Merge https://github.com/zsloan/genenetwork2

4 files changed, 70 insertions, 65 deletions

diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index fc1edf2a..e41ade7c 100755
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -59,6 +59,9 @@
             <button class="btn btn-default" id="select_all"><span class="glyphicon glyphicon-ok"></span> Select All</button>
             <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" id="add" disabled="disabled"><i class="icon-plus-sign"></i> Add Record to Other Collection</button>
+            <button class="btn" id="remove" disabled="disabled"><i class="icon-minus-sign"></i> Remove Record</button>
+            <button class="btn btn-primary pull-right"><i class="icon-download icon-white"></i> Download Table</button>
             <br />
             <br />
         <table class="table table-hover table-striped" id='trait_table'>
diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html
index 5e0a92e3..cb29a07c 100755
--- a/wqflask/wqflask/templates/index_page.html
+++ b/wqflask/wqflask/templates/index_page.html
@@ -206,12 +206,12 @@
                     <h3>GN1 Mirror and development sites</h3>
 
                     <ul>
-                        <li><a href="http://www.genenetwork.org/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Main GN1 site at UTHSC</a> (main site)</li>
-                        <li><a href="http://www.genenetwork.waimr.uwa.edu.au/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Australia at the UWA</a></li>
-                        <li><a href="http://gn.genetics.ucla.edu/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">California at UCLA</a></li>
-                        <li><a href="http://genenetwork.helmholtz-hzi.de/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Germany at the HZI</a></li>
-                        <li><a href="http://genenetwork.memphis.edu/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Memphis at the U of M</a></li>
-                        <li><a href="http://genenetwork.epfl.ch/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Switzerland at the EPFL</a></li>
+                        <li><a href="http://www.genenetwork.org/" target="_blank">Main GN1 site at UTHSC</a> (main site)</li>
+                        <li><a href="http://www.genenetwork.waimr.uwa.edu.au/" target="_blank">Australia at the UWA</a></li>
+                        <li><a href="http://gn.genetics.ucla.edu/" target="_blank">California at UCLA</a></li>
+                        <li><a href="http://genenetwork.helmholtz-hzi.de/" target="_blank">Germany at the HZI</a></li>
+                        <li><a href="http://genenetwork.memphis.edu/" target="_blank">Memphis at the U of M</a></li>
+                        <li><a href="http://genenetwork.epfl.ch/" target="_blank">Switzerland at the EPFL</a></li>
                     </ul>
                 </section>
 
diff --git a/wqflask/wqflask/templates/pair_scan_results.html b/wqflask/wqflask/templates/pair_scan_results.html
index f46d7cbf..ab4a36bb 100644
--- a/wqflask/wqflask/templates/pair_scan_results.html
+++ b/wqflask/wqflask/templates/pair_scan_results.html
@@ -44,7 +44,7 @@
                    </tr>
                 </thead>
                 <tbody>
-                    {% for marker in pair_scan_results %}
+                    {% for marker in filtered_markers %}
                         <tr>
                             <td>{{loop.index}}</td>
                             <td>{{marker.name}}</td>
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 27504e51..bd1e6f1e 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -4,14 +4,16 @@
         
             <ul class="nav nav-pills">
                 <li class="active">
-                    <a href="#interval_mapping" data-toggle="tab">Interval Mapping</a>
-                </li>
-                <li>
                     <a href="#pylmm" data-toggle="tab">pyLMM</a>
                 </li>
                 <li>
                     <a href="#rqtl_geno" data-toggle="tab">rqtl</a>
                 </li>
+                {% if dataset.group.species != 'human' %}
+                <li>
+                    <a href="#interval_mapping" data-toggle="tab">Interval Mapping</a>
+                </li>
+                {% endif %}
                 {% if dataset.group.species == 'human' %}
                 <li>
                     <a href="#plink" data-toggle="tab">PLINK</a>
@@ -26,60 +28,7 @@
             </ul>
 
             <div class="tab-content">
-                <div class="tab-pane active" id="interval_mapping">
-                    <div style="padding: 20px" class="form-horizontal">
-                        <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_perm_reaper" value="2000" type="text" class="form-control">
-                            </div>
-                        </div>
-    
-                        <div class="mapping_method_fields form-group">
-                            <label for="mapping_bootstraps" class="col-xs-2 control-label" title="Bootstrapping Resamples">Bootstrap</label>
-                            <div style="margin-left: 20px;" class="col-xs-4 controls">
-                                <input name="mapping_bootstraps" value="2000" type="text" class="form-control">
-                            </div>
-                        </div>
-                    
-                        <div class="mapping_method_fields form-group">
-                            <label style="text-align:left;" class="col-xs-12 control-label">Display Additive Effect</label>
-                            <div class="col-xs-12 controls" id="display_additive_effect">                      
-                                <label class="radio-inline">
-                                    <input type="radio" name="display_additive" id="display_additive" value="yes" checked="">
-                                    Yes
-                                </label>
-                                <label class="radio-inline">
-                                    <input type="radio" name="display_additive" id="display_additive" value="no">
-                                    No
-                                </label>
-                            </div>
-                        </div>
-
-                        <div class="mapping_method_fields form-group">
-                            <label style="text-align:left;" class="col-xs-12 control-label">Manhattan Plot</label>
-                            <div class="col-xs-12 controls">                      
-                                <label class="radio-inline">
-                                    <input type="radio" name="manhattan_plot_reaper" value="true">
-                                    Yes
-                                </label>
-                                <label class="radio-inline">
-                                    <input type="radio" name="manhattan_plot_reaper" value="false" checked="">
-                                    No
-                               </label>
-                            </div>
-                        </div>
-                        <div class="form-group">
-                            <div style="padding-left:15px;" class="controls">
-                                <button id="interval_mapping_compute" class="btn submit_special btn-primary" data-url="/interval_mapping" title="Compute Interval Mapping">
-                                    <i class="icon-ok-circle icon-white"></i> Open Mapping Tool
-                                </button>
-                            </div>
-                        </div>
-                    </div>
-                </div>
-                
-                <div class="tab-pane" id="pylmm">
+                <div class="tab-pane active" id="pylmm">
                     
                     <div style="padding: 20px" class="form-horizontal">
                         <div class="mapping_method_fields form-group">
@@ -211,7 +160,60 @@
                         </div>
                     </div>
                 </div>
-                
+                {% if dataset.group.species != 'human' %}
+                <div class="tab-pane" id="interval_mapping">
+                    <div style="padding: 20px" class="form-horizontal">
+                        <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_perm_reaper" value="2000" type="text" class="form-control">
+                            </div>
+                        </div>
+    
+                        <div class="mapping_method_fields form-group">
+                            <label for="mapping_bootstraps" class="col-xs-2 control-label" title="Bootstrapping Resamples">Bootstrap</label>
+                            <div style="margin-left: 20px;" class="col-xs-4 controls">
+                                <input name="mapping_bootstraps" value="2000" type="text" class="form-control">
+                            </div>
+                        </div>
+                    
+                        <div class="mapping_method_fields form-group">
+                            <label style="text-align:left;" class="col-xs-12 control-label">Display Additive Effect</label>
+                            <div class="col-xs-12 controls" id="display_additive_effect">                      
+                                <label class="radio-inline">
+                                    <input type="radio" name="display_additive" id="display_additive" value="yes" checked="">
+                                    Yes
+                                </label>
+                                <label class="radio-inline">
+                                    <input type="radio" name="display_additive" id="display_additive" value="no">
+                                    No
+                                </label>
+                            </div>
+                        </div>
+
+                        <div class="mapping_method_fields form-group">
+                            <label style="text-align:left;" class="col-xs-12 control-label">Manhattan Plot</label>
+                            <div class="col-xs-12 controls">                      
+                                <label class="radio-inline">
+                                    <input type="radio" name="manhattan_plot_reaper" value="true">
+                                    Yes
+                                </label>
+                                <label class="radio-inline">
+                                    <input type="radio" name="manhattan_plot_reaper" value="false" checked="">
+                                    No
+                               </label>
+                            </div>
+                        </div>
+                        <div class="form-group">
+                            <div style="padding-left:15px;" class="controls">
+                                <button id="interval_mapping_compute" class="btn submit_special btn-primary" data-url="/interval_mapping" title="Compute Interval Mapping">
+                                    <i class="icon-ok-circle icon-white"></i> Open Mapping Tool
+                                </button>
+                            </div>
+                        </div>
+                    </div>
+                </div>
+                {% endif %}
                 {% if dataset.group.species == 'human' %}
                 <div class="tab-pane" id="plink">
                     <div style="padding: 20px" class="form-horizontal">