diff options
-rw-r--r-- | bh20simplewebuploader/main.py | 5 | ||||
-rw-r--r-- | bh20simplewebuploader/templates/export.html | 28 | ||||
-rw-r--r-- | doc/web/export.html | 307 | ||||
-rw-r--r-- | doc/web/export.org | 32 | ||||
-rw-r--r-- | test/rest-api.html | 41 | ||||
-rw-r--r-- | test/rest-api.org | 17 |
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>‎</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 |