diff options
Diffstat (limited to 'bh20simplewebuploader/templates')
| -rw-r--r-- | bh20simplewebuploader/templates/form.html | 325 |
1 files changed, 100 insertions, 225 deletions
diff --git a/bh20simplewebuploader/templates/form.html b/bh20simplewebuploader/templates/form.html index 02ae84d..ffd4158 100644 --- a/bh20simplewebuploader/templates/form.html +++ b/bh20simplewebuploader/templates/form.html @@ -1,152 +1,9 @@ <!DOCTYPE html> <html> - <style> - hr { - margin: auto 0; - } - - body { - color: #101010; - background-color: #F9EDE1; - } - - h1, h2, h3, h4 { - font-family: 'Roboto Slab', serif; - color: darkblue; - } - - h1 { - text-align: center; - } - - p { - color: #505050; - font-style: italic; - } - .header { - background-color: white; - margin: 0 auto; - padding: 20px; - text-align: center; - height: 150px; - } - - .logo { - float: right; - } - - p, form, .about, .footer { - font-family: 'Raleway', sans-serif; - line-height: 1.5; - } - - form h4 { - text-transform: 'uppercase'; - } - - .intro, form { - padding: 20px; - } - - .intro { - background-color: lightgrey; - margin: 0 auto; - padding: 20px; - } - - .about { - background-color: lightgrey; - margin: 0 auto; - padding: 20px; - } - .footer { - background-color: white; - margin: 0 auto; - } - - span.dropt {border-bottom: thin dotted; background: #ffeedd;} - span.dropt:hover {text-decoration: none; background: #ffffff; z-index: 6; } - - .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 { - padding: 1em; - grid-area: b; - } - - .metadata { - padding: 1em; - grid-area: c; - } - .metadata_upload_form { - padding: 1em; - 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; - -webkit-column-break-inside: avoid; /* Chrome, Safari, Opera */ - page-break-inside: avoid; /* Firefox */ - break-inside: avoid; - } - - .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"> + <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> </head> @@ -158,28 +15,67 @@ <small>Disabled until we got everything wired up</small> </section> - <hr> + + <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()">Tech</button> + <button class="button" onclick="fetchAllaccessions()">Allaccessions</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"> - <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="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> + + </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 (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> @@ -189,16 +85,16 @@ </div> <div class="metadata"> - <label>Select metadata submission method:</label> - <br> - <input type="radio" id="metadata_form" name="metadata_type" value="fill" onchange="setMode()" checked 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> + <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_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> @@ -206,9 +102,9 @@ <input type="file" id="metadata" name="metadata" accept=".json,.yml,.yaml" required> <br> </div> - </div> - </div> + </div> + </div> <div id="metadata_fill_form_spot"> <div id="metadata_fill_form"> {% for record in fields %} @@ -246,40 +142,44 @@ {% 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> + <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"> + <a href="https://arvados.org/"><img src="static/image/arvados-logo.png"></a> + <a href="https://www.commonwl.org/"><img src="static/image/CWL-Logo-Header.png"></a> + + <a href="https://github.com/virtual-biohackathons/covid-19-bh20"> + <img src="static/image/covid19biohackathon.png"></a> + </div> </div> - - <hr> <div class="footer"> - <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> + <!-- Sponsors --> - <a href="https://github.com/virtual-biohackathons/covid-19-bh20"> - <img src="static/image/covid19biohackathon.png" align="right" height="70"></a> <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> @@ -289,35 +189,10 @@ </div> - <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() - } - } +<script type="text/javascript"> + let scriptRoot = {{ request.script_root|tojson|safe }}; +</script> - // Start in mode appropriate to selected form item - setMode() - </script> +<script type="text/javascript" src="/static/main.js"></script> </body> </html> |