Adding the port as a parameter to runserver; this should just be temporary until

I figure out how to get it to read the port from the config file instead

Using runserver.py instead of secure_server.py because of an error with the latter
that I haven't figured out how to fix yet

Improved the appearance of several of the tables

6 files changed, 138 insertions, 134 deletions

diff --git a/wqflask/cfg/default_settings.py b/wqflask/cfg/default_settings.py
index c9d2a934..8fca3d77 100755
--- a/wqflask/cfg/default_settings.py
+++ b/wqflask/cfg/default_settings.py
@@ -1,7 +1,5 @@
 LOGFILE = """/tmp/flask_gn_log"""
 
-SERVER_PORT = 5002
-
 #This is needed because Flask turns key errors into a
 #400 bad request response with no exception/log
 TRAP_BAD_REQUEST_ERRORS = True
diff --git a/wqflask/runserver.py b/wqflask/runserver.py
index 1cf38f8e..8ab88580 100755
--- a/wqflask/runserver.py
+++ b/wqflask/runserver.py
@@ -28,6 +28,7 @@ import logging_tree
 logging_tree.printout()
 
 app.run(host='0.0.0.0',
+        port=5002,
         use_debugger=False,
         threaded=True,
         use_reloader=True)
diff --git a/wqflask/wqflask/static/new/packages/DataTables/css/jquery.dataTables.css b/wqflask/wqflask/static/new/packages/DataTables/css/jquery.dataTables.css
index 68d5e4fa..7a674d3a 100755
--- a/wqflask/wqflask/static/new/packages/DataTables/css/jquery.dataTables.css
+++ b/wqflask/wqflask/static/new/packages/DataTables/css/jquery.dataTables.css
@@ -50,6 +50,7 @@ table.dataTable tr.outlier td{ background-color: #FFFF00; }
 .dataTables_wrapper {
 	position: relative;
 	clear: both;
+       float: left;
 	*zoom: 1;
 }
 
diff --git a/wqflask/wqflask/templates/marker_regression.html b/wqflask/wqflask/templates/marker_regression.html
index 2c8f42a1..6aed69d5 100755
--- a/wqflask/wqflask/templates/marker_regression.html
+++ b/wqflask/wqflask/templates/marker_regression.html
@@ -1,127 +1,126 @@
-{% extends "base.html" %}

-{% block title %}Interval Mapping{% endblock %}

-{% block css %}

-<!--    <link rel="stylesheet" type="text/css" href="/static/new/css/interval_mapping.css" />-->

-    <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />

-    <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />

-    <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" />

-    <link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" />

-    <link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" />

-{% endblock %}

-{% block content %} <!-- Start of body -->

-

-    {{ header("Mapping",

-        '{}: {}'.format(this_trait.name, this_trait.description_fmt)) }}

-

-    <div class="container">

-        <div>

-            <h2>

-                Whole Genome Mapping

-            </h2>

-            <form style ='float: left; padding: 5px;' id="exportform" action="export" method="post">

-              <input type="hidden" id="data" name="data" value="">

-              <input type="hidden" id="filename" name="filename" value="">

-              <input type="submit" id="export" value="Download SVG">

-            </form>

-            <form style ='float: left; padding: 5px;' id="exportpdfform" action="export_pdf" method="post">

-              <input type="hidden" id="data" name="data" value="">

-              <input type="hidden" id="filename" name="filename" value="">

-              <input type="submit" id="export_pdf" value="Download PDF">

-            </form>

-<!--            <button id="export_pdf" class="btn">Export PDF</button>-->

-        </div>

-        <div id="chart_container">

-            <div class="qtlcharts" id="topchart">

-                

-            </div>

-        </div>

-        <div>

-            <h2>

-                Results

-            </h2>

-        </div>

-        <table cellpadding="0" cellspacing="0" border="0" id="qtl_results" class="table table-hover table-striped table-bordered">

-            <thead>

-                <tr>

-                    <td>Index</td>

-                    <td>LOD Score</td>

-                    <td>Chr</td>

-                    <td>Mb</td>

-                    <td>Locus</td>

-                </tr>

-            </thead>

-            <tbody>

-                {% for marker in filtered_markers %}

-                    {% if marker.lod_score > lod_cutoff %}

-                    <tr>

-                        <td>{{loop.index}}</td>

-                        <td>{{marker.lod_score}}</td>

-                        <td>{{marker.chr}}</td>

-                        <td>{{marker.Mb}}</td>

-                        <td>{{marker.name}}</td>

-                    </tr>

-                    {% endif %}

-                {% endfor %}

-            </tbody>

-        </table>

-    

-    </div>

-

-    <!-- End of body -->

-

-{% endblock %}

-

-{% block js %}  

-    <script>

-        js_data = {{ js_data | safe }}

-    </script>

-

-    <!--[if lt IE 9]>

-<!--        <script language="javascript" type="text/javascript" src="/static/packages/jqplot/excanvas.js"></script>-->

-    <![endif]-->

-    <script language="javascript" type="text/javascript" src="http://d3js.org/d3.v3.min.js"></script>

-    <script language="javascript" type="text/javascript" src="/static/new/js_external/d3-tip.min.js"></script>

-<!--    <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/jspdf.js"></script>

-    <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/libs/FileSaver.js/FileSaver.js"></script>

-    <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/libs/Blob.js/BlobBuilder.js"></script>

-    <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/jspdf.plugin.standard_fonts_metrics.js"></script>

-    <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/jspdf.plugin.from_html.js"></script>-->

-    <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/manhattan_plot.js"></script>-->

-    <script language="javascript" type="text/javascript" src="/static/new/javascript/lod_chart.js"></script>

-    <script language="javascript" type="text/javascript" src="/static/new/javascript/create_lodchart.js"></script>

-    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>

-    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>

-    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.scientific.js"></script>

-    <script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script>

-    <script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script>

-    <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>

-

-    <script type="text/javascript" charset="utf-8">

-        $(document).ready( function () {

-            console.time("Creating table");

-            $('#qtl_results').dataTable( {

-                //"sDom": "<<'span3'l><'span3'T><'span4'f>'row-fluid'r>t<'row-fluid'<'span6'i><'span6'p>>",

-                "sDom": "lTftipr",

-                "oTableTools": {

-                    "aButtons": [

-                        "copy",

-                        "print",

-                        {

-                            "sExtends":    "collection",

-                            "sButtonText": 'Save <span class="caret" />',

-                            "aButtons":    [ "csv", "xls", "pdf" ]

-                        }

-                    ],

-                    "sSwfPath": "/static/packages/TableTools/media/swf/copy_csv_xls_pdf.swf"

-                },

-                "iDisplayLength": 50,

-                "bLengthChange": true,

-                "bDeferRender": true,

-                "bSortClasses": false

-            } );

-            console.timeEnd("Creating table");

-        });

-    </script>

+{% extends "base.html" %}
+{% block title %}Interval Mapping{% endblock %}
+{% block css %}
+<!--    <link rel="stylesheet" type="text/css" href="/static/new/css/interval_mapping.css" />-->
+    <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
+    <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />
+    <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" />
+    <link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" />
+    <link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" />
+{% endblock %}
+{% block content %} <!-- Start of body -->
+
+    {{ header("Mapping",
+        '{}: {}'.format(this_trait.name, this_trait.description_fmt)) }}
+
+    <div class="container">
+        <div>
+            <h2>
+                Whole Genome Mapping
+            </h2>
+            <form style ='float: left; padding: 5px;' id="exportform" action="export" method="post">
+              <input type="hidden" id="data" name="data" value="">
+              <input type="hidden" id="filename" name="filename" value="">
+              <input type="submit" id="export" value="Download SVG">
+            </form>
+            <form style ='float: left; padding: 5px;' id="exportpdfform" action="export_pdf" method="post">
+              <input type="hidden" id="data" name="data" value="">
+              <input type="hidden" id="filename" name="filename" value="">
+              <input type="submit" id="export_pdf" value="Download PDF">
+            </form>
+<!--            <button id="export_pdf" class="btn">Export PDF</button>-->
+        </div>
+        <div id="chart_container">
+            <div class="qtlcharts" id="topchart">
+                
+            </div>
+        </div>
+        <div>
+            <h2>
+                Results
+            </h2>
+            <table cellpadding="0" cellspacing="0" border="0" id="qtl_results" class="table table-hover table-striped table-bordered">
+                <thead>
+                    <tr>
+                        <td>Index</td>
+                        <td>LOD Score</td>
+                        <td>Chr</td>
+                        <td>Mb</td>
+                        <td>Locus</td>
+                   </tr>
+                </thead>
+                <tbody>
+                    {% for marker in filtered_markers %}
+                        {% if marker.lod_score > lod_cutoff %}
+                        <tr>
+                            <td>{{loop.index}}</td>
+                            <td>{{marker.lod_score}}</td>
+                            <td>{{marker.chr}}</td>
+                            <td>{{marker.Mb}}</td>
+                            <td>{{marker.name}}</td>
+                        </tr>
+                        {% endif %}
+                    {% endfor %}
+                </tbody>
+            </table>
+        </div>
+    </div>
+
+    <!-- End of body -->
+
+{% endblock %}
+
+{% block js %}  
+    <script>
+        js_data = {{ js_data | safe }}
+    </script>
+
+    <!--[if lt IE 9]>
+<!--        <script language="javascript" type="text/javascript" src="/static/packages/jqplot/excanvas.js"></script>-->
+    <![endif]-->
+    <script language="javascript" type="text/javascript" src="http://d3js.org/d3.v3.min.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/new/js_external/d3-tip.min.js"></script>
+<!--    <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/jspdf.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/libs/FileSaver.js/FileSaver.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/libs/Blob.js/BlobBuilder.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/jspdf.plugin.standard_fonts_metrics.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/jspdf.plugin.from_html.js"></script>-->
+    <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/manhattan_plot.js"></script>-->
+    <script language="javascript" type="text/javascript" src="/static/new/javascript/lod_chart.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/new/javascript/create_lodchart.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.scientific.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
+
+    <script type="text/javascript" charset="utf-8">
+        $(document).ready( function () {
+            console.time("Creating table");
+            $('#qtl_results').dataTable( {
+                //"sDom": "<<'span3'l><'span3'T><'span4'f>'row-fluid'r>t<'row-fluid'<'span6'i><'span6'p>>",
+                "sDom": "lTftipr",
+                "oTableTools": {
+                    "aButtons": [
+                        "copy",
+                        "print",
+                        {
+                            "sExtends":    "collection",
+                            "sButtonText": 'Save <span class="caret" />',
+                            "aButtons":    [ "csv", "xls", "pdf" ]
+                        }
+                    ],
+                    "sSwfPath": "/static/packages/TableTools/media/swf/copy_csv_xls_pdf.swf"
+                },
+                "iDisplayLength": 50,
+                "bLengthChange": true,
+                "bDeferRender": true,
+                "bSortClasses": false
+            } );
+            console.timeEnd("Creating table");
+        });
+    </script>
 {% endblock %}
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 0baac2d3..286ead6c 100755
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -84,12 +84,15 @@
 
             <br />
             <br />
-            
-            <button class="btn" id="select_all"><i class="icon-ok"></i> Select All</button>
-            <button class="btn" id="deselect_all"><i class="icon-remove"></i> Deselect All</button>
-            <button class="btn" id="invert"><i class="icon-resize-vertical"></i> Invert</button>
-            <button class="btn" id="add"><i class="icon-plus-sign"></i> Add</button>
-            <button class="btn btn-primary pull-right"><i class="icon-download icon-white"></i> Download Table</button>
+	     <br />
+
+            <div style="clear:both">
+                <button class="btn" id="select_all"><i class="icon-ok"></i> Select All</button>
+                <button class="btn" id="deselect_all"><i class="icon-remove"></i> Deselect All</button>
+                <button class="btn" id="invert"><i class="icon-resize-vertical"></i> Invert</button>
+                <button class="btn" id="add"><i class="icon-plus-sign"></i> Add</button>
+                <button class="btn btn-primary pull-right"><i class="icon-download icon-white"></i> Download Table</button>
+            </div>
         </div>
     </div>
 
diff --git a/wqflask/wqflask/templates/show_trait_edit_data.html b/wqflask/wqflask/templates/show_trait_edit_data.html
index e7df3b13..5d6346ca 100755
--- a/wqflask/wqflask/templates/show_trait_edit_data.html
+++ b/wqflask/wqflask/templates/show_trait_edit_data.html
@@ -119,6 +119,7 @@
                         {# Todo: Add IDs #}
                         <td class="column_name-Value">
                           <input type="text" data-value="{{ sample.display_value }}" name="{{ 'value:' + sample.name }}"
+                                 style="text-align:right;"
                                  class="trait_value_input edit_sample_value"
                                  value="{{ sample.display_value }}"
                                  size=8 maxlength=8
@@ -133,6 +134,7 @@
                         {# Todo: Add IDs #}
                         <td class="column_name-SE">
                           <input type="text" data-value="{{ sample.display_variance }}" name="{{ 'variance:' + sample.name}}"
+                                 style="text-align:right;"
                                  class="trait_value_input edit_sample_se"
                                  value="{{ sample.display_variance }}"
                                  size=8 maxlength=8