1a3c324b528c57e4b6211d872a3b4e666b032259
jnavarr5
  Mon Apr 14 16:27:03 2025 -0700
Adding function for listing GenArk genomes, refs #32897

diff --git src/hg/htdocs/goldenPath/help/api.html src/hg/htdocs/goldenPath/help/api.html
index 743f10d5733..11e3c49ccc5 100755
--- src/hg/htdocs/goldenPath/help/api.html
+++ src/hg/htdocs/goldenPath/help/api.html
@@ -199,66 +199,62 @@
 question mark <b>?</b>, and multiple parameters are separated with
 the semi-colon <b>;</b>.  For example:
 <pre>
 https://api.genome.ucsc.edu/getData/sequence?genome=hg38;chrom=chrM
 </pre>
 </p>
 
 <!-- ========== Required and optional parameters  ======================= -->
 <a id="Parameter_use"></a>
 <h2>Required and optional parameters</h2>
 <p>
 <table>
 <tr><th>Endpoint function</th><th>Required</th><th>Optional</th></tr>
 <tr><th>/list/publicHubs</th><td>(none)</td><td>(none)</td></tr>
 <tr><th>/list/ucscGenomes</th><td>(none)</td><td>(none)</td></tr>
-<!-- not yet
 <tr><th>/list/genarkGenomes</th><td>(none)</td><td>genome</td></tr>
--->
 <tr><th>/list/hubGenomes</th><td>hubUrl</td><td>(none)</td></tr>
 <tr><th>/list/files</th><td>genome</td><td>format=text, maxItemsOutput</td></tr>
 <tr><th>/list/tracks</th><td>genome or (hubUrl and genome)</td><td>trackLeavesOnly=1</td></tr>
 <tr><th>/list/chromosomes</th><td>genome or (hubUrl and genome)</td><td>track</td></tr>
 <tr><th>/list/schema</th><td>(genome or (hubUrl and genome)) and track</td><td>(none)</td></tr>
 <tr><th>/getData/sequence</th><td>(genome or (hubUrl and genome)) and chrom</td><td>start, end, revComp=1</td></tr>
 <tr><th>/getData/track</th><td>(genome or (hubUrl and genome)) and track</td><td>chrom,
 (start and end), maxItemsOutput, jsonOutputArrays</td></tr>
 <tr><th>/search</th><td>search and genome</td><td>categories=helpDocs,
 categories=publicHubs, categories=trackDb</td></tr>
 </table>
 </p>
 <p>
 The <b>hubUrl</b> and <b>genome</b> parameters are required together to
 specify a unique genome in an assembly or track hub.  The <b>genome</b> for
 a track hub will usually be a UCSC database genome.  Assembly hubs will
 have their own unique <b>genome</b> sequences.  Specify <b>genome</b> without
 a <b>hubUrl</b> to refer to a UCSC Genome Browser assembly.
 </p>
 <p>
 Using the <b>chrom=&lt;name&gt;</b> parameter will limit the request
 to the single specified chromosome.  To limit the request to a specific
 position, both <b>start=4321</b> and <b>end=5678</b> must be given together.
 Using the <b>revComp=1</b> parameter returns the reverse complement.
 </p>
-<!-- not yet
 <p>
 Use the <b>genome</b> argument with the <b>/list/genarkGenomes</b> function
 to test for the existence of a specific genome assembly in the
 <a href='https://hgdownload.soe.ucsc.edu/hubs/' target=_blank>Genark</a> set
 of assembly hubs.
 </p>
--->
 <p>
 The <b>/list/files</b> endpoint only works for UCSC hosted genome assemblies,
 not for external hosted assembly hubs.
 </p>
 <p>
 Any extra parameters not allowed in a function will be flagged as an error.
 </p>
 
 <!-- ========== Supported track types ======================= -->
 <a id="Track_types"></a>
 <h2>Supported track types for getData functions</h2>
 <div class="row">
   <!-- Left column -->
   <div class="col-md-6">
     <p>
@@ -327,36 +323,34 @@
 <a id="list_examples"></a>
 <h2>Example data access</h2>
 <p>
 Your WEB browser can be configured to interpret JSON data and format
 in a convenient browsing format.  Firefox has this function built in,
 other browsers have add-ons that can be turned on to format JSON data.
 With your browser thus configured, the following links can demonstrate
 the functions of the API interface.
 </p>
 <h3>Listing functions</h3>
 <ol>
 <li><a href='https://api.genome.ucsc.edu/list/publicHubs' target=_blank>list public hubs</a> -
 <b>api.genome.ucsc.edu/list/publicHubs</b></li>
 <li><a href='https://api.genome.ucsc.edu/list/ucscGenomes' target=_blank>list UCSC database genomes</a> -
 <b>api.genome.ucsc.edu/list/ucscGenomes</b></li>
-<!-- not yet
-<li><a href='https://api.genome.ucsc.edu/list/genarkGenomes;maxItemsOutput=5' target=_blank>list GenArk assembly hub genomes</a> -
-<b>api.genome.ucsc.edu/list/genarkGenomes;maxItemsOutput=5</b></li>
-<li><a href='https://api.genome.ucsc.edu/list/genarkGenomes;genome=GCF_028858775.2' target=_blank>test if genome GCF_028858775.2 exists in the GenArk assembly hub genomes</a> -
-<b>api.genome.ucsc.edu/list/genarkGenomes;genome=GCF_028858775.2</b></li>
--->
+<li><a href='https://api.genome.ucsc.edu/list/genarkGenomes?maxItemsOutput=5' target=_blank>list GenArk assembly hub genomes</a> -
+<b>api.genome.ucsc.edu/list/genarkGenomes?maxItemsOutput=5</b></li>
+<li><a href='https://api.genome.ucsc.edu/list/genarkGenomes?genome=GCF_028858775.2' target=_blank>test if genome GCF_028858775.2 exists in the GenArk assembly hub genomes</a> -
+<b>api.genome.ucsc.edu/list/genarkGenomes?genome=GCF_028858775.2</b></li>
 <li><a href='https://api.genome.ucsc.edu/list/hubGenomes?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt'
 target=_blank>list genomes from specified hub</a> -
 <b>api.genome.ucsc.edu/list/hubGenomes?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt</b></li>
 <li><a href='https://api.genome.ucsc.edu/list/tracks?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ'
 target=_blank>list tracks from specified hub and genome</a> -
 <b>api.genome.ucsc.edu/list/tracks?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ</b></li>
 <li><a href='https://api.genome.ucsc.edu/list/tracks?genome=hg38' target=_blank>list tracks from UCSC database genome</a> -
 <b>api.genome.ucsc.edu/list/tracks?genome=hg38</b></li>
 <li><a href='https://api.genome.ucsc.edu/list/chromosomes?genome=hg38' target=_blank>list chromosomes from UCSC database genome</a> -
 <b>api.genome.ucsc.edu/list/chromosomes?genome=hg38</b></li>
 <li><a href='https://api.genome.ucsc.edu/list/chromosomes?genome=hg38;track=gold'
 target=_blank>list chromosomes from specified track in UCSC database genome</a> -
 <b>api.genome.ucsc.edu/list/chromosomes?genome=hg38;track=gold</b></li>
 <li><a href='https://api.genome.ucsc.edu/list/chromosomes?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ'
 target=_blank>list chromosomes from assembly hub genome</a> -