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-rw-r--r--bh20simplewebuploader/static/main.css72
-rw-r--r--bh20simplewebuploader/templates/form.html95
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> &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>