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rebuild docs

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james hadfield 2 years ago
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  1. 4
      docs/customise-client/api.html
  2. 4
      docs/customise-client/api/index.html
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      docs/customise-client/introduction.html
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      docs/introduction/how-to-run.html
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      docs/introduction/how-to-run/index.html
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4
docs/customise-client/api.html

@ -68,7 +68,7 @@ They are contained in a JSON file supplied to Auspice via</p>
<em>Thus, while you can run <code>auspice develop --extend &lt;JSON&gt;</code> it will not update as you may expect!</em></p>
<h2><a class="anchor" aria-hidden="true" id="available-customisations"></a><a href="#available-customisations" 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>Available Customisations</h2>
<p>The following are definable as top-level keys of the JSON file.
A useful reference may be the <a href="https://github.com/nextstrain/nextstrain.org/blob/master/auspice/client/config.json">customisation JSON file</a> used by nextstrain.org.</p>
A useful reference may be the <a href="https://github.com/nextstrain/nextstrain.org/blob/master/auspice-client/customisations/config.json">customisation JSON file</a> used by nextstrain.org.</p>
<ul>
<li><code>sidebarTheme</code> allows modifications to the aesthetics of the sidebar. See below.</li>
<li><code>navbarComponent</code> a (relative) path to a JS file exporting a React component to be rendered as the nav bar. See below.</li>
@ -163,4 +163,4 @@ This can be changed by specifying <code>serverAddress</code> in the customisatio
<p>Note that currently you can't specify a different domain due to CORS headers.
This may well be a simple fix -- please get in touch if you can help here!</p>
</blockquote>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 1/28/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/customise-client/introduction"><span class="arrow-prev"></span><span>Customising Auspice</span></a><a class="docs-next button" href="/auspice/customise-client/requests"><span>Requests Made from the Client</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#available-customisations">Available Customisations</a></li><li><a href="#sidebar-theme">Sidebar Theme</a></li><li><a href="#nav-bar-component">Nav-bar Component</a></li><li><a href="#splash-component">Splash component</a></li><li><a href="#specifying-the-api-server-address">Specifying the API server address</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 &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 3/22/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/customise-client/introduction"><span class="arrow-prev"></span><span>Customising Auspice</span></a><a class="docs-next button" href="/auspice/customise-client/requests"><span>Requests Made from the Client</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#available-customisations">Available Customisations</a></li><li><a href="#sidebar-theme">Sidebar Theme</a></li><li><a href="#nav-bar-component">Nav-bar Component</a></li><li><a href="#splash-component">Splash component</a></li><li><a href="#specifying-the-api-server-address">Specifying the API server address</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 &amp; Trevor Bedford</section></footer></div></body></html>

4
docs/customise-client/api/index.html

@ -68,7 +68,7 @@ They are contained in a JSON file supplied to Auspice via</p>
<em>Thus, while you can run <code>auspice develop --extend &lt;JSON&gt;</code> it will not update as you may expect!</em></p>
<h2><a class="anchor" aria-hidden="true" id="available-customisations"></a><a href="#available-customisations" 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>Available Customisations</h2>
<p>The following are definable as top-level keys of the JSON file.
A useful reference may be the <a href="https://github.com/nextstrain/nextstrain.org/blob/master/auspice/client/config.json">customisation JSON file</a> used by nextstrain.org.</p>
A useful reference may be the <a href="https://github.com/nextstrain/nextstrain.org/blob/master/auspice-client/customisations/config.json">customisation JSON file</a> used by nextstrain.org.</p>
<ul>
<li><code>sidebarTheme</code> allows modifications to the aesthetics of the sidebar. See below.</li>
<li><code>navbarComponent</code> a (relative) path to a JS file exporting a React component to be rendered as the nav bar. See below.</li>
@ -163,4 +163,4 @@ This can be changed by specifying <code>serverAddress</code> in the customisatio
<p>Note that currently you can't specify a different domain due to CORS headers.
This may well be a simple fix -- please get in touch if you can help here!</p>
</blockquote>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 1/28/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/customise-client/introduction"><span class="arrow-prev"></span><span>Customising Auspice</span></a><a class="docs-next button" href="/auspice/customise-client/requests"><span>Requests Made from the Client</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#available-customisations">Available Customisations</a></li><li><a href="#sidebar-theme">Sidebar Theme</a></li><li><a href="#nav-bar-component">Nav-bar Component</a></li><li><a href="#splash-component">Splash component</a></li><li><a href="#specifying-the-api-server-address">Specifying the API server address</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 &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 3/22/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/customise-client/introduction"><span class="arrow-prev"></span><span>Customising Auspice</span></a><a class="docs-next button" href="/auspice/customise-client/requests"><span>Requests Made from the Client</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#available-customisations">Available Customisations</a></li><li><a href="#sidebar-theme">Sidebar Theme</a></li><li><a href="#nav-bar-component">Nav-bar Component</a></li><li><a href="#splash-component">Splash component</a></li><li><a href="#specifying-the-api-server-address">Specifying the API server address</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 &amp; Trevor Bedford</section></footer></div></body></html>

4
docs/customise-client/introduction.html

@ -61,6 +61,6 @@ This is how Auspice running locally and nextstrain.org look different, despite b
<p>This is achieved by providing a JSON at build time to Auspice which defines the desired customisations via:</p>
<pre><code class="hljs css language-bash">auspice build --extend &lt;JSON&gt;
</code></pre>
<p><a href="https://github.com/nextstrain/nextstrain.org/blob/master/auspice/client/config.json">Here's</a> the file used by nextstrain.org to change the appearance of Auspice in the above image.</p>
<p><a href="https://github.com/nextstrain/nextstrain.org/blob/master/auspice-client/customisations/config.json">Here's</a> the file used by nextstrain.org to change the appearance of Auspice in the above image.</p>
<p>See the <a href="/auspice/customise-client/api">client customisation API</a> for the available options.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/17/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/advanced-functionality/misc"><span class="arrow-prev"></span><span>Miscellaneous</span></a><a class="docs-next button" href="/auspice/customise-client/api"><span>Client Customisation API</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"></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 &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 3/22/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/advanced-functionality/misc"><span class="arrow-prev"></span><span>Miscellaneous</span></a><a class="docs-next button" href="/auspice/customise-client/api"><span>Client Customisation API</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"></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 &amp; Trevor Bedford</section></footer></div></body></html>

4
docs/customise-client/introduction/index.html

@ -61,6 +61,6 @@ This is how Auspice running locally and nextstrain.org look different, despite b
<p>This is achieved by providing a JSON at build time to Auspice which defines the desired customisations via:</p>
<pre><code class="hljs css language-bash">auspice build --extend &lt;JSON&gt;
</code></pre>
<p><a href="https://github.com/nextstrain/nextstrain.org/blob/master/auspice/client/config.json">Here's</a> the file used by nextstrain.org to change the appearance of Auspice in the above image.</p>
<p><a href="https://github.com/nextstrain/nextstrain.org/blob/master/auspice-client/customisations/config.json">Here's</a> the file used by nextstrain.org to change the appearance of Auspice in the above image.</p>
<p>See the <a href="/auspice/customise-client/api">client customisation API</a> for the available options.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/17/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/advanced-functionality/misc"><span class="arrow-prev"></span><span>Miscellaneous</span></a><a class="docs-next button" href="/auspice/customise-client/api"><span>Client Customisation API</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"></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 &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 3/22/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/advanced-functionality/misc"><span class="arrow-prev"></span><span>Miscellaneous</span></a><a class="docs-next button" href="/auspice/customise-client/api"><span>Client Customisation API</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"></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 &amp; Trevor Bedford</section></footer></div></body></html>

6
docs/introduction/how-to-run.html

@ -113,9 +113,9 @@ Currently, it only converts &quot;Auspice v1&quot; JSONs into &quot;Auspice v2&q
<h3><a class="anchor" aria-hidden="true" id="dataset-jsons"></a><a href="#dataset-jsons" 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>Dataset JSONs</h3>
<p>For datasets, Auspice (v2.x) can currently load either</p>
<ul>
<li>&quot;Auspice v1&quot; JSONs (metadata + tree JSONs) -- see the JSON schemas <a href="https://github.com/nextstrain/augur/blob/v6/augur/data/schema-export-v1-meta.json">here</a> and <a href="https://github.com/nextstrain/augur/blob/v6/augur/data/schema-export-v1-tree.json">here</a>.
<li>&quot;Auspice v1&quot; JSONs (metadata + tree JSONs) -- see the JSON schemas <a href="https://github.com/nextstrain/augur/blob/master/augur/data/schema-export-v1-meta.json">here</a> and <a href="https://github.com/nextstrain/augur/blob/master/augur/data/schema-export-v1-tree.json">here</a>.
<em>The zika dataset we download above is in this format</em></li>
<li>&quot;Auspice v2&quot; JSONs. See the JSON schema <a href="https://github.com/nextstrain/augur/blob/v6/augur/data/schema-export-v2.json">here</a>.</li>
<li>&quot;Auspice v2&quot; JSONs. See the JSON schema <a href="https://github.com/nextstrain/augur/blob/master/augur/data/schema-export-v2.json">here</a>.</li>
</ul>
<p>See the <a href="/auspice/server/api">Server API</a> for more details about the file formats an Auspice server (e.g. <code>auspice view</code>) sends to the client.</p>
<p>Currently we mainly use <a href="https://github.com/nextstrain/augur">Augur</a> to create these datasets.
@ -133,4 +133,4 @@ Using BEAST trees is possible, but you have to use Augur to convert them first.<
<li>You can download the narrative Markdown files by running <a href="https://github.com/nextstrain/auspice/blob/master/scripts/get-narratives.sh">this script</a> which will create a <code>./narratives</code> directory for you.</li>
</ul>
<p>You can then run <code>auspice view --datasetDir data --narrativeDir narratives</code> to visualise all of the <a href="https://nextstrain.org">nextstrain.org</a> datasets locally.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 11/14/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/introduction/install"><span class="arrow-prev"></span><span>Install Auspice</span></a><a class="docs-next button" href="/auspice/advanced-functionality/second-trees"><span>Displaying multiple trees</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#how-to-get-an-example-dataset-up-and-running">How to Get an Example Dataset Up and Running</a></li><li><a href="#auspice-view"><code>auspice view</code></a></li><li><a href="#auspice-build"><code>auspice build</code></a></li><li><a href="#auspice-develop"><code>auspice develop</code></a></li><li><a href="#auspice-convert"><code>auspice convert</code></a></li><li><a href="#input-file-formats">Input File Formats</a><ul class="toc-headings"><li><a href="#dataset-jsons">Dataset JSONs</a></li><li><a href="#narratives">Narratives</a></li></ul></li><li><a href="#obtaining-a-set-of-input-files">Obtaining a Set of Input Files</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 &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 3/22/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/introduction/install"><span class="arrow-prev"></span><span>Install Auspice</span></a><a class="docs-next button" href="/auspice/advanced-functionality/second-trees"><span>Displaying multiple trees</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#how-to-get-an-example-dataset-up-and-running">How to Get an Example Dataset Up and Running</a></li><li><a href="#auspice-view"><code>auspice view</code></a></li><li><a href="#auspice-build"><code>auspice build</code></a></li><li><a href="#auspice-develop"><code>auspice develop</code></a></li><li><a href="#auspice-convert"><code>auspice convert</code></a></li><li><a href="#input-file-formats">Input File Formats</a><ul class="toc-headings"><li><a href="#dataset-jsons">Dataset JSONs</a></li><li><a href="#narratives">Narratives</a></li></ul></li><li><a href="#obtaining-a-set-of-input-files">Obtaining a Set of Input Files</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 &amp; Trevor Bedford</section></footer></div></body></html>

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@ -113,9 +113,9 @@ Currently, it only converts &quot;Auspice v1&quot; JSONs into &quot;Auspice v2&q
<h3><a class="anchor" aria-hidden="true" id="dataset-jsons"></a><a href="#dataset-jsons" 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>Dataset JSONs</h3>
<p>For datasets, Auspice (v2.x) can currently load either</p>
<ul>
<li>&quot;Auspice v1&quot; JSONs (metadata + tree JSONs) -- see the JSON schemas <a href="https://github.com/nextstrain/augur/blob/v6/augur/data/schema-export-v1-meta.json">here</a> and <a href="https://github.com/nextstrain/augur/blob/v6/augur/data/schema-export-v1-tree.json">here</a>.
<li>&quot;Auspice v1&quot; JSONs (metadata + tree JSONs) -- see the JSON schemas <a href="https://github.com/nextstrain/augur/blob/master/augur/data/schema-export-v1-meta.json">here</a> and <a href="https://github.com/nextstrain/augur/blob/master/augur/data/schema-export-v1-tree.json">here</a>.
<em>The zika dataset we download above is in this format</em></li>
<li>&quot;Auspice v2&quot; JSONs. See the JSON schema <a href="https://github.com/nextstrain/augur/blob/v6/augur/data/schema-export-v2.json">here</a>.</li>
<li>&quot;Auspice v2&quot; JSONs. See the JSON schema <a href="https://github.com/nextstrain/augur/blob/master/augur/data/schema-export-v2.json">here</a>.</li>
</ul>
<p>See the <a href="/auspice/server/api">Server API</a> for more details about the file formats an Auspice server (e.g. <code>auspice view</code>) sends to the client.</p>
<p>Currently we mainly use <a href="https://github.com/nextstrain/augur">Augur</a> to create these datasets.
@ -133,4 +133,4 @@ Using BEAST trees is possible, but you have to use Augur to convert them first.<
<li>You can download the narrative Markdown files by running <a href="https://github.com/nextstrain/auspice/blob/master/scripts/get-narratives.sh">this script</a> which will create a <code>./narratives</code> directory for you.</li>
</ul>
<p>You can then run <code>auspice view --datasetDir data --narrativeDir narratives</code> to visualise all of the <a href="https://nextstrain.org">nextstrain.org</a> datasets locally.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 11/14/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/introduction/install"><span class="arrow-prev"></span><span>Install Auspice</span></a><a class="docs-next button" href="/auspice/advanced-functionality/second-trees"><span>Displaying multiple trees</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#how-to-get-an-example-dataset-up-and-running">How to Get an Example Dataset Up and Running</a></li><li><a href="#auspice-view"><code>auspice view</code></a></li><li><a href="#auspice-build"><code>auspice build</code></a></li><li><a href="#auspice-develop"><code>auspice develop</code></a></li><li><a href="#auspice-convert"><code>auspice convert</code></a></li><li><a href="#input-file-formats">Input File Formats</a><ul class="toc-headings"><li><a href="#dataset-jsons">Dataset JSONs</a></li><li><a href="#narratives">Narratives</a></li></ul></li><li><a href="#obtaining-a-set-of-input-files">Obtaining a Set of Input Files</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 &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 3/22/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/introduction/install"><span class="arrow-prev"></span><span>Install Auspice</span></a><a class="docs-next button" href="/auspice/advanced-functionality/second-trees"><span>Displaying multiple trees</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#how-to-get-an-example-dataset-up-and-running">How to Get an Example Dataset Up and Running</a></li><li><a href="#auspice-view"><code>auspice view</code></a></li><li><a href="#auspice-build"><code>auspice build</code></a></li><li><a href="#auspice-develop"><code>auspice develop</code></a></li><li><a href="#auspice-convert"><code>auspice convert</code></a></li><li><a href="#input-file-formats">Input File Formats</a><ul class="toc-headings"><li><a href="#dataset-jsons">Dataset JSONs</a></li><li><a href="#narratives">Narratives</a></li></ul></li><li><a href="#obtaining-a-set-of-input-files">Obtaining a Set of Input Files</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 &amp; Trevor Bedford</section></footer></div></body></html>

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@ -95,9 +95,9 @@ Additionally the format of the input JSONs to Auspice changed a bit throughout t
<tr><th>file</th><th>schema</th><th>auspice versions</th><th>description</th></tr>
</thead>
<tbody>
<tr><td>&quot;tree&quot; JSON</td><td><a href="https://github.com/nextstrain/augur/blob/v6/augur/data/schema-export-v1-tree.json">Link</a></td><td>v1, v2</td><td>Decorated phylogenetic tree</td></tr>
<tr><td>&quot;meta&quot; JSON</td><td><a href="https://github.com/nextstrain/augur/blob/v6/augur/data/schema-export-v1-meta.json">Link</a></td><td>v1, v2</td><td>The &quot;metadata&quot; associated with a phylogenetic tree</td></tr>
<tr><td>&quot;v2&quot; JSON</td><td><a href="https://github.com/nextstrain/augur/blob/v6/augur/data/schema-export-v2.json">Link</a></td><td>v2</td><td>The single input format required for Auspice v2</td></tr>
<tr><td>&quot;tree&quot; JSON</td><td><a href="https://github.com/nextstrain/augur/blob/master/augur/data/schema-export-v1-tree.json">Link</a></td><td>v1, v2</td><td>Decorated phylogenetic tree</td></tr>
<tr><td>&quot;meta&quot; JSON</td><td><a href="https://github.com/nextstrain/augur/blob/master/augur/data/schema-export-v1-meta.json">Link</a></td><td>v1, v2</td><td>The &quot;metadata&quot; associated with a phylogenetic tree</td></tr>
<tr><td>&quot;v2&quot; JSON</td><td><a href="https://github.com/nextstrain/augur/blob/master/augur/data/schema-export-v2.json">Link</a></td><td>v2</td><td>The single input format required for Auspice v2</td></tr>
</tbody>
</table>
<p>If you use Augur to construct your JSONs, then the next version of Augur (v6) will give you the option to produce &quot;v1&quot; or &quot;v2&quot; JSONs.
@ -206,4 +206,4 @@ We have now generalised this, and the <a href="/auspice/server/api#charon-getava
<p>It's possible to use <code>auspice build</code> to <a href="/auspice/customise-client/introduction">build a custom auspice client</a>.
If this has been done, then running <code>auspice view</code> will serve it -- before you had to run <code>auspice view --customBuild</code>.
This streamlines generating custom auspice bundles and serving them locally.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/21/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/releases/changelog"><span class="arrow-prev"></span><span>Changelog</span></a><a class="docs-next button" href="/auspice/contributing/overview"><span>Contributing to Auspice</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#whats-new">What's New</a></li><li><a href="#backstory">Backstory</a></li><li><a href="#i-dont-want-to-upgrade-how-can-i-continue-to-use-auspice-v1">I don't want to upgrade - how can I continue to use Auspice v1?</a></li><li><a href="#pie-charts-to-represent-discrete-variables-on-a-map">Pie charts to represent discrete variables on a map</a></li><li><a href="#new-dataset-json-format">New dataset JSON format</a></li><li><a href="#more-information-in-tree-info-boxes">More information in tree info boxes</a></li><li><a href="#display-of-second-trees">Display of second trees</a></li><li><a href="#display-better-dates-on-the-tree-axis">Display better dates on the tree axis</a></li><li><a href="#map-quot-reset-zoom-quot-button-zooms-to-include-all-demes">Map &quot;reset zoom&quot; button zooms to include all demes</a></li><li><a href="#consistent-colouring-of-missing-data-in-the-tree">Consistent colouring of missing data in the tree</a></li><li><a href="#removal-of-twitter-amp-google-analytics">Removal of Twitter &amp; Google Analytics</a></li><li><a href="#improvements-in-the-entropy-panel">Improvements in the entropy panel</a></li><li><a href="#auspice-responds-to-server-redirects-for-datasets">Auspice responds to server redirects for datasets</a></li><li><a href="#importing-server-code-from-auspice">Importing (server) code from Auspice</a></li><li><a href="#new-auspice-subcommand-auspice-convert">New Auspice subcommand: <code>auspice convert</code></a></li><li><a href="#ability-to-show-a-quot-build-quot-source-url-in-the-sidebar">Ability to show a &quot;build&quot; source URL in the sidebar</a></li><li><a href="#auspice-view-uses-a-custom-auspice-client-if-present"><code>auspice view</code> uses a custom Auspice client if present</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 &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 3/22/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/releases/changelog"><span class="arrow-prev"></span><span>Changelog</span></a><a class="docs-next button" href="/auspice/contributing/overview"><span>Contributing to Auspice</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#whats-new">What's New</a></li><li><a href="#backstory">Backstory</a></li><li><a href="#i-dont-want-to-upgrade-how-can-i-continue-to-use-auspice-v1">I don't want to upgrade - how can I continue to use Auspice v1?</a></li><li><a href="#pie-charts-to-represent-discrete-variables-on-a-map">Pie charts to represent discrete variables on a map</a></li><li><a href="#new-dataset-json-format">New dataset JSON format</a></li><li><a href="#more-information-in-tree-info-boxes">More information in tree info boxes</a></li><li><a href="#display-of-second-trees">Display of second trees</a></li><li><a href="#display-better-dates-on-the-tree-axis">Display better dates on the tree axis</a></li><li><a href="#map-quot-reset-zoom-quot-button-zooms-to-include-all-demes">Map &quot;reset zoom&quot; button zooms to include all demes</a></li><li><a href="#consistent-colouring-of-missing-data-in-the-tree">Consistent colouring of missing data in the tree</a></li><li><a href="#removal-of-twitter-amp-google-analytics">Removal of Twitter &amp; Google Analytics</a></li><li><a href="#improvements-in-the-entropy-panel">Improvements in the entropy panel</a></li><li><a href="#auspice-responds-to-server-redirects-for-datasets">Auspice responds to server redirects for datasets</a></li><li><a href="#importing-server-code-from-auspice">Importing (server) code from Auspice</a></li><li><a href="#new-auspice-subcommand-auspice-convert">New Auspice subcommand: <code>auspice convert</code></a></li><li><a href="#ability-to-show-a-quot-build-quot-source-url-in-the-sidebar">Ability to show a &quot;build&quot; source URL in the sidebar</a></li><li><a href="#auspice-view-uses-a-custom-auspice-client-if-present"><code>auspice view</code> uses a custom Auspice client if present</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 &amp; Trevor Bedford</section></footer></div></body></html>

8
docs/releases/v2/index.html

@ -95,9 +95,9 @@ Additionally the format of the input JSONs to Auspice changed a bit throughout t
<tr><th>file</th><th>schema</th><th>auspice versions</th><th>description</th></tr>
</thead>
<tbody>
<tr><td>&quot;tree&quot; JSON</td><td><a href="https://github.com/nextstrain/augur/blob/v6/augur/data/schema-export-v1-tree.json">Link</a></td><td>v1, v2</td><td>Decorated phylogenetic tree</td></tr>
<tr><td>&quot;meta&quot; JSON</td><td><a href="https://github.com/nextstrain/augur/blob/v6/augur/data/schema-export-v1-meta.json">Link</a></td><td>v1, v2</td><td>The &quot;metadata&quot; associated with a phylogenetic tree</td></tr>
<tr><td>&quot;v2&quot; JSON</td><td><a href="https://github.com/nextstrain/augur/blob/v6/augur/data/schema-export-v2.json">Link</a></td><td>v2</td><td>The single input format required for Auspice v2</td></tr>
<tr><td>&quot;tree&quot; JSON</td><td><a href="https://github.com/nextstrain/augur/blob/master/augur/data/schema-export-v1-tree.json">Link</a></td><td>v1, v2</td><td>Decorated phylogenetic tree</td></tr>
<tr><td>&quot;meta&quot; JSON</td><td><a href="https://github.com/nextstrain/augur/blob/master/augur/data/schema-export-v1-meta.json">Link</a></td><td>v1, v2</td><td>The &quot;metadata&quot; associated with a phylogenetic tree</td></tr>
<tr><td>&quot;v2&quot; JSON</td><td><a href="https://github.com/nextstrain/augur/blob/master/augur/data/schema-export-v2.json">Link</a></td><td>v2</td><td>The single input format required for Auspice v2</td></tr>
</tbody>
</table>
<p>If you use Augur to construct your JSONs, then the next version of Augur (v6) will give you the option to produce &quot;v1&quot; or &quot;v2&quot; JSONs.
@ -206,4 +206,4 @@ We have now generalised this, and the <a href="/auspice/server/api#charon-getava
<p>It's possible to use <code>auspice build</code> to <a href="/auspice/customise-client/introduction">build a custom auspice client</a>.
If this has been done, then running <code>auspice view</code> will serve it -- before you had to run <code>auspice view --customBuild</code>.
This streamlines generating custom auspice bundles and serving them locally.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/21/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/releases/changelog"><span class="arrow-prev"></span><span>Changelog</span></a><a class="docs-next button" href="/auspice/contributing/overview"><span>Contributing to Auspice</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#whats-new">What's New</a></li><li><a href="#backstory">Backstory</a></li><li><a href="#i-dont-want-to-upgrade-how-can-i-continue-to-use-auspice-v1">I don't want to upgrade - how can I continue to use Auspice v1?</a></li><li><a href="#pie-charts-to-represent-discrete-variables-on-a-map">Pie charts to represent discrete variables on a map</a></li><li><a href="#new-dataset-json-format">New dataset JSON format</a></li><li><a href="#more-information-in-tree-info-boxes">More information in tree info boxes</a></li><li><a href="#display-of-second-trees">Display of second trees</a></li><li><a href="#display-better-dates-on-the-tree-axis">Display better dates on the tree axis</a></li><li><a href="#map-quot-reset-zoom-quot-button-zooms-to-include-all-demes">Map &quot;reset zoom&quot; button zooms to include all demes</a></li><li><a href="#consistent-colouring-of-missing-data-in-the-tree">Consistent colouring of missing data in the tree</a></li><li><a href="#removal-of-twitter-amp-google-analytics">Removal of Twitter &amp; Google Analytics</a></li><li><a href="#improvements-in-the-entropy-panel">Improvements in the entropy panel</a></li><li><a href="#auspice-responds-to-server-redirects-for-datasets">Auspice responds to server redirects for datasets</a></li><li><a href="#importing-server-code-from-auspice">Importing (server) code from Auspice</a></li><li><a href="#new-auspice-subcommand-auspice-convert">New Auspice subcommand: <code>auspice convert</code></a></li><li><a href="#ability-to-show-a-quot-build-quot-source-url-in-the-sidebar">Ability to show a &quot;build&quot; source URL in the sidebar</a></li><li><a href="#auspice-view-uses-a-custom-auspice-client-if-present"><code>auspice view</code> uses a custom Auspice client if present</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 &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 3/22/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/releases/changelog"><span class="arrow-prev"></span><span>Changelog</span></a><a class="docs-next button" href="/auspice/contributing/overview"><span>Contributing to Auspice</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#whats-new">What's New</a></li><li><a href="#backstory">Backstory</a></li><li><a href="#i-dont-want-to-upgrade-how-can-i-continue-to-use-auspice-v1">I don't want to upgrade - how can I continue to use Auspice v1?</a></li><li><a href="#pie-charts-to-represent-discrete-variables-on-a-map">Pie charts to represent discrete variables on a map</a></li><li><a href="#new-dataset-json-format">New dataset JSON format</a></li><li><a href="#more-information-in-tree-info-boxes">More information in tree info boxes</a></li><li><a href="#display-of-second-trees">Display of second trees</a></li><li><a href="#display-better-dates-on-the-tree-axis">Display better dates on the tree axis</a></li><li><a href="#map-quot-reset-zoom-quot-button-zooms-to-include-all-demes">Map &quot;reset zoom&quot; button zooms to include all demes</a></li><li><a href="#consistent-colouring-of-missing-data-in-the-tree">Consistent colouring of missing data in the tree</a></li><li><a href="#removal-of-twitter-amp-google-analytics">Removal of Twitter &amp; Google Analytics</a></li><li><a href="#improvements-in-the-entropy-panel">Improvements in the entropy panel</a></li><li><a href="#auspice-responds-to-server-redirects-for-datasets">Auspice responds to server redirects for datasets</a></li><li><a href="#importing-server-code-from-auspice">Importing (server) code from Auspice</a></li><li><a href="#new-auspice-subcommand-auspice-convert">New Auspice subcommand: <code>auspice convert</code></a></li><li><a href="#ability-to-show-a-quot-build-quot-source-url-in-the-sidebar">Ability to show a &quot;build&quot; source URL in the sidebar</a></li><li><a href="#auspice-view-uses-a-custom-auspice-client-if-present"><code>auspice view</code> uses a custom Auspice client if present</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 &amp; Trevor Bedford</section></footer></div></body></html>

8
docs/server/api.html

@ -96,7 +96,7 @@ Unused by the default Auspice handler.</li>
</ul>
<p><strong>JSON Response (on success):</strong></p>
<p>The JSON response depends on the file-type being requested.</p>
<p>If the type is not specified, i.e. we're requesting the &quot;main&quot; dataset JSON then <a href="https://github.com/nextstrain/augur/blob/v6/augur/data/schema-export-v2.json">see this JSON schema</a>.
<p>If the type is not specified, i.e. we're requesting the &quot;main&quot; dataset JSON then <a href="https://github.com/nextstrain/augur/blob/master/augur/data/schema-export-v2.json">see this JSON schema</a>.
Note that the Auspice client <em>cannot</em> process v1 (meta / tree) JSONs -- <a href="/auspice/server/api#importing-code-from-auspice">see below</a> for how to convert these.</p>
<p>Alternative file type reponses are to be documented.</p>
<p><strong>Alternative responses:</strong></p>
@ -132,7 +132,7 @@ The provided JavaScript file must export three functions, each of which handles
</tbody>
</table>
<p>For information about the <code>req</code> and <code>res</code> arguments see the express documentation for the <a href="https://expressjs.com/en/api.html#req">request object</a> and <a href="https://expressjs.com/en/api.html#res">response object</a>, respectively.</p>
<p>You can see <a href="https://nextstrain.org">nextstrain.org</a>'s implementation of these handlers <a href="https://github.com/nextstrain/nextstrain.org/blob/master/auspice/server/index.js">here</a>.</p>
<p>You can see <a href="https://nextstrain.org">nextstrain.org</a>'s implementation of these handlers <a href="https://github.com/nextstrain/nextstrain.org/blob/master/server.js">here</a>.</p>
<p>Here's a pseudocode example of an implementation for the <code>getAvailable</code> handler which may help understanding:</p>
<pre><code class="hljs css language-js"><span class="hljs-keyword">const</span> getAvailable = <span class="hljs-function">(<span class="hljs-params">req, res</span>) =&gt;</span> {
<span class="hljs-keyword">try</span> {
@ -159,7 +159,7 @@ For instance, the code to convert v1 dataset JSONs to v2 JSONs (which the client
</code></pre>
<p>where <code>tree</code> is the v1 tree JSON, and <code>meta</code> the v1 meta JSON.</p>
<p><strong>Returns:</strong></p>
<p>An object representing the v2 JSON <a href="https://github.com/nextstrain/augur/blob/v6/augur/data/schema-export-v2.json">defined by this schema</a>.</p>
<p>An object representing the v2 JSON <a href="https://github.com/nextstrain/augur/blob/master/augur/data/schema-export-v2.json">defined by this schema</a>.</p>
<h3><a class="anchor" aria-hidden="true" id="parsenarrativefile"></a><a href="#parsenarrativefile" 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><code>parseNarrativeFile</code></h3>
<p><strong>Signature:</strong></p>
<pre><code class="hljs css language-js"><span class="hljs-keyword">const</span> blocks = parseNarrativeFile(fileContents);
@ -173,4 +173,4 @@ Each object has properties</p>
<li><code>dataset</code> -- the dataset associated with this block</li>
<li><code>query</code> -- the query associated with this block</li>
</ul>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/17/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/server/introduction"><span class="arrow-prev"></span><span>Auspice servers</span></a><a class="docs-next button" href="/auspice/server/authentication"><span>Authentication</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#auspice-client-requests">Auspice client requests</a><ul class="toc-headings"><li><a href="#charon-getavailable"><code>/charon/getAvailable</code></a></li><li><a href="#charon-getdataset"><code>/charon/getDataset</code></a></li><li><a href="#charon-getnarrative"><code>/charon/getNarrative</code></a></li></ul></li><li><a href="#suppling-custom-handlers-to-the-auspice-server">Suppling custom handlers to the Auspice server</a></li><li><a href="#importing-code-from-auspice">Importing code from Auspice</a><ul class="toc-headings"><li><a href="#convertfromv1"><code>convertFromV1</code></a></li><li><a href="#parsenarrativefile"><code>parseNarrativeFile</code></a></li></ul></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 &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 3/22/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/server/introduction"><span class="arrow-prev"></span><span>Auspice servers</span></a><a class="docs-next button" href="/auspice/server/authentication"><span>Authentication</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#auspice-client-requests">Auspice client requests</a><ul class="toc-headings"><li><a href="#charon-getavailable"><code>/charon/getAvailable</code></a></li><li><a href="#charon-getdataset"><code>/charon/getDataset</code></a></li><li><a href="#charon-getnarrative"><code>/charon/getNarrative</code></a></li></ul></li><li><a href="#suppling-custom-handlers-to-the-auspice-server">Suppling custom handlers to the Auspice server</a></li><li><a href="#importing-code-from-auspice">Importing code from Auspice</a><ul class="toc-headings"><li><a href="#convertfromv1"><code>convertFromV1</code></a></li><li><a href="#parsenarrativefile"><code>parseNarrativeFile</code></a></li></ul></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 &amp; Trevor Bedford</section></footer></div></body></html>

8
docs/server/api/index.html

@ -96,7 +96,7 @@ Unused by the default Auspice handler.</li>
</ul>
<p><strong>JSON Response (on success):</strong></p>
<p>The JSON response depends on the file-type being requested.</p>
<p>If the type is not specified, i.e. we're requesting the &quot;main&quot; dataset JSON then <a href="https://github.com/nextstrain/augur/blob/v6/augur/data/schema-export-v2.json">see this JSON schema</a>.
<p>If the type is not specified, i.e. we're requesting the &quot;main&quot; dataset JSON then <a href="https://github.com/nextstrain/augur/blob/master/augur/data/schema-export-v2.json">see this JSON schema</a>.
Note that the Auspice client <em>cannot</em> process v1 (meta / tree) JSONs -- <a href="/auspice/server/api#importing-code-from-auspice">see below</a> for how to convert these.</p>
<p>Alternative file type reponses are to be documented.</p>
<p><strong>Alternative responses:</strong></p>
@ -132,7 +132,7 @@ The provided JavaScript file must export three functions, each of which handles
</tbody>
</table>
<p>For information about the <code>req</code> and <code>res</code> arguments see the express documentation for the <a href="https://expressjs.com/en/api.html#req">request object</a> and <a href="https://expressjs.com/en/api.html#res">response object</a>, respectively.</p>
<p>You can see <a href="https://nextstrain.org">nextstrain.org</a>'s implementation of these handlers <a href="https://github.com/nextstrain/nextstrain.org/blob/master/auspice/server/index.js">here</a>.</p>
<p>You can see <a href="https://nextstrain.org">nextstrain.org</a>'s implementation of these handlers <a href="https://github.com/nextstrain/nextstrain.org/blob/master/server.js">here</a>.</p>
<p>Here's a pseudocode example of an implementation for the <code>getAvailable</code> handler which may help understanding:</p>
<pre><code class="hljs css language-js"><span class="hljs-keyword">const</span> getAvailable = <span class="hljs-function">(<span class="hljs-params">req, res</span>) =&gt;</span> {
<span class="hljs-keyword">try</span> {
@ -159,7 +159,7 @@ For instance, the code to convert v1 dataset JSONs to v2 JSONs (which the client
</code></pre>
<p>where <code>tree</code> is the v1 tree JSON, and <code>meta</code> the v1 meta JSON.</p>
<p><strong>Returns:</strong></p>
<p>An object representing the v2 JSON <a href="https://github.com/nextstrain/augur/blob/v6/augur/data/schema-export-v2.json">defined by this schema</a>.</p>
<p>An object representing the v2 JSON <a href="https://github.com/nextstrain/augur/blob/master/augur/data/schema-export-v2.json">defined by this schema</a>.</p>
<h3><a class="anchor" aria-hidden="true" id="parsenarrativefile"></a><a href="#parsenarrativefile" 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><code>parseNarrativeFile</code></h3>
<p><strong>Signature:</strong></p>
<pre><code class="hljs css language-js"><span class="hljs-keyword">const</span> blocks = parseNarrativeFile(fileContents);
@ -173,4 +173,4 @@ Each object has properties</p>
<li><code>dataset</code> -- the dataset associated with this block</li>
<li><code>query</code> -- the query associated with this block</li>
</ul>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/17/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/server/introduction"><span class="arrow-prev"></span><span>Auspice servers</span></a><a class="docs-next button" href="/auspice/server/authentication"><span>Authentication</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#auspice-client-requests">Auspice client requests</a><ul class="toc-headings"><li><a href="#charon-getavailable"><code>/charon/getAvailable</code></a></li><li><a href="#charon-getdataset"><code>/charon/getDataset</code></a></li><li><a href="#charon-getnarrative"><code>/charon/getNarrative</code></a></li></ul></li><li><a href="#suppling-custom-handlers-to-the-auspice-server">Suppling custom handlers to the Auspice server</a></li><li><a href="#importing-code-from-auspice">Importing code from Auspice</a><ul class="toc-headings"><li><a href="#convertfromv1"><code>convertFromV1</code></a></li><li><a href="#parsenarrativefile"><code>parseNarrativeFile</code></a></li></ul></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 &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 3/22/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/server/introduction"><span class="arrow-prev"></span><span>Auspice servers</span></a><a class="docs-next button" href="/auspice/server/authentication"><span>Authentication</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#auspice-client-requests">Auspice client requests</a><ul class="toc-headings"><li><a href="#charon-getavailable"><code>/charon/getAvailable</code></a></li><li><a href="#charon-getdataset"><code>/charon/getDataset</code></a></li><li><a href="#charon-getnarrative"><code>/charon/getNarrative</code></a></li></ul></li><li><a href="#suppling-custom-handlers-to-the-auspice-server">Suppling custom handlers to the Auspice server</a></li><li><a href="#importing-code-from-auspice">Importing code from Auspice</a><ul class="toc-headings"><li><a href="#convertfromv1"><code>convertFromV1</code></a></li><li><a href="#parsenarrativefile"><code>parseNarrativeFile</code></a></li></ul></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 &amp; Trevor Bedford</section></footer></div></body></html>
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