- Temporary traits can be created, viewed, and added to collections

- Correct PCA trait data is created but can't be saved yet
- Added inner margins by increasing xDomain and yDomain of probability plot on trait page
- Increased X/Y-axis label font size
- Turned "processes" to 0 on runserver.py for PROD setting, since it doesn't work with threading
- Improved appearance of correlation page table
- Added links to github to index page
- Removed js_data from GEMMA/PLINK mapping results, since it isn't used for those
- Removed "Tissue" from trait page for phenotype traits

7 files changed, 99 insertions, 67 deletions

diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index cedb65a1..3bde7dc7 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -32,65 +32,65 @@
         <br />
         <br />
 
-        <div style="width: {% if target_dataset.type == "ProbeSet" %}1600px{% elif target_dataset.type == "Publish" %}1200px{% else %}800px{% endif %}; background-color: #eeeeee; border: 1px solid black;">
+        <div style="width: {% if target_dataset.type == "ProbeSet" %}1600px{% elif target_dataset.type == "Publish" %}1400px{% else %}800px{% endif %};">
             <table width="1600px" id="trait_table" class="table table-hover table-striped">
                 <thead>
                     <tr>
-                        <th style="width: 30px; background-color: #eeeeee;"></th>
+                        <th style="width: 30px;"></th>
                     {% for header in target_dataset.header_fields %}
                         {% if header == 'Year' %}
-                        <th style="text-align: right; background-color: #eeeeee;">{{header}}</th>
+                        <th>{{header}}</th>
                         {% elif header == 'Max LRS' %}
-                        <th style="text-align: right; background-color: #eeeeee;">Max&nbsp;&nbsp;<br>LRS<a href="http://genenetwork.org//glossary.html#L" target="_blank"><sup style="color:#f00"> ?</sup></a></th>
+                        <th>Max LRS<a href="http://genenetwork.org//glossary.html#L" target="_blank"><sup style="color:#f00"> ?</sup></a></th>
                         {% elif header == 'Max LRS Location' %}
-                        <th style="text-align: right; background-color: #eeeeee;">{{header}}</th>
+                        <th>{{header}}</th>
                         {% elif header == 'Location' %}
-                        <th style="text-align: right; background-color: #eeeeee;">{{header}}</th>
+                        <th>{{header}}</th>
                         {% elif header == 'Mean' %}
-                        <th style="text-align: right; background-color: #eeeeee;">{{header}}</th>
+                        <th>{{header}}</th>
                         {% elif header == 'Additive Effect' %}
-                        <th style="text-align: right; background-color: #eeeeee;">Add&nbsp;&nbsp;<br>Effect<a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup style="color:#f00"> ?</sup></a></th>
+                        <th>Additive Effect<a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup style="color:#f00"> ?</sup></a></th>
                         {% elif header == 'Index' %}
-                        <th style="text-align: right; background-color: #eeeeee; padding-left: 0px; margin-left: 0px;">{{header}}</th>
+                        <th>{{header}}</th>
                         {% elif header == 'N' %}
-                        <th style="text-align: right; background-color: #eeeeee;">{{header}}</th>
+                        <th>{{header}}</th>
                         {% else %}
-                        <th style="background-color: #eeeeee;">{{header}}</th>
+                        <th>{{header}}</th>
                         {% endif %}
                     {% endfor %}
                     {% if target_dataset.type == "ProbeSet" %}
                         {% if corr_method == 'pearson' %}
-                        <th style="text-align: right; background-color: #eeeeee;">Sample r</th>
-                        <th style="text-align: right; background-color: #eeeeee;">&nbsp;&nbsp;N</th>
-                        <th style="text-align: right; background-color: #eeeeee;">Sample p(r)</th>
-                        <th style="text-align: right; background-color: #eeeeee;">Lit r</th>
-                        <th style="text-align: right; background-color: #eeeeee;">Tissue r</th>
+                        <th>Sample r</th>
+                        <th>&nbsp;&nbsp;N</th>
+                        <th>Sample p(r)</th>
+                        <th>Lit r</th>
+                        <th>Tissue r</th>
                         {% else %}
-                        <th style="text-align: right; background-color: #eeeeee;">Sample rho</th>
-                        <th style="text-align: right; background-color: #eeeeee;">N</th>
-                        <th style="text-align: right; background-color: #eeeeee;">Sample p(rho)</th>
-                        <th style="text-align: right; background-color: #eeeeee;">Lit r</th>
-                        <th style="text-align: right; background-color: #eeeeee;">Tissue rho</th>
+                        <th>Sample rho</th>
+                        <th>N</th>
+                        <th>Sample p(rho)</th>
+                        <th>Lit r</th>
+                        <th>Tissue rho</th>
                         {% endif %}
                     {% elif target_dataset.type == "Publish" %}
                         {% if corr_method == 'pearson' %}
-                        <th style="text-align: right; background-color: #eeeeee;">Sample r</th>
-                        <th style="text-align: right; background-color: #eeeeee;">&nbsp;&nbsp;N</th>
-                        <th style="text-align: right; background-color: #eeeeee;">Sample p(r)</th>
+                        <th>Sample r</th>
+                        <th>&nbsp;&nbsp;N</th>
+                        <th>Sample p(r)</th>
                         {% else %}
-                        <th style="text-align: right; background-color: #eeeeee;">Sample rho</th>
-                        <th style="text-align: right; background-color: #eeeeee;">&nbsp;&nbsp;N</th>
-                        <th style="text-align: right; background-color: #eeeeee;">Sample p(rho)</th>
+                        <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 style="text-align: right; background-color: #eeeeee;">Sample r</th>
-                        <th style="text-align: right; background-color: #eeeeee;">N</th>
-                        <th style="text-align: right; background-color: #eeeeee;">Sample p(r)</th>
+                        <th>Sample r</th>
+                        <th>N</th>
+                        <th>Sample p(r)</th>
                         {% else %}
-                        <th style="text-align: right; background-color: #eeeeee;">Sample rho</th>
-                        <th style="text-align: right; background-color: #eeeeee;">N</th>
-                        <th style="text-align: right; background-color: #eeeeee;">Sample p(rho)</th>
+                        <th>Sample rho</th>
+                        <th>N</th>
+                        <th>Sample p(rho)</th>
                         {% endif %}
                     {% endif %}
                     </tr>
@@ -99,7 +99,7 @@
                 <tbody>
                 {% for trait in correlation_results %}
                     <tr>
-                        <td>&nbsp;<INPUT TYPE="checkbox" NAME="searchResult" class="checkbox trait_checkbox" style="transform: scale(1.5);" VALUE="{{ data_hmac('{}:{}'.format(trait.name, trait.dataset.name)) }}"></td>
+                        <td align="center" style="padding-right: 0px;">&nbsp;<INPUT TYPE="checkbox" NAME="searchResult" class="checkbox trait_checkbox" style="padding-right: 0px;" VALUE="{{ data_hmac('{}:{}'.format(trait.name, trait.dataset.name)) }}"></td>
                         <td align="right">{{ loop.index }}</td>
                         <td>
                             <a href="{{ url_for('show_trait_page',
@@ -114,21 +114,21 @@
                         <td>{{ trait.description_display }}</TD>
                         <td align="right"style="white-space: nowrap;">{{ trait.location_repr }}</td>
                         <td align="right">{{ '%0.3f' % trait.mean|float }}</td>
-                        <td align="right" style="padding-right: 15px;">{% if trait.LRS_score_repr != "N/A" %}{{ '%0.1f' % trait.LRS_score_repr|float }}{% else %}N/A{% endif %}</td>
-                        <td align="right" style="padding-right: 15px;">{{ trait.LRS_location_repr }}</td>
-                        <td align="right" style="padding-right: 15px;">{% if trait.additive != "" %}{{ '%0.3f' % trait.additive|float }}{% else %}N/A{% endif %}</td>
-                        <td align="right" style="padding-right: 15px;"><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" style="padding-right: 15px;">{{ trait.num_overlap }}</td>
-                        <td align="right" style="padding-right: 15px;">{{'%0.3e'|format(trait.sample_p)}}</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>
                         {% if trait.lit_corr == "" or trait.lit_corr == 0.000 %}
-                        <td align="right" style="padding-right: 15px;">--</td>
+                        <td align="right">--</td>
                         {% else %}
-                        <td align="right" style="padding-right: 15px;">{{'%0.3f'|format(trait.lit_corr)}}</td>
+                        <td align="right">{{'%0.3f'|format(trait.lit_corr)}}</td>
                         {% endif %}
                         {% if trait.tissue_corr == "" or trait.tissue_corr == 0.000 %}
-                        <td align="right" style="padding-right: 15px;">--</td>
+                        <td align="right">--</td>
                         {% else %}
-                        <td align="right" style="padding-right: 15px;">{{'%0.3f'|format(trait.tissue_corr)}}</td>
+                        <td align="right">{{'%0.3f'|format(trait.tissue_corr)}}</td>
                         {% endif %}
                       {% elif target_dataset.type == "Publish" %}
                         <td>{{ trait.description_display }}</td>
@@ -138,17 +138,17 @@
                                 {{ trait.pubmed_text }}
                             </a>
                         </td>
-                        <td align="right" style="padding-right: 15px;">{{ trait.LRS_score_repr }}</td>
-                        <td align="right" style="padding-right: 15px;">{{ trait.LRS_location_repr }}</td>
-                        <td align="right" style="padding-right: 15px;">{% if trait.additive != "" %}{{ '%0.3f' % trait.additive|float }}{% else %}N/A{% endif %}</td>
-                        <td align="right" style="padding-right: 15px;"><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" style="padding-right: 15px;">{{ trait.num_overlap }}</td>
-                        <td align="right" style="padding-right: 15px;">{{'%0.3e'|format(trait.sample_p)}}</td>
+                        <td align="right">{{ trait.LRS_score_repr }}</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>
                       {% elif target_dataset.type == "Geno" %}
-                        <td align="right" style="padding-right: 15px;">{{ trait.location_repr }}</TD>
-                        <td align="right" style="padding-right: 15px;"><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" style="padding-right: 15px;">{{ trait.num_overlap }}</td>
-                        <td align="right" style="padding-right: 15px;">{{'%0.3e'|format(trait.sample_p)}}</td>
+                        <td align="right">{{ trait.location_repr }}</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>
                       {% endif %}
                     </tr>
                 {% endfor %}
@@ -278,6 +278,13 @@
                     { "type": "natural" },
                     { "type": "natural" }
                 ],
+                "createdRow": function ( row, data, index ) {
+                    $('td', row).eq(4).attr('title', $('td', row).eq(4).text());
+                    if ($('td', row).eq(4).text().length > 60) {
+                        $('td', row).eq(4).text($('td', row).eq(4).text().substring(0, 60));
+                        $('td', row).eq(4).text($('td', row).eq(4).text() + '...')
+                    }
+                },
                 "order": [[12, "asc" ]],
                 "sDom": "Btir",
                 "autoWidth": false,
@@ -287,7 +294,6 @@
             } );
 
             var table = $('#trait_table').DataTable();
-            new $.fn.dataTable.FixedHeader( table );
 
             {% elif target_dataset.type == "Publish" %}
             $('#trait_table').dataTable( {
@@ -311,7 +317,7 @@
                     { "type": "natural" },
                     { "type": "natural" },
                     { "type": "natural", "width": "25%" },
-                    { "type": "natural", "width": "10%" },
+                    { "type": "natural", "width": "15%" },
                     { "type": "natural" },
                     { "type": "natural" },
                     { "type": "natural" },
@@ -320,6 +326,13 @@
                     { "type": "natural" },
                     { "type": "scientific" }
                 ],
+                "createdRow": function ( row, data, index ) {
+                    $('td', row).eq(4).attr('title', $('td', row).eq(4).text());
+                    if ($('td', row).eq(4).text().length > 60) {
+                        $('td', row).eq(4).text($('td', row).eq(4).text().substring(0, 60));
+                        $('td', row).eq(4).text($('td', row).eq(4).text() + '...')
+                    }
+                },
                 "order": [[11, "asc" ]],
                 "sDom": "Btir",
                 "autoWidth": false,
diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html
index 1694eae5..72ced084 100755
--- a/wqflask/wqflask/templates/index_page_orig.html
+++ b/wqflask/wqflask/templates/index_page_orig.html
@@ -173,6 +173,16 @@
             </div>
 
             <div style="padding-left:120px" class="col-xs-4" style="width: 600px !important;">
+                <section id="websites">
+                    <div class="page-header">
+                        <h1>Github</h1>
+                    </div>
+                    <ul>
+                      <li><a href="https://github.com/genenetwork/genenetwork2">GN2 Source Code</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>
+                    </ul>
+               </section>
                 <section id="news-section">
                     <div class="page-header">
                         <h1>News</h1>
@@ -212,7 +222,7 @@
 
                 <section id="websites">
                     <div class="page-header">
-                        <h2>Links</h2>
+                        <h1>Links</h1>
                     </div>
                     <h3>GeneNetwork v2:</h3>
                       <ul>
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html
index 6d3f9326..4cea51b2 100644
--- a/wqflask/wqflask/templates/marker_regression_gn1.html
+++ b/wqflask/wqflask/templates/marker_regression_gn1.html
@@ -137,9 +137,9 @@
             <li id="gn1_map_tab">
               <a href="#gn1_map" data-toggle="tab" aria-expanded="true">GN1 Map</a>
             </li>
-            {% if mapping_method != "gemma" %}
+            {% if mapping_method != "gemma" and mapping_method != "plink" %}
             <li id="vector_map_tab">
-              <a href="#vector_map" data-toggle="tab" {% if mapping_method != "gemma" %}aria-expanded="false"{% else %}aria-expanded="true"{% endif %}>Vector Map</a>
+              <a href="#vector_map" data-toggle="tab" {% if mapping_method != "gemma" and mapping_method != "plink" %}aria-expanded="false"{% else %}aria-expanded="true"{% endif %}>Vector Map</a>
             </li>
             {% endif %}
           </ul>
@@ -161,7 +161,7 @@
                   {% endif %}
               </div>
             </div>
-            {% if mapping_method != "gemma" %}
+            {% if mapping_method != "gemma" and mapping_method != "plink" %}
             <div class="tab-pane {% if mapping_method == "gemma" %}active{% endif %}" id="vector_map">
               <div id="chart_container">
                 <div class="qtlcharts" id="topchart"></div>
@@ -277,11 +277,13 @@
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.scientific.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
 
+    {% if mapping_method != "gemma" and mapping_method != "plink" %}
     <script>
         js_data = {{ js_data | safe }}
     </script>
+    {% endif %}
 
-    {% if mapping_method != "gemma" %}
+    {% if mapping_method != "gemma" and mapping_method != "plink" %}
     <script language="javascript" type="text/javascript" src="/static/new/javascript/panelutil.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/chr_lod_chart.js"></script> 
     <script language="javascript" type="text/javascript" src="/static/new/javascript/lod_chart.js"></script>
@@ -385,6 +387,7 @@
             return $('#marker_regression_form').submit(); 
         };
 
+        {% if mapping_method != "gemma" and mapping_method != "plink" %}
         export_perm_data = function() {
             var num_perm, perm_data;
             num_perm = js_data.num_perm
@@ -393,7 +396,8 @@
             $('input[name=perm_results]').val(json_perm_data);
             $('#marker_regression_form').attr('action', '/export_perm_data');
             return $('#marker_regression_form').submit();
-    };
+        }
+        {% endif %}
 
     </script>
 
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 772c4314..56b6cc62 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -17,7 +17,9 @@
 {% block content %} <!-- Start of body -->
 
 <!--
-    {% if this_trait.dataset.type != 'Geno' %}
+    {% if dataset.type == 'Temp' %}
+	{{ header("{}".format("Temporary Trait")) }}
+    {% elif dataset.type != 'Geno' %}
 	{{ header("{}".format(this_trait.name_header_fmt),
 	    '{}: {}'.format(this_trait.name, this_trait.description_fmt)) }}
     {% else %}
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 547c3c27..a0c40c7f 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -3,10 +3,12 @@
         <td>Species and Group</td>
         <td>{{ this_trait.dataset.group.species }}, {{ this_trait.dataset.group.name }}</td>
     </tr>
+    {% if this_trait.dataset.type == 'Publish' %}
     <tr>
         <td>Tissue</td>
         <td>{{ this_trait.dataset.tissue }}</td>
     </tr>
+    {% endif %}
     {% if this_trait.dataset.type == 'ProbeSet' %}
     {% if this_trait.symbol != None %}
     <tr>
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 12ba80b9..23c09d05 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -17,16 +17,17 @@
                 </li>
                 {% endif %}
                 {# if use_plink_gemma #}
-                {% if dataset.group.mapping_id == "2" or dataset.group.mapping_id == "4" %}
+                {% for mapping_method in dataset.group.mapping_names %}
+                {% if mapping_method == "GEMMA" %}
                 <li class="active">
                     <a href="#gemma" data-toggle="tab">GEMMA</a>
                 </li>
-                {% if dataset.group.mapping_id == "4" %}
+                {% elif mapping_method == "PLINK" %}
                 <li>
                     <a href="#plink" data-toggle="tab">PLINK</a>
                 </li>
                 {% endif %}
-                {% endif %}
+                {% endfor %}
                 <!--<li>
                     <a href="#pair_scan" data-toggle="tab">Pair Scan</a>
                 </li>-->
diff --git a/wqflask/wqflask/templates/submit_trait.html b/wqflask/wqflask/templates/submit_trait.html
index 2529a4f4..8d624ffd 100644
--- a/wqflask/wqflask/templates/submit_trait.html
+++ b/wqflask/wqflask/templates/submit_trait.html
@@ -2,7 +2,7 @@
 {% block title %}Trait Submission{% endblock %}
 {% block content %}
 <!-- Start of body -->
-  <form method="post" action="/show_trait">
+  <form method="post" action="/show_temp_trait">
     <div class="container-fluid">
 
         {{ flash_me() }}