diff options
Diffstat (limited to 'bh20simplewebuploader/templates')
| -rw-r--r-- | bh20simplewebuploader/templates/footer.html | 14 | ||||
| -rw-r--r-- | bh20simplewebuploader/templates/form.html | 49 | ||||
| -rw-r--r-- | bh20simplewebuploader/templates/home.html | 50 | ||||
| -rw-r--r-- | bh20simplewebuploader/templates/menu.html | 4 | ||||
| -rw-r--r-- | bh20simplewebuploader/templates/resource.html | 27 | ||||
| -rw-r--r-- | bh20simplewebuploader/templates/status.html | 17 |
6 files changed, 111 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..91b6c20 --- /dev/null +++ b/bh20simplewebuploader/templates/resource.html @@ -0,0 +1,27 @@ +<!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/projects/lugli-j7d0g-5ct8p1i1wrgyjvp#Data_collections">All sequences project</a></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> |