        'corr_type',
+        'trait_id',
+        'dataset',
+        'group',
+        'corr_sample_method',
+        'corr_samples_group',
+        'corr_dataset',
+        'min_expr',
+        'corr_return_results',
+        'loc_chr',
+        'min_loc_mb',
+        'max_loc_mb',
+        'p_range_lower',
+        'p_range_upper'
+    )
+    start_vars_container = {}
+    start_vars = {}
+    for key, value in initial_start_vars.iteritems():
+        if key in wanted or key.startswith(('value:')):
+            start_vars[key] = value
+
+    start_vars_container['start_vars'] = start_vars
+    rendered_template = render_template("loading_correlation.html", **start_vars_container)
+
+    return rendered_template
+
+
 @app.route("/corr_compute", methods=('POST',))
 def corr_compute_page():
     logger.info("In corr_compute, request.form is:", pf(request.form))
-- 
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