From 99af299197dfc527155cd3257388b784810518c4 Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Wed, 8 Jul 2020 00:16:23 -0400 Subject: Split upload tab. Add upload status tab. Add more direct links on download page. Arvados-DCO-1.1-Signed-off-by: Peter Amstutz --- bh20simplewebuploader/templates/footer.html | 14 ++++++++ bh20simplewebuploader/templates/form.html | 49 -------------------------- bh20simplewebuploader/templates/home.html | 50 +++++++++++++++++++++++++++ bh20simplewebuploader/templates/menu.html | 4 ++- bh20simplewebuploader/templates/resource.html | 26 ++++++++++++++ bh20simplewebuploader/templates/status.html | 17 +++++++++ 6 files changed, 110 insertions(+), 50 deletions(-) create mode 100644 bh20simplewebuploader/templates/home.html create mode 100644 bh20simplewebuploader/templates/resource.html create mode 100644 bh20simplewebuploader/templates/status.html (limited to 'bh20simplewebuploader/templates') 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 @@ + + 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 @@
-
-

- Make your sequence - data FAIR. Upload - your SARS-CoV-2 sequence (FASTA or FASTQ - formats) with metadata (JSONLD) to - the public sequence - resource. The upload will trigger a - recompute with all available sequences into a - Pangenome available for - download! -

-

- 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 here. All - data is published under - a Creative - Commons license 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 REDCap. -

-

- Note that form fields contain - web ontology - URI's - for disambiguation - and machine readable metadata. For examples of - use, see the BLOG. -

-
-

@@ -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); - }); -}); - 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 @@ + + + {% include 'header.html' %} + + {% include 'banner.html' %} + {% include 'menu.html' %} + +
+
+

+ Make your sequence + data FAIR. Upload + your SARS-CoV-2 sequence (FASTA or FASTQ + formats) with metadata (JSONLD) to + the public sequence + resource. The upload will trigger a + recompute with all available sequences into a + Pangenome available for + download! +

+

+ 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 here. All + data is published under + a Creative + Commons license 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 REDCap. +

+

+ Note that form fields contain + web ontology + URI's + for disambiguation + and machine readable metadata. For examples of + use, see the BLOG. +

+
+
+ +{% include 'footer.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 @@
- COVID-19 + PUBSEQ DOWNLOAD + UPLOAD + STATUS DEMO BLOG ABOUT 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 @@ + + + {% include 'header.html' %} + + {% include 'banner.html' %} + {% include 'menu.html' %} + +
+

+

All sequences (FASTA) relabled and deduplicated

+

Metadata (RDF) for all sequences

+

All sequences in Graphical Fragment Assembly (GFA) - More about GFA

+

All sequences in Optimized Dynamic Genome/Graph Implementation (ODGI) - More about ODGI

+

All sequences in RDF using spodgi - More about spodgi

+ + +

SPARQL endpoint - Sample query for accessions + + {{ embed|safe }} + +

+ +{% include 'footer.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 @@ + + + {% include 'header.html' %} + + {% include 'banner.html' %} + {% include 'menu.html' %} + +

Sequence upload processing status

+ +
+ {{ table }} +
+ +{% include 'footer.html' %} + + + -- cgit v1.2.3