Fixed gen_select_dataset so that it does not include Phenotype and

Genotype groups when the corresponding data sets do not exist

Interval Mapping no longer shows up for human traits

Fixed the appearance of the mirror links on the main page

2 files changed, 66 insertions, 64 deletions

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/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">