diff options
Diffstat (limited to 'bh20simplewebuploader')
| -rw-r--r-- | bh20simplewebuploader/static/main.css | 72 | ||||
| -rw-r--r-- | bh20simplewebuploader/templates/form.html | 95 |
2 files changed, 114 insertions, 53 deletions
diff --git a/bh20simplewebuploader/static/main.css b/bh20simplewebuploader/static/main.css index 20003f9..57e29ef 100644 --- a/bh20simplewebuploader/static/main.css +++ b/bh20simplewebuploader/static/main.css @@ -4,23 +4,24 @@ hr { body { color: #101010; - background-color: #F9EDE1; + background-color: #F5FFFF; margin: 0; } h1, h2, h3, h4 { - font-family: 'Roboto Slab', serif; - color: darkblue; + font-family: 'Inter', sans-serif; + color: #0ED1CD; } h1 { text-align: center; } -p { +.intro { color: #505050; - font-style: italic; + font-weight: 300; } + .header { background-color: white; margin: 0 auto; @@ -29,12 +30,17 @@ p { height: 150px; } +h2 > svg { + position: relative; + top: 8px; +} + .logo { float: right; } p, form, .about, .footer { - font-family: 'Raleway', sans-serif; + font-family: 'Inter', sans-serif; line-height: 1.5; } @@ -47,15 +53,17 @@ form h4 { } .intro { - background-color: lightgrey; + background-color: inherit; margin: 0 auto; padding: 20px; } .about { - background-color: lightgrey; - margin: 0 auto; + background-color: #B2F8F8; + margin: 30px auto; padding: 20px; + width: 95%; + border-radius: 20px; } .button { @@ -66,8 +74,13 @@ form h4 { } .footer { - background-color: white; + background: #058280;; margin: 0 auto; + color: #fff; +} + +.footer a { + color: #fff; } span.dropt {border-bottom: thin dotted; background: #ffeedd;} @@ -87,6 +100,21 @@ span.dropt:hover {text-decoration: none; background: #ffffff; z-index: 6; } grid-auto-flow: column; } +.about { + display: grid; + grid-template-columns: repeat(2, 1fr); + grid-auto-flow: row; +} + +.about h1 { + text-align: left; +} + +.about p { + font-weight: 300; + color: #505050; +} + .intro { grid-area: a; } @@ -96,6 +124,15 @@ span.dropt:hover {text-decoration: none; background: #ffffff; z-index: 6; } grid-area: b; } +a { + color: #40DBD8; + font-weight: 700; +} + +.fasta-file-select label, .metadata label { + font-weight: 600; +} + .metadata { padding: 1em; grid-area: c; @@ -179,9 +216,22 @@ footer { display: flex; flex-direction: row; flex-wrap: wrap; - justify-content: space-around; + justify-content: space-evenly; + align-content: space-evenly; } +.sponsors a { + flex-grow: 4; + height: 200px; + margin: 10px; + background: white; + display: flex; + flex-direction: column; + justify-content: center; +} +.sponsors img { + width: 100%; +} .metadata input#metadata_upload:checked ~ #metadata_upload_form_spot { display: block; } diff --git a/bh20simplewebuploader/templates/form.html b/bh20simplewebuploader/templates/form.html index 5d1e1b1..ffd4158 100644 --- a/bh20simplewebuploader/templates/form.html +++ b/bh20simplewebuploader/templates/form.html @@ -2,7 +2,7 @@ <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="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> @@ -47,24 +47,35 @@ <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> @@ -138,37 +149,37 @@ <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> + <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> - <hr> + </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> <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> · 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> |