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authorPjotr Prins2020-04-12 15:10:29 -0500
committerPjotr Prins2020-04-12 15:10:29 -0500
commit2e4d12e9890c36421d60ab06f6131f029844bc77 (patch)
tree4315449ff2a75e423c852e335a2251f0a6d0acb7 /bh20simplewebuploader
parentaa93ecf387182896e6dc84bdd145ebce9aba3745 (diff)
downloadbh20-seq-resource-2e4d12e9890c36421d60ab06f6131f029844bc77.tar.gz
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Website: working on layout
Diffstat (limited to 'bh20simplewebuploader')
-rw-r--r--bh20simplewebuploader/main.py1
-rw-r--r--bh20simplewebuploader/static/image/coronasmallcomp.gifbin0 -> 7335879 bytes
-rw-r--r--bh20simplewebuploader/static/image/covid19biohackathon.pngbin0 -> 21756 bytes
-rw-r--r--bh20simplewebuploader/templates/form.html45
4 files changed, 39 insertions, 7 deletions
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py
index 383ef84..81f2ef9 100644
--- a/bh20simplewebuploader/main.py
+++ b/bh20simplewebuploader/main.py
@@ -126,6 +126,7 @@ def generate_form(schema):
return list(walk_fields(root_name))
+
# At startup, we need to load the current metadata schema so we can make a form for it
METADATA_SCHEMA = yaml.safe_load(urllib.request.urlopen('https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-schema.yml'))
FORM_ITEMS = generate_form(METADATA_SCHEMA)
diff --git a/bh20simplewebuploader/static/image/coronasmallcomp.gif b/bh20simplewebuploader/static/image/coronasmallcomp.gif
new file mode 100644
index 0000000..7a16637
--- /dev/null
+++ b/bh20simplewebuploader/static/image/coronasmallcomp.gif
Binary files differ
diff --git a/bh20simplewebuploader/static/image/covid19biohackathon.png b/bh20simplewebuploader/static/image/covid19biohackathon.png
new file mode 100644
index 0000000..7a744b6
--- /dev/null
+++ b/bh20simplewebuploader/static/image/covid19biohackathon.png
Binary files differ
diff --git a/bh20simplewebuploader/templates/form.html b/bh20simplewebuploader/templates/form.html
index afae4c7..839f22f 100644
--- a/bh20simplewebuploader/templates/form.html
+++ b/bh20simplewebuploader/templates/form.html
@@ -7,6 +7,7 @@
body {
color: #101010;
+ background-color: #F9EDE1;
}
h1, h4 {
@@ -21,6 +22,17 @@
color: #505050;
font-style: italic;
}
+ .header {
+ margin: 0 auto;
+ padding: 20px;
+ color: blue;
+ text-align: center;
+ height: 150px;
+ }
+
+ .logo {
+ float: right;
+ }
p, form {
font-family: 'Raleway', sans-serif;
@@ -112,18 +124,35 @@
<meta charset="UTF-8">
<link href="https://fonts.googleapis.com/css2?family=Raleway:wght@500&family=Roboto+Slab&display=swap" rel="stylesheet">
<meta name="viewport" content="width=device-width, initial-scale=1">
- <title>Simple Web Uploader for Public SARS-CoV-2 Sequence Resource</title>
+ <title>Web Uploader for Public SARS-CoV-2 Sequence Resource</title>
</head>
<body>
- <h1>Simple Web Uploader for Public SARS-CoV-2 Sequence Resource</h1>
+ <section class="header">
+ <div class="logo"><a href="https://github.com/tylermorganwall/coronaobj/"><img src="static/image/coronasmallcomp.gif" width="150" /></a></div>
+ <h1>Web Uploader for Public SARS-CoV-2 Sequence Resource</h1>
+ </section>
<hr>
+
<section>
<form action="/submit" method="POST" enctype="multipart/form-data" id="main_form" class="grid-container">
- <p class="intro">
- This tool can be used to upload sequenced genomes of SARS-CoV-2 samples to the <a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca">Public SARS-CoV-2 Sequence Resource</a>. Your uploaded sequence will automatically be processed and incorporated into the public pangenome.
- </p>
+ <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. 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.
+ 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, or FASTQ of reads (max 50MB):</label>
+ <label for="fasta">Select FASTA file of assembled genome (max 40K), or FASTQ of reads (max 50MB):</label>
<br>
<input type="file" id="fasta" name="fasta" accept=".fa,.fasta,.fna,.fq" required>
<br>
@@ -154,7 +183,7 @@
{% for record in fields %}
{% if 'heading' in record %}
- {% if loop.index > 1 %}
+ {% if loop.index > 1 and 2 < 3 %}
</div>
{% endif %}
<div class="record">
@@ -182,6 +211,8 @@
</section>
<hr>
<small><a href="https://github.com/arvados/bh20-seq-resource">Source</a> &middot; Made for <a href="https://github.com/virtual-biohackathons/covid-19-bh20">COVID-19-BH20</a></small>
+ <a href="https://github.com/virtual-biohackathons/covid-19-bh20">
+ <img src="static/image/covid19biohackathon.png" align="right" width="300"></a>
<script type="text/javascript">
let uploadForm = document.getElementById('metadata_upload_form')