auspice
Version:
Web app for visualizing pathogen evolution
98 lines (91 loc) • 15.1 kB
HTML
<html lang="en"><head><meta charSet="utf-8"/><meta http-equiv="X-UA-Compatible" content="IE=edge"/><title>Converting a narrative to PDF · Auspice</title><meta name="viewport" content="width=device-width"/><meta name="generator" content="Docusaurus"/><meta name="description" content="This documentation will walk through how to turn a narrative into a static PDF."/><meta name="docsearch:language" content="en"/><meta property="og:title" content="Converting a narrative to PDF · Auspice"/><meta property="og:type" content="website"/><meta property="og:url" content="https://nextstrain.github.io/auspice/"/><meta property="og:description" content="This documentation will walk through how to turn a narrative into a static PDF."/><meta property="og:image" content="https://nextstrain.github.io/auspice/img/icon.svg"/><meta name="twitter:card" content="summary"/><meta name="twitter:image" content="https://nextstrain.github.io/auspice/img/icon.svg"/><link rel="shortcut icon" href="/auspice/img/favicon.ico"/><link rel="stylesheet" href="//cdnjs.cloudflare.com/ajax/libs/highlight.js/9.12.0/styles/solarized-dark.min.css"/><script type="text/javascript" src="https://buttons.github.io/buttons.js"></script><script src="/auspice/js/scrollSpy.js"></script><link rel="stylesheet" href="/auspice/css/main.css"/><script src="/auspice/js/codetabs.js"></script></head><body class="sideNavVisible separateOnPageNav"><div class="fixedHeaderContainer"><div class="headerWrapper wrapper"><header><a href="/auspice/"><img class="logo" src="/auspice/img/logo-light.svg" alt="Auspice"/><h2 class="headerTitleWithLogo">Auspice</h2></a><div class="navigationWrapper navigationSlider"><nav class="slidingNav"><ul class="nav-site nav-site-internal"><li class="siteNavGroupActive"><a href="/auspice/introduction/overview" target="_self">Docs</a></li></ul></nav></div></header></div></div><div class="navPusher"><div class="docMainWrapper wrapper"><div class="docsNavContainer" id="docsNav"><nav class="toc"><div class="toggleNav"><section class="navWrapper wrapper"><div class="navBreadcrumb wrapper"><div class="navToggle" id="navToggler"><div class="hamburger-menu"><div class="line1"></div><div class="line2"></div><div class="line3"></div></div></div><h2><i>›</i><span>Narratives</span></h2><div class="tocToggler" id="tocToggler"><i class="icon-toc"></i></div></div><div class="navGroups"><div class="navGroup"><h3 class="navGroupCategoryTitle">Introduction</h3><ul class=""><li class="navListItem"><a class="navItem" href="/auspice/introduction/overview">Overview</a></li><li class="navListItem"><a class="navItem" href="/auspice/introduction/install">Install Auspice</a></li><li class="navListItem"><a class="navItem" href="/auspice/introduction/how-to-run">How to Run Auspice</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Advanced Functionality</h3><ul class=""><li class="navListItem"><a class="navItem" href="/auspice/advanced-functionality/second-trees">Displaying mutliple trees</a></li><li class="navListItem"><a class="navItem" href="/auspice/advanced-functionality/misc">Miscellaneous</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Customising Auspice</h3><ul class=""><li class="navListItem"><a class="navItem" href="/auspice/customise-client/introduction">Customising Auspice</a></li><li class="navListItem"><a class="navItem" href="/auspice/customise-client/api">Client Customisation API</a></li><li class="navListItem"><a class="navItem" href="/auspice/customise-client/requests">Requests Made from the Client</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Using a Custom Server</h3><ul class=""><li class="navListItem"><a class="navItem" href="/auspice/server/introduction">Auspice servers</a></li><li class="navListItem"><a class="navItem" href="/auspice/server/api">Server API</a></li><li class="navListItem"><a class="navItem" href="/auspice/server/authentication">Authentication</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Narratives</h3><ul class=""><li class="navListItem"><a class="navItem" href="/auspice/narratives/introduction">Communicating Results Using Narratives</a></li><li class="navListItem"><a class="navItem" href="/auspice/narratives/how-to-write">Writing a Narrative</a></li><li class="navListItem navListItemActive"><a class="navItem" href="/auspice/narratives/create-pdf">Converting a narrative to PDF</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Release Notes</h3><ul class=""><li class="navListItem"><a class="navItem" href="/auspice/releases/changelog">Changelog</a></li><li class="navListItem"><a class="navItem" href="/auspice/releases/v2">Auspice Version 2.0</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Contributing</h3><ul class=""><li class="navListItem"><a class="navItem" href="/auspice/contributing/overview">Contributing to Auspice</a></li></ul></div></div></section></div><script>
var coll = document.getElementsByClassName('collapsible');
var checkActiveCategory = true;
for (var i = 0; i < coll.length; i++) {
var links = coll[i].nextElementSibling.getElementsByTagName('*');
if (checkActiveCategory){
for (var j = 0; j < links.length; j++) {
if (links[j].classList.contains('navListItemActive')){
coll[i].nextElementSibling.classList.toggle('hide');
coll[i].childNodes[1].classList.toggle('rotate');
checkActiveCategory = false;
break;
}
}
}
coll[i].addEventListener('click', function() {
var arrow = this.childNodes[1];
arrow.classList.toggle('rotate');
var content = this.nextElementSibling;
content.classList.toggle('hide');
});
}
document.addEventListener('DOMContentLoaded', function() {
createToggler('#navToggler', '#docsNav', 'docsSliderActive');
createToggler('#tocToggler', 'body', 'tocActive');
var headings = document.querySelector('.toc-headings');
headings && headings.addEventListener('click', function(event) {
var el = event.target;
while(el !== headings){
if (el.tagName === 'A') {
document.body.classList.remove('tocActive');
break;
} else{
el = el.parentNode;
}
}
}, false);
function createToggler(togglerSelector, targetSelector, className) {
var toggler = document.querySelector(togglerSelector);
var target = document.querySelector(targetSelector);
if (!toggler) {
return;
}
toggler.onclick = function(event) {
event.preventDefault();
target.classList.toggle(className);
};
}
});
</script></nav></div><div class="container mainContainer"><div class="wrapper"><div class="post"><header class="postHeader"><h1 class="postHeaderTitle">Converting a narrative to PDF</h1></header><article><div><span><p>This documentation will walk through how to turn a narrative into a static PDF.
We understand that there are multiple reasons why PDFs may be a necessary method of distribution, but stress that narratives are designed to be viewed through auspice where you have the ability to interact with and interrogate the data.</p>
<p>If you run into any bugs, please <a href="mailto:hello@nextstrain.org">get in contact with us (email)</a>.</p>
<h2><a class="anchor" aria-hidden="true" id="prerequisites"></a><a href="#prerequisites" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Prerequisites</h2>
<p>This requires <a href="https://github.com/astefanutti/decktape">Decktape</a> to be installed, which itself requires Node.js.
If you've followed the <a href="../introduction/install">auspice install instructions</a> and are using a conda environment then this is straightforward.
If not, you can create the necessary conda environment via:</p>
<pre><code class="hljs css language-bash">conda create --name auspice nodejs=10
</code></pre>
<p>Install Decktape via:</p>
<pre><code class="hljs css language-bash">conda activate auspice <span class="hljs-comment"># or whichever conda environment has nodejs</span>
npm install --global decktape
</code></pre>
<h2><a class="anchor" aria-hidden="true" id="saving-an-online-narrative-to-pdf"></a><a href="#saving-an-online-narrative-to-pdf" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Saving an online narrative to PDF</h2>
<p>Let's say we want to save the example Genomic-Epi Situation Report for Ebola in the DRC available at <a href="https://nextstrain.org/narratives/inrb-ebola-example-sit-rep">nextstrain.org/narratives/inrb-ebola-example-sit-rep</a> which you can see has 6 different "pages" of content.
We use decktape to access these different pages & save their output as PDF via:</p>
<pre><code class="hljs css language-bash">decktape generic --load-pause 3000 --key ArrowDown --size 1600x900 \
https://nextstrain.org/narratives/inrb-ebola-example-sit-rep example.pdf
</code></pre>
<p>You'll see a lot of bad-looking warning messages printed in the terminal 😱, but as long as you see "Printed 7 slides" or similar then the command has worked.
You should now be able to view a static PDF of the narrative, in this case at <code>example.pdf</code>.
Feel free to play around with the different options available to decktape (run <code>decktape generic --help</code> to see them).</p>
<blockquote>
<p>Note that this technique won't work if authentication is required. Please refer to the section on saving local narratives to PDF for how to do this.</p>
</blockquote>
<h2><a class="anchor" aria-hidden="true" id="saving-a-local-narrative-to-pdf"></a><a href="#saving-a-local-narrative-to-pdf" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Saving a local narrative to PDF</h2>
<p>If you have a local narrative then the concept is similar to saving an online narrative, except we need to start a auspice server locally to display our narrative & allow it to be accessed by decktape.
These instructions assume you have installed auspice into a conda enviornment as per the <a href="../introduction/install">auspice install instructions</a>.</p>
<p>Start up auspice locally, sourcing your own datasets & narratives via:</p>
<pre><code class="hljs css language-bash">conda activate auspice <span class="hljs-comment"># or whichever conda environment has auspice installed</span>
auspice view --datasetDir <path-to-datasets> --narrativeDir <path-to-narratives>
</code></pre>
<p>You should now be able to view your narrative at <a href="http://localhost:4000">localhost:4000</a>.
For the purposes of this guide, i'll assume that we've followed the <a href="how-to-write">Writing a Narrative</a> guide, and thus have a narrative describing mumps in North America available at <a href="http://localhost:4000/narratives/example">localhost:4000/narratives/example</a>.</p>
<p>In a separate terminal window, run</p>
<pre><code class="hljs css language-bash">conda activate auspice <span class="hljs-comment"># or whichever conda environment has dectape installed from earlier</span>
decktape generic --load-pause 3000 --key ArrowDown --size 1600x900 \
http://localhost:4000/narratives/example example.pdf
</code></pre>
<p>You'll see a lot of bad-looking warning messages printed in the terminal 😱, but as long as you see "Printed 11 slides" or similar then the command has worked.
You should now be able to view a static PDF of the narrative, in this case at <code>example.pdf</code>.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 11/15/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/narratives/how-to-write"><span class="arrow-prev">← </span><span>Writing a Narrative</span></a><a class="docs-next button" href="/auspice/releases/changelog"><span>Changelog</span><span class="arrow-next"> →</span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#prerequisites">Prerequisites</a></li><li><a href="#saving-an-online-narrative-to-pdf">Saving an online narrative to PDF</a></li><li><a href="#saving-a-local-narrative-to-pdf">Saving a local narrative to PDF</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher & Trevor Bedford</section></footer></div></body></html>