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-rw-r--r--bh20simplewebuploader/main.py5
-rw-r--r--bh20simplewebuploader/templates/export.html28
-rw-r--r--doc/web/export.html307
-rw-r--r--doc/web/export.org32
-rw-r--r--test/rest-api.html41
-rw-r--r--test/rest-api.org17
6 files changed, 388 insertions, 42 deletions
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py
index 029c2e3..c306749 100644
--- a/bh20simplewebuploader/main.py
+++ b/bh20simplewebuploader/main.py
@@ -632,7 +632,8 @@ def validated_page():
@app.route('/export')
def export_page():
- return render_template('export.html',menu='EXPORT')
+ buf = get_html_body('doc/web/export.html',"https://github.com/arvados/bh20-seq-resource/blob/master/doc/web/export.org")
+ return render_template('export.html',menu='EXPORT',embed=buf)
@app.route('/demo')
def demo_page():
@@ -641,7 +642,7 @@ def demo_page():
@app.route('/apidoc')
def apidoc_page():
buf = get_html_body('test/rest-api.html',"https://github.com/arvados/bh20-seq-resource/blob/master/test/rest-api.org")
- return render_template('blog.html',menu='BLOG',embed=buf)
+ return render_template('blog.html',menu='BLOG',embed=buf,blog=True)
@app.route('/blog',methods=['GET'])
def blog_page():
diff --git a/bh20simplewebuploader/templates/export.html b/bh20simplewebuploader/templates/export.html
index aaceac9..3588e57 100644
--- a/bh20simplewebuploader/templates/export.html
+++ b/bh20simplewebuploader/templates/export.html
@@ -5,30 +5,10 @@
{% include 'banner.html' %}
{% include 'menu.html' %}
- <h1>Export Data</h1>
- <section class="blog">
-
- COVID-19 PubSeq allows for exporting forms and data for other
- services.
-
- <h2>SPARQL</h2>
-
- <p>
- First of all, PubSeq exports a SPARQL endpoint
- <a href="http://sparql.genenetwork.org/sparql/">here</a> that allows
- you do do any query on the data. See this
- <a href="/blog?id=using-covid-19-pubseq-part1">document</a> for
- examples.
- </p>
-
- <h2>Export EBI/ENA Forms</h2>
-
- <p>
- Uploading data to EBI/ENA with PubSeq is described
- <a href="/blog?id=using-covid-19-pubseq-part6">here</a>. To
- export, first search for an uploaded entry through its
- identifier:
- </p>
+
+ {% if embed %}
+ {{ embed|safe }}
+ {% endif %}
<div class="search">
<input id="search-input" type="search" placeholder="e.g. MT326090.1" required>
diff --git a/doc/web/export.html b/doc/web/export.html
new file mode 100644
index 0000000..cc92d4f
--- /dev/null
+++ b/doc/web/export.html
@@ -0,0 +1,307 @@
+<?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>
+<!-- 2020-07-21 Tue 01:51 -->
+<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; }
+ 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%; }
+ /*]]>*/-->
+</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>
+<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="#org1b344eb">1. Export data</a></li>
+<li><a href="#orgc7785c0">2. SPARQL API</a></li>
+<li><a href="#org5b66ee0">3. REST API</a></li>
+<li><a href="#org3f92e6f">4. Export EBI/ENA Forms</a></li>
+</ul>
+</div>
+</div>
+
+<div id="outline-container-org1b344eb" class="outline-2">
+<h2 id="org1b344eb"><span class="section-number-2">1</span> Export data</h2>
+<div class="outline-text-2" id="text-1">
+<p>
+Apart from straight file <a href="http://covid19.genenetwork.org/download">downloads</a> COVID-19 PubSeq allows for
+exporting forms and data for other services.
+</p>
+</div>
+</div>
+
+<div id="outline-container-orgc7785c0" class="outline-2">
+<h2 id="orgc7785c0"><span class="section-number-2">2</span> SPARQL API</h2>
+<div class="outline-text-2" id="text-2">
+<p>
+First of all, PubSeq exports a SPARQL endpoint <a href="http://sparql.genenetwork.org/sparql/">here</a> that allows you do
+do any query on the data. See this <a href="http://covid19.genenetwork.org/blog?id=using-covid-19-pubseq-part1">document</a> for examples.
+</p>
+</div>
+</div>
+
+<div id="outline-container-org5b66ee0" class="outline-2">
+<h2 id="org5b66ee0"><span class="section-number-2">3</span> REST API</h2>
+<div class="outline-text-2" id="text-3">
+<p>
+In addition to above flexible SPARQL endpoint - which is essentially
+is a query REST API - PubSeq exports its own
+<a href="http://covid19.genenetwork.org/apidoc">REST API</a>.
+</p>
+</div>
+</div>
+
+<div id="outline-container-org3f92e6f" class="outline-2">
+<h2 id="org3f92e6f"><span class="section-number-2">4</span> Export EBI/ENA Forms</h2>
+<div class="outline-text-2" id="text-4">
+<p>
+Uploading data to EBI/ENA with PubSeq is described <a href="http://covid19.genenetwork.org/blog?id=using-covid-19-pubseq-part6">here</a>.
+</p>
+
+<p>
+To export,
+first search for an uploaded entry through its identifier:
+</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 2020-07-21 Tue 01:51</small>.
+</div>
+</body>
+</html>
diff --git a/doc/web/export.org b/doc/web/export.org
new file mode 100644
index 0000000..aa7d680
--- /dev/null
+++ b/doc/web/export.org
@@ -0,0 +1,32 @@
+#+TITLE: About/FAQ
+#+AUTHOR: Pjotr Prins
+
+* Table of Contents :TOC:noexport:
+ - [[#export-data][Export data]]
+ - [[#sparql-api][SPARQL API]]
+ - [[#rest-api][REST API]]
+ - [[#export-ebiena-forms][Export EBI/ENA Forms]]
+
+* Export data
+
+Apart from straight file [[http://covid19.genenetwork.org/download][downloads]] COVID-19 PubSeq allows for
+exporting forms and data for other services.
+
+* SPARQL API
+
+
+First of all, PubSeq exports a SPARQL endpoint [[http://sparql.genenetwork.org/sparql/][here]] that allows you do
+do any query on the data. See this [[http://covid19.genenetwork.org/blog?id=using-covid-19-pubseq-part1][document]] for examples.
+
+* REST API
+
+In addition to above flexible SPARQL endpoint - which is essentially
+is a query REST API - PubSeq exports its own
+[[http://covid19.genenetwork.org/apidoc][REST API]].
+
+* Export EBI/ENA Forms
+
+Uploading data to EBI/ENA with PubSeq is described [[http://covid19.genenetwork.org/blog?id=using-covid-19-pubseq-part6][here]].
+
+To export,
+first search for an uploaded entry through its identifier:
diff --git a/test/rest-api.html b/test/rest-api.html
index c50d116..421d75a 100644
--- a/test/rest-api.html
+++ b/test/rest-api.html
@@ -3,10 +3,10 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
-<!-- 2020-07-20 Mon 06:13 -->
+<!-- 2020-07-21 Tue 01:32 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
-<title>&lrm;</title>
+<title>PubSeq REST API</title>
<meta name="generator" content="Org mode" />
<meta name="author" content="Pjotr Prins" />
<style type="text/css">
@@ -193,6 +193,7 @@
.org-svg { width: 90%; }
/*]]>*/-->
</style>
+<link rel="Blog stylesheet" type="text/css" href="blog.css" />
<script type="text/javascript">
/*
@licstart The following is the entire license notice for the
@@ -241,23 +242,31 @@ for the JavaScript code in this tag.
</script>
</head>
<body>
-<div id="content">
+<div id="org-div-home-and-up">
+ <a accesskey="h" href=""> UP </a>
+ |
+ <a accesskey="H" href="http://covid19.genenetwork.org/apidoc"> HOME </a>
+</div><div id="content">
+<h1 class="title">PubSeq REST API</h1>
<div id="table-of-contents">
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
-<li><a href="#orgb24ef14">1. PubSeq REST API</a>
+<li><a href="#org0db7287">1. PubSeq REST API</a>
<ul>
-<li><a href="#orgd7c015d">1.1. Introduction</a></li>
-<li><a href="#orgb2caa89">1.2. Fetch EBI XML</a></li>
+<li><a href="#orgd98cd95">1.1. Introduction</a></li>
+<li><a href="#org8951ab6">1.2. Fetch EBI XML</a></li>
</ul>
</li>
-<li><a href="#org68f26b2">2. Configure emacs to run tests</a></li>
+<li><a href="#orgbde9911">2. Configure emacs to run tests</a></li>
</ul>
</div>
</div>
-<div id="outline-container-orgb24ef14" class="outline-2">
-<h2 id="orgb24ef14"><span class="section-number-2">1</span> PubSeq REST API</h2>
+
+
+
+<div id="outline-container-org0db7287" class="outline-2">
+<h2 id="org0db7287"><span class="section-number-2">1</span> PubSeq REST API</h2>
<div class="outline-text-2" id="text-1">
<p>
Here we document the public REST API that comes with PubSeq. The tests
@@ -266,8 +275,8 @@ for running the tests inside emacs.
</p>
</div>
-<div id="outline-container-orgd7c015d" class="outline-3">
-<h3 id="orgd7c015d"><span class="section-number-3">1.1</span> Introduction</h3>
+<div id="outline-container-orgd98cd95" class="outline-3">
+<h3 id="orgd98cd95"><span class="section-number-3">1.1</span> Introduction</h3>
<div class="outline-text-3" id="text-1-1">
<p>
We built a REST API for COVID-19 PubSeq. The API source code can be
@@ -330,8 +339,8 @@ response_body
</div>
</div>
-<div id="outline-container-orgb2caa89" class="outline-3">
-<h3 id="orgb2caa89"><span class="section-number-3">1.2</span> Fetch EBI XML</h3>
+<div id="outline-container-org8951ab6" class="outline-3">
+<h3 id="org8951ab6"><span class="section-number-3">1.2</span> Fetch EBI XML</h3>
<div class="outline-text-3" id="text-1-2">
<p>
PubSeq provides an API that is used to export formats that are
@@ -401,8 +410,8 @@ documented <a href="http://covid19.genenetwork.org/blog?id=using-covid-19-pubseq
</div>
</div>
-<div id="outline-container-org68f26b2" class="outline-2">
-<h2 id="org68f26b2"><span class="section-number-2">2</span> Configure emacs to run tests</h2>
+<div id="outline-container-orgbde9911" class="outline-2">
+<h2 id="orgbde9911"><span class="section-number-2">2</span> Configure emacs to run tests</h2>
<div class="outline-text-2" id="text-2">
<p>
Execute a code
@@ -428,7 +437,7 @@ To skip confirmations you may also want to set
</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 2020-07-20 Mon 06:13</small>.
+<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 2020-07-21 Tue 01:32</small>.
</div>
</body>
</html>
diff --git a/test/rest-api.org b/test/rest-api.org
index 6d118b5..31fc792 100644
--- a/test/rest-api.org
+++ b/test/rest-api.org
@@ -1,3 +1,17 @@
+# C-c C-e h h publish
+# C-c ! insert date (use . for active agenda, C-u C-c ! for date+time, C-u C-c . for time)
+# C-c C-t task rotate
+# RSS_IMAGE_URL: http://xxxx.xxxx.free.fr/rss_icon.png
+
+#+TITLE: PubSeq REST API
+#+AUTHOR: Pjotr Prins
+#+HTML_LINK_HOME: http://covid19.genenetwork.org/apidoc
+# OPTIONS: section-numbers: nil, with-drawers: t
+
+#+HTML_HEAD: <link rel="Blog stylesheet" type="text/css" href="blog.css" />
+
+
+
* PubSeq REST API
Here we document the public REST API that comes with PubSeq. The tests
@@ -33,6 +47,9 @@ response_body
#+RESULTS:
| service | : | PubSeq | version | : | 0.1 |
+** Fetch metadata
+
+
** Fetch EBI XML
PubSeq provides an API that is used to export formats that are
generated by cgit v1.2.3 (git 2.45.2) at 2024-11-22 04:09:45 +0000