{%extends "base.html"%}
{%from "flash_messages.html" import flash_all_messages%}

{%block title%}Data Upload{%endblock%}

{%block contents%}
<div class="row">
  {{flash_all_messages()}}

  <h1 class="heading">data upload</h1>

  <div class="explainer">
    <p>Each of the sections below gives you a different option for data upload.
      Please read the documentation for each section carefully to understand what
      each section is about.</p>
  </div>
</div>

<div class="row">
  <h2 class="heading">R/qtl2 Bundles</h2>

  <div class="explainer">
    <p>This feature combines and extends the two upload methods below. Instead of
      uploading one item at a time, the R/qtl2 bundle you upload can contain both
      the genotypes data (samples/individuals/cases and their data) and the
      expression data.</p>
    <p>The R/qtl2 bundle, additionally, can contain extra metadata, that neither
      of the methods below can handle.</p>

    <a href="{{url_for('upload.rqtl2.select_species')}}"
       title="Upload a zip bundle of R/qtl2 files">
      <button class="btn btn-primary">upload R/qtl2 bundle</button></a>
  </div>
</div>


<div class="row">
  <h2 class="heading">Expression Data</h2>

  <div class="explainer">
    <p>This feature enables you to upload expression data. It expects the data to
      be in <strong>tab-separated values (TSV)</strong> files. The data should be
      a simple matrix of <em>phenotype × sample</em>, i.e. The first column is a
      list of the <em>phenotypes</em> and the first row is a list of
      <em>samples/cases</em>.</p>

    <p>If you haven't done so please go to this page to learn the requirements for
      file formats and helpful suggestions to enter your data in a fast and easy
      way.</p>

    <ol>
      <li><strong>PLEASE REVIEW YOUR DATA.</strong>Make sure your data complies
        with our system requirements. (
        <a href="{{url_for('entry.data_review')}}#data-concerns"
	   title="Details for the data expectations.">Help</a>
        )</li>
      <li><strong>UPLOAD YOUR DATA FOR DATA VERIFICATION.</strong> We accept
        <strong>.csv</strong>, <strong>.txt</strong> and <strong>.zip</strong>
        files (<a href="{{url_for('entry.data_review')}}#file-types"
	          title="Details for the data expectations.">Help</a>)</li>
    </ol>
  </div>

  <a href="{{url_for('entry.upload_file')}}"
     title="Upload your expression data"
     class="btn btn-primary">upload expression data</a>
</div>

<div class="row">
  <h2 class="heading">samples/cases</h2>

  <div class="explainer">
    <p>For the expression data above, you need the samples/cases in your file to
      already exist in the GeneNetwork database. If there are any samples that do
      not already exist the upload of the expression data will fail.</p>
    <p>This section gives you the opportunity to upload any missing samples</p>
  </div>

  <a href="{{url_for('samples.select_species')}}"
     title="Upload samples/cases/individuals for your data"
     class="btn btn-primary">upload Samples/Cases</a>
</div>

{%endblock%}