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authorPjotr Prins2020-08-22 11:04:56 +0100
committerPjotr Prins2020-08-22 11:04:56 +0100
commitcab2f4ca70c08d9f44442ba01bdfa5639017084b (patch)
treec4d52887fc9b6314d37e45f92c90235a7d9c55c3 /bh20simplewebuploader
parented0bef1505c50c49479d794bbac6ad2fd2a99db1 (diff)
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Repositioning content
Diffstat (limited to 'bh20simplewebuploader')
-rw-r--r--bh20simplewebuploader/main.py5
-rw-r--r--bh20simplewebuploader/templates/banner.html2
-rw-r--r--bh20simplewebuploader/templates/blurb.html13
-rw-r--r--bh20simplewebuploader/templates/footer.html2
-rw-r--r--bh20simplewebuploader/templates/home.html78
-rw-r--r--bh20simplewebuploader/templates/menu.html1
6 files changed, 63 insertions, 38 deletions
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py
index 62ec5cd..3dbe49a 100644
--- a/bh20simplewebuploader/main.py
+++ b/bh20simplewebuploader/main.py
@@ -658,6 +658,11 @@ def about_page():
buf = get_html_body('doc/web/about.html','https://github.com/arvados/bh20-seq-resource/blob/master/doc/web/about.org')
return render_template('about.html',menu='ABOUT',embed=buf)
+@app.route('/contact')
+def contact_page():
+ buf = get_html_body('doc/web/contact.html','https://github.com/arvados/bh20-seq-resource/blob/master/doc/web/contact.org')
+ return render_template('about.html',menu='CONTACT',embed=buf)
+
## Dynamic API functions starting here
## This is quick and dirty for now, just to get something out and demonstrate the queries
## Feel free to rename the functions/endpoints, feel free to process result so we get nicer JSON
diff --git a/bh20simplewebuploader/templates/banner.html b/bh20simplewebuploader/templates/banner.html
index 8f2b09a..32db983 100644
--- a/bh20simplewebuploader/templates/banner.html
+++ b/bh20simplewebuploader/templates/banner.html
@@ -2,6 +2,6 @@
<div class="logo"><a href="http://covid-19.genenetwork.org/"><img src="static/image/coronasmallcomp.gif" width="150" title="COVID-19 image by Tyler Morgan-Wall"></a></div>
<h1>COVID-19 PubSeq: Public SARS-CoV-2 Sequence Resource</h1>
- <p>Database contains <span id="Counter"></span> public sequences!</p>
+ <p><span id="Counter"></span> public sequences ready for <a href="/download">download</a>!</p>
</section>
diff --git a/bh20simplewebuploader/templates/blurb.html b/bh20simplewebuploader/templates/blurb.html
index 8b65afa..e58bf78 100644
--- a/bh20simplewebuploader/templates/blurb.html
+++ b/bh20simplewebuploader/templates/blurb.html
@@ -6,7 +6,15 @@
virus strains. PubSeq allows anyone to upload sequence material in
the form of FASTA or fastq files with accompanying metadata through
a web interface or REST API.
-
+</p>
+<p>
+ PubSeq accepts sequence material from all sources (notably in FASTA
+ format). PubSeq also provides specific workflows for Oxford Nanopore
+ analysis in FASTQ format. If you need help analysing FAST5 or FASTQ
+ data, feel free to <a href="/contact">contact us</a>! Also for
+ commercial support and Cloud pipelines you can reach out to us.
+</p>
+<p>
COVID-19 PubSeq is also a repository for sequences with a low
barrier to entry for uploading sequence data using best practices,
including <a href="https://en.wikipedia.org/wiki/FAIR_data">FAIR
@@ -14,7 +22,8 @@
standards and, perhaps most importantly, providing standardised
workflows that get triggered on upload, so that results are
immediately available in standardised data formats.
-
+</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
diff --git a/bh20simplewebuploader/templates/footer.html b/bh20simplewebuploader/templates/footer.html
index 3a405de..f78e8bf 100644
--- a/bh20simplewebuploader/templates/footer.html
+++ b/bh20simplewebuploader/templates/footer.html
@@ -19,7 +19,7 @@
<a href="static/image/BCC2020_AndreaGuarracino_COVID19PubSeq_Poster.pdf">
<img src="static/image/BCC2020_AndreaGuarracino_COVID19PubSeq_Poster.png" alt="BCC2020 COVID19 PubSeq Poster"/>
</a>
- <h3>SPONSORS</h3>
+ <h3>OUR SPONSORS</h3>
<div class="sponsorimg">
<a href="https://github.com/virtual-biohackathons/covid-19-bh20">
<img src="static/image/covid19biohackathon.png"></a>
diff --git a/bh20simplewebuploader/templates/home.html b/bh20simplewebuploader/templates/home.html
index bede611..367f6e2 100644
--- a/bh20simplewebuploader/templates/home.html
+++ b/bh20simplewebuploader/templates/home.html
@@ -8,40 +8,50 @@
<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>
+
+ <p>
+ COVID-19 PubSeq is a free and open online
+ bioinformatics public sequence resource with
+ on-the-fly analysis of sequenced SARS-CoV-2
+ samples that allows for a quick turnaround in
+ identification of new virus strains. PubSeq allows
+ anyone to upload sequence material in the form of
+ FASTA or fastq files with accompanying metadata
+ through the <a href="/upload">web interface</a> or <a href="/apidoc">REST API</a>.
+ </p>
+ <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 simple 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>
diff --git a/bh20simplewebuploader/templates/menu.html b/bh20simplewebuploader/templates/menu.html
index d408171..5d5fdc8 100644
--- a/bh20simplewebuploader/templates/menu.html
+++ b/bh20simplewebuploader/templates/menu.html
@@ -8,6 +8,7 @@
<a href="/export" class="{{ 'active' if menu=='EXPORT' }}">EXPORT</a>
<a href="/blog" class="{{ 'active' if menu=='BLOG' }}">BLOG</a>
<a href="/about" class="{{ 'active' if menu=='ABOUT' }}">ABOUT</a>
+ <a href="/contact" class="{{ 'active' if menu=='CONTACT' }}">CONTACT</a>
<a href="javascript:void(0);" class="icon" onclick="myFunction()">
<i class="fa fa-bars"></i>
</a>