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| -rw-r--r-- | bh20simplewebuploader/main.py | 1 | ||||
| -rw-r--r-- | bh20simplewebuploader/static/image/coronasmallcomp.gif | bin | 0 -> 7335879 bytes | |||
| -rw-r--r-- | bh20simplewebuploader/static/image/covid19biohackathon.png | bin | 0 -> 21756 bytes | |||
| -rw-r--r-- | bh20simplewebuploader/templates/form.html | 45 |
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 Binary files differnew file mode 100644 index 0000000..7a16637 --- /dev/null +++ b/bh20simplewebuploader/static/image/coronasmallcomp.gif diff --git a/bh20simplewebuploader/static/image/covid19biohackathon.png b/bh20simplewebuploader/static/image/covid19biohackathon.png Binary files differnew file mode 100644 index 0000000..7a744b6 --- /dev/null +++ b/bh20simplewebuploader/static/image/covid19biohackathon.png 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> · 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') |
