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<!DOCTYPE html>
<html>
    <head>
        <meta charset="UTF-8">
        <link href="https://fonts.googleapis.com/css2?family=Raleway:wght@500&family=Roboto+Slab&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>
    </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>

<small>Disabled until we got everything wired up</small>

      </section>

      <section class="search-section">
          <div class="filter-options" action="#">
              <p>[Demo] Display content sequences by: </p>

              <button class="button">Source</button>
              <button class="button">Location</button>
          </div>

          <form 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>
          </form>
      </section>

      <section class="results">
      </section>

        <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 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>

                <div class="fasta-file-select">
                    <label for="fasta">Select FASTA file of assembled genome (max 50K), or FASTQ of reads (<span class="dropt" title="For a larger fastq file you'll need to use a CLI uploader">max 150MB<span style="width:500px;"></span></span>) : </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="displayForm()" required>
                    <label for="metadata_form">Fill in metadata manually</label>
                    <input type="radio" id="metadata_upload" name="metadata_type" value="upload" onchange="displayForm()" 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/metadata.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  %}
                    </div>
                    {% endif %}
                    <div class="record">
                        <h4>{{ record['heading'] }}</h4>
                        {% else %}
                        <label for="{{ record['id'] }}" 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 id="{{ record['id'] }}" name="{{ record['id'] }}" {{ "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 type="{{ record['type'] }}" id="{{ record['id'] }}" name="{{ record['id'] }}" {{ "required" if record['required'] else "" }} {{ ("step=" + record['step']) if 'step' in record else ""}}>
                        {% endif %}
                        {% endif %}
                        {% if loop.index == loop.length %}
                    </div>
                    {% endif %}
                    {% endfor %}
                </div>

                </div>


<input class="submit" type="submit" value="Add to Pangenome">
            </form>
        </section>
<hr>
<br>
<div class="about">
  <h3>ABOUT</h3>
  <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>
                    <br>
</div>

                    <hr>
<div class="footer">
    <!-- Sponsors -->
    <div class="sponsors">
        <a href="https://arvados.org/"><img src="static/image/arvados-logo.png" align="top"></a>
        <a href="https://www.commonwl.org/"><img src="static/image/CWL-Logo-Header.png" height="70"></a>

        <a href="https://github.com/virtual-biohackathons/covid-19-bh20">
            <img src="static/image/covid19biohackathon.png" align="right" height="70"></a>
    </div>

        <center>
        <small><a href="https://github.com/arvados/bh20-seq-resource">Source code</a> &middot; Powered by <a href="https://www.commonwl.org/">Common Workflow Language</a> &amp; <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 }};
</script>

<script type="text/javascript" src="/static/main.js"></script>
    </body>
</html>