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{%extends "base.html"%}
{%from "flash_messages.html" import flash_all_messages%}
{%block title%}Data Upload{%endblock%}
{%block contents%}
<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>
<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-main">upload R/qtl2 bundle</button></a>
</div>
<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>
<form action="{{url_for('entry.upload_file')}}"
method="POST" enctype="multipart/form-data">
<legend class="heading">upload expression data</legend>
{%with messages = get_flashed_messages(with_categories=True) %}
{%if messages %}
<div class="alerts">
{%for category, message in messages %}
<span class="alert {{category}}">{{message}}</span>
{%endfor%}
</div>
{%endif%}
{%endwith%}
<fieldset>
<label for="select_species01">Species</label>
<select id="select_species01"
name="speciesid"
required="required">
<option value="">Select species</option>
{%for aspecies in species%}
<option value="{{aspecies.SpeciesId}}">{{aspecies.MenuName}}</option>
{%endfor%}
</select>
</fieldset>
<fieldset>
<legend>file type</legend>
<input type="radio" name="filetype" value="average" id="filetype_average"
required="required" class="form-col-1" />
<label for="filetype_average" class="form-col-2">average</label>
<input type="radio" name="filetype" value="standard-error"
id="filetype_standard_error" required="required"
class="form-col-1" />
<label for="filetype_standard_error" class="form-col-2">
standard error
</label>
</fieldset>
<fieldset>
<span id="no-file-error" class="alert-error" style="display: none;">
No file selected
</span>
<label for="file_upload" class="form-col-1">select file</label>
<input type="file" name="qc_text_file" id="file_upload"
accept="text/plain, text/tab-separated-values, application/zip"
class="form-col-2"/>
</fieldset>
<fieldset>
<input type="submit" value="upload file" class="btn btn-main form-col-2" />
</fieldset>
</form>
<div id="progress-indicator" class="hidden">
<h3>Uploading file</h3>
<p id="progress-filename">the-file</p>
<progress id="progress-bar" value="0" max="100">
0
</progress>
<p id="progress-text">Uploading 0%</p>
<p id="progress-extra-text">Processing</p>
<form id="frm-cancel-upload" style="border-style: none;">
<button id="btn-cancel-upload" type="submit" class="btn btn-danger">
Cancel
</button>
</form>
</div>
<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>
<form method="POST" action="{{url_for('samples.select_species')}}">
<legend class="heading">upload samples</legend>
<fieldset>
<label for="select_species02">Species</label>
<select id="select_species02" name="species_id" required="required">
<option value="">Select species</option>
{%for spec in species%}
<option value="{{spec.SpeciesId}}">{{spec.MenuName}}</option>
{%endfor%}
</select>
</fieldset>
<fieldset>
<input type="submit" value="submit" class="btn btn-main form-col-2" />
</fieldset>
</form>
{%endblock%}
{%block javascript%}
<script type="text/javascript" src="static/js/upload_progress.js"></script>
<script type="text/javascript">
setup_upload_handlers();
</script>
{%endblock%}
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