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<!DOCTYPE html>
<html>
<style>
hr {
margin: auto 0;
}
body {
color: #101010;
background-color: #F9EDE1;
}
h1, h4 {
font-family: 'Roboto Slab', serif;
}
h1 {
text-align: center;
}
p {
color: #505050;
font-style: italic;
}
.header {
margin: 0 auto;
padding: 20px;
color: blue;
text-align: center;
height: 150px;
}
.logo {
float: right;
}
p, form {
font-family: 'Raleway', sans-serif;
line-height: 1.5;
}
form h4 {
text-transform: 'uppercase';
}
.intro, form {
padding: 20px;
}
.intro {
margin: 0 auto;
padding: 20px;
}
.grid-container {
display: grid;
grid-template-columns: repeat(4, 1fr);
grid-template-rows: auto;
row-gap:5px;
grid-template-areas:
"a a b b"
"a a c c"
"a a d d"
"e e e e"
"f f f f";
grid-auto-flow: column;
}
.intro {
grid-area: a;
}
.fasta-file-select {
grid-area: b;
}
.metadata {
grid-area: c;
}
#metadata_upload_form_spot {
grid-area: d;
}
#metadata_fill_form_spot {
grid-area: e;
}
#metadata_fill_form {
column-count: 4;
margin-top: 0.5em;
column-width: 250px;
}
.record {
display: flex;
flex-direction: column;
border: solid 1px #808080;
padding: 1em;
background: #F8F8F8;
margin-bottom: 1em;
}
.record label {
font-size: small;
margin-top: 10px;
}
.submit {
grid-area: f;
width: 17em;
justify-self: center;
}
@media only screen and (max-device-width: 480px) {
.grid-container {
display: flex;
flex-direction: column;
}
}
</style>
<head>
<meta charset="UTF-8">
<link href="https://fonts.googleapis.com/css2?family=Raleway:wght@500&family=Roboto+Slab&display=swap" rel="stylesheet">
<meta name="viewport" content="width=device-width, initial-scale=1">
<title>Web Uploader for Public SARS-CoV-2 Sequence Resource</title>
</head>
<body>
<section class="header">
<div class="logo"><a href="https://github.com/tylermorganwall/coronaobj/"><img src="static/image/coronasmallcomp.gif" width="150" /></a></div>
<h1>Web Uploader for Public SARS-CoV-2 Sequence Resource</h1>
</section>
<hr>
<section>
<form action="/submit" method="POST" enctype="multipart/form-data" id="main_form" class="grid-container">
<p class="intro">
Upload your SARS-CoV-2 sequence (FASTA or FASTQ formats) with metadata (JSONLD) to the <a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca">public sequence resource</a>. The upload will trigger a
recompute with all available sequences into a Pangenome
available for
<a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca">download</a>!
Your uploaded sequence will automatically be processed
and incorporated into the public pangenome with
metadata. All data is published under
a <a href="https://creativecommons.org/licenses/by/4.0/">Creative
Commons 4.0 attribution license</a> (CC-BY-4.0). You
can take the published (GFA/RDF/FASTA) data and store it in
a triple store for further processing.
A free command line version of the uploader can be
installed from <a href="https://github.com/arvados/bh20-seq-resource">source</a>.
</p>
<div class="fasta-file-select">
<label for="fasta">Select FASTA file of assembled genome (max 40K), or FASTQ of reads (max 50MB):</label>
<br>
<input type="file" id="fasta" name="fasta" accept=".fa,.fasta,.fna,.fq" required>
<br>
</div>
<div class="metadata">
<label>Select metadata submission method:</label>
<br>
<input type="radio" id="metadata_upload" name="metadata_type" value="upload" onchange="setMode()" checked required>
<label for="metadata_upload">Upload metadata file</label>
<input type="radio" id="metadata_form" name="metadata_type" value="fill" onchange="setMode()" required>
<label for="metadata_form">Fill in metadata manually</label>
<br>
</div>
<div id="metadata_upload_form_spot">
<div id="metadata_upload_form">
<label for="metadata">Select JSON or YAML metadata file following <a href="https://github.com/arvados/bh20-seq-resource/blob/master/bh20sequploader/bh20seq-schema.yml" target="_blank">this schema</a> (<a href="https://github.com/arvados/bh20-seq-resource/blob/master/example/metadata.yaml" target="_blank">Example 1</a>, <a href="https://github.com/arvados/bh20-seq-resource/blob/master/example/minimal_example.yaml" target="_blank">Example 2</a>, max 1MB):</label>
<br>
<input type="file" id="metadata" name="metadata" accept=".json,.yml,.yaml" required>
<br>
</div>
</div>
<div id="metadata_fill_form_spot">
<div id="metadata_fill_form">
{{ record }}
{% for record in fields %}
{% if 'heading' in record %}
{% if loop.index > 1 and 2 < 3 %}
</div>
{% endif %}
<div class="record">
<h4>{{ record['heading'] }}</h4>
{% else %}
<label for="{{ record['id'] }}">
{{ record['label'] }}
{{ "*" if record['required'] else "" }}
{% if 'ref_url' in record %}
<a href="{{ record['ref_url'] }}" title="More Info" target="_blank">?</a>
{% endif %}
</label>
<input type="{{ record['type'] }}" id="{{ record['id'] }}" name="{{ record['id'] }}" {{ "required" if record['required'] else "" }}>
{% endif %}
{% if loop.index == loop.length %}
</div>
{% endif %}
{% endfor %}
</div>
</div>
<input class="submit" type="submit" value="Add to Pangenome">
</form>
</section>
<hr>
<small><a href="https://github.com/arvados/bh20-seq-resource">Source</a> · Made for <a href="https://github.com/virtual-biohackathons/covid-19-bh20">COVID-19-BH20</a></small>
<a href="https://github.com/virtual-biohackathons/covid-19-bh20">
<img src="static/image/covid19biohackathon.png" align="right" width="300"></a>
<script type="text/javascript">
let uploadForm = document.getElementById('metadata_upload_form')
let uploadFormSpot = document.getElementById('metadata_upload_form_spot')
let fillForm = document.getElementById('metadata_fill_form')
let fillFormSpot = document.getElementById('metadata_fill_form_spot')
function setUploadMode() {
// Make the upload form the one in use
uploadFormSpot.appendChild(uploadForm)
fillFormSpot.removeChild(fillForm)
}
function setFillMode() {
// Make the fillable form the one in use
uploadFormSpot.removeChild(uploadForm)
fillFormSpot.appendChild(fillForm)
}
function setMode() {
// Pick mode based on radio
if (document.getElementById('metadata_upload').checked) {
setUploadMode()
} else {
setFillMode()
}
}
// Start in mode appropriate to selected form item
setMode()
</script>
</body>
</html>
|
