4 files changed, 202 insertions, 6 deletions
diff --git a/uploader/templates/background-jobs/default-success-page.html b/uploader/templates/background-jobs/default-success-page.html
new file mode 100644
index 0000000..5732456
--- /dev/null
+++ b/uploader/templates/background-jobs/default-success-page.html
@@ -0,0 +1,17 @@
+{%extends "phenotypes/base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+
+{%block title%}Background Jobs: Success{%endblock%}
+
+{%block pagetitle%}Background Jobs: Success{%endblock%}
+
+{%block contents%}
+{{flash_all_messages()}}
+
+<div class="row">
+  <p>Job <strong>{{job.job_id}}</strong>,
+    {%if job.get("metadata", {}).get("job-type")%}
+    of type '<em>{{job.metadata["job-type"]}}</em>
+    {%endif%}' completed successfully.</p>
+</div>
+{%endblock%}
diff --git a/uploader/templates/base2.html b/uploader/templates/base2.html
new file mode 100644
index 0000000..4c5d613
--- /dev/null
+++ b/uploader/templates/base2.html
@@ -0,0 +1,111 @@
+<!DOCTYPE html>
+<html lang="en">
+
+  <head>
+
+    <meta charset="UTF-8" />
+    <meta application-name="GeneNetwork Quality-Control Application" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    {%block extrameta%}{%endblock%}
+
+    <title>Data Upload and Quality Control: {%block title%}{%endblock%}</title>
+
+    <link rel="stylesheet" type="text/css"
+	  href="{{url_for('base.bootstrap',
+                filename='css/bootstrap.min.css')}}" />
+    <link rel="stylesheet" type="text/css"
+          href="{{url_for('base.datatables',
+                filename='css/dataTables.bootstrap5.min.css')}}" />
+    <link rel="stylesheet" type="text/css" href="/static/css/styles2.css" />
+    <link rel="stylesheet" type="text/css" href="/static/css/layout-large.css" />
+    <link rel="stylesheet" type="text/css" href="/static/css/layout-medium.css" />
+    <link rel="stylesheet" type="text/css" href="/static/css/layout-small.css" />
+    <link rel="stylesheet" type="text/css" href="/static/css/theme.css" />
+
+    {%block css%}{%endblock%}
+
+  </head>
+
+  <body>
+    <header id="header">
+      <span id="header-text">GeneNetwork</span>
+      <nav id="header-nav">
+        <ul class="nav justify-content-end">
+          <li>
+            {%if user_logged_in()%}
+            <a href="{{url_for('oauth2.logout')}}"
+               title="Log out of the system">
+              <span class="glyphicon glyphicon-user"></span>
+              {{user_email()}} Sign Out</a>
+            {%else%}
+            <a href="{{authserver_authorise_uri()}}"
+               title="Log in to the system">Sign In</a>
+            {%endif%}
+          </li>
+        </ul>
+      </nav>
+    </header>
+
+
+    <main id="main" class="main">
+      <nav id="breadcrumbs" aria-label="breadcrumb">
+        <ol class="breadcrumb">
+          <li class="breadcrumb-item">
+            <a href="{{url_for('base.index')}}">Home</a></li>
+          {%block extra_breadcrumbs%}
+          <li class="breadcrumb-item">
+            <a href="{{url_for('base.index')}}">Page01</a></li>
+          <li class="breadcrumb-item">
+            <a href="{{url_for('base.index')}}">Page02</a></li>
+          <li class="breadcrumb-item">
+            <a href="{{url_for('base.index')}}">Page03</a></li>
+          <li class="breadcrumb-item">
+            <a href="{{url_for('base.index')}}">Page04</a></li>
+          {%endblock%}
+        </ol>
+      </nav>
+
+      <div id="main-content">
+          {%block contents%}{%endblock%}
+        </div>
+
+      <div id="sidebar-content">
+          {%block sidebarcontents%}{%endblock%}
+        </div>
+    </main>
+
+
+
+    <script type="text/javascript" src="/static/js/debug.js"></script>
+    <!--
+        Core dependencies
+      -->
+    <script src="{{url_for('base.jquery',
+                 filename='jquery.min.js')}}"></script>
+    <script src="{{url_for('base.bootstrap',
+                 filename='js/bootstrap.min.js')}}"></script>
+
+    <!--
+        DataTables dependencies
+      -->
+    <script type="text/javascript"
+            src="{{url_for('base.datatables',
+                 filename='js/dataTables.min.js')}}"></script>
+    <script type="text/javascript"
+        src="{{url_for('base.datatables_extensions',
+             filename='scroller/js/dataTables.scroller.min.js')}}"></script>
+    <script type="text/javascript"
+            src="{{url_for('base.datatables_extensions',
+                 filename='buttons/js/dataTables.buttons.min.js')}}"></script>
+    <script type="text/javascript"
+            src="{{url_for('base.datatables_extensions',
+                 filename='select/js/dataTables.select.min.js')}}"></script>
+
+    <!--
+        local dependencies
+      -->
+    <script type="text/javascript" src="/static/js/utils.js"></script>
+    <script type="text/javascript" src="/static/js/datatables.js"></script>
+    {%block javascript%}{%endblock%}
+  </body>
+</html>
diff --git a/uploader/templates/index2.html b/uploader/templates/index2.html
new file mode 100644
index 0000000..72fea2f
--- /dev/null
+++ b/uploader/templates/index2.html
@@ -0,0 +1,48 @@
+{%extends "base2.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+
+{%block title%}Home{%endblock%}
+
+{%block pagetitle%}Home{%endblock%}
+
+{%block extra_breadcrumbs%}{%endblock%}
+
+{%block contents%}
+
+<div class="row">{{flash_all_messages()}}</div>
+
+{%if user_logged_in()%}
+<div class="row">
+  <p>Select from:</p>
+  <ul>
+    <li>Species</li>
+    <li>Publications</li>
+  </ul>
+</div>
+{%else%}
+<div class="row">
+  <p>
+    <a href="{{authserver_authorise_uri()}}"
+       title="Sign in to the system"
+       class="btn btn-primary">Sign in</a>
+    to continue.</p>
+</div>
+{%endif%}
+
+{%endblock%}
+
+
+
+{%block sidebarcontents%}
+<div class="row">
+  <form id="frm-quick-navigation">
+    <legend>Quick Navigation</legend>
+    <div class="form-group">
+      <label for="fqn-species-id">Species</label>
+      <select name="species_id">
+        <option value="">Select species</option>
+      </select>
+    </div>
+  </form>
+</div>
+{%endblock%}
diff --git a/uploader/templates/phenotypes/view-dataset.html b/uploader/templates/phenotypes/view-dataset.html
index 306dcce..6a261fc 100644
--- a/uploader/templates/phenotypes/view-dataset.html
+++ b/uploader/templates/phenotypes/view-dataset.html
@@ -46,12 +46,32 @@
 </div>
 
 <div class="row">
-  <p><a href="{{url_for('species.populations.phenotypes.add_phenotypes',
-              species_id=species.SpeciesId,
-              population_id=population.Id,
-              dataset_id=dataset.Id)}}"
-        title="Add a bunch of phenotypes"
-        class="btn btn-primary">Add phenotypes</a></p>
+  <div class="col">
+    <a href="{{url_for('species.populations.phenotypes.add_phenotypes',
+             species_id=species.SpeciesId,
+             population_id=population.Id,
+             dataset_id=dataset.Id)}}"
+       title="Add a bunch of phenotypes"
+       class="btn btn-primary">Add phenotypes</a>
+  </div>
+
+  <div class="col">
+    <form id="frm-recompute-phenotype-means"
+          method="POST"
+          action="{{url_for(
+                  'species.populations.phenotypes.recompute_means',
+                  species_id=species['SpeciesId'],
+                  population_id=population['Id'],
+                  dataset_id=dataset['Id'])}}"
+          class="d-flex flex-row align-items-center flex-wrap"
+          style="display: inline;">
+      <input type="submit"
+             title="Compute/Recompute the means for all phenotypes."
+             class="btn btn-info"
+             value="(rec/c)ompute means"
+             id="submit-frm-recompute-phenotype-means" />
+    </form>
+  </div>
 </div>
 
 <div class="row">