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changelog & rebuild docs

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james hadfield 2 years ago
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  1. 4
      CHANGELOG.md
  2. 5
      docs/narratives/introduction.html
  3. 5
      docs/narratives/introduction/index.html
  4. 29
      docs/releases/changelog.html
  5. 29
      docs/releases/changelog/index.html
  6. 29
      docs/server/api.html
  7. 29
      docs/server/api/index.html

4
CHANGELOG.md

@ -3,11 +3,9 @@ title: Changelog
---
## version 2.18.1 - 2020/08/07
* Add between-paragraph padding for text rendering in (non-mobile) narratives.
## version 2.18.0 - 2020/08/03
* Parse narratives client side.
See [PR 1193](https://github.com/nextstrain/auspice/pull/1193) and [PR 1172](https://github.com/nextstrain/auspice/pull/1172).
This shifts the default client behavior to request a narrative in markdown format and parse it client-side.

5
docs/narratives/introduction.html

@ -88,12 +88,9 @@ The <a href="/auspice/narratives/how-to-write">writing a narrative</a> tutorial
<p>Narratives are now being used in various settings, however some bugs remain.
Please <a href="mailto:hello@nextstrain.org">get in touch (email)</a> with any and all questions about narratives, or <a href="https://github.com/nextstrain/auspice/issues/new">file an issue on GitHub</a> 🙏</p>
<ul>
<li><p>Datasets currently cannot be changed between paragraphs (i.e. the initial dataset is used for all subsequent paragraphs).</p></li>
<li><p>Text which is larger than the sidebar / page height is cut off.</p></li>
<li><p>Styling may be slightly off on different browsers.</p></li>
<li><p>Not all state is mirrored in the URLs (for instance, map bounds are not set in the URL).
This limits what views can be defined by paragraphs in the narratives.</p></li>
<li><p>The frontmatter parsing will be extended to allow arrays of authors (etc).</p></li>
</ul>
<p>Take a look at the <a href="https://github.com/nextstrain/auspice/labels/narratives">GitHub issues tagged as related to narrative functionality</a> for a potentially more up-to-date list of these.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 17/10/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/server/authentication"><span class="arrow-prev"></span><span>Authentication</span></a><a class="docs-next button" href="/auspice/narratives/how-to-write"><span>Writing a Narrative</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#examples">Examples</a></li><li><a href="#how-to-write-a-narrative">How to Write a Narrative</a></li><li><a href="#sharing-narratives">Sharing Narratives</a></li><li><a href="#known-bugs-limitations">Known Bugs / Limitations</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 03/08/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/server/authentication"><span class="arrow-prev"></span><span>Authentication</span></a><a class="docs-next button" href="/auspice/narratives/how-to-write"><span>Writing a Narrative</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#examples">Examples</a></li><li><a href="#how-to-write-a-narrative">How to Write a Narrative</a></li><li><a href="#sharing-narratives">Sharing Narratives</a></li><li><a href="#known-bugs-limitations">Known Bugs / Limitations</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>

5
docs/narratives/introduction/index.html

@ -88,12 +88,9 @@ The <a href="/auspice/narratives/how-to-write">writing a narrative</a> tutorial
<p>Narratives are now being used in various settings, however some bugs remain.
Please <a href="mailto:hello@nextstrain.org">get in touch (email)</a> with any and all questions about narratives, or <a href="https://github.com/nextstrain/auspice/issues/new">file an issue on GitHub</a> 🙏</p>
<ul>
<li><p>Datasets currently cannot be changed between paragraphs (i.e. the initial dataset is used for all subsequent paragraphs).</p></li>
<li><p>Text which is larger than the sidebar / page height is cut off.</p></li>
<li><p>Styling may be slightly off on different browsers.</p></li>
<li><p>Not all state is mirrored in the URLs (for instance, map bounds are not set in the URL).
This limits what views can be defined by paragraphs in the narratives.</p></li>
<li><p>The frontmatter parsing will be extended to allow arrays of authors (etc).</p></li>
</ul>
<p>Take a look at the <a href="https://github.com/nextstrain/auspice/labels/narratives">GitHub issues tagged as related to narrative functionality</a> for a potentially more up-to-date list of these.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 17/10/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/server/authentication"><span class="arrow-prev"></span><span>Authentication</span></a><a class="docs-next button" href="/auspice/narratives/how-to-write"><span>Writing a Narrative</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#examples">Examples</a></li><li><a href="#how-to-write-a-narrative">How to Write a Narrative</a></li><li><a href="#sharing-narratives">Sharing Narratives</a></li><li><a href="#known-bugs-limitations">Known Bugs / Limitations</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 03/08/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/server/authentication"><span class="arrow-prev"></span><span>Authentication</span></a><a class="docs-next button" href="/auspice/narratives/how-to-write"><span>Writing a Narrative</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#examples">Examples</a></li><li><a href="#how-to-write-a-narrative">How to Write a Narrative</a></li><li><a href="#sharing-narratives">Sharing Narratives</a></li><li><a href="#known-bugs-limitations">Known Bugs / Limitations</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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docs/server/api.html

@ -106,16 +106,26 @@ Any other non-200 reponse behaves similarly but also displays a large &quot;erro
<p><strong>URL query arguments:</strong></p>
<ul>
<li><code>prefix</code> (required) - the pathname of the requesting page in Auspice. Use this to determine which narrative to return.</li>
<li><code>type</code> (optional) - the format of the data returned (see below for more information).
Current valid values are &quot;json&quot; and &quot;md&quot;.
If no type is specified the server will use &quot;json&quot; as a default (for backwards compatibility reasons).
Requests to this API from the Auspice client are made with `type=md.</li>
</ul>
<p><strong>JSON Response (on success):</strong></p>
<p>The output from the <a href="/auspice/server/api#parsenarrativefile">parseNarrativeFile</a> function defined below.
For instance, here is the code from the default Auspice handler:</p>
<p><strong>Response (on success):</strong></p>
<p>The response depends on the <code>type</code> specified in the query.</p>
<p>If a markdown format is requested, then the narrative file is sent to the client unmodified to be parsed on the client.</p>
<p>If a JSON is requested then the narrative file is parsed into JSON format by the server.
For Auspice versions prior to v2.18 this was the only expected behavior.
The transformation from markdown (i.e. the narrative file itself) to JSON is via the <code>parseNarrativeFile()</code> function (see below for how this is exported from Auspice for use in other servers).
Here, roughly, is the code we use in the auspice server for this transformation:</p>
<pre><code class="hljs css language-js"><span class="hljs-keyword">const</span> fileContents = fs.readFileSync(pathName, <span class="hljs-string">'utf8'</span>);
<span class="hljs-keyword">const</span> blocks = parseNarrative(fileContents);
res.send(<span class="hljs-built_in">JSON</span>.stringify(blocks).replace(<span class="hljs-regexp">/&lt;/g</span>, <span class="hljs-string">'\\u003c'</span>));
<span class="hljs-keyword">if</span> (type === <span class="hljs-string">"json"</span>) {
<span class="hljs-keyword">const</span> blocks = parseNarrative(fileContents);
res.send(<span class="hljs-built_in">JSON</span>.stringify(blocks).replace(<span class="hljs-regexp">/&lt;/g</span>, <span class="hljs-string">'\\u003c'</span>));
}
</code></pre>
<blockquote>
<p>Note that in a future version of Auspice we plan to move the parsing of the narrative to the client.</p>
<p>While the Auspice client (from v2.18 onwards) always requests the <code>type=md</code>, it will attempt to parse the response as JSON if markdown parsing fails, in an effort to remain backwards compatable with servers which may be using an earlier API.</p>
</blockquote>
<hr>
<h2><a class="anchor" aria-hidden="true" id="suppling-custom-handlers-to-the-auspice-server"></a><a href="#suppling-custom-handlers-to-the-auspice-server" 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>Suppling custom handlers to the Auspice server</h2>
@ -161,6 +171,11 @@ For instance, the code to convert v1 dataset JSONs to v2 JSONs (which the client
<p><strong>Returns:</strong></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>
<blockquote>
<p>This function is deprecated as of vXXX.
You can now send the untransformed contents of the narrative file (markdown) for client-side parsing.
See <a href="#charon-getnarrative">above</a> for more details.</p>
</blockquote>
<p><strong>Signature:</strong></p>
<pre><code class="hljs css language-js"><span class="hljs-keyword">const</span> blocks = parseNarrativeFile(fileContents);
</code></pre>
@ -173,4 +188,4 @@ 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 10/07/2020</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>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 03/08/2020</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>

29
docs/server/api/index.html

@ -106,16 +106,26 @@ Any other non-200 reponse behaves similarly but also displays a large &quot;erro
<p><strong>URL query arguments:</strong></p>
<ul>
<li><code>prefix</code> (required) - the pathname of the requesting page in Auspice. Use this to determine which narrative to return.</li>
<li><code>type</code> (optional) - the format of the data returned (see below for more information).
Current valid values are &quot;json&quot; and &quot;md&quot;.
If no type is specified the server will use &quot;json&quot; as a default (for backwards compatibility reasons).
Requests to this API from the Auspice client are made with `type=md.</li>
</ul>
<p><strong>JSON Response (on success):</strong></p>
<p>The output from the <a href="/auspice/server/api#parsenarrativefile">parseNarrativeFile</a> function defined below.
For instance, here is the code from the default Auspice handler:</p>
<p><strong>Response (on success):</strong></p>
<p>The response depends on the <code>type</code> specified in the query.</p>
<p>If a markdown format is requested, then the narrative file is sent to the client unmodified to be parsed on the client.</p>
<p>If a JSON is requested then the narrative file is parsed into JSON format by the server.
For Auspice versions prior to v2.18 this was the only expected behavior.
The transformation from markdown (i.e. the narrative file itself) to JSON is via the <code>parseNarrativeFile()</code> function (see below for how this is exported from Auspice for use in other servers).
Here, roughly, is the code we use in the auspice server for this transformation:</p>
<pre><code class="hljs css language-js"><span class="hljs-keyword">const</span> fileContents = fs.readFileSync(pathName, <span class="hljs-string">'utf8'</span>);
<span class="hljs-keyword">const</span> blocks = parseNarrative(fileContents);
res.send(<span class="hljs-built_in">JSON</span>.stringify(blocks).replace(<span class="hljs-regexp">/&lt;/g</span>, <span class="hljs-string">'\\u003c'</span>));
<span class="hljs-keyword">if</span> (type === <span class="hljs-string">"json"</span>) {
<span class="hljs-keyword">const</span> blocks = parseNarrative(fileContents);
res.send(<span class="hljs-built_in">JSON</span>.stringify(blocks).replace(<span class="hljs-regexp">/&lt;/g</span>, <span class="hljs-string">'\\u003c'</span>));
}
</code></pre>
<blockquote>
<p>Note that in a future version of Auspice we plan to move the parsing of the narrative to the client.</p>
<p>While the Auspice client (from v2.18 onwards) always requests the <code>type=md</code>, it will attempt to parse the response as JSON if markdown parsing fails, in an effort to remain backwards compatable with servers which may be using an earlier API.</p>
</blockquote>
<hr>
<h2><a class="anchor" aria-hidden="true" id="suppling-custom-handlers-to-the-auspice-server"></a><a href="#suppling-custom-handlers-to-the-auspice-server" 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>Suppling custom handlers to the Auspice server</h2>
@ -161,6 +171,11 @@ For instance, the code to convert v1 dataset JSONs to v2 JSONs (which the client
<p><strong>Returns:</strong></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>
<blockquote>
<p>This function is deprecated as of vXXX.
You can now send the untransformed contents of the narrative file (markdown) for client-side parsing.
See <a href="#charon-getnarrative">above</a> for more details.</p>
</blockquote>
<p><strong>Signature:</strong></p>
<pre><code class="hljs css language-js"><span class="hljs-keyword">const</span> blocks = parseNarrativeFile(fileContents);
</code></pre>
@ -173,4 +188,4 @@ 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 10/07/2020</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>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 03/08/2020</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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