Made some more aesthetic changes to various pages and charts/figures

Added some information to the mapping loading page

12 files changed, 194 insertions, 136 deletions

diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 0527449b..39dd075e 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -3,6 +3,7 @@ from __future__ import absolute_import, division, print_function
 import string
 import resource
 import codecs
+import requests
 
 import redis
 Redis = redis.StrictRedis()
@@ -120,11 +121,17 @@ class GeneralTrait(object):
     @property
     def alias_fmt(self):
         '''Return a text formatted alias'''
-        if self.alias:
-            alias = string.replace(self.alias, ";", " ")
-            alias = string.join(string.split(alias), ", ")
-        else:
-            alias = 'Not available'
+
+        alias = 'Not available'
+        if self.symbol:
+            response = requests.get("http://gn2.genenetwork.org/gn3/gene/aliases/" + self.symbol)
+            alias_list = json.loads(response.content)
+            alias = "; ".join(alias_list)
+
+        if alias == 'Not available':
+            if self.alias:
+                alias = string.replace(self.alias, ";", " ")
+                alias = string.join(string.split(alias), ", ")
 
         return alias
 
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 1dd80962..f1f5840f 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -142,40 +142,6 @@ class ShowTrait(object):
         self.qnorm_vals = quantile_normalize_vals(self.sample_groups)
         self.z_scores = get_z_scores(self.sample_groups)
 
-        # Todo: Add back in the ones we actually need from below, as we discover we need them
-        hddn = OrderedDict()
-
-        if self.dataset.group.allsamples:
-            hddn['allsamples'] = string.join(self.dataset.group.allsamples, ' ')
-
-        hddn['trait_id'] = self.trait_id
-        hddn['dataset'] = self.dataset.name
-        hddn['temp_trait'] = False
-        if self.temp_trait:
-           hddn['temp_trait'] = True
-           hddn['group'] = self.temp_group
-           hddn['species'] = self.temp_species
-        hddn['use_outliers'] = False
-        hddn['method'] = "gemma"
-        hddn['selected_chr'] = -1
-        hddn['mapping_display_all'] = True
-        hddn['suggestive'] = 0
-        hddn['num_perm'] = 0
-        hddn['manhattan_plot'] = ""
-        hddn['control_marker'] = ""
-        if not self.temp_trait:
-            if hasattr(self.this_trait, 'locus_chr') and self.this_trait.locus_chr != "" and self.dataset.type != "Geno" and self.dataset.type != "Publish":
-                hddn['control_marker'] = self.nearest_marker
-                #hddn['control_marker'] = self.nearest_marker1+","+self.nearest_marker2
-        hddn['do_control'] = False
-        hddn['maf'] = 0.05
-        hddn['compare_traits'] = []
-        hddn['export_data'] = ""
-        hddn['export_format'] = "excel"
-
-        # We'll need access to this_trait and hddn in the Jinja2 Template, so we put it inside self
-        self.hddn = hddn
-
         self.temp_uuid = uuid.uuid4()
 
         self.sample_group_types = OrderedDict()
@@ -216,18 +182,61 @@ class ShowTrait(object):
 
         sample_column_width = max_samplename_width * 8
 
-        if self.num_values >= 500:
+        if self.num_values >= 5000:
             self.maf = 0.01
         else:
             self.maf = 0.05
 
         trait_symbol = None
+        short_description = None
         if not self.temp_trait:
             if self.this_trait.symbol:
                 trait_symbol = self.this_trait.symbol
+                short_description = trait_symbol
+
+            elif self.this_trait.post_publication_abbreviation:
+                short_description = self.this_trait.post_publication_abbreviation
+
+            elif self.this_trait.pre_publication_abbreviation:
+                short_description = self.this_trait.pre_publication_abbreviation
+
+        # Todo: Add back in the ones we actually need from below, as we discover we need them
+        hddn = OrderedDict()
+
+        if self.dataset.group.allsamples:
+            hddn['allsamples'] = string.join(self.dataset.group.allsamples, ' ')
+        hddn['primary_samples'] = string.join(self.primary_sample_names, ',')
+        hddn['trait_id'] = self.trait_id
+        hddn['dataset'] = self.dataset.name
+        hddn['temp_trait'] = False
+        if self.temp_trait:
+           hddn['temp_trait'] = True
+           hddn['group'] = self.temp_group
+           hddn['species'] = self.temp_species
+        hddn['use_outliers'] = False
+        hddn['method'] = "gemma"
+        hddn['selected_chr'] = -1
+        hddn['mapping_display_all'] = True
+        hddn['suggestive'] = 0
+        hddn['num_perm'] = 0
+        hddn['manhattan_plot'] = ""
+        hddn['control_marker'] = ""
+        if not self.temp_trait:
+            if hasattr(self.this_trait, 'locus_chr') and self.this_trait.locus_chr != "" and self.dataset.type != "Geno" and self.dataset.type != "Publish":
+                hddn['control_marker'] = self.nearest_marker
+                #hddn['control_marker'] = self.nearest_marker1+","+self.nearest_marker2
+        hddn['do_control'] = False
+        hddn['maf'] = 0.05
+        hddn['compare_traits'] = []
+        hddn['export_data'] = ""
+        hddn['export_format'] = "excel"
+
+        # We'll need access to this_trait and hddn in the Jinja2 Template, so we put it inside self
+        self.hddn = hddn
 
         js_data = dict(trait_id = self.trait_id,
                        trait_symbol = trait_symbol,
+                       short_description = short_description,
                        unit_type = trait_units,
                        dataset_type = self.dataset.type,
                        data_scale = self.dataset.data_scale,
@@ -396,6 +405,8 @@ class ShowTrait(object):
                                             sample_group_type='primary',
                                             header="%s Only" % (self.dataset.group.name))
             self.sample_groups = (primary_samples,)
+
+        self.primary_sample_names = primary_sample_names
         self.dataset.group.allsamples = all_samples_ordered
 
 def quantile_normalize_vals(sample_groups):
@@ -493,7 +504,7 @@ def get_genofiles(this_dataset):
     return jsondata['genofile']
 
 def get_table_widths(sample_groups, has_num_cases=False):
-    stats_table_width = 200
+    stats_table_width = 250
     if len(sample_groups) > 1:
         stats_table_width = 450
 
diff --git a/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js b/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js
index a9c5676c..cc4195e4 100644
--- a/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js
+++ b/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js
@@ -171,22 +171,23 @@
     }
 
     var layout = {
-        title: js_data.trait_id,
+        title: "<b>Trait " + js_data.trait_id + ": " + js_data.short_description + "</b>",
         margin: {
-            l: 65,
+            l: 100,
             r: 30,
             t: 80,
-            b: 80
+            b: 60
         },
         xaxis: {
-            title: "Normal Theoretical Quantiles",
+            title: "<b>Normal Theoretical Quantiles</b>",
             range: [first_x, last_x],
             zeroline: false,
             visible: true,
             linecolor: 'black',
             linewidth: 1,
             titlefont: {
-              size: 16
+              family: "arial",
+              size: 20
             },
             ticklen: 4,
             tickfont: {
@@ -194,19 +195,21 @@
             }
         },
         yaxis: {
-            title: "Data Quantiles",
+            title: "<b>Data Quantiles</b>",
             zeroline: false,
             visible: true,
             linecolor: 'black',
             linewidth: 1,
             titlefont: {
-              size: 16
+              family: "arial",
+              size: 20
             },
             ticklen: 4,
             tickfont: {
               size: 16
             },
-            tickformat: tick_digits
+            tickformat: tick_digits,
+            automargin: true
         },
         hovermode: "closest"
     }
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 8366ec0a..48b6da5e 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -30,11 +30,11 @@ Stat_Table_Rows = [
   }, {
     vn: "min",
     pretty: "Minimum",
-    digits: 2
+    digits: 3
   }, {
     vn: "max",
     pretty: "Maximum",
-    digits: 2
+    digits: 3
   }
 ]
 
@@ -67,7 +67,7 @@ Stat_Table_Rows.push(
     digits: 3
   }, {
     vn: "interquartile",
-    pretty: "<font color='blue'>Interquartile Range</font>",
+    pretty: "<font color='black'>Interquartile Range</font>",
     url: "http://www.genenetwork.org/glossary.html#Interquartile",
     digits: 3
   }, {
@@ -334,9 +334,9 @@ update_prob_plot = function() {
 make_table = function() {
   var header, key, row, row_line, table, the_id, the_rows, value, _i, _len, _ref, _ref1;
   if (js_data.trait_symbol != null) {
-    header = "<thead><tr><th style=\"text-align: center;\" colspan=\"100%\">Trait: " + js_data.trait_id + " - " + js_data.trait_symbol + "</th></tr><tr><th style=\"text-align: right; padding-left: 5px;\">Statistic</th>";
+    header = "<thead><tr><th style=\"color: white; background-color: #369; text-align: center;\" colspan=\"100%\">Trait " + js_data.trait_id + " - " + js_data.trait_symbol + "</th></tr><tr><th style=\"text-align: right; padding-left: 5px;\">Statistic</th>";
   } else {
-    header = "<thead><tr><th style=\"text-align: center;\" colspan=\"100%\">Trait: " + js_data.trait_id + "</th></tr><tr><th style=\"text-align: right; padding-left: 5px;\">Statistic</th>";
+    header = "<thead><tr><th style=\"color: white; background-color: #369; text-align: center;\" colspan=\"100%\">Trait " + js_data.trait_id + "</th></tr><tr><th style=\"text-align: right; padding-left: 5px;\">Statistic</th>";
   }
   _ref = js_data.sample_group_types;
   for (key in _ref) {
@@ -990,12 +990,13 @@ var hist_trace = {
 root.histogram_data = [hist_trace];
 root.histogram_layout = {
   bargap: 0.05,
-  title: js_data.trait_id,
+  title: "<b>Trait " + js_data.trait_id + ": " + js_data.short_description + "</b>",
   xaxis: {
            autorange: true,
-           title: "Value",
+           title: "<b>Value</b>",
            titlefont: {
-             size: 16
+             family: "arial",
+             size: 20
            },
            ticklen: 4,
            tickfont: {
@@ -1004,23 +1005,25 @@ root.histogram_layout = {
          },
   yaxis: {
            autorange: true,
-           title: "Count",
+           title: "<b>Count</b>",
            titlefont: {
-             size: 16
+             family: "arial",
+             size: 20
            },
            showline: true,
            ticklen: 4,
            tickfont: {
              size: 16
-           }
+           },
+           automargin: true
          },
   width: 500,
   height: 600,
   margin: {
-      l: 50,
+      l: 70,
       r: 30,
       t: 100,
-      b: 60
+      b: 50
   }
 };
 
@@ -1036,25 +1039,34 @@ $('.histogram_samples_group').change(function() {
 });
 
 root.box_layout = {
-    title: js_data.trait_id,
     xaxis: {
         showline: true,
+        titlefont: {
+          family: "arial",
+          size: 20
+        },
         tickfont: {
           size: 16
         },
     },
     yaxis: {
-        title: js_data.unit_type,
+        title: "<b>" + js_data.unit_type +"</b>",
         autorange: true,
         showline: true,
+        titlefont: {
+          family: "arial",
+          size: 20
+        },
         ticklen: 4,
         tickfont: {
           size: 16
         },
-        tickformat: tick_digits
+        tickformat: tick_digits,
+        zeroline: false,
+        automargin: true
     },
     margin: {
-        l: 50,
+        l: 90,
         r: 30,
         t: 30,
         b: 80
@@ -1122,7 +1134,7 @@ if (full_sample_lists.length > 1) {
       {
         type: 'box',
         y: get_sample_vals(full_sample_lists[0]),
-        name: sample_group_list[0],
+        name: "<b>Trait " + js_data.trait_id + "</b>",
         boxpoints: 'Outliers',
         jitter: 0.5,
         whiskerwidth: 0.2,
@@ -1150,28 +1162,36 @@ $('.box_plot_tab').click(function() {
 // Violin Plot
 
 root.violin_layout = {
-  title: js_data.trait_id,
   xaxis: {
       showline: true,
+      titlefont: {
+        family: "arial",
+        size: 20
+      },
       tickfont: {
         size: 16
       }
   },
   yaxis: {
-      title: js_data.unit_type,
+      title: "<b>"+js_data.unit_type+"</b>",
       autorange: true,
       showline: true,
+      titlefont: {
+        family: "arial",
+        size: 20
+      },
       ticklen: 4,
       tickfont: {
         size: 16
       },
       tickformat: tick_digits,
-      zeroline: false
+      zeroline: false,
+      automargin: true
   },
   margin: {
-        l: 50,
+        l: 90,
         r: 30,
-        t: 80,
+        t: 30,
         b: 80
   }
 };
@@ -1239,14 +1259,11 @@ if (full_sample_lists.length > 1) {
         box: {
           visible: true
         },
-        line: {
-          color: 'green',
-        },
         meanline: {
           visible: true
         },
-        name: sample_group_list[0],
-        x0: sample_group_list[0]
+        name: "<b>Trait " + js_data.trait_id + "</b>",
+        x0: "<b>Trait " + js_data.trait_id + "</b>"
       }
     ]
 }
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 8001dfc9..8db9522c 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -156,7 +156,7 @@
                             'score_type', 'suggestive', 'significant', 'num_perm', 'permCheck', 'perm_output', 'num_bootstrap', 'bootCheck', 'bootstrap_results',
                             'LRSCheck', 'covariates', 'maf', 'use_loco', 'manhattan_plot', 'control_marker', 'control_marker_db', 'do_control', 'genofile', 
                             'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', 'additiveCheck', 'showSNP', 'showGenes', 'viewLegend', 'haplotypeAnalystCheck', 
-                            'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', 'group', 'species', 'reaper_version']
+                            'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', 'group', 'species', 'reaper_version', 'primary_samples']
 
   $("#rqtl_geno_compute").on("click", (function(_this) {
     return function() {
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index 80bbd7f5..2366bdec 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -94,7 +94,7 @@
 
         <form method="get" action="/gsearch">
             <div class="row" style="width: 100%; position: absolute; bottom: 0; top: 30px;">
-                <select style="width: 170px; margin-top: 15px; margin-left: 10px;" name="type">
+                <select style="width: 150px; margin-top: 15px; margin-left: 20px;" name="type">
                     <option value="gene">Genes / Molecules</option>
                     <option value="phenotype" {% if type=="phenotype" %}selected{% endif %}>Phenotypes</option>
                 </select>
diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html
index 7e67ece2..34a15c6a 100644
--- a/wqflask/wqflask/templates/correlation_matrix.html
+++ b/wqflask/wqflask/templates/correlation_matrix.html
@@ -10,7 +10,7 @@
 
 <div class="container" width="100%">
 <h1>Correlation Matrix</h1>
-<div style="width: 100%; max-width: 850px;">Lower left cells list Pearson product-moment correlations; upper right cells list Spearman rank order correlations. Each cell also contains the n of cases. Values ranging from 0.4 to 1.0 range from dark blue to white, while values ranging from -0.4 to -1.0 range from orange to white. Select any cell to generate a scatter plot. Select trait labels for more information.</div>
+<div style="width: 100%; max-width: 850px;">Lower left cells list Pearson product-moment correlations; upper right cells list Spearman rank order correlations. Each cell also contains the n of cases. Values ranging from 0.4 to 1.0 range from orange to white, while values ranging from -0.4 to -1.0 range from dark blue to white. Select any cell to generate a scatter plot. Select trait labels for more information.</div>
 <hr style="height: 1px; background-color: #A9A9A9;">
 {% if lowest_overlap < 8 %}
 <div style="margin-bottom: 10px;"><i><font style="color: red;">Caution</font>: This matrix of correlations contains some cells with small sample sizes of fewer than 8.</i></div>
diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html
index 286f6c1f..ed91a886 100755
--- a/wqflask/wqflask/templates/index_page_orig.html
+++ b/wqflask/wqflask/templates/index_page_orig.html
@@ -28,7 +28,7 @@
                     <div class="page-header">
                         <h1>Select and search</h1>
                     </div>
-                    <form method="get" action="/search" name="SEARCHFORM">
+                    <form method="get" action="/search" target="_blank" name="SEARCHFORM">
                         <fieldset>
                             <div style="padding: 20px" class="form-horizontal">
 
@@ -199,9 +199,9 @@
                         <h1>Github</h1>
                         <ul>
                           <li><a href="https://github.com/genenetwork/genenetwork2">GN2 Source Code</a></li>
-                          <li><a href="https://github.com/genenetwork/gn-docs/wiki">GN2 Document Wiki</a></li>
-                          <li><a href="https://github.com/genenetwork/sysmaintenance">System Maintenance Code</a></li>
                           <li><a href="https://github.com/genenetwork/genenetwork">GN1 Source Code</a></li>
+                          <!--<li><a href="https://github.com/genenetwork/gn-docs/wiki">GN2 Document Wiki</a></li>-->
+                          <li><a href="https://github.com/genenetwork/sysmaintenance">System Maintenance Code</a></li>
                         </ul>
                     </div>
                </section>
@@ -241,7 +241,7 @@
                     <h3>GeneNetwork v2:</h3>
                       <ul>
                         <li><a href="http://gn2.genenetwork.org/">Main website</a> at UTHSC</li>
-                        <li><a href="http://test-gn2.genenetwork.org/">Testing website</a> at UTHSC</li>
+                        <!--<li><a href="http://test-gn2.genenetwork.org/">Testing website</a> at UTHSC</li>-->
                       </ul>
                     <h3>GeneNetwork v1:</h3>
                     <ul>
diff --git a/wqflask/wqflask/templates/loading.html b/wqflask/wqflask/templates/loading.html
index 25560249..3eb061e5 100644
--- a/wqflask/wqflask/templates/loading.html
+++ b/wqflask/wqflask/templates/loading.html
@@ -7,10 +7,24 @@
   <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;">
+        <div style="margin-bottom: 5px; left: 50%; margin-right: -50%; transform: translate(-50%, -50%); position: absolute;">
+        {% if start_vars.tool_used == "Mapping" %}
+        <h1>Computing the Map</h1>
+        <br>
+        <i>n</i> = {{ start_vars.num_vals }}
+        <br>
+        Method = {{ start_vars.method }}
+        <br>
+        {% if start_vars.transform != "" %}
+        transform = {{ start_vars.transform }}
+        <br>
+        {% endif %}
+        MAF = {{ start_vars.maf }}
+        {% else %}
         <h1>Loading&nbsp;{{ start_vars.tool_used }}&nbsp;Results...</h1>
+        {% endif %}
         </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 center-block" style="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>
@@ -22,5 +36,5 @@
 <script  type="text/javascript">
 
 $("#loading_form").attr("action", "{{ start_vars.form_url }}");
-$("#loading_form").submit();
+setTimeout(function(){ $("#loading_form").submit()}, 350);
 </script>
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/new_security/login_user.html b/wqflask/wqflask/templates/new_security/login_user.html
index 27b20ebf..c9aaf028 100644
--- a/wqflask/wqflask/templates/new_security/login_user.html
+++ b/wqflask/wqflask/templates/new_security/login_user.html
@@ -2,53 +2,11 @@
 {% block title %}Register{% endblock %}
 {% block content %}
 
-    <div class="container">
+    <div class="container" style="min-width: 1250px;">
 
         {{ flash_me() }}
 
-        <div class="page-header">
-            <h1>&nbsp;&nbsp;&nbsp;&nbsp;Login</h1>
-        </div>
-
-
-        <div class="security_box">
-
-            <h4>Don't have an account?</h4>
-
-            {% if es_server: %}
-	    <a href="/n/register" class="btn btn-primary modalize">Create a new account</a>
-	    {% else: %}
-	    <div class="alert alert-warning">
-	      <p>You cannot create an account at this moment.<br />
-		Please try again later.</p>
-	    </div>
-	    {% endif %}
-
-	    <hr />
-	    <h4>Login with external services</h4>
-
-	    {% if external_login: %}
-	    <div>
-	      {% if external_login["github"]: %}
-	      <a href="{{external_login['github']}}" title="Login with GitHub" class="btn btn-info btn-group">Login with Github</a>
-              {% else %}
-              <p>Github login is not available right now</p>
-	      {% endif %}
-
-	      {% if external_login["orcid"]: %}
-	      <a href="{{external_login['orcid']}}" title="Login with ORCID" class="btn btn-info btn-group">Login with ORCID</a>
-              {% else %}
-              <p>ORCID login is not available right now</p>
-	      {% endif %}
-	    </div>
-	    {% else: %}
-	    <div class="alert alert-warning">
-	      <p>Sorry, you cannot login with Github or ORCID at this time.</p>
-	    </div>
-	    {% endif %}
-	    <hr />
-
-            <h4>Already have an account? Sign in here.</h4>
+        <h4>Already have an account? Sign in here.</h4>
 
 	    {% if es_server: %}
             <form class="form-horizontal" action="/n/login" method="POST" name="login_user_form" id="loginUserForm">
@@ -69,7 +27,6 @@
                         </div>
                     </div>
 
-
                     <div class="form-group">
                         <label class="col-xs-1 control-label" for="remember"></label>
                         <div style="margin-left:20px;" class="col-xs-4 controls">
@@ -87,6 +44,42 @@
                     </div>
               </fieldset>
 
+              <div class="security_box">
+
+                    <h4>Don't have an account?</h4>
+
+                    {% if es_server: %}
+                <a href="/n/register" class="btn btn-primary modalize">Create a new account</a>
+                {% else: %}
+                <div class="alert alert-warning">
+                  <p>You cannot create an account at this moment.<br />
+                Please try again later.</p>
+                </div>
+                {% endif %}
+
+                <hr />
+                <h4>Login with external services</h4>
+
+                {% if external_login: %}
+                <div>
+                  {% if external_login["github"]: %}
+                  <a href="{{external_login['github']}}" title="Login with GitHub" class="btn btn-info btn-group">Login with Github</a>
+                      {% else %}
+                      <p>Github login is not available right now</p>
+                  {% endif %}
+
+                  {% if external_login["orcid"]: %}
+                  <a href="{{external_login['orcid']}}" title="Login with ORCID" class="btn btn-info btn-group">Login with ORCID</a>
+                      {% else %}
+                      <p>ORCID login is not available right now</p>
+                  {% endif %}
+                </div>
+                {% else: %}
+                <div class="alert alert-warning">
+                  <p>Sorry, you cannot login with Github or ORCID at this time.</p>
+                </div>
+                {% endif %}
+
             </form>
 	    {% else: %}
 	    <div class="alert alert-warning">
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index f5978196..2dded69f 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -13,7 +13,7 @@
 
         <div style="padding-top: 10px; padding-bottom: 10px; font-size: 16px;">
         <!-- Need to customize text more for other types of searches -->
-        <p>We searched <a href="http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&{% if dataset.accession_id != 'None' %}GN_AccessionId={{ dataset.accession_id }}{% else %}InfoPageName={{ dataset.name }}{% endif %}">{{ dataset.fullname }}</a>
+        <p><b>Search Results:</b> We searched <a href="http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&{% if dataset.accession_id != 'None' %}GN_AccessionId={{ dataset.accession_id }}{% else %}InfoPageName={{ dataset.name }}{% endif %}">{{ dataset.fullname }}</a>
            to find all records
                 {% for word in search_terms %}
                     {% if word.key|lower == "rif" %}
@@ -249,6 +249,7 @@
                 'columns': [
                     {
                       'data': null,
+                      'width': "30px",
                       'orderDataType': "dom-checkbox",
                       'orderSequence': [ "desc", "asc"],
                       'render': function(data, type, row, meta) {
@@ -258,12 +259,14 @@
                     {
                       'title': "Index",
                       'type': "natural",
+                      'width': "30px",
                       'data': "index"
                     },
                     {
                       'title': "Record",
                       'type': "natural",
                       'data': null,
+                      'width': "60px",
                       'orderDataType': "dom-inner-text",
                       'render': function(data, type, row, meta) {
                         return '<a href="/show_trait?trait_id=' + data.name + '&dataset=' + data.dataset + '">' + data.name + '</a>'
@@ -277,7 +280,6 @@
                     {
                       'title': "Description",
                       'type': "natural",
-                      'width': "300px",
                       'data': null,
                       'render': function(data, type, row, meta) {
                         try {
@@ -290,12 +292,13 @@
                     {
                       'title': "Location",
                       'type': "natural",
-                      'width': "140px",
+                      'width': "120px",
                       'data': "location"
                     },
                     {
                       'title': "Mean",
                       'type': "natural",
+                      'width': "40px",
                       'data': "mean",
                       'orderSequence': [ "desc", "asc"]
                     },
@@ -308,7 +311,7 @@
                     {
                       'title': "Max LRS Location",
                       'type': "natural",
-                      'width': "140px",
+                      'width': "120px",
                       'data': "lrs_location"
                     },
                     {
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index fe858d52..7b585b03 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -560,6 +560,7 @@ def loading_page():
     logger.info(request.url)
     initial_start_vars = request.form
     start_vars_container = {}
+    num_vals = 0 #ZS: So it can be displayed on loading page
     if 'wanted_inputs' in initial_start_vars:
         wanted = initial_start_vars['wanted_inputs'].split(",")
         start_vars = {}
@@ -567,6 +568,15 @@ def loading_page():
             if key in wanted or key.startswith(('value:')):
                 start_vars[key] = value
 
+        if 'primary_samples' in start_vars:
+            samples = start_vars['primary_samples'].split(",")
+            for sample in samples:
+                value = start_vars.get('value:' + sample)
+                if value != "x":
+                    num_vals += 1
+
+        start_vars['num_vals'] = num_vals
+
         start_vars_container['start_vars'] = start_vars
     else:
         start_vars_container['start_vars'] = initial_start_vars