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<!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>GN Uploader: {%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.bootstrap',
filename='css/bootstrap-theme.min.css')}}" />
<link rel="stylesheet" type="text/css" href="/static/css/styles.css" />
{%block css%}{%endblock%}
</head>
<body>
<header id="header" class="container-fluid">
<div class="row">
<span class="header col-lg-9">GeneNetwork Data Quality Control and Upload</span>
<nav class="header-nav col-lg-3">
<ul class="nav justify-content-end">
<li>
{%if user_logged_in()%}
<a href="{{url_for('oauth2.logout')}}"
title="Log out of the system">{{user_email()}} — Log Out</a>
{%else%}
<a href="{{authserver_authorise_uri()}}"
title="Log in to the system">Log In</a>
{%endif%}
</li>
</ul>
</nav>
</header>
<aside id="nav-sidebar" class="container-fluid">
<ul class="nav flex-column">
<li {%if activemenu=="home"%}class="activemenu"{%endif%}>
<a href="/" >Home</a></li>
<li {%if activemenu=="species"%}class="activemenu"{%endif%}>
<a href="{{url_for('species.list_species')}}"
title="View and manage species information.">Species</a></li>
<li {%if activemenu=="platforms"%}class="activemenu"{%endif%}>
<a href="{{url_for('species.platforms.index')}}"
title="View and manage species platforms.">Sequencing Platforms</a></li>
<li {%if activemenu=="populations"%}class="activemenu"{%endif%}>
<a href="{{url_for('species.populations.index')}}"
title="View and manage species populations.">Populations</a></li>
<li {%if activemenu=="samples"%}class="activemenu"{%endif%}>
<a href="{{url_for('species.populations.samples.index')}}"
title="Upload population samples.">Samples</a></li>
<li {%if activemenu=="genotypes"%}class="activemenu"{%endif%}>
<a href="{{url_for('species.populations.genotypes.index')}}"
title="Upload Genotype data.">Genotype Data</a></li>
<!--
TODO: Maybe include menus here for managing studies and dataset or
maybe have the studies/datasets managed under their respective
sections, e.g. "Publish*" studies/datasets under the "Phenotypes"
section, "ProbeSet*" studies/datasets under the "Expression Data"
sections, etc.
-->
<li {%if activemenu=="phenotypes"%}class="activemenu"{%endif%}>
<a href="{{url_for('species.populations.phenotypes.index')}}"
title="Upload phenotype data.">Phenotype Data</a></li>
<li {%if activemenu=="expression-data"%}class="activemenu"{%endif%}>
<a href="{{url_for('species.populations.expression-data.index')}}"
title="Upload expression data."
class="not-implemented">Expression Data</a></li>
<li {%if activemenu=="individuals"%}class="activemenu"{%endif%}>
<a href="#"
class="not-implemented"
title="Upload individual data.">Individual Data</a></li>
<li {%if activemenu=="rna-seq"%}class="activemenu"{%endif%}>
<a href="#"
class="not-implemented"
title="Upload RNA-Seq data.">RNA-Seq Data</a></li>
<li {%if activemenu=="async-jobs"%}class="activemenu"{%endif%}>
<a href="#"
class="not-implemented"
title="View and manage the backgroud jobs you have running">
Background Jobs</a></li>
</ul>
</aside>
<main id="main" class="main container-fluid">
<div class="pagetitle row">
<h1>GN Uploader: {%block pagetitle%}{%endblock%}</h1>
<nav>
<ol class="breadcrumb">
<li {%if activelink is not defined or activelink=="home"%}
class="breadcrumb-item active"
{%else%}
class="breadcrumb-item"
{%endif%}>
<a href="{{url_for('base.index')}}">Home</a>
</li>
{%block lvl1_breadcrumbs%}{%endblock%}
</ol>
</nav>
</div>
<div class="row">
<div class="container-fluid">
<div class="col-md-8 main-content">
{%block contents%}{%endblock%}
</div>
<div class="sidebar-content col-md-4">
{%block sidebarcontents%}{%endblock%}
</div>
</div>
</div>
</main>
<script src="{{url_for('base.jquery',
filename='jquery.min.js')}}"></script>
<script src="{{url_for('base.bootstrap',
filename='js/bootstrap.min.js')}}"></script>
<script type="text/javascript" src="/static/js/misc.js"></script>
{%block javascript%}{%endblock%}
</body>
</html>
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