Really should have split this into many more commits:

- Now use proxy to pull trait data and hide traits/results that the user
doesn't have view permission for

- Created a factory method for creating trait ob so it can return None
when user doesn't have view permissions (this is why such a large number
of files are changed)

- Added metadata to permutation export

- Added current group management code

- Added fixed password verification e-mail code

5 files changed, 61 insertions, 25 deletions

diff --git a/wqflask/wqflask/templates/admin/group_manager.html b/wqflask/wqflask/templates/admin/group_manager.html
index ac5c1350..b7df1aad 100644
--- a/wqflask/wqflask/templates/admin/group_manager.html
+++ b/wqflask/wqflask/templates/admin/group_manager.html
@@ -2,17 +2,25 @@
 {% block title %}Group Manager{% endblock %}
 {% block content %}
 <!-- Start of body -->
-     {{ header("List of groups", "" )}}
-
     <div class="container">
         <div class="page-header">
             <h1>Manage Groups</h1>
+            <button type="button" id="remove_groups" class="btn btn-primary" data-url="/groups/remove">Remove Selected Groups</button>
         </div>
-        <form action="/manage/groups" method="POST">
+        <form id="groups_form" action="/groups/manage" method="POST">
+            <input type="hidden" name="selected_group_ids" value="">
             <div class="container" style="margin-bottom: 30px;">
+                {% if admin_groups|length == 0 and user_groups|length == 0 %}
+                <h4>You currently aren't a member or admin of any groups.</h4>
+                <br>
+                <button type="submit" name="add_new_group" class="btn btn-primary">Create a new group</button>
+                {% else %}
                 <div><h3>Admin Groups</h3></div>
                 <hr>
-                <table id="admin_groups" class="table table-hover">
+                {% if admin_groups|length == 0 %}
+                <h4>You currently aren't the administrator of any groups.</h4>
+                {% else %}
+                <table id="admin_groups" class="table table-hover" style="min-width: 800px; max-width: 1000px;">
                     <thead>
                         <tr>
                             <th></th>
@@ -26,7 +34,7 @@
                     <tbody>
                         {% for group in admin_groups %}
                         <tr>
-                            <td><input type="checkbox" name="read" value="{{ group.id }}"></td>
+                            <td><input type="checkbox" name="group_id" value="{{ group.id }}"></td>
                             <td>{{ loop.index }}</td>
                             <td>{{ group.name }}</td>
                             <td>{{ group.admins|length + group.users|length }}</td>
@@ -36,12 +44,16 @@
                         {% endfor %}
                     </tbody>
                 </table>
+                {% endif %}
             </div>
             <hr>
             <div class="container">
                 <div><h3>User Groups</h3></div>
                 <hr>
-                <table id="user_groups" class="table table-hover">
+                {% if user_groups|length == 0 %}
+                <h4>You currently aren't a member of any groups.</h4>
+                {% else %}
+                <table id="user_groups" class="table table-hover" style="min-width: 800px; max-width: 1000px;">
                     <thead>
                         <tr>
                             <th></th>
@@ -65,12 +77,12 @@
                         {% endfor %}
                     </tbody>
                 </table>
+                {% endif %}
+                {% endif %}
             </div>
         </form>
     </div>
 
-
-
 <!-- End of body -->
 
 {% endblock %}
@@ -79,7 +91,6 @@
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.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">
@@ -113,6 +124,22 @@
                 "paging": false,
                 "orderClasses": true
             } );
+
+            submit_special = function(url) {
+                $("#groups_form").attr("action", url);
+                return $("#groups_form").submit();
+            };
+
+            $("#remove_groups").on("click", function() {
+                url = $(this).data("url")
+                groups = []
+                $("input[name=group_id]:checked").each(function() {
+                    groups.push($(this).val());
+                });
+                groups_string = groups.join(":")
+                $("input[name=selected_group_ids]").val(groups_string)
+                return submit_special(url)
+            });
         });
     </script>
 {% endblock %}
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 1c84239c..71705390 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -1,4 +1,5 @@
 {% extends "base.html" %}
+{% block title %}Correlation Results{% endblock %}
 {% block css %}
     <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
     <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.bootstrap.css" />
diff --git a/wqflask/wqflask/templates/email/verification.txt b/wqflask/wqflask/templates/email/verification.txt
deleted file mode 100644
index 76149a3a..00000000
--- a/wqflask/wqflask/templates/email/verification.txt
+++ /dev/null
@@ -1,7 +0,0 @@
-Thank you for signing up for GeneNetwork.
-
-We need to verify your email address.
-
-To do that please click the following link, or cut and paste it into your browser window:
-
-{{ url_for_hmac("verify_email", code = verification_code, _external=True )}}
diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/wqflask/wqflask/templates/gsearch_pheno.html
index 05b2f988..04b45659 100644
--- a/wqflask/wqflask/templates/gsearch_pheno.html
+++ b/wqflask/wqflask/templates/gsearch_pheno.html
@@ -31,7 +31,7 @@
             </form>
             <br />
             <br />
-            <div style="width: 100%;">
+            <div style="min-width: 2000px; width: 100%;">
               <table id="trait_table" class="table-hover table-striped cell-border" style="float: left;">
                 <tbody>
                  <td colspan="100%" align="center"><br><b><font size="15">Loading...</font></b><br></td>
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index b4429b46..c5d49168 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -41,7 +41,8 @@
         <input type="hidden" name="selected_chr" value="{{ selectedChr }}">
         <input type="hidden" name="manhattan_plot" value="{{ manhattan_plot }}">
         <input type="hidden" name="num_perm" value="{{ nperm }}">
-        <input type="hidden" name="perm_results" value="">
+        <input type="hidden" name="perm_info" value="">
+        <input type="hidden" name="perm_strata" value="{{ perm_strata }}">
         <input type="hidden" name="num_bootstrap" value="{{ nboot }}">
         <input type="hidden" name="do_control" value="{{ doControl }}">
         <input type="hidden" name="control_marker" value="{{ controlLocus }}">
@@ -464,13 +465,27 @@
 
         {% if mapping_method != "gemma" and mapping_method != "plink" %}
         $('#download_perm').click(function(){
-          var num_perm, perm_data;
-            num_perm = js_data.num_perm
-            perm_data = js_data.perm_results
-            json_perm_data = JSON.stringify(perm_data);
-            $('input[name=perm_results]').val(json_perm_data);
-            $('#marker_regression_form').attr('action', '/export_perm_data');
-            return $('#marker_regression_form').submit();
+          perm_info_dict = {
+            perm_data: js_data.perm_results,
+            num_perm: "{{ nperm }}",
+            trait_name: "{{ this_trait.display_name }}",
+            trait_description: "{{ this_trait.description_display }}",
+            cofactors: "{{ covariates }}",
+            n_samples: {{ n_samples }},
+            n_genotypes: {{ qtl_results|length }},
+            {% if genofile_string is defined %}
+            genofile: "{{ genofile_string }}",
+            {% else %}
+            genofile: "",
+            {% endif %}
+            units_linkage: "{{ LRS_LOD }}",
+            strat_cofactors: js_data.categorical_vars
+          }
+          json_perm_data = JSON.stringify(perm_info_dict);
+
+          $('input[name=perm_info]').val(json_perm_data);
+          $('#marker_regression_form').attr('action', '/export_perm_data');
+          return $('#marker_regression_form').submit();
         });
 
         modebar_options = {