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<!DOCTYPE html>
<html>
<head>
<meta charset="UTF-8">
<link href="https://fonts.googleapis.com/css2?family=Inter:wght@100;200;300;400;500;600;700;800;900&display=swap" rel="stylesheet">
<link href="/static/main.css" rel="stylesheet" type="text/css">
<meta name="viewport" content="width=device-width, initial-scale=1">
<title>Web uploader for Public SARS-CoV-2 Sequence Resource</title>
<script type="text/javascript" src="/static/main.js"></script>
</head>
<body>
<section class="header">
<div class="logo"><a href="http://covid-19.genenetwork.org/"><img src="static/image/coronasmallcomp.gif" width="150" title="COVID-19 image by Tyler Morgan-Wall"></a></div>
<h1>Web uploader for Public SARS-CoV-2 Sequence Resource</h1>
<p>Database contains <span id="Counter"></span> public sequences!</p>
</section>
<section class="search-section">
<div class="filter-options" action="#">
<p>[Demo] Display content sequences by: </p>
<div>
<button class="button" onclick="fetchSEQBySpecimen()">Specimen source</button>
<button class="button" onclick="fetchSEQByLocation()">Location</button>
<button class="button" onclick="fetchSEQByTech()">Sequencer</button>
<button class="button" onclick="fetchAllaccessions()">All accessions</button>
</div>
</div>
<div class="search">
<input id="search-input" id="global-search" type="search" placeholder="FASTA uri" required>
<button class="button search-button" type="submit" onclick="search()">
<span class="icon ion-search">
<span class="sr-only">Search</span>
</span>
</button>
</div>
</section>
<div id="loader" class="loader invisible"></div>
<section id="results" class="invisible">
<pre><code id="json"></code></pre>
</section>
<section>
<form action="/submit" method="POST" enctype="multipart/form-data" id="main_form" class="grid-container">
<div class="intro">
<p>
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>!
</p>
<p>
Your uploaded sequence will automatically be processed
and incorporated into the public pangenome with
metadata using worklows from the High Performance Open Biology Lab defined <a href="https://github.com/hpobio-lab/viral-analysis/tree/master/cwl/pangenome-generate">here</a>. 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. We also plan to
combine identifiers with clinical data stored securely at <a href="https://redcap-covid19.elixir-luxembourg.org/redcap/">REDCap</a>.
A free command line version of the uploader can be
installed from <a href="https://github.com/arvados/bh20-seq-resource">source</a>.
</p>
<p>
Note that form fields contain web <a href="https://en.wikipedia.org/wiki/Web_Ontology_Language">onthology URI's</a> for <a href="https://en.wikipedia.org/wiki/Wikipedia:Disambiguation">disambiguation</a> and machine readable metadata. For examples of use, see the <a href="https://github.com/arvados/bh20-seq-resource/blob/master/doc/blog/using-covid-19-pubseq-part1.org">BLOG</a>.
</p>
</div>
<div class="fasta-file-select">
<h2><svg class="bi bi-cloud-upload" width="1.2em" height="1.2em" viewBox="0 0 16 16" fill="currentColor" xmlns="http://www.w3.org/2000/svg">
<path d="M4.887 6.2l-.964-.165A2.5 2.5 0 103.5 11H6v1H3.5a3.5 3.5 0 11.59-6.95 5.002 5.002 0 119.804 1.98A2.501 2.501 0 0113.5 12H10v-1h3.5a1.5 1.5 0 00.237-2.981L12.7 7.854l.216-1.028a4 4 0 10-7.843-1.587l-.185.96z"/>
<path fill-rule="evenodd" d="M5 8.854a.5.5 0 00.707 0L8 6.56l2.293 2.293A.5.5 0 1011 8.146L8.354 5.5a.5.5 0 00-.708 0L5 8.146a.5.5 0 000 .708z" clip-rule="evenodd"/>
<path fill-rule="evenodd" d="M8 6a.5.5 0 01.5.5v8a.5.5 0 01-1 0v-8A.5.5 0 018 6z" clip-rule="evenodd"/>
</svg> Upload SARS-CoV-2 Sequence</h2>
<label for="fasta">Select FASTA file of assembled genome (form upload <span class="dropt" title="For larger files or bulk uploads you can use a CLI uploader">max 50K<span style="width:500px;"></span></span>; FASTQ and BAM is coming soon): </label>
<br>
<input type="file" id="fasta" name="fasta" accept=".fa,.fasta,.fna,.fq" required>
<br>
<small>
Note that by uploading your data you automatically agree to a <a href="https://creativecommons.org/licenses/by/4.0/">CC-BY-4.0 license</a>. </small>
</div>
<div class="metadata">
<label>Select metadata submission method:</label>
<br>
<input type="radio" id="metadata_form" name="metadata_type" value="fill" checked onchange="setMode()" required>
<label for="metadata_form">Fill in metadata manually</label>
<input type="radio" id="metadata_upload" name="metadata_type" value="upload" onchange="setMode()" required>
<label for="metadata_upload">Upload metadata file</label>
<br>
<small>Make sure the metadata has submitter attribution details.</small>
<div id="metadata_upload_form_spot">
<div id="metadata_upload_form">
<br>
<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> and <a href="https://github.com/arvados/bh20-seq-resource/blob/master/example/maximum_metadata_example.yaml" target="_blank">example</a> (max 50K):</label>
<br>
<input type="file" id="metadata" name="metadata" accept=".json,.yml,.yaml" required>
<br>
</div>
</div>
</div>
<div id="metadata_fill_form_spot">
<div id="metadata_fill_form">
{% for record in fields %}
{% if 'heading' in record %}
{% if loop.index > 1 and 2 < 3 %} <!-- for emacs matching elements -->
</div>
{% endif %}
<div class="record"> <!-- from block, e.g. host fields -->
<h4>{{ record['heading'] }}</h4>
{% else %} <!-- handles one field -->
<div class="field-group" data-keypath="{{ record['id'] }}">
<div class="field" data-number="0">
<label for="{{ record['id'] }}{{ '[0]' if record['list'] else ''}}" title="{{ record.get('docstring', '') }}">
{{ record['label'] }}
{{ "*" if record['required'] else "" }}
{% if 'docstring' in record %}
<a href='javascript:alert({{ record['docstring'] | tojson }})'>❓</a>
{% endif %}
{% if 'ref_iri' in record %}
<a href="{{ record['ref_iri'] }}" target="_blank" title="Ontology Link">🔗</a>
{% endif %}
</label>
{% if record['type'] == 'select' %}
<select class="control" id="{{ record['id'] }}{{ '[0]' if record['list'] else ''}}" name="{{ record['id'] }}{{ '[0]' if record['list'] else ''}}" {{ "required" if record['required'] else "" }}>
<option value="" selected>Choose one...</option>
{% for option in record['options'] %}
<option value="{{ option[1] }}">{{ option[0] }}</option>
{% endfor %}
</select>
{% else %} <!-- input field -->
<input class="control"
type="{{ record['type'] }}"
id="{{ record['id'] }}{{ '[0]' if record['list'] else ''}}"
{{ 'value=http://purl.obolibrary.org/obo/NCBITaxon_9606' if record['id']=='metadata.host.host_species'}}
{{ 'placeholder=http://www.wikidata.org/entity/Q30' if record['id']=='metadata.sample.collection_location'}}
{{ 'placeholder=MyUniqueSampleId.1' if record['id']=='metadata.sample.sample_id'}}
{{ 'value=http://purl.obolibrary.org/obo/NCBITaxon_2697049' if record['id']=='metadata.virus.virus_species'}}
{{ 'readonly=1 value=http://genenetwork.org/submission' if record['id']=='metadata.id'}}
name="{{ record['id'] }}{{ '[0]' if record['list'] else ''}}"
{{ "required" if record['required'] else "" }} {{ ("step=" + record['step']) if 'step' in record else ""}}>
{% endif %}
</div>
{% if record['list'] %}
<button type="button" title="Remove field" class="remove-field invisible">➖</button>
<button type="button" title="Add field" class="add-field">➕</button>
{% endif %}
</div>
{% endif %}
{% if loop.index == loop.length %}
</div>
{% endif %}
{% endfor %}
</div>
</div>
<input class="submit" id="submit" onclick="on_submit_button()" type="submit" value="Add to Pangenome">
</form>
</section>
<br>
<div class="about">
<div>
<h1>ABOUT</h1>
<p>
This a public repository created at the COVID-19 BioHackathon
that has a low barrier to entry for uploading sequence data using
best practices. I.e., data is published with a creative commons
4.0 (CC-4.0) license with metadata using state-of-the art
standards and, perhaps most importantly, providing standardized
workflows that get triggered on upload, so that results are
immediately available in standardized data formats. The repository
will be maintained and expanded for the duration of the
pandemic. To contribute data simply upload it! To contribute code
and/or workflows see
the <a href="https://github.com/arvados/bh20-seq-resource">project
repository</a>. For more information see the <a href="https://github.com/arvados/bh20-seq-resource/blob/master/paper/paper.md">paper</a> (WIP).
</p>
</div>
<div class="sponsors">
<div class="sponsorimg">
<a href="https://github.com/virtual-biohackathons/covid-19-bh20">
<img src="static/image/covid19biohackathon.png"></a>
</div>
<div class="sponsorimg">
<a href="https://www.commonwl.org/"><img src="static/image/CWL-Logo-Header.png"></a>
</div>
<div class="sponsorimg">
<a href="https://arvados.org/"><img src="static/image/arvados-logo.png"></a>
</div>
</div>
</div>
<div class="footer">
<!-- Sponsors -->
<center>
<small><a href="https://github.com/arvados/bh20-seq-resource">Source code</a> · Powered by <a href="https://www.commonwl.org/">Common Workflow Language</a> & <a href="https://arvados.org/">Arvados</a>; Made for <a href="https://github.com/virtual-biohackathons/covid-19-bh20">COVID-19-BH20</a>
</small>
</center>
</div>
<script type="text/javascript">
let scriptRoot = {{ request.script_root|tojson|safe }};
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')
setMode()
document.addEventListener("DOMContentLoaded", function(){
var count = fetch("/api/getCount")
.then((resp) => resp.json())
.then(function (data) {
count = data["sequences"];
console.log(count);
span = document.getElementById("Counter");
txt = document.createTextNode(count);
span.appendChild(txt);
});
});
</script>
</body>
</html>
|
