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-rw-r--r--bh20simplewebuploader/main.py14
-rw-r--r--bh20simplewebuploader/templates/about.html4
-rw-r--r--bh20simplewebuploader/templates/form.html2
-rw-r--r--bh20simplewebuploader/templates/org-header.html293
-rw-r--r--doc/blog/using-covid-19-pubseq-part1.org2
-rw-r--r--doc/web/about.html462
-rw-r--r--doc/web/about.org134
7 files changed, 906 insertions, 5 deletions
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py
index a30d350..eb9a0f5 100644
--- a/bh20simplewebuploader/main.py
+++ b/bh20simplewebuploader/main.py
@@ -428,7 +428,19 @@ def blog_page():
@app.route('/about')
def about_page():
- return render_template('about.html',menu='ABOUT')
+ buf = ""
+ in_body = False
+ begin_body = re.compile(r"<body>",re.IGNORECASE)
+ end_body = re.compile(r"(</body>|.*=\"postamble\")",re.IGNORECASE)
+ with open('doc/web/about.html') as f:
+ for line in f:
+ if end_body.match(line):
+ break
+ if in_body:
+ buf += line
+ elif begin_body.match(line):
+ in_body = True
+ return render_template('about.html',menu='ABOUT',embed=buf)
## Dynamic API functions starting here
## This is quick and dirty for now, just to get something out and demonstrate the queries
diff --git a/bh20simplewebuploader/templates/about.html b/bh20simplewebuploader/templates/about.html
index 286a211..07b6951 100644
--- a/bh20simplewebuploader/templates/about.html
+++ b/bh20simplewebuploader/templates/about.html
@@ -1,11 +1,11 @@
<!DOCTYPE html>
<html>
- {% include 'header.html' %}
+ {% include 'org-header.html' %}
<body>
{% include 'banner.html' %}
{% include 'menu.html' %}
- WIP
+ {{ embed|safe }}
{% include 'footer.html' %}
diff --git a/bh20simplewebuploader/templates/form.html b/bh20simplewebuploader/templates/form.html
index b1bbad2..3a1b03b 100644
--- a/bh20simplewebuploader/templates/form.html
+++ b/bh20simplewebuploader/templates/form.html
@@ -12,7 +12,7 @@
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>!
+ <a href="https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/">download</a>!
</p>
<p>
Your uploaded sequence will automatically be processed
diff --git a/bh20simplewebuploader/templates/org-header.html b/bh20simplewebuploader/templates/org-header.html
new file mode 100644
index 0000000..915bcb7
--- /dev/null
+++ b/bh20simplewebuploader/templates/org-header.html
@@ -0,0 +1,293 @@
+<head>
+ <link href="https://fonts.googleapis.com/css2?family=Inter:wght@100;200;300;400;500;600;700;800;900&display=swap" rel="stylesheet">
+ <link href="/static/main.css" rel="stylesheet" type="text/css">
+ <meta name="viewport" content="width=device-width, initial-scale=1">
+ <title>Web uploader for Public SARS-CoV-2 Sequence Resource</title>
+ <script type="text/javascript" src="/static/main.js"></script>
+<!-- 2020-05-24 Sun 08:10 -->
+<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
+<meta name="viewport" content="width=device-width, initial-scale=1" />
+<meta name="generator" content="Org mode" />
+<meta name="author" content="Pjotr Prins" />
+<style type="text/css">
+ <!--/*--><![CDATA[/*><!--*/
+ .title { text-align: center;
+ margin-bottom: .2em; }
+ .subtitle { text-align: center;
+ font-size: medium;
+ font-weight: bold;
+ margin-top:0; }
+ .todo { font-family: monospace; color: red; }
+ .done { font-family: monospace; color: green; }
+ .priority { font-family: monospace; color: orange; }
+ .tag { background-color: #eee; font-family: monospace;
+ padding: 2px; font-size: 80%; font-weight: normal; }
+ .timestamp { color: #bebebe; }
+ .timestamp-kwd { color: #5f9ea0; }
+ .org-right { margin-left: auto; margin-right: 0px; text-align: right; }
+ .org-left { margin-left: 0px; margin-right: auto; text-align: left; }
+ .org-center { margin-left: auto; margin-right: auto; text-align: center; }
+ .underline { text-decoration: underline; }
+ #postamble p, #preamble p { font-size: 90%; margin: .2em; }
+ p.verse { margin-left: 3%; }
+ pre {
+ border: 1px solid #ccc;
+ box-shadow: 3px 3px 3px #eee;
+ padding: 8pt;
+ font-family: monospace;
+ overflow: auto;
+ margin: 1.2em;
+ }
+ pre.src {
+ position: relative;
+ overflow: visible;
+ padding-top: 1.2em;
+ }
+ pre.src:before {
+ display: none;
+ position: absolute;
+ background-color: white;
+ top: -10px;
+ right: 10px;
+ padding: 3px;
+ border: 1px solid black;
+ }
+ pre.src:hover:before { display: inline;}
+ /* Languages per Org manual */
+ pre.src-asymptote:before { content: 'Asymptote'; }
+ pre.src-awk:before { content: 'Awk'; }
+ pre.src-C:before { content: 'C'; }
+ /* pre.src-C++ doesn't work in CSS */
+ pre.src-clojure:before { content: 'Clojure'; }
+ pre.src-css:before { content: 'CSS'; }
+ pre.src-D:before { content: 'D'; }
+ pre.src-ditaa:before { content: 'ditaa'; }
+ pre.src-dot:before { content: 'Graphviz'; }
+ pre.src-calc:before { content: 'Emacs Calc'; }
+ pre.src-emacs-lisp:before { content: 'Emacs Lisp'; }
+ pre.src-fortran:before { content: 'Fortran'; }
+ pre.src-gnuplot:before { content: 'gnuplot'; }
+ pre.src-haskell:before { content: 'Haskell'; }
+ pre.src-hledger:before { content: 'hledger'; }
+ pre.src-java:before { content: 'Java'; }
+ pre.src-js:before { content: 'Javascript'; }
+ pre.src-latex:before { content: 'LaTeX'; }
+ pre.src-ledger:before { content: 'Ledger'; }
+ pre.src-lisp:before { content: 'Lisp'; }
+ pre.src-lilypond:before { content: 'Lilypond'; }
+ pre.src-lua:before { content: 'Lua'; }
+ pre.src-matlab:before { content: 'MATLAB'; }
+ pre.src-mscgen:before { content: 'Mscgen'; }
+ pre.src-ocaml:before { content: 'Objective Caml'; }
+ pre.src-octave:before { content: 'Octave'; }
+ pre.src-org:before { content: 'Org mode'; }
+ pre.src-oz:before { content: 'OZ'; }
+ pre.src-plantuml:before { content: 'Plantuml'; }
+ pre.src-processing:before { content: 'Processing.js'; }
+ pre.src-python:before { content: 'Python'; }
+ pre.src-R:before { content: 'R'; }
+ pre.src-ruby:before { content: 'Ruby'; }
+ pre.src-sass:before { content: 'Sass'; }
+ pre.src-scheme:before { content: 'Scheme'; }
+ pre.src-screen:before { content: 'Gnu Screen'; }
+ pre.src-sed:before { content: 'Sed'; }
+ pre.src-sh:before { content: 'shell'; }
+ pre.src-sql:before { content: 'SQL'; }
+ pre.src-sqlite:before { content: 'SQLite'; }
+ /* additional languages in org.el's org-babel-load-languages alist */
+ pre.src-forth:before { content: 'Forth'; }
+ pre.src-io:before { content: 'IO'; }
+ pre.src-J:before { content: 'J'; }
+ pre.src-makefile:before { content: 'Makefile'; }
+ pre.src-maxima:before { content: 'Maxima'; }
+ pre.src-perl:before { content: 'Perl'; }
+ pre.src-picolisp:before { content: 'Pico Lisp'; }
+ pre.src-scala:before { content: 'Scala'; }
+ pre.src-shell:before { content: 'Shell Script'; }
+ pre.src-ebnf2ps:before { content: 'ebfn2ps'; }
+ /* additional language identifiers per "defun org-babel-execute"
+ in ob-*.el */
+ pre.src-cpp:before { content: 'C++'; }
+ pre.src-abc:before { content: 'ABC'; }
+ pre.src-coq:before { content: 'Coq'; }
+ pre.src-groovy:before { content: 'Groovy'; }
+ /* additional language identifiers from org-babel-shell-names in
+ ob-shell.el: ob-shell is the only babel language using a lambda to put
+ the execution function name together. */
+ pre.src-bash:before { content: 'bash'; }
+ pre.src-csh:before { content: 'csh'; }
+ pre.src-ash:before { content: 'ash'; }
+ pre.src-dash:before { content: 'dash'; }
+ pre.src-ksh:before { content: 'ksh'; }
+ pre.src-mksh:before { content: 'mksh'; }
+ pre.src-posh:before { content: 'posh'; }
+ /* Additional Emacs modes also supported by the LaTeX listings package */
+ pre.src-ada:before { content: 'Ada'; }
+ pre.src-asm:before { content: 'Assembler'; }
+ pre.src-caml:before { content: 'Caml'; }
+ pre.src-delphi:before { content: 'Delphi'; }
+ pre.src-html:before { content: 'HTML'; }
+ pre.src-idl:before { content: 'IDL'; }
+ pre.src-mercury:before { content: 'Mercury'; }
+ pre.src-metapost:before { content: 'MetaPost'; }
+ pre.src-modula-2:before { content: 'Modula-2'; }
+ pre.src-pascal:before { content: 'Pascal'; }
+ pre.src-ps:before { content: 'PostScript'; }
+ pre.src-prolog:before { content: 'Prolog'; }
+ pre.src-simula:before { content: 'Simula'; }
+ pre.src-tcl:before { content: 'tcl'; }
+ pre.src-tex:before { content: 'TeX'; }
+ pre.src-plain-tex:before { content: 'Plain TeX'; }
+ pre.src-verilog:before { content: 'Verilog'; }
+ pre.src-vhdl:before { content: 'VHDL'; }
+ pre.src-xml:before { content: 'XML'; }
+ pre.src-nxml:before { content: 'XML'; }
+ /* add a generic configuration mode; LaTeX export needs an additional
+ (add-to-list 'org-latex-listings-langs '(conf " ")) in .emacs */
+ pre.src-conf:before { content: 'Configuration File'; }
+
+ table { border-collapse:collapse; }
+ caption.t-above { caption-side: top; }
+ caption.t-bottom { caption-side: bottom; }
+ td, th { vertical-align:top; }
+ th.org-right { text-align: center; }
+ th.org-left { text-align: center; }
+ th.org-center { text-align: center; }
+ td.org-right { text-align: right; }
+ td.org-left { text-align: left; }
+ td.org-center { text-align: center; }
+ dt { font-weight: bold; }
+ .footpara { display: inline; }
+ .footdef { margin-bottom: 1em; }
+ .figure { padding: 1em; }
+ .figure p { text-align: center; }
+ .equation-container {
+ display: table;
+ text-align: center;
+ width: 100%;
+ }
+ .equation {
+ vertical-align: middle;
+ }
+ .equation-label {
+ display: table-cell;
+ text-align: right;
+ vertical-align: middle;
+ }
+ .inlinetask {
+ padding: 10px;
+ border: 2px solid gray;
+ margin: 10px;
+ background: #ffffcc;
+ }
+ #org-div-home-and-up
+ { text-align: right; font-size: 70%; white-space: nowrap; }
+ textarea { overflow-x: auto; }
+ .linenr { font-size: smaller }
+ .code-highlighted { background-color: #ffff00; }
+ .org-info-js_info-navigation { border-style: none; }
+ #org-info-js_console-label
+ { font-size: 10px; font-weight: bold; white-space: nowrap; }
+ .org-info-js_search-highlight
+ { background-color: #ffff00; color: #000000; font-weight: bold; }
+ .org-svg { width: 90%; }
+ /*]]>*/-->
+
+.title { font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,monospace }
+.table-of-contents { font-family: monospace; color: red; }
+/* .text-table-of-contents { font-family: monospace; color: black; font-size:80%; } */
+.timestamp { font-family: monospace; color: darkgreen; }
+
+h1,h2 { font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,monospace; color
+:black;background-color:#F0F8FF; }
+h2,h3,h4 { color: darkblue; }
+code { color: darkblue; }
+body {font-family: Palatino, 'Palatino Linotype', serif; color:black; font-size: l
+arge }
+
+div.verbatim { color: black; background-color: white; border-style:outset; font-family: palatino font, mono
+space; font-size:80%; font-weight:bold; }
+div.quote { font-family: palatino font, monospace; font-size:80%; }
+div.quotation { font-family: palatino font, monospace; font-size:80%; }
+pre.example { font-family: prestige, monospace; color:black; font-size:70%; background-color: lightyellow;
+ }
+pre.src { font-family: prestige, monospace; font-weight: bold; color:white; font-size:80%; background-color
+: black; }
+
+div[id="text-table-of-contents"]{
+ font-family: palatino font, monospace; background-color:white;
+ border-style: dotted;
+ border-color: #98bf21;
+ border-width: 1px;
+}
+div[class^="outline-text"] {
+ background-color:#ebe6f0;
+ border-style: dotted;
+ border-color: #98bf21;
+ border-width: 1px;
+ font-family: Palatino, 'Palatino Linotype', serif; color:black; font-size: large
+}
+span[class="todo TESTING"] {
+ color:purple;
+}
+span[class="todo IN_PROGRESS"] {
+ color:brown;
+}
+span[class^="section-number"] {
+ color:grey;
+}
+span[class="journal"] {
+ color:darkblue;
+}
+span[class="year"] {
+ color:darkred;
+}
+
+</style>
+<script type="text/javascript">
+/*
+@licstart The following is the entire license notice for the
+JavaScript code in this tag.
+
+Copyright (C) 2012-2020 Free Software Foundation, Inc.
+
+The JavaScript code in this tag is free software: you can
+redistribute it and/or modify it under the terms of the GNU
+General Public License (GNU GPL) as published by the Free Software
+Foundation, either version 3 of the License, or (at your option)
+any later version. The code is distributed WITHOUT ANY WARRANTY;
+without even the implied warranty of MERCHANTABILITY or FITNESS
+FOR A PARTICULAR PURPOSE. See the GNU GPL for more details.
+
+As additional permission under GNU GPL version 3 section 7, you
+may distribute non-source (e.g., minimized or compacted) forms of
+that code without the copy of the GNU GPL normally required by
+section 4, provided you include this license notice and a URL
+through which recipients can access the Corresponding Source.
+
+
+@licend The above is the entire license notice
+for the JavaScript code in this tag.
+*/
+<!--/*--><![CDATA[/*><!--*/
+ function CodeHighlightOn(elem, id)
+ {
+ var target = document.getElementById(id);
+ if(null != target) {
+ elem.cacheClassElem = elem.className;
+ elem.cacheClassTarget = target.className;
+ target.className = "code-highlighted";
+ elem.className = "code-highlighted";
+ }
+ }
+ function CodeHighlightOff(elem, id)
+ {
+ var target = document.getElementById(id);
+ if(elem.cacheClassElem)
+ elem.className = elem.cacheClassElem;
+ if(elem.cacheClassTarget)
+ target.className = elem.cacheClassTarget;
+ }
+/*]]>*///-->
+</script>
+</head>
diff --git a/doc/blog/using-covid-19-pubseq-part1.org b/doc/blog/using-covid-19-pubseq-part1.org
index 8d3dae5..b1edbad 100644
--- a/doc/blog/using-covid-19-pubseq-part1.org
+++ b/doc/blog/using-covid-19-pubseq-part1.org
@@ -11,7 +11,7 @@ most importantly, providing standardised workflows that get triggered
on upload, so that results are immediately available in standardised
data formats.
-* Table of Contents :TOC:
+* Table of Contents :TOC:noexport:
- [[#what-does-this-mean][What does this mean?]]
- [[#fetch-sequence-data][Fetch sequence data]]
- [[#predicates][Predicates]]
diff --git a/doc/web/about.html b/doc/web/about.html
new file mode 100644
index 0000000..1f8b1a1
--- /dev/null
+++ b/doc/web/about.html
@@ -0,0 +1,462 @@
+<?xml version="1.0" encoding="utf-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
+<head>
+<!-- 2020-05-24 Sun 10:27 -->
+<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
+<meta name="viewport" content="width=device-width, initial-scale=1" />
+<title>About/FAQ</title>
+<meta name="generator" content="Org mode" />
+<meta name="author" content="Pjotr Prins" />
+<style type="text/css">
+ <!--/*--><![CDATA[/*><!--*/
+ .title { text-align: center;
+ margin-bottom: .2em; }
+ .subtitle { text-align: center;
+ font-size: medium;
+ font-weight: bold;
+ margin-top:0; }
+ .todo { font-family: monospace; color: red; }
+ .done { font-family: monospace; color: green; }
+ .priority { font-family: monospace; color: orange; }
+ .tag { background-color: #eee; font-family: monospace;
+ padding: 2px; font-size: 80%; font-weight: normal; }
+ .timestamp { color: #bebebe; }
+ .timestamp-kwd { color: #5f9ea0; }
+ .org-right { margin-left: auto; margin-right: 0px; text-align: right; }
+ .org-left { margin-left: 0px; margin-right: auto; text-align: left; }
+ .org-center { margin-left: auto; margin-right: auto; text-align: center; }
+ .underline { text-decoration: underline; }
+ #postamble p, #preamble p { font-size: 90%; margin: .2em; }
+ p.verse { margin-left: 3%; }
+ pre {
+ border: 1px solid #ccc;
+ box-shadow: 3px 3px 3px #eee;
+ padding: 8pt;
+ font-family: monospace;
+ overflow: auto;
+ margin: 1.2em;
+ }
+ pre.src {
+ position: relative;
+ overflow: visible;
+ padding-top: 1.2em;
+ }
+ pre.src:before {
+ display: none;
+ position: absolute;
+ background-color: white;
+ top: -10px;
+ right: 10px;
+ padding: 3px;
+ border: 1px solid black;
+ }
+ pre.src:hover:before { display: inline;}
+ /* Languages per Org manual */
+ pre.src-asymptote:before { content: 'Asymptote'; }
+ pre.src-awk:before { content: 'Awk'; }
+ pre.src-C:before { content: 'C'; }
+ /* pre.src-C++ doesn't work in CSS */
+ pre.src-clojure:before { content: 'Clojure'; }
+ pre.src-css:before { content: 'CSS'; }
+ pre.src-D:before { content: 'D'; }
+ pre.src-ditaa:before { content: 'ditaa'; }
+ pre.src-dot:before { content: 'Graphviz'; }
+ pre.src-calc:before { content: 'Emacs Calc'; }
+ pre.src-emacs-lisp:before { content: 'Emacs Lisp'; }
+ pre.src-fortran:before { content: 'Fortran'; }
+ pre.src-gnuplot:before { content: 'gnuplot'; }
+ pre.src-haskell:before { content: 'Haskell'; }
+ pre.src-hledger:before { content: 'hledger'; }
+ pre.src-java:before { content: 'Java'; }
+ pre.src-js:before { content: 'Javascript'; }
+ pre.src-latex:before { content: 'LaTeX'; }
+ pre.src-ledger:before { content: 'Ledger'; }
+ pre.src-lisp:before { content: 'Lisp'; }
+ pre.src-lilypond:before { content: 'Lilypond'; }
+ pre.src-lua:before { content: 'Lua'; }
+ pre.src-matlab:before { content: 'MATLAB'; }
+ pre.src-mscgen:before { content: 'Mscgen'; }
+ pre.src-ocaml:before { content: 'Objective Caml'; }
+ pre.src-octave:before { content: 'Octave'; }
+ pre.src-org:before { content: 'Org mode'; }
+ pre.src-oz:before { content: 'OZ'; }
+ pre.src-plantuml:before { content: 'Plantuml'; }
+ pre.src-processing:before { content: 'Processing.js'; }
+ pre.src-python:before { content: 'Python'; }
+ pre.src-R:before { content: 'R'; }
+ pre.src-ruby:before { content: 'Ruby'; }
+ pre.src-sass:before { content: 'Sass'; }
+ pre.src-scheme:before { content: 'Scheme'; }
+ pre.src-screen:before { content: 'Gnu Screen'; }
+ pre.src-sed:before { content: 'Sed'; }
+ pre.src-sh:before { content: 'shell'; }
+ pre.src-sql:before { content: 'SQL'; }
+ pre.src-sqlite:before { content: 'SQLite'; }
+ /* additional languages in org.el's org-babel-load-languages alist */
+ pre.src-forth:before { content: 'Forth'; }
+ pre.src-io:before { content: 'IO'; }
+ pre.src-J:before { content: 'J'; }
+ pre.src-makefile:before { content: 'Makefile'; }
+ pre.src-maxima:before { content: 'Maxima'; }
+ pre.src-perl:before { content: 'Perl'; }
+ pre.src-picolisp:before { content: 'Pico Lisp'; }
+ pre.src-scala:before { content: 'Scala'; }
+ pre.src-shell:before { content: 'Shell Script'; }
+ pre.src-ebnf2ps:before { content: 'ebfn2ps'; }
+ /* additional language identifiers per "defun org-babel-execute"
+ in ob-*.el */
+ pre.src-cpp:before { content: 'C++'; }
+ pre.src-abc:before { content: 'ABC'; }
+ pre.src-coq:before { content: 'Coq'; }
+ pre.src-groovy:before { content: 'Groovy'; }
+ /* additional language identifiers from org-babel-shell-names in
+ ob-shell.el: ob-shell is the only babel language using a lambda to put
+ the execution function name together. */
+ pre.src-bash:before { content: 'bash'; }
+ pre.src-csh:before { content: 'csh'; }
+ pre.src-ash:before { content: 'ash'; }
+ pre.src-dash:before { content: 'dash'; }
+ pre.src-ksh:before { content: 'ksh'; }
+ pre.src-mksh:before { content: 'mksh'; }
+ pre.src-posh:before { content: 'posh'; }
+ /* Additional Emacs modes also supported by the LaTeX listings package */
+ pre.src-ada:before { content: 'Ada'; }
+ pre.src-asm:before { content: 'Assembler'; }
+ pre.src-caml:before { content: 'Caml'; }
+ pre.src-delphi:before { content: 'Delphi'; }
+ pre.src-html:before { content: 'HTML'; }
+ pre.src-idl:before { content: 'IDL'; }
+ pre.src-mercury:before { content: 'Mercury'; }
+ pre.src-metapost:before { content: 'MetaPost'; }
+ pre.src-modula-2:before { content: 'Modula-2'; }
+ pre.src-pascal:before { content: 'Pascal'; }
+ pre.src-ps:before { content: 'PostScript'; }
+ pre.src-prolog:before { content: 'Prolog'; }
+ pre.src-simula:before { content: 'Simula'; }
+ pre.src-tcl:before { content: 'tcl'; }
+ pre.src-tex:before { content: 'TeX'; }
+ pre.src-plain-tex:before { content: 'Plain TeX'; }
+ pre.src-verilog:before { content: 'Verilog'; }
+ pre.src-vhdl:before { content: 'VHDL'; }
+ pre.src-xml:before { content: 'XML'; }
+ pre.src-nxml:before { content: 'XML'; }
+ /* add a generic configuration mode; LaTeX export needs an additional
+ (add-to-list 'org-latex-listings-langs '(conf " ")) in .emacs */
+ pre.src-conf:before { content: 'Configuration File'; }
+
+ table { border-collapse:collapse; }
+ caption.t-above { caption-side: top; }
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+ display: table;
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+ .org-svg { width: 90%; }
+ /*]]>*/-->
+</style>
+<script type="text/javascript">
+/*
+@licstart The following is the entire license notice for the
+JavaScript code in this tag.
+
+Copyright (C) 2012-2020 Free Software Foundation, Inc.
+
+The JavaScript code in this tag is free software: you can
+redistribute it and/or modify it under the terms of the GNU
+General Public License (GNU GPL) as published by the Free Software
+Foundation, either version 3 of the License, or (at your option)
+any later version. The code is distributed WITHOUT ANY WARRANTY;
+without even the implied warranty of MERCHANTABILITY or FITNESS
+FOR A PARTICULAR PURPOSE. See the GNU GPL for more details.
+
+As additional permission under GNU GPL version 3 section 7, you
+may distribute non-source (e.g., minimized or compacted) forms of
+that code without the copy of the GNU GPL normally required by
+section 4, provided you include this license notice and a URL
+through which recipients can access the Corresponding Source.
+
+
+@licend The above is the entire license notice
+for the JavaScript code in this tag.
+*/
+<!--/*--><![CDATA[/*><!--*/
+ function CodeHighlightOn(elem, id)
+ {
+ var target = document.getElementById(id);
+ if(null != target) {
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+</script>
+</head>
+<body>
+<div id="content">
+<h1 class="title">About/FAQ</h1>
+<div id="table-of-contents">
+<h2>Table of Contents</h2>
+<div id="text-table-of-contents">
+<ul>
+<li><a href="#org4fc5d3e">1. What is the 'public sequence resource' about?</a></li>
+<li><a href="#orga424b3d">2. Who created the public sequence resource?</a></li>
+<li><a href="#org250dbae">3. How does the public sequence resource compare to other data resources?</a></li>
+<li><a href="#orgd065057">4. Why should I upload my data here?</a></li>
+<li><a href="#org5f94b02">5. Why should I not upload by data here?</a></li>
+<li><a href="#orgbaaaeaf">6. How does the public sequence resource work?</a></li>
+<li><a href="#org68363cb">7. Is this about open data?</a></li>
+<li><a href="#orgb6aaf34">8. Is this about free software?</a></li>
+<li><a href="#orga01eab2">9. How do I upload raw data?</a></li>
+<li><a href="#org57f1ee0">10. How do I change metadata?</a></li>
+<li><a href="#org5585441">11. How do I change the work flows?</a></li>
+<li><a href="#orgc51ee58">12. How do I change the source code?</a></li>
+<li><a href="#org79c6c9b">13. How do I deal with private data and privacy?</a></li>
+<li><a href="#org8ed8b69">14. Who are the sponsors?</a></li>
+</ul>
+</div>
+</div>
+
+<div id="outline-container-org4fc5d3e" class="outline-2">
+<h2 id="org4fc5d3e"><span class="section-number-2">1</span> What is the 'public sequence resource' about?</h2>
+<div class="outline-text-2" id="text-1">
+<p>
+The <b>public sequence resource</b> aims to provide a generic and useful
+resource for COVID-19 research. The focus is on providing the best
+possible sequence data with associated metadata that can be used for
+sequence comparison and protein prediction.
+</p>
+</div>
+</div>
+
+<div id="outline-container-orga424b3d" class="outline-2">
+<h2 id="orga424b3d"><span class="section-number-2">2</span> Who created the public sequence resource?</h2>
+<div class="outline-text-2" id="text-2">
+<p>
+The <b>public sequence resource</b> is an initiative by <a href="https://github.com/arvados/bh20-seq-resource/graphs/contributors">bioinformatics</a> and
+ontology experts who want to create something agile and useful for
+the wider research community. The initiative started at the COVID-19
+biohackathon in April 2020 and is ongoing. The main project drivers
+are Pjotr Prins (UTHSC), Peter Amstutz (Curii), Michael Crusoe (Common
+Workflow Language) and Thomas Liener (consultant, formerly EBI). But
+as this is a free software initiative the project represents major
+work by hundreds of software developers and ontology and data
+wrangling experts. Thank you everyone!
+</p>
+</div>
+</div>
+
+<div id="outline-container-org250dbae" class="outline-2">
+<h2 id="org250dbae"><span class="section-number-2">3</span> How does the public sequence resource compare to other data resources?</h2>
+<div class="outline-text-2" id="text-3">
+<p>
+The short version is that we use state-of-the-art practices in
+bioinformatics using agile methods. Unlike the resources from large
+institutes we can improve things on a dime and anyone can contribute
+to building out this resource!
+</p>
+
+<p>
+Importantly: all data is published under the <a href="https://creativecommons.org/licenses/by/4.0/">Creative Commons 4.0
+attribution license</a> which means it data can be published and workflows
+can run in public environments allowing for improved access for
+research and reproducible results. This contrasts with some other
+public resources, including GISAID.
+</p>
+</div>
+</div>
+
+<div id="outline-container-orgd065057" class="outline-2">
+<h2 id="orgd065057"><span class="section-number-2">4</span> Why should I upload my data here?</h2>
+<div class="outline-text-2" id="text-4">
+<ol class="org-ol">
+<li>We champion truly shareable data without licensing restrictions - with proper
+attribution</li>
+<li>We provide full metadata support using state-of-the-art ontology's</li>
+<li>We provide a web-based sequence uploader and a command-line version
+for bulk uploads</li>
+<li>We provide a live SPARQL end-point for all metadata</li>
+<li>We provide free data analysis and sequence comparison triggered on data upload</li>
+<li>We provide free downloads of all computed output</li>
+<li>There is no need to set up pipelines and/or compute clusters</li>
+<li>All workflows get triggered on uploading a new sequence</li>
+<li>When someone (you?) improves the software/workflows and everyone benefits</li>
+</ol>
+
+<p>
+Finally, if you upload your data here we have workflows that output
+formatted data suitable for uploading to EBI resources (and soon
+others). Uploading your data here get your data ready for upload to
+multiple resources.
+</p>
+</div>
+</div>
+
+<div id="outline-container-org5f94b02" class="outline-2">
+<h2 id="org5f94b02"><span class="section-number-2">5</span> Why should I not upload by data here?</h2>
+<div class="outline-text-2" id="text-5">
+<p>
+Funny question. There is no good reason not to upload your data here!
+In fact, you can upload your data here as well as to other
+resources. It is your data after all. No one can prevent you from
+uploading your data to multiple resources. We recommend uploading to
+EBI and NCBI resources. Use our data conversion tools to only enter
+data once and make the process smooth.
+</p>
+</div>
+</div>
+
+<div id="outline-container-orgbaaaeaf" class="outline-2">
+<h2 id="orgbaaaeaf"><span class="section-number-2">6</span> How does the public sequence resource work?</h2>
+<div class="outline-text-2" id="text-6">
+<p>
+On uploading a sequence with metadata it will automatically be
+processed and incorporated into the public pangenome with metadata
+using workflows from the High Performance Open Biology Lab defined
+<a href="https://github.com/hpobio-lab/viral-analysis/tree/master/cwl/pangenome-generate">here</a>.
+</p>
+</div>
+</div>
+
+<div id="outline-container-org68363cb" class="outline-2">
+<h2 id="org68363cb"><span class="section-number-2">7</span> Is this about open data?</h2>
+<div class="outline-text-2" id="text-7">
+<p>
+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 download the raw and published (GFA/RDF/FASTA)
+data and store it for further processing.
+</p>
+</div>
+</div>
+
+<div id="outline-container-orgb6aaf34" class="outline-2">
+<h2 id="orgb6aaf34"><span class="section-number-2">8</span> Is this about free software?</h2>
+<div class="outline-text-2" id="text-8">
+<p>
+Absolutely. Free software allows for fully reproducible pipelines. You
+can take our workflows and data and run it elsewhere!
+</p>
+</div>
+</div>
+
+<div id="outline-container-orga01eab2" class="outline-2">
+<h2 id="orga01eab2"><span class="section-number-2">9</span> How do I upload raw data?</h2>
+<div class="outline-text-2" id="text-9">
+<p>
+We are preparing raw sequence data pipelines (fastq and BAM). The
+reason is that we want the best data possible for downstream analysis
+(including protein prediction and test development). The current
+approach where people publish final sequences of SARS-CoV-2 is lacking
+because it hides how this sequence was created. For reasons of
+reproducible and improved results we want/need to work with the raw
+sequence reads (both short reads and long reads) and take alternative
+assembly variations into consideration. This is all work in progress.
+</p>
+</div>
+</div>
+
+<div id="outline-container-org57f1ee0" class="outline-2">
+<h2 id="org57f1ee0"><span class="section-number-2">10</span> How do I change metadata?</h2>
+<div class="outline-text-2" id="text-10">
+<p>
+See the <a href="http://covid19.genenetwork.org/blog">http://covid19.genenetwork.org/blog</a>!
+</p>
+</div>
+</div>
+
+<div id="outline-container-org5585441" class="outline-2">
+<h2 id="org5585441"><span class="section-number-2">11</span> How do I change the work flows?</h2>
+<div class="outline-text-2" id="text-11">
+<p>
+See the <a href="http://covid19.genenetwork.org/blog">http://covid19.genenetwork.org/blog</a>!
+</p>
+</div>
+</div>
+
+<div id="outline-container-orgc51ee58" class="outline-2">
+<h2 id="orgc51ee58"><span class="section-number-2">12</span> How do I change the source code?</h2>
+<div class="outline-text-2" id="text-12">
+<p>
+Go to our <a href="https://github.com/arvados/bh20-seq-resource">source code repositories</a>, fork/clone the repository, change
+something and submit a <a href="https://github.com/arvados/bh20-seq-resource/pulls">pull request</a> (PR). That easy! Check out how
+many PRs we already merged.
+</p>
+</div>
+</div>
+
+<div id="outline-container-org79c6c9b" class="outline-2">
+<h2 id="org79c6c9b"><span class="section-number-2">13</span> How do I deal with private data and privacy?</h2>
+<div class="outline-text-2" id="text-13">
+<p>
+A public sequence resource is about public data. Metadata can refer to
+private data. You can use your own (anonymous) identifiers. We also
+plan to combine identifiers with clinical data stored securely at
+<a href="https://redcap-covid19.elixir-luxembourg.org/redcap/">REDCap</a>. Contact Pjotr Prins if you want to work on this.
+</p>
+</div>
+</div>
+
+<div id="outline-container-org8ed8b69" class="outline-2">
+<h2 id="org8ed8b69"><span class="section-number-2">14</span> Who are the sponsors?</h2>
+<div class="outline-text-2" id="text-14">
+<p>
+The main sponsors are listed in the footer. In addition to the time
+generously donated by many contributors we also acknowledge Amazon AWS
+for donating COVID-19 related compute time.
+</p>
+</div>
+</div>
+</div>
+<div id="postamble" class="status">
+<hr><small>Created by <a href="http://thebird.nl/">Pjotr Prins</a> (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!<br />Modified 2020-05-24 Sun 10:26</small>.
+</div>
+</body>
+</html>
diff --git a/doc/web/about.org b/doc/web/about.org
new file mode 100644
index 0000000..fc9d1ff
--- /dev/null
+++ b/doc/web/about.org
@@ -0,0 +1,134 @@
+#+TITLE: About/FAQ
+#+AUTHOR: Pjotr Prins
+
+* Table of Contents :TOC:noexport:
+ - [[#what-is-the-public-sequence-resource-about][What is the 'public sequence resource' about?]]
+ - [[#who-created-the-public-sequence-resource][Who created the public sequence resource?]]
+ - [[#how-does-the-public-sequence-resource-compare-to-other-data-resources][How does the public sequence resource compare to other data resources?]]
+ - [[#why-should-i-upload-my-data-here][Why should I upload my data here?]]
+ - [[#why-should-i-not-upload-by-data-here][Why should I not upload by data here?]]
+ - [[#how-does-the-public-sequence-resource-work][How does the public sequence resource work?]]
+ - [[#is-this-about-open-data][Is this about open data?]]
+ - [[#is-this-about-free-software][Is this about free software?]]
+ - [[#how-do-i-upload-raw-data][How do I upload raw data?]]
+ - [[#how-do-i-change-metadata][How do I change metadata?]]
+ - [[#how-do-i-change-the-work-flows][How do I change the work flows?]]
+ - [[#how-do-i-change-the-source-code][How do I change the source code?]]
+ - [[#how-do-i-deal-with-private-data-and-privacy][How do I deal with private data and privacy?]]
+ - [[#who-are-the-sponsors][Who are the sponsors?]]
+
+* What is the 'public sequence resource' about?
+
+The *public sequence resource* aims to provide a generic and useful
+resource for COVID-19 research. The focus is on providing the best
+possible sequence data with associated metadata that can be used for
+sequence comparison and protein prediction.
+
+* Who created the public sequence resource?
+
+The *public sequence resource* is an initiative by [[https://github.com/arvados/bh20-seq-resource/graphs/contributors][bioinformatics]] and
+ontology experts who want to create something agile and useful for
+the wider research community. The initiative started at the COVID-19
+biohackathon in April 2020 and is ongoing. The main project drivers
+are Pjotr Prins (UTHSC), Peter Amstutz (Curii), Michael Crusoe (Common
+Workflow Language) and Thomas Liener (consultant, formerly EBI). But
+as this is a free software initiative the project represents major
+work by hundreds of software developers and ontology and data
+wrangling experts. Thank you everyone!
+
+* How does the public sequence resource compare to other data resources?
+
+The short version is that we use state-of-the-art practices in
+bioinformatics using agile methods. Unlike the resources from large
+institutes we can improve things on a dime and anyone can contribute
+to building out this resource!
+
+Importantly: all data is published under the [[https://creativecommons.org/licenses/by/4.0/][Creative Commons 4.0
+attribution license]] which means it data can be published and workflows
+can run in public environments allowing for improved access for
+research and reproducible results. This contrasts with some other
+public resources, including GISAID.
+
+* Why should I upload my data here?
+
+1. We champion truly shareable data without licensing restrictions - with proper
+ attribution
+2. We provide full metadata support using state-of-the-art ontology's
+2. We provide a web-based sequence uploader and a command-line version
+ for bulk uploads
+3. We provide a live SPARQL end-point for all metadata
+2. We provide free data analysis and sequence comparison triggered on data upload
+4. We provide free downloads of all computed output
+3. There is no need to set up pipelines and/or compute clusters
+4. All workflows get triggered on uploading a new sequence
+4. When someone (you?) improves the software/workflows and everyone benefits
+
+Finally, if you upload your data here we have workflows that output
+formatted data suitable for uploading to EBI resources (and soon
+others). Uploading your data here get your data ready for upload to
+multiple resources.
+
+* Why should I not upload by data here?
+
+Funny question. There is no good reason not to upload your data here!
+In fact, you can upload your data here as well as to other
+resources. It is your data after all. No one can prevent you from
+uploading your data to multiple resources. We recommend uploading to
+EBI and NCBI resources. Use our data conversion tools to only enter
+data once and make the process smooth.
+
+* How does the public sequence resource work?
+
+On uploading a sequence with metadata it will automatically be
+processed and incorporated into the public pangenome with metadata
+using workflows from the High Performance Open Biology Lab defined
+[[https://github.com/hpobio-lab/viral-analysis/tree/master/cwl/pangenome-generate][here]].
+
+* Is this about open data?
+
+All data is published under a [[https://creativecommons.org/licenses/by/4.0/][Creative Commons 4.0 attribution license]]
+(CC-BY-4.0). You can download the raw and published (GFA/RDF/FASTA)
+data and store it for further processing.
+
+* Is this about free software?
+
+Absolutely. Free software allows for fully reproducible pipelines. You
+can take our workflows and data and run it elsewhere!
+
+* How do I upload raw data?
+
+We are preparing raw sequence data pipelines (fastq and BAM). The
+reason is that we want the best data possible for downstream analysis
+(including protein prediction and test development). The current
+approach where people publish final sequences of SARS-CoV-2 is lacking
+because it hides how this sequence was created. For reasons of
+reproducible and improved results we want/need to work with the raw
+sequence reads (both short reads and long reads) and take alternative
+assembly variations into consideration. This is all work in progress.
+
+* How do I change metadata?
+
+See the [[http://covid19.genenetwork.org/blog]]!
+
+* How do I change the work flows?
+
+See the [[http://covid19.genenetwork.org/blog]]!
+
+* How do I change the source code?
+
+Go to our [[https://github.com/arvados/bh20-seq-resource][source code repositories]], fork/clone the repository, change
+something and submit a [[https://github.com/arvados/bh20-seq-resource/pulls][pull request]] (PR). That easy! Check out how
+many PRs we already merged.
+
+* How do I deal with private data and privacy?
+
+A public sequence resource is about public data. Metadata can refer to
+private data. You can use your own (anonymous) identifiers. We also
+plan to combine identifiers with clinical data stored securely at
+[[https://redcap-covid19.elixir-luxembourg.org/redcap/][REDCap]]. Contact Pjotr Prins if you want to work on this.
+
+* Who are the sponsors?
+
+The main sponsors are listed in the footer. In addition to the time
+generously donated by many contributors we also acknowledge Amazon AWS
+for donating COVID-19 related compute time.