From 3f1049827499e1647769d37f27aabf524dbe9690 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 26 Aug 2015 22:15:25 +0000
Subject: Fixed issue with colums for the gene global search (still need to
 change for phenotype)

Fixed issue where LRS and LOD are sometimes labeled incorrectly

Changed the header of the trait page

Added link to GN1 in header

Fixxed an issue that made permutations not work with pylmm

Fixed "sign in" button when creating a collection while not logged in
---
 wqflask/base/data_set.py                           | 52 +++++++------
 wqflask/wqflask/collect.py                         |  2 +
 .../wqflask/marker_regression/marker_regression.py |  5 +-
 .../static/new/javascript/dataset_select_menu.js   |  1 +
 wqflask/wqflask/static/new/javascript/histogram.js |  2 +-
 .../static/packages/bootstrap/css/bootstrap.css    |  4 +-
 wqflask/wqflask/templates/base.html                |  3 +-
 wqflask/wqflask/templates/collections/add.html     |  6 +-
 wqflask/wqflask/templates/gsearch_gene.html        |  4 +-
 wqflask/wqflask/templates/marker_regression.html   |  7 +-
 wqflask/wqflask/templates/search_result_page.html  | 87 ++++++++++++++++++----
 wqflask/wqflask/templates/show_trait.html          | 48 ++++--------
 wqflask/wqflask/templates/show_trait_details.html  |  6 +-
 .../templates/show_trait_mapping_tools.html        |  2 +-
 14 files changed, 145 insertions(+), 84 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index c60efe65..e98258f6 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -559,29 +559,39 @@ class DataSet(object):
         This is not meant to retrieve the data set info if no name at all is passed.
 
         """
-
-        query_args = tuple(escape(x) for x in (
-            (self.type + "Freeze"),
-            str(webqtlConfig.PUBLICTHRESH),
-            self.name,
-            self.name,
-            self.name))
-        print("query_args are:", query_args)
-
-        #print("""
-        #        SELECT Id, Name, FullName, ShortName
-        #        FROM %s
-        #        WHERE public > %s AND
-        #             (Name = '%s' OR FullName = '%s' OR ShortName = '%s')
-        #  """ % (query_args))
         
         try:
-            self.id, self.name, self.fullname, self.shortname = g.db.execute("""
-                    SELECT Id, Name, FullName, ShortName
-                    FROM %s
-                    WHERE public > %s AND
-                         (Name = '%s' OR FullName = '%s' OR ShortName = '%s')
-              """ % (query_args)).fetchone()
+            if self.type == "ProbeSet":
+                query_args = tuple(escape(x) for x in (
+                    str(webqtlConfig.PUBLICTHRESH),
+                    self.name,
+                    self.name,
+                    self.name))
+
+                self.id, self.name, self.fullname, self.shortname, self.tissue = g.db.execute("""
+                        SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName, ProbeSetFreeze.ShortName, Tissue.Name
+                        FROM ProbeSetFreeze, ProbeFreeze, Tissue
+                        WHERE ProbeSetFreeze.public > %s AND
+                              ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND
+                              ProbeFreeze.TissueId = Tissue.Id AND
+                             (ProbeSetFreeze.Name = '%s' OR ProbeSetFreeze.FullName = '%s' OR ProbeSetFreeze.ShortName = '%s')
+                  """ % (query_args)).fetchone()
+            else:
+                query_args = tuple(escape(x) for x in (
+                    (self.type + "Freeze"),
+                    str(webqtlConfig.PUBLICTHRESH),
+                    self.name,
+                    self.name,
+                    self.name))
+
+                self.tissue = "N/A"
+                self.id, self.name, self.fullname, self.shortname = g.db.execute("""
+                        SELECT Id, Name, FullName, ShortName
+                        FROM %s
+                        WHERE public > %s AND
+                             (Name = '%s' OR FullName = '%s' OR ShortName = '%s')
+                  """ % (query_args)).fetchone()
+
         except TypeError:
             print("Dataset {} is not yet available in GeneNetwork.".format(self.name))
             pass
diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index c7c1e744..750f4757 100755
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -181,6 +181,8 @@ def collections_new():
     if "anonymous_add" in params:
         AnonCollection().add_traits(params, "Default")
         return redirect(url_for('view_collection'))
+    elif "sign_in" in params:
+        return redirect(url_for('login'))
 
     collection_name = params['new_collection']
 
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 850dfc7f..1c5757a6 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -165,7 +165,10 @@ class MarkerRegression(object):
                 else:
                     self.json_data['chr'].append(str(qtl['chr']))
                 self.json_data['pos'].append(qtl['Mb'])
-                self.json_data['lod.hk'].append(str(qtl['lod_score']))
+                if self.score_type == "LRS":
+                    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
diff --git a/wqflask/wqflask/static/new/javascript/dataset_select_menu.js b/wqflask/wqflask/static/new/javascript/dataset_select_menu.js
index fb9fdcf3..f91504be 100644
--- a/wqflask/wqflask/static/new/javascript/dataset_select_menu.js
+++ b/wqflask/wqflask/static/new/javascript/dataset_select_menu.js
@@ -94,6 +94,7 @@ $(function() {
   $('#dataset_info').click(dataset_info);
   make_default = function() {
     var holder, item, jholder, _i, _len, _ref;
+    alert("The current settings are now your default.")
     holder = {};
     _ref = ['species', 'group', 'type', 'dataset'];
     for (_i = 0, _len = _ref.length; _i < _len; _i++) {
diff --git a/wqflask/wqflask/static/new/javascript/histogram.js b/wqflask/wqflask/static/new/javascript/histogram.js
index d872a3ba..d26d0c03 100755
--- a/wqflask/wqflask/static/new/javascript/histogram.js
+++ b/wqflask/wqflask/static/new/javascript/histogram.js
@@ -68,7 +68,7 @@
     Histogram.prototype.get_histogram_data = function() {
       var n_bins;
       console.log("sample_vals:", this.sample_vals);
-      n_bins = Math.sqrt(this.sample_vals.length);
+      n_bins = 2*Math.sqrt(this.sample_vals.length); //Was originally just the square root, but increased to 2*; ideally would be a GUI for changing this
       this.histogram_data = d3.layout.histogram().bins(this.x_scale.ticks(n_bins))(this.sample_vals);
       return console.log("histogram_data:", this.histogram_data[0]);
     };
diff --git a/wqflask/wqflask/static/packages/bootstrap/css/bootstrap.css b/wqflask/wqflask/static/packages/bootstrap/css/bootstrap.css
index dd6fa736..4145e73f 100755
--- a/wqflask/wqflask/static/packages/bootstrap/css/bootstrap.css
+++ b/wqflask/wqflask/static/packages/bootstrap/css/bootstrap.css
@@ -1215,7 +1215,7 @@ a.bg-danger:hover {
 }
 .page-header {
   padding-bottom: 9px;
-  margin: 20px 0 20px;
+  margin: 10px 0 10px;
   border-bottom: 1px solid #eee;
 }
 ul,
@@ -4674,7 +4674,7 @@ a.list-group-item.active > .badge,
   margin-left: 3px;
 }
 .jumbotron {
-  margin-bottom: 30px;
+  margin-bottom: 10px;
   color: inherit;
   background-color: #eee;
 }
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index 75af8ba5..90acd0da 100755
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -83,7 +83,8 @@
                     <option value="phenotype" {% if type=="phenotype" %}selected{% endif %}>Phenotypes</option>
                 </select>
                 <input class="btn btn-primary form-control col-xs-2" style="width: 100px; margin-top: 15px; margin-left: 10px;" type="submit" value="Search All">
-                <input class="form-control col-xs-6" style="width: 980px; margin-top: 15px; margin-left: 10px;" type="text" name="terms" required>
+                <input class="form-control col-xs-6" style="width: 600px; margin-top: 15px; margin-left: 10px;" type="text" name="terms" required>
+                <a href="http://www.genenetwork.org"><input class="btn btn-primary form-control col-xs-2" style="width: 175px; margin-top: 15px; margin-left: 50px;" value="Use GeneNetwork 1"></a>
             </div>
         </form>
     </div>
diff --git a/wqflask/wqflask/templates/collections/add.html b/wqflask/wqflask/templates/collections/add.html
index faee4f78..07fcba22 100755
--- a/wqflask/wqflask/templates/collections/add.html
+++ b/wqflask/wqflask/templates/collections/add.html
@@ -1,11 +1,12 @@
 <div id="myModal">
     <div class="modal-header">
         <h3>Add to collection</h3>
-        <p>You have three choices: Use your default collection, create a new named collection,
+        <p>You have two choices: Create and name a collection,
         or add the traits to an existing collection.</p>
     </div>
     <div class="modal-body">
         <form action="/collections/new" data-validate="parsley" id="add_form">
+<!--
             <fieldset>
                 <legend>Use your default collection</legend>
                 <span class="help-block">Choose this if you're in a hurry or don't plan on using the collection again.</span>
@@ -13,11 +14,12 @@
                 <button type="submit" name="Default" class="btn">Continue</button>
             </fieldset>
             <hr />
+-->
 
 
             <input type="hidden" name="traits" value="{{ traits }}" />
             <fieldset>
-                <legend>Or create a new named collection</legend>
+                <legend>Create a new named collection</legend>
                 <label>New collection name</label>
                 <input type="text" name="new_collection" placeholder="Name of new collection..."
                     data-trigger="change" data-minlength="5" data-maxlength="50">
diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/wqflask/wqflask/templates/gsearch_gene.html
index 6beefb01..c7e50a16 100755
--- a/wqflask/wqflask/templates/gsearch_gene.html
+++ b/wqflask/wqflask/templates/gsearch_gene.html
@@ -52,8 +52,8 @@
                         <TD>{{ loop.index }}</TD>
                         <TD>{{ this_trait.dataset.group.species }}</TD>
                         <TD>{{ this_trait.dataset.group.name }}</TD>
-                        <TD>{{ this_trait.dataset.name }}</TD>
-                        <TD>{{ this_trait.dataset.name }}</TD>
+                        <TD>{{ this_trait.dataset.tissue }}</TD>
+                        <TD>{{ this_trait.dataset.fullname }}</TD>
                         <TD><a href="{{ url_for('show_trait_page', trait_id = this_trait.name, dataset = this_trait.dataset.name)}}">{{ this_trait.name }}</a></TD>
                         <TD>{{ this_trait.symbol }}</TD>
                         <TD>{{ this_trait.description_display }}</TD>
diff --git a/wqflask/wqflask/templates/marker_regression.html b/wqflask/wqflask/templates/marker_regression.html
index 91808fcf..d83730a2 100755
--- a/wqflask/wqflask/templates/marker_regression.html
+++ b/wqflask/wqflask/templates/marker_regression.html
@@ -34,7 +34,7 @@
                 <thead>
                     <tr>
                         <th>Index</th>
-                        <th>LOD Score</th>
+                        <th>{{ score_type }}</th>
                         <th>Chr</th>
                         <th>Mb</th>
                         <th>Locus</th>
@@ -87,7 +87,10 @@
                     { "type": "natural" },
                     { "type": "natural" }
                     ],
-                "sDom": "ZRtir",
+                "buttons": [
+                    'csv'
+                ],
+                "sDom": "RZBtir",
                 "iDisplayLength": -1,
                 "autoWidth": true,
                 "bDeferRender": true,
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 117e2dcd..d0875b71 100755
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -2,8 +2,6 @@
 {% block title %}Search Results{% endblock %}
 {% block 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/packages/DataTables/extensions/dataTables.fixedHeader.css" >
     <link rel="stylesheet" type="text/css" href="//cdn.datatables.net/fixedcolumns/3.0.4/css/dataTables.fixedColumns.css">
     <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.bootstrap.css" />
@@ -45,12 +43,21 @@
           <button class="btn btn-default" id="deselect_all"><span class="glyphicon glyphicon-remove"></span> Deselect All</button>
           <button class="btn btn-default" id="invert"><span class="glyphicon glyphicon-resize-vertical"></span> Invert</button>
           <button class="btn btn-default" id="add" disabled><span class="glyphicon glyphicon-plus-sign"></span> Add</button>
-          <button class="btn btn-default"><span class="glyphicon glyphicon-download"></span> Download Table</button>
+          <!--<button class="btn btn-default"><span class="glyphicon glyphicon-download"></span> Download Table</button>-->
           <button id="redraw" class="btn btn-default">Reset Columns</button>
           <input type="text" id="searchbox" class="form-control" style="width: 200px; display: inline;" placeholder="Search This Table For ...">
           <input type="text" id="select_top" class="form-control" style="width: 200px; display: inline;" placeholder="Select Top ...">
           <br />
           <br />
+          <button class="btn btn-default" id="open_options">Open Extra Options</button>
+          <br />
+          <br />
+          <div id="extra_options" style="display:none;">
+          Min LRS <input type="text" id="min" class="form-control" style="width: 60px; display: inline;">
+          Max LRS <input type="text" id="max" class="form-control" style="width: 60px; display: inline;">
+          </div>
+          <br />
+          <br />
           <div id="table_container">
             <table class="table table-hover table-striped" id='trait_table' {% if dataset.type == 'Geno' %}width="400px"{% endif %} style="float: left;">
                 <thead>
@@ -58,7 +65,7 @@
                         <th style="width: 30px;"></th>
                     {% for header in header_fields %}
                         {% if header == 'Max LRS' %}
-                        <th style="text-align: right;">Max&nbsp;&nbsp;<br>LRS<a href="http://genenetwork.org//glossary.html#L" target="_blank"><sup style="color:#f00"> ?</sup></a></th>
+                        <th style="text-align: right;">Max&nbsp;&nbsp;<br>LRS</th>
                         {% elif header == 'Additive Effect' %}
                         <th style="text-align: right;">Additive<br>Effect<a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup style="color:#f00"> ?</sup></a></th>
                         {% else %}
@@ -73,7 +80,7 @@
                     <TR id="trait:{{ this_trait.name }}:{{ this_trait.dataset.name }}">
                         <TD><INPUT TYPE="checkbox" NAME="searchResult" class="checkbox trait_checkbox" style="transform: scale(1.5);" VALUE="{{ data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset.name)) }}">
                         </TD>
-                        <TD>{{ loop.index }}</TD>
+                        <TD align="right">{{ loop.index }}</TD>
                         <TD>
                             <a href="{{ url_for('show_trait_page',
                                     trait_id = this_trait.name,
@@ -132,8 +139,6 @@
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colReorder.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.fixedHeader.js"></script>
     <script language="javascript" type="text/javascript" src="//cdn.datatables.net/fixedcolumns/3.0.4/js/dataTables.fixedColumns.min.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 type="text/javascript" charset="utf-8">
         function getValue(x) {
@@ -150,7 +155,41 @@
             }
             return parseFloat(x);
         }
-            
+
+
+        function filtering( oSettings, aData, iDataIndex, column) {
+            var iColumn = column;
+            if (document.getElementById('min').value){
+                var iMin = document.getElementById('min').value * 1;
+            } else {
+                var iMin = 0
+            }
+            if (document.getElementById('max').value){
+                var iMax = document.getElementById('max').value * 1;
+            } else {
+                var iMax = 10000
+            }
+
+            var iVersion = aData[iColumn] == "-" ? 0 : aData[iColumn]*1;
+            if ( iMin === "" && iMax === "" )
+            {
+                return true;
+            }
+            else if ( iMin === "" && iVersion < iMax )
+            {
+                return true;
+            }
+            else if ( iMin < iVersion && "" === iMax )
+            {
+                return true;
+            }
+            else if ( iMin < iVersion && iVersion < iMax )
+            {
+                return true;
+            }
+                return false;
+        }
+
         jQuery.fn.dataTableExt.oSort['cust-txt-asc'] = function (a, b) {
             var x = getValue(a);
             var y = getValue(b); 
@@ -183,13 +222,21 @@
 
             console.time("Creating table");
             {% if dataset.type == 'ProbeSet' %}
+
+            jQuery.fn.dataTableExt.afnFiltering.push(
+                function( oSettings, aData, iDataIndex ) {
+                    return filtering( oSettings, aData, iDataIndex, 7 );
+
+                }
+            );
+
             $('#trait_table').DataTable( {
                 "columns": [
                     { "type": "natural" },
                     { "type": "natural" },
                     { "type": "natural" },
                     { "type": "natural" },
-                    { "type": "natural", "width": "30%" },
+                    { "type": "natural", "width": "40%" },
                     { "type": "natural", "width": "15%" },
                     { "type": "natural" },
                     { "type": "natural" },
@@ -201,7 +248,6 @@
                 ],
                 "sDom": "RZBtir",
                 "iDisplayLength": -1,
-                "autoWidth": false,
                 "bDeferRender": true,
                 "bSortClasses": false,
                 "scrollY": "700px",
@@ -222,7 +268,10 @@
                     { "type": "natural", "width": "15%"},
                     { "type": "natural" }
                 ],
-                "sDom": "RZtir",
+                "buttons": [
+                    'csv'
+                ],
+                "sDom": "RZBtir",
                 "iDisplayLength": -1,
                 "autoWidth": false,
                 "bDeferRender": true,
@@ -239,7 +288,10 @@
                     { "type": "natural" },
                     { "type": "natural", "width": "40%"}
                 ],
-                "sDom": "RZtir",
+                "buttons": [
+                    'csv'
+                ],
+                "sDom": "RZBtir",
                 "iDisplayLength": -1,
                 "autoWidth": true,
                 "bDeferRender": true,
@@ -251,13 +303,18 @@
             {% endif %}
             console.timeEnd("Creating table");
             
+            var table = $('#trait_table').DataTable();
             $('#redraw').click(function() {
                 var table = $('#trait_table').DataTable();
                 table.colReorder.reset()
             });
-            
-            //new $.fn.dataTable.FixedHeader( table );
-            //new $.fn.dataTable.FixedColumns( table );
+
+            $('#min').keyup( function() { table.draw(); } );
+            $('#max').keyup( function() { table.draw(); } );
+
+            $('#open_options').click( function () {
+                $('#extra_options').toggle();
+            });
 
         });
     </script>
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 6199f931..0709a82f 100755
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -11,8 +11,8 @@
     <link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" />
     <link rel="stylesheet" type="text/css" href="/static/new/packages/nvd3/nv.d3.min.css" />
     <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
+    <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.bootstrap.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" />
 
 {% endblock %}
 {% block content %} <!-- Start of body -->
@@ -37,12 +37,6 @@
         <input type="hidden" name="temp_uuid" id="temp_uuid" value="{{ temp_uuid }}">
 
         <div class="container">
-            <div class="page-header">
-                <h1>{{ dataset.group.species.capitalize() }} -
-                    {{ dataset.group.name }} -
-                    {{ this_trait.name_header_fmt }}
-                </h1>
-            </div>
             
             {% include 'show_trait_details.html' %}
             <div class="panel-group" id="accordion">
@@ -145,12 +139,14 @@
     <script language="javascript" type="text/javascript" src="/static/new/javascript/lod_chart.js"></script>
 
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.js"></script>
+    <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/dataTables.buttons.min.js"></script>
+    <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/buttons.html5.min.js"></script>
+    <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/buttons.bootstrap.min.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.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/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colResize.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colReorder.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 type="text/javascript" charset="utf-8">
             
            function getValue(x) {
@@ -209,19 +205,10 @@
                         { "bSortable": false },
                         { "type": "cust-txt" }
                         ],
-                    "sDom": "RZtir",
-                    "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"
-                    },
+                    "buttons": [
+                        'csv'
+                    ],
+                    "sDom": "RZBtir",
                     "iDisplayLength": -1,
                     "autoWidth": false,
                     "bLengthChange": true,
@@ -245,19 +232,10 @@
                         null,
                         { "type": "cust-txt" }
                     ],
-                    "sDom": "RZtir",
-                    "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"
-                    },
+                    "buttons": [
+                        'csv'
+                    ],
+                    "sDom": "RZBtir",
                     "iDisplayLength": -1,
                     "autoWidth": false,
                     "bLengthChange": true,
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 108fcd92..04db915a 100755
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -1,4 +1,8 @@
 <dl class="dl-horizontal">
+    <dt>Species</dt>
+    <dd>{{ this_trait.dataset.group.species }}</dd>
+    <dt>Group</dt>
+    <dd>{{ this_trait.dataset.group.name }}</dd>
     {% if this_trait.dataset.type == 'ProbeSet' %}
     <dt>Aliases</dt>
     <dd>{{ this_trait.alias_fmt }}</dd>
@@ -33,7 +37,7 @@
     {% if this_trait.dataset.type == 'ProbeSet' %}
     <dd>
         {% if this_trait.symbol != None %}
-        <a href="http://bioinformatics-dev/Getd2g.pl?gene_list={{ this_trait.symbol }}" target="_blank" title="Related descriptive, genomic, clinical, functional and drug-therapy information">
+        <a href="http://www.genotation.org/Getd2g.pl?gene_list={{ this_trait.symbol }}" target="_blank" title="Related descriptive, genomic, clinical, functional and drug-therapy information">
             Genotation
         </a>
         &nbsp;&nbsp;
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index eea9b295..b9ac80bf 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -35,7 +35,7 @@
                         <div class="mapping_method_fields form-group">
                             <label for="mapping_permutations" class="col-xs-2 control-label">Permutations</label>
                             <div style="margin-left: 20px;" class="col-xs-4 controls">
-                                <input name="num_pylmm" value="" type="text" class="form-control">
+                                <input name="num_perm_pylmm" value="" type="text" class="form-control">
                             </div>
                         </div>
                         <div id="permutations_alert" class="alert alert-error alert-warning" style="display:none;">
-- 
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