Added default Loading text for dropdowns

Changed order of columns for correlatoin page and removed Y scrolling

Changed name and order of top menu items some

4 files changed, 90 insertions, 75 deletions

diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index b7b349d5..1fa47920 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -148,6 +148,8 @@ class CorrelationResults(object):
             self.target_dataset = data_set.create_dataset(start_vars['corr_dataset'])
             self.target_dataset.get_trait_data(self.sample_data.keys())
 
+            self.header_fields = get_header_fields(self.target_dataset.type, self.corr_method)
+
             self.correlation_results = []
 
             self.correlation_data = {}
@@ -537,3 +539,74 @@ def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_ap
         results_list.append(results_dict)
 
     return json.dumps(results_list)
+
+def get_header_fields(data_type, corr_method):
+    if data_type == "ProbeSet":
+        if corr_method == "pearson":
+            header_fields = ['Index',
+                                'Record',
+                                'Symbol',
+                                'Description',
+                                'Location',
+                                'Mean',
+                                'Sample r',
+                                'N',
+                                'Sample p(r)',
+                                'Lit r',
+                                'Tissue r',
+                                'Tissue p(r)',
+                                'Max LRS',
+                                'Max LRS Location',
+                                'Additive Effect']
+        else:
+            header_fields = ['Index',
+                                'Record',
+                                'Symbol',
+                                'Description',
+                                'Location',
+                                'Mean',
+                                'Sample rho',
+                                'N',
+                                'Sample p(rho)',
+                                'Lit rho',
+                                'Tissue rho',
+                                'Tissue p(rho)',
+                                'Max LRS',
+                                'Max LRS Location',
+                                'Additive Effect']
+    elif data_type == "Publish":
+        if corr_method == "pearson":
+            header_fields = ['Index',
+                            'Record',
+                            'Description',
+                            'Authors',
+                            'Year',
+                            'Sample r',
+                            'N',
+                            'Sample p(r)']
+        else:
+            header_fields = ['Index',
+                            'Record',
+                            'Description',
+                            'Authors',
+                            'Year',
+                            'Sample rho',
+                            'N',
+                            'Sample p(rho)']
+    else:
+        if corr_method == "pearson":
+            header_fields = ['Index',
+                                'ID',
+                                'Location'
+                                'Sample r',
+                                'N',
+                                'Sample p(r)']
+        else:
+            header_fields = ['Index',
+                                'ID',
+                                'Location'
+                                'Sample rho',
+                                'N',
+                                'Sample p(rho)']
+
+    return header_fields
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index f9bc1055..42e57523 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -49,15 +49,15 @@
                             </ul>
                         </li>
                         <li class="">
-                            <a href="/help" class="dropdow-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">Info <span class="caret"></a>
+                            <a href="/help" class="dropdow-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">Help <span class="caret"></a>
                             <ul class="dropdown-menu">
-                              <li><a href="/news">News</a></li>
-                              <li><a href="http://genenetwork.org/faq.html">FAQ</a></li>
-                              <li><a href="http://genenetwork.org/glossary.html">Glossary of Term</a></li>
                               <li><a href="/references">References</a></li>
+                              <li><a href="http://genenetwork.org/glossary.html">Glossary of Term</a></li>
+                              <li><a href="http://genenetwork.org/faq.html">FAQ</a></li>
                               <li><a href="/policies">Policies</a></li>
                               <li><a href="/links">Links</a></li>
                               <li><a href="/environments">Environments</a></li>
+                              <li><a href="/news">GN1 News</a></li>
                             </ul>
                         </li>
                         <li class="">
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 258936e1..fffdfd75 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -111,64 +111,9 @@
                 <thead>
                     <tr>
                         <th></th>
-                    {% for header in target_dataset.header_fields %}
-                        {% if header == 'Year' %}
+                    {% for header in header_fields %}
                         <th>{{header}}</th>
-                        {% elif header == 'Max LRS' %}
-                        <th>Max LRS</th>
-                        {% elif header == 'Max LRS Location' %}
-                        <th>{{header}}</th>
-                        {% elif header == 'Location' %}
-                        <th>{{header}}</th>
-                        {% elif header == 'Mean' %}
-                        <th>{{header}}</th>
-                        {% elif header == 'Additive Effect' %}
-                        <th>Additive Effect</th>
-                        {% elif header == 'Index' %}
-                        <th>{{header}}</th>
-                        {% elif header == 'N' %}
-                        <th>{{header}}</th>
-                        {% else %}
-                        <th>{{header}}</th>
-                        {% endif %}
                     {% endfor %}
-                    {% if target_dataset.type == "ProbeSet" %}
-                        {% if corr_method == 'pearson' %}
-                        <th>Sample r</th>
-                        <th>N</th>
-                        <th>Sample p(r)</th>
-                        <th>Lit r</th>
-                        <th>Tissue r</th>
-                        <th>Tissue p(r)</th>
-                        {% else %}
-                        <th>Sample rho</th>
-                        <th>N</th>
-                        <th>Sample p(rho)</th>
-                        <th>Lit r</th>
-                        <th>Tissue rho</th>
-                        <th>Tissue p(rho)</th>
-                        {% endif %}
-                    {% elif target_dataset.type == "Publish" %}
-                        {% if corr_method == 'pearson' %}
-                        <th>Sample r</th>
-                        <th>&nbsp;&nbsp;N</th>
-                        <th>Sample p(r)</th>
-                        {% else %}
-                        <th>Sample rho</th>
-                        <th>&nbsp;&nbsp;N</th>
-                        <th>Sample p(rho)</th>
-                        {% endif %}
-                    {% elif target_dataset.type == "Geno" %}
-                        {% if corr_method == 'pearson' %}
-                        <th>Sample r</th>
-                        <th>N</th>
-                        <th>Sample p(r)</th>
-                        {% else %}
-                        <th>Sample rho</th>
-                        <th>N</th>
-                        <th>Sample p(rho)</th>
-                        {% endif %}
-                    {% endif %}
                     </tr>
                 </thead>
 
@@ -190,9 +135,6 @@
                         <td>{{ trait.description_display }}</TD>
                         <td style="white-space: nowrap;">{{ trait.location_repr }}</td>
                         <td align="right">{{ '%0.3f' % trait.mean|float }}</td>
-                        <td align="right">{% if trait.LRS_score_repr != "N/A" %}{{ '%0.1f' % trait.LRS_score_repr|float }}{% else %}N/A{% endif %}</td>
-                        <td align="right">{{ trait.LRS_location_repr }}</td>
-                        <td align="right">{% if trait.additive != "" %}{{ '%0.3f' % trait.additive|float }}{% else %}N/A{% endif %}</td>
                         <td align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{'%0.3f'|format(trait.sample_r)}}</a></td>
                         <td align="right">{{ trait.num_overlap }}</td>
                         <td align="right">{{'%0.3e'|format(trait.sample_p)}}</td>
@@ -208,6 +150,9 @@
                         <td align="right">{{'%0.3f'|format(trait.tissue_corr)}}</td>
                         <td align="right">{{'%0.3e'|format(trait.tissue_pvalue)}}</td>
                         {% endif %}
+                        <td align="right">{% if trait.LRS_score_repr != "N/A" %}{{ '%0.1f' % trait.LRS_score_repr|float }}{% else %}N/A{% endif %}</td>
+                        <td align="right">{{ trait.LRS_location_repr }}</td>
+                        <td align="right">{% if trait.additive != "" %}{{ '%0.3f' % trait.additive|float }}{% else %}N/A{% endif %}</td>
                       {% elif target_dataset.type == "Publish" %}
                         <td>{{ trait.description_display }}</td>
                         <td>{{ trait.authors }}</td>
@@ -398,15 +343,15 @@
                     { "type": "natural", "width": "15%" },
                     { "type": "natural" },
                     { "type": "natural" },
-                    { "type": "natural" },
-                    { "type": "natural" },
-                    { "type": "natural" },
                     { "orderDataType": "dom-innertext", 'orderSequence': [ "desc", "asc"] },
                     { "type": "natural" },
                     { "type": "scientific" },
                     { "type": "numeric-html", 'orderSequence': [ "desc", "asc"] },
                     { "type": "numeric-html", 'orderSequence': [ "desc", "asc"] },
-                    { "type": "scientific" }
+                    { "type": "scientific" },
+                    { "type": "natural" },
+                    { "type": "natural" },
+                    { "type": "natural" }
                 ],
                 "createdRow": function ( row, data, index ) {
                     $('td', row).eq(4).attr('title', $('td', row).eq(4).text());
@@ -416,14 +361,11 @@
                     }
                 },
                 "order": [[12, "asc" ]],
-                "sDom": "BRZtir",
+                "sDom": "tir",
                 "iDisplayLength": -1,
                 "autoWidth": false,
                 "deferRender": true,
                 "bSortClasses": false,
-                "scrollY": "800px",
-                "scrollCollapse": false,
-                "scroller": true,
                 "paging": false,
                 "orderClasses": true
             }
diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html
index 5706c870..48ed0ec5 100755
--- a/wqflask/wqflask/templates/index_page_orig.html
+++ b/wqflask/wqflask/templates/index_page_orig.html
@@ -36,7 +36,7 @@
                                     <label for="species" class="col-xs-1 control-label" style="width: 65px !important;">Species:</label>
                                     <div class="col-xs-10 controls input-append" style="display: flex; padding-left: 20px;">
                                         <div class="col-8">
-                                          <select name="species" id="species" class="form-control" style="width: 280px !important;"></select>
+                                          <select name="species" id="species" class="form-control" style="width: 280px !important;"><option>Loading...</option></select>
                                         </div>
                                         <div class="col-4" style="margin-left: 10px;">
                                           <button type="button" id="make_default" class="btn btn-primary form-control">Make Default</button>
@@ -48,7 +48,7 @@
                                     <label for="group" class="col-xs-1 control-label" style="width: 65px !important;">Group:</label>
                                     <div class="col-xs-10 controls input-append" style="padding-left: 20px;">
                                         <div class="col-8">
-                                          <select name="group" id="group" class="form-control" style="width: 280px !important;"></select>
+                                          <select name="group" id="group" class="form-control" style="width: 280px !important;"><option>Loading...</option></select>
                                           <i class="icon-question-sign"></i>
                                         </div>
                                     </div>
@@ -58,7 +58,7 @@
                                     <label for="tissue" class="col-xs-1 control-label" style="width: 65px !important;">Type:</label>
                                     <div class="col-xs-10 controls" style="padding-left: 20px;">
                                         <div class="col-8">
-                                          <select name="type" id="type" class="form-control" style="width: 280px !important;"></select>
+                                          <select name="type" id="type" class="form-control" style="width: 280px !important;"><option>Loading...</option></select>
                                         </div>
                                     </div>
                                 </div>
@@ -67,7 +67,7 @@
                                     <label for="dataset" class="col-xs-1 control-label" style="width: 65px !important;">Dataset:</label>
                                     <div class="col-xs-10 controls input-append" style="display: flex; padding-left: 20px;">
                                         <div class="col-9">
-                                          <select name="dataset" id="dataset" class="form-control" style="width: 340px !important;"></select>
+                                          <select name="dataset" id="dataset" class="form-control" style="width: 340px !important;"><option>Loading...</option></select>
                                           <i class="icon-question-sign"></i>
                                         </div>
                                         <div class="col-3" style="margin-left: 10px;">