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-rw-r--r--bh20simplewebuploader/templates/footer.html14
-rw-r--r--bh20simplewebuploader/templates/form.html49
-rw-r--r--bh20simplewebuploader/templates/home.html50
-rw-r--r--bh20simplewebuploader/templates/menu.html4
-rw-r--r--bh20simplewebuploader/templates/resource.html26
-rw-r--r--bh20simplewebuploader/templates/status.html17
6 files changed, 110 insertions, 50 deletions
diff --git a/bh20simplewebuploader/templates/footer.html b/bh20simplewebuploader/templates/footer.html
index 9326b1e..a1dd4fd 100644
--- a/bh20simplewebuploader/templates/footer.html
+++ b/bh20simplewebuploader/templates/footer.html
@@ -41,3 +41,17 @@
</div>
</section>
<script type="text/javascript" src="/static/main.js"></script>
+
+<script type="text/javascript">
+ document.addEventListener("DOMContentLoaded", function(){
+ var count = fetch("/api/getCount")
+ .then((resp) => resp.json())
+ .then(function (data) {
+ count = data["sequences"];
+ console.log(count);
+ span = document.getElementById("Counter");
+ txt = document.createTextNode(count);
+ span.appendChild(txt);
+ });
+ });
+</script>
diff --git a/bh20simplewebuploader/templates/form.html b/bh20simplewebuploader/templates/form.html
index 0ad2080..b9b3776 100644
--- a/bh20simplewebuploader/templates/form.html
+++ b/bh20simplewebuploader/templates/form.html
@@ -7,43 +7,6 @@
<section>
<form action="/submit" method="POST" enctype="multipart/form-data" id="main_form" class="grid-container">
- <div class="intro">
- <p>
- Make your sequence
- data <a href="https://en.wikipedia.org/wiki/FAIR_data">FAIR</a>. Upload
- your SARS-CoV-2 sequence (FASTA or FASTQ
- formats) with metadata (JSONLD) to
- the <a href="/about">public sequence
- resource</a>. The upload will trigger a
- recompute with all available sequences into a
- Pangenome available for
- <a href="/download">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 license</a> You can take the published
- (GFA/RDF/FASTA) data and store it in a triple
- store for further processing. Clinical
- data can be stored
- securely
- at <a href="https://redcap-covid19.elixir-luxembourg.org/redcap/">REDCap</a>.
- </p>
- <p>
- Note that form fields contain
- web <a href="https://en.wikipedia.org/wiki/Web_Ontology_Language">ontology
- URI's</a>
- for <a href="https://en.wikipedia.org/wiki/Wikipedia:Disambiguation">disambiguation</a>
- and machine readable metadata. For examples of
- use, see the <a href="/blog">BLOG</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"/>
@@ -160,18 +123,6 @@
setMode()
- document.addEventListener("DOMContentLoaded", function(){
- var count = fetch("/api/getCount")
- .then((resp) => resp.json())
- .then(function (data) {
- count = data["sequences"];
- console.log(count);
- span = document.getElementById("Counter");
- txt = document.createTextNode(count);
- span.appendChild(txt);
- });
-});
-
</script>
</body>
diff --git a/bh20simplewebuploader/templates/home.html b/bh20simplewebuploader/templates/home.html
new file mode 100644
index 0000000..b90a18d
--- /dev/null
+++ b/bh20simplewebuploader/templates/home.html
@@ -0,0 +1,50 @@
+<!DOCTYPE html>
+<html>
+ {% include 'header.html' %}
+ <body>
+ {% include 'banner.html' %}
+ {% include 'menu.html' %}
+
+ <section>
+ <div class="intro">
+ <p>
+ Make your sequence
+ data <a href="https://en.wikipedia.org/wiki/FAIR_data">FAIR</a>. Upload
+ your SARS-CoV-2 sequence (FASTA or FASTQ
+ formats) with metadata (JSONLD) to
+ the <a href="/about">public sequence
+ resource</a>. The upload will trigger a
+ recompute with all available sequences into a
+ Pangenome available for
+ <a href="/download">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 license</a> You can take the published
+ (GFA/RDF/FASTA) data and store it in a triple
+ store for further processing. Clinical
+ data can be stored
+ securely
+ at <a href="https://redcap-covid19.elixir-luxembourg.org/redcap/">REDCap</a>.
+ </p>
+ <p>
+ Note that form fields contain
+ web <a href="https://en.wikipedia.org/wiki/Web_Ontology_Language">ontology
+ URI's</a>
+ for <a href="https://en.wikipedia.org/wiki/Wikipedia:Disambiguation">disambiguation</a>
+ and machine readable metadata. For examples of
+ use, see the <a href="/blog">BLOG</a>.
+ </p>
+ </div>
+ </section>
+
+{% include 'footer.html' %}
+
+ </body>
+</html>
diff --git a/bh20simplewebuploader/templates/menu.html b/bh20simplewebuploader/templates/menu.html
index 6f97e19..0f6003f 100644
--- a/bh20simplewebuploader/templates/menu.html
+++ b/bh20simplewebuploader/templates/menu.html
@@ -1,7 +1,9 @@
<section class="menu">
<div class="topnav" id="myTopnav">
- <a href="/" class="{{ 'active' if menu=='HOME' }}">COVID-19</a>
+ <a href="/" class="{{ 'active' if menu=='HOME' }}">PUBSEQ</a>
<a href="/download" class="{{ 'active' if menu=='DOWNLOAD' }}">DOWNLOAD</a>
+ <a href="/upload" class="{{ 'active' if menu=='UPLOAD' }}">UPLOAD</a>
+ <a href="/status" class="{{ 'active' if menu=='STATUS' }}">STATUS</a>
<a href="/demo" class="{{ 'active' if menu=='DEMO' }}">DEMO</a>
<a href="/blog" class="{{ 'active' if menu=='BLOG' }}">BLOG</a>
<a href="/about" class="{{ 'active' if menu=='ABOUT' }}">ABOUT</a>
diff --git a/bh20simplewebuploader/templates/resource.html b/bh20simplewebuploader/templates/resource.html
new file mode 100644
index 0000000..e0d344f
--- /dev/null
+++ b/bh20simplewebuploader/templates/resource.html
@@ -0,0 +1,26 @@
+<!DOCTYPE html>
+<html>
+ {% include 'header.html' %}
+ <body>
+ {% include 'banner.html' %}
+ {% include 'menu.html' %}
+
+ <div class="status">
+ <p><img src="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/relabeledSeqs_dedup_relabeledSeqs_dedup.png" height="300px"></p>
+ <p><a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/relabeledSeqs_dedup.fasta">All sequences (FASTA) relabled and deduplicated</a></p>
+ <p><a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/mergedmetadata.ttl">Metadata (RDF) for all sequences</a></p>
+ <p><a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/relabeledSeqs_dedup_relabeledSeqs_dedup.gfa">All sequences in Graphical Fragment Assembly (GFA)</a> - <a href="https://github.com/GFA-spec/GFA-spec">More about GFA</a></p>
+ <p><a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/relabeledSeqs_dedup_relabeledSeqs_dedup.gfa">All sequences in Optimized Dynamic Genome/Graph Implementation (ODGI)</a> - <a href="https://github.com/vgteam/odgi">More about ODGI</a></p>
+ <p><a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/relabeledSeqs_dedup_relabeledSeqs_dedup.ttl.xz">All sequences in RDF using spodgi</a> - <a href="https://github.com/pangenome/spodgi">More about spodgi</a></p>
+
+
+ <p><a href="http://sparql.genenetwork.org/sparql/">SPARQL endpoint</a> - <a href="http://sparql.genenetwork.org/sparql/?default-graph-uri=&query=SELECT+DISTINCT+%3Ffasta+%3Fvalue+WHERE+%7B%3Ffasta+%3Fx%5B+%3Chttp%3A%2F%2Fedamontology.org%2Fdata_2091%3E+%3Fvalue+%5D%7D%0D%0A&format=text%2Fhtml&timeout=0&debug=on&run=+Run+Query+">Sample query for accessions</a>
+
+ {{ embed|safe }}
+
+ </div>
+
+{% include 'footer.html' %}
+
+ </body>
+</html>
diff --git a/bh20simplewebuploader/templates/status.html b/bh20simplewebuploader/templates/status.html
new file mode 100644
index 0000000..a1cf28f
--- /dev/null
+++ b/bh20simplewebuploader/templates/status.html
@@ -0,0 +1,17 @@
+<!DOCTYPE html>
+<html>
+ {% include 'header.html' %}
+ <body>
+ {% include 'banner.html' %}
+ {% include 'menu.html' %}
+
+ <h1>Sequence upload processing status</h1>
+
+ <div class="status">
+ {{ table }}
+ </div>
+
+{% include 'footer.html' %}
+
+ </body>
+</html>
generated by cgit v1.2.3 (git 2.44.0) at 2024-05-20 05:33:00 +0000