720de849b76a5a3d95e66050d5a2c2683d60351a
hiram
  Fri Jul 5 12:58:50 2024 -0700
adding list/genarkGenomes endpoint and examples refs #34045

diff --git src/hg/htdocs/goldenPath/help/api.html src/hg/htdocs/goldenPath/help/api.html
index a8cf210..168ea69 100755
--- src/hg/htdocs/goldenPath/help/api.html
+++ src/hg/htdocs/goldenPath/help/api.html
@@ -102,64 +102,64 @@
 </p>
 
 <!-- ========== Endpoint functions ======================= -->
 <a id="Endpoint"></a>
 <h2>Endpoint functions to return data</h2>
 <p>
 The URL <b>https://api.genome.ucsc.edu/</b> is used to access
 the endpoint functions.  For example:
 <pre>
     curl -L 'https://api.genome.ucsc.edu/list/ucscGenomes'
 </pre>
 </p>
 <p>
 <ul>
 <li><b>/list/publicHubs</b> - list public hubs</li>
-<li><b>/list/ucscGenomes</b> - list UCSC Genome Browser database genomes</li>
+<li><b>/list/ucscGenomes</b> - list UCSC Genome Browser database genomes from database host</li>
+<li><b>/list/genarkGenomes</b> - list UCSC Genome Browser database genomes from assembly hub host</li>
 <li><b>/list/hubGenomes</b> - list genomes from specified hub</li>
 <li><b>/list/files</b> - list download files available for specified genome</li>
 <li><b>/list/tracks</b> - list data tracks available in specified hub or database genome
 (see also: <a href='trackDb/trackDbHub.html' target=_blank>track definition help</a>)</li>
 <li><b>/list/chromosomes</b> - list chromosomes from a data track in specified hub or database
 <li><b>/list/schema</b> - list the schema for a data track in specified hub or database
 genome</li>
 <li><b>/getData/sequence</b> - return sequence from specified hub or database genome</li>
 <li><b>/getData/track</b> - return data from specified track in hub or database genome</li>
 <li><b>/search</b> - return search matches within a UCSC Genome Browser genome assembly</li>
 </ul>
 </p>
 
 <!-- ========== Parameters to endpoint functions ======================= -->
 <a id="Parameters"></a>
 <h2>Parameters to endpoint functions</h2>
 <p>
 <ul>
 <li>hubUrl=&lt;url&gt; - specify track hub or assembly hub URL</li>
-<li>genome=&lt;name&gt; - specify genome assembly in UCSC Genome Browser or track/assembly hub</li>
+<li>genome=&lt;name&gt; - specify genome assembly in UCSC Genome Browser or track/assembly hub.  Use with with /list/genarkGenomes to test for existence.</li>
 <li>track=&lt;trackName&gt; - specify data track in track/assembly hub or UCSC database genome
 assembly</li>
 <li>chrom=&lt;chrN&gt; - specify chromosome name for sequence or track data</li>
 <li>start=&lt;123&gt; - specify start coordinate (0 relative) for data from track or sequence
 retrieval (start and end required together). See also: <a
  href='https://genome-blog.gi.ucsc.edu/blog/the-ucsc-genome-browser-coordinate-counting-systems/'
 target=_blank>UCSC browser coordinate counting systems</a></li>
 <li>end=&lt;456&gt; - specify end coordinate (1 relative) for data from track or sequence
 retrieval (start and end required together). See also: <a
  href='https://genome-blog.gi.ucsc.edu/blog/the-ucsc-genome-browser-coordinate-counting-systems/'
 target=_blank>UCSC browser coordinate counting systems</a></li>
-<li>revComp=1 - on <em>/getData/sequence</em> function, return reverse complement of sequence data
- together)</li>
+<li>revComp=1 - on <em>/getData/sequence</em> function, return reverse complement of sequence data</li>
 <li>maxItemsOutput=1000 - limit number of items to output, default: 1,000, maximum limit:
 1,000,000 (use <em>-1</em> to get maximum output)</li>
 <li>trackLeavesOnly=1 - on <em>/list/tracks</em> function, only show tracks, do not show
 composite container information</li>
 <li>jsonOutputArrays=1 - on <em>/getData/track</em> function, JSON format is array type
 for each item of data, instead of the default object type</li>
 <li>format=text - on <em>/list/files</em> function, return plain text listing
 of download files instead of JSON format output (which includes more meta-data information).  Text output contains less meta-data in comment lines prefixed by the '#' hash character.</li>
 <li>search=&lt;term&gt;&genome=&lt;name&gt; - on <em>/search</em> function, specify term to be
 search within a UCSC Genome Browser genome assembly</li>
 <li>categories=helpDocs - on <em>/search?search=&lt;term&gt;&genome=&lt;name&gt;</em> function, restrict the search
 within the UCSC Genome Browser help documentation</li>
 <li>categories=publicHubs - on <em>/search?search=&lt;term&gt;&genome=&lt;name&gt;</em> function, restrict the search
 within the UCSC Genome Browser Public Hubs</li>
 <li>categories=trackDb - on <em>/search?search=&lt;term&gt;&genome=&lt;name&gt;</em> function, restrict the search
@@ -171,79 +171,88 @@
 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>
+<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>
 <p>
+Use the <em>genome</em> argument with the <em>/list/genarkGenomes</em> 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>
 <p>
 <ul>
-<li><a href='/FAQ/FAQformat.html#format21' target=_blank>barChart</a></li>
+<li><a href='/goldenPath/help/bigBarChart.html' target=_blank>barChart/bigBarChart</a></li>
 <li><a href='/FAQ/FAQformat.html#format1' target=_blank>bed</a></li>
-<li><a href='/FAQ/FAQformat.html#format1.5' target=_blank>bigBed</a></li>
-<!--  not yet
-<li><a href='/FAQ/FAQformat.html#format9.1' target=_blank>bigGenePred</a></li>
--->
-<li><a href='/FAQ/FAQformat.html#format9.5' target=_blank>bigNarrowPeak</a></li>
-<li><a href='/FAQ/FAQformat.html#format6.1' target=_blank>bigWig</a></li>
+<li><a href='/goldenPath/help/bigBed.html' target=_blank>bigBed</a></li>
+<li><a href='/goldenPath/help/bigChain.html' target=_blank>bigChain</a></li>
+<li><a href='/goldenPath/help/bigGenePred.html' target=_blank>bigGenePred</a></li>
+<li><a href='/goldenPath/help/bigLolly.html' target=_blank>bigLolly</a></li>
+<li><a href='/goldenPath/help/bigNarrowPeak.html' target=_blank>bigNarrowPeak</a></li>
+<li><a href='/goldenPath/help/bigMaf.html' target=_blank>bigMaf</a></li>
+<li><a href='/goldenPath/help/bigPsl.html' target=_blank>bigPsl</a></li>
+<li><a href='/goldenPath/help/bigWig.html' target=_blank>bigWig</a></li>
 <li><a href='/goldenPath/help/chain.html' target=_blank>chain</a></li>
 <li><a href='/FAQ/FAQformat.html#format9' target=_blank>genePred</a></li>
-<li><a href='/FAQ/FAQformat.html#format22' target=_blank>interact</a></li>
+<li><a href='/goldenPath/help/interact.html' target=_blank>interact/bigInteract</a></li>
 <li><a href='/FAQ/FAQformat.html#format9.5' target=_blank>narrowPeak</a></li>
 <li><a href='/FAQ/FAQformat.html#format17' target=_blank>peptideMapping</a></li>
 <li><a href='/FAQ/FAQformat.html#format2' target=_blank>psl</a></li>
 <li><a href='http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/rmsk.sql' target=_blank>rmsk - repeat masker</a></li>
 <li><a href='/FAQ/FAQformat.html#format6' target=_blank>wig</a></li>
 <li>(Work is underway to support additional track types)</li>
 </ul>
 </p>
 
 <!-- ========== API on mirrors and local installations ======================= -->
 <a id="Mirrors"></a>
 <h2>Using the API on mirrors and local installations</h2>
 <p>
 In order to access the API from a <a href='/mirror.html' target=_blank>mirror installation</a>
 or one of the UCSC official mirrors, the complete URL with the cgi-bin should be used:</p>
@@ -268,30 +277,34 @@
 <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>
+<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> -