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docs/customise-client/api.html

@ -160,4 +160,4 @@ 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 22/03/2020</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 27/05/2020</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>

2
docs/customise-client/api/index.html

@ -160,4 +160,4 @@ 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 22/03/2020</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 27/05/2020</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>

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@ -105,25 +105,58 @@ hot-reloading to allow automatic updating as you edit the code.</p>
Currently, it only converts &quot;Auspice v1&quot; JSONs into &quot;Auspice v2&quot; JSONs, using the same code that is <a href="/auspice/server/api#convertfromv1">programatically importable</a>.</p>
<p>Right now, <code>auspice view</code> will automatically convert &quot;v1&quot; JSONs into &quot;v2&quot; JSONs, so there's no need to do this yourself.</p>
<h2><a class="anchor" aria-hidden="true" id="input-file-formats"></a><a href="#input-file-formats" 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>Input File Formats</h2>
<blockquote>
<p>Auspice is agnostic about the data it visualises -- they don't have to be viral genomes, or real-time, or generated in Augur.
(They do, however have to be in a specific file format.)</p>
</blockquote>
<p>Auspice takes two different file types: datasets (the tree, map, etc.), which are defined as one or more JSON files and narratives, which are specified as a Markdown file.</p>
<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>
<p>Auspice takes two different file types:</p>
<ul>
<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/master/augur/data/schema-export-v2.json">here</a>.</li>
<li>Datasets (the tree, map, etc.), which are defined as one or more JSON files.</li>
<li>Narratives, which are specified as a Markdown file.</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>
<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>Currently we mainly use <a href="https://github.com/nextstrain/augur">Augur</a> to create these datasets.
See <a href="https://nextstrain.org/docs/bioinformatics/introduction-to-augur">the Nextstrain documentation</a> for more details.</p>
See <a href="https://nextstrain.org/docs/bioinformatics/introduction-to-augur">the Nextstrain documentation</a> for more details on this process.</p>
<p>Datasets JSONs include:</p>
<ul>
<li>Auspice v2 JSON (required) - <a href="https://github.com/nextstrain/augur/blob/master/augur/data/schema-export-v2.json">schema here</a>. It includes the following information:
<ul>
<li><code>tree</code>: The tree structure encoded as a deeply nested JSON object.
<ul>
<li>Traits (such as country, divergence, collection date, attributions, etc.) are stored on each node.</li>
<li>The presence of a <code>children</code> property indicates that it's an internal node and contains the child objects.</li>
</ul></li>
<li><code>metadata</code>: Additional data to control and inform the visualization.</li>
</ul></li>
<li>Frequency JSON (optional) - <a href="http://data.nextstrain.org/flu_seasonal_h3n2_ha_2y_tip-frequencies.json">example here</a>
<ul>
<li>Generates the frequencies panel, e.g. on <a href="https://nextstrain.org/flu">nextstrain.org/flu</a>.</li>
</ul></li>
</ul>
<blockquote>
<p>We are working on ways to make datasets in Newick / Nexus formats available. You can see an early prototype of this at <a href="https://auspice-us.herokuapp.com/">auspice-us.herokuapp.com</a> where you can drop on Newick (and CSV) files.
Using BEAST trees is possible, but you have to use Augur to convert them first.</p>
</blockquote>
<blockquote>
<p>If you happen to maintain builds that rely on Auspice v1, don’t worry - Auspice v2 is backward compatible and accepts the v1 format as well. The v1 schema is also available below.
See <a href="/auspice/releases/v2">the v2 release notes</a> for details and motivation for the v2 format.</p>
</blockquote>
<h4><a class="anchor" aria-hidden="true" id="auspice-v1-jsons-for-backwards-compatibility-use-only"></a><a href="#auspice-v1-jsons-for-backwards-compatibility-use-only" 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>Auspice v1 JSONs (for backwards compatibility use only)</h4>
<p>Auspice works with the v1 format for backwards compatibility. <em>The zika dataset we download above is in this format.</em></p>
<p>This format includes:</p>
<ul>
<li>Tree JSON (required) - <a href="https://github.com/nextstrain/augur/blob/master/augur/data/schema-export-v1-tree.json">schema here</a>
<ul>
<li>The same tree information as in the v2 JSON above in a separate file whose name <em>must</em> end with <code>_tree.json</code>.</li>
</ul></li>
<li>Metadata JSON (required) - <a href="https://github.com/nextstrain/augur/blob/master/augur/data/schema-export-v1-meta.json">schema here</a>
<ul>
<li>The same metadata information as in the v2 JSON above in a separate file whose name <em>must</em> end with <code>_meta.json</code> and have the same prefix as the tree JSON above.</li>
</ul></li>
<li>Frequency JSON (optional) - <a href="http://data.nextstrain.org/flu_seasonal_h3n2_ha_2y_tip-frequencies.json">example here</a>
<ul>
<li>Generates the frequencies panel, e.g. on <a href="https://nextstrain.org/flu">nextstrain.org/flu</a>.</li>
</ul></li>
</ul>
<h3><a class="anchor" aria-hidden="true" id="narratives"></a><a href="#narratives" 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>Narratives</h3>
<p>For narratives, please see <a href="/auspice/narratives/how-to-write">Writing a Narrative</a> for a description of the file format.</p>
<h2><a class="anchor" aria-hidden="true" id="obtaining-a-set-of-input-files"></a><a href="#obtaining-a-set-of-input-files" 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>Obtaining a Set of Input Files</h2>
@ -133,4 +166,4 @@ 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 22/03/2020</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>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 23/05/2020</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>

53
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@ -105,25 +105,58 @@ hot-reloading to allow automatic updating as you edit the code.</p>
Currently, it only converts &quot;Auspice v1&quot; JSONs into &quot;Auspice v2&quot; JSONs, using the same code that is <a href="/auspice/server/api#convertfromv1">programatically importable</a>.</p>
<p>Right now, <code>auspice view</code> will automatically convert &quot;v1&quot; JSONs into &quot;v2&quot; JSONs, so there's no need to do this yourself.</p>
<h2><a class="anchor" aria-hidden="true" id="input-file-formats"></a><a href="#input-file-formats" 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>Input File Formats</h2>
<blockquote>
<p>Auspice is agnostic about the data it visualises -- they don't have to be viral genomes, or real-time, or generated in Augur.
(They do, however have to be in a specific file format.)</p>
</blockquote>
<p>Auspice takes two different file types: datasets (the tree, map, etc.), which are defined as one or more JSON files and narratives, which are specified as a Markdown file.</p>
<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>
<p>Auspice takes two different file types:</p>
<ul>
<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/master/augur/data/schema-export-v2.json">here</a>.</li>
<li>Datasets (the tree, map, etc.), which are defined as one or more JSON files.</li>
<li>Narratives, which are specified as a Markdown file.</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>
<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>Currently we mainly use <a href="https://github.com/nextstrain/augur">Augur</a> to create these datasets.
See <a href="https://nextstrain.org/docs/bioinformatics/introduction-to-augur">the Nextstrain documentation</a> for more details.</p>
See <a href="https://nextstrain.org/docs/bioinformatics/introduction-to-augur">the Nextstrain documentation</a> for more details on this process.</p>
<p>Datasets JSONs include:</p>
<ul>
<li>Auspice v2 JSON (required) - <a href="https://github.com/nextstrain/augur/blob/master/augur/data/schema-export-v2.json">schema here</a>. It includes the following information:
<ul>
<li><code>tree</code>: The tree structure encoded as a deeply nested JSON object.
<ul>
<li>Traits (such as country, divergence, collection date, attributions, etc.) are stored on each node.</li>
<li>The presence of a <code>children</code> property indicates that it's an internal node and contains the child objects.</li>
</ul></li>
<li><code>metadata</code>: Additional data to control and inform the visualization.</li>
</ul></li>
<li>Frequency JSON (optional) - <a href="http://data.nextstrain.org/flu_seasonal_h3n2_ha_2y_tip-frequencies.json">example here</a>
<ul>
<li>Generates the frequencies panel, e.g. on <a href="https://nextstrain.org/flu">nextstrain.org/flu</a>.</li>
</ul></li>
</ul>
<blockquote>
<p>We are working on ways to make datasets in Newick / Nexus formats available. You can see an early prototype of this at <a href="https://auspice-us.herokuapp.com/">auspice-us.herokuapp.com</a> where you can drop on Newick (and CSV) files.
Using BEAST trees is possible, but you have to use Augur to convert them first.</p>
</blockquote>
<blockquote>
<p>If you happen to maintain builds that rely on Auspice v1, don’t worry - Auspice v2 is backward compatible and accepts the v1 format as well. The v1 schema is also available below.
See <a href="/auspice/releases/v2">the v2 release notes</a> for details and motivation for the v2 format.</p>
</blockquote>
<h4><a class="anchor" aria-hidden="true" id="auspice-v1-jsons-for-backwards-compatibility-use-only"></a><a href="#auspice-v1-jsons-for-backwards-compatibility-use-only" 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>Auspice v1 JSONs (for backwards compatibility use only)</h4>
<p>Auspice works with the v1 format for backwards compatibility. <em>The zika dataset we download above is in this format.</em></p>
<p>This format includes:</p>
<ul>
<li>Tree JSON (required) - <a href="https://github.com/nextstrain/augur/blob/master/augur/data/schema-export-v1-tree.json">schema here</a>
<ul>
<li>The same tree information as in the v2 JSON above in a separate file whose name <em>must</em> end with <code>_tree.json</code>.</li>
</ul></li>
<li>Metadata JSON (required) - <a href="https://github.com/nextstrain/augur/blob/master/augur/data/schema-export-v1-meta.json">schema here</a>
<ul>
<li>The same metadata information as in the v2 JSON above in a separate file whose name <em>must</em> end with <code>_meta.json</code> and have the same prefix as the tree JSON above.</li>
</ul></li>
<li>Frequency JSON (optional) - <a href="http://data.nextstrain.org/flu_seasonal_h3n2_ha_2y_tip-frequencies.json">example here</a>
<ul>
<li>Generates the frequencies panel, e.g. on <a href="https://nextstrain.org/flu">nextstrain.org/flu</a>.</li>
</ul></li>
</ul>
<h3><a class="anchor" aria-hidden="true" id="narratives"></a><a href="#narratives" 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>Narratives</h3>
<p>For narratives, please see <a href="/auspice/narratives/how-to-write">Writing a Narrative</a> for a description of the file format.</p>
<h2><a class="anchor" aria-hidden="true" id="obtaining-a-set-of-input-files"></a><a href="#obtaining-a-set-of-input-files" 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>Obtaining a Set of Input Files</h2>
@ -133,4 +166,4 @@ 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 22/03/2020</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>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 23/05/2020</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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