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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()}} &mdash; 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="#"
             class="not-implemented"
             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.">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>