438e3f1d32b858255405c7bb3fccb7190d06fca1
hiram
  Sun Apr 28 13:12:25 2019 -0700
eliminating the db= argument everywhere, only need genome= refs #18869

diff --git src/hg/htdocs/goldenPath/help/api.html src/hg/htdocs/goldenPath/help/api.html
index 413bf32..b52332a 100755
--- src/hg/htdocs/goldenPath/help/api.html
+++ src/hg/htdocs/goldenPath/help/api.html
@@ -75,75 +75,71 @@
 <li><b>/list/ucscGenomes</b> - list UCSC database genomes</li>
 <li><b>/list/hubGenomes</b> - list genomes from specified hub</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 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>
 </ul>
 </p>
 
 <!-- ========== Parameters to endpoint functions ======================= -->
 <a name="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 assemby in track or assembly hub (only used with hubUrl)</li>
-<li>db=&lt;ucscDb&gt; - specify database (aka genome assembly) in UCSC genome browser (either hubUrl or db specified, not both)</li>
+<li>genome=&lt;name&gt; - specify genome assembly in UCSC genome browser, track or assembly hub</li>
 <li>track=&lt;trackName&gt; - specify data track in 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)</li>
 <li>end=&lt;456&gt; - specify end coordinate (1 relative) for data from track or sequence retrieval (start and end required together)</li>
 <li>(see also: <a href='http://genome.ucsc.edu/blog/the-ucsc-genome-browser-coordinate-counting-systems/' target=_blank>UCSC browser coordinate counting systems)</a></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
 </ul>
 </p>
 <p>
 The parameters are added to the endpoint URL beginning with a
 question mark <b>?</b>, and multiple parameters are separated with
 the semi-colon <b>;</b>.  For example:
 <pre>
-https://api-test.gi.ucsc.edu/getData/sequence?db=ce11;chrom=chrM
+https://api-test.gi.ucsc.edu/getData/sequence?genome=ce11;chrom=chrM
 </pre>
 </p>
 
 <!-- ========== Required and optional parameters  ======================= -->
 <a name="Parameter use"></a>
 <h2>Required and optional parameters</h2>
 <p>
 <table border=1>
 <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/hubGenomes</th><td>hubUrl</td><td>(none)</td></tr>
-<tr><th>/list/tracks</th><td>(hubUrl and genome) or db</td><td>trackLeavesOnly=1</td></tr>
-<tr><th>/list/chromosomes</th><td>((hubUrl and genome) or db) and track</td><td>(none)</td></tr>
-<tr><th>/getData/sequence</th><td>((hubUrl and genome) or db) and chrom</td><td>start and end</td></tr>
-<tr><th>/getData/track</th><td>((hubUrl and genome) or db) and track</td><td>chrom, (start and end), maxItemsOutput, jsonOutputArrays</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>/getData/sequence</th><td>(genome or (hubUrl and genome)) and chrom</td><td>start and end</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>
 </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.
-</p>
-<p>
-When not an assembly or track hub, to access UCSC database assemblies,
-the parameter <b>db=&lt;name&gt;</b> is required.
+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.
 </p>
 
 <!-- ========== Supported track types ======================= -->
 <a name="Track types"></a>
 <h2>Supported track types, at this time (April 2019), for getData functions</h2>
 <p>
 <ul>
 <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
@@ -157,51 +153,51 @@
 <li><a href='http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/rmsk.sql' target=_blank>rmsk - repeat masker</li>
 <li><a href='/FAQ/FAQformat.html#format6' target=_blank>wig</a></li>
 <li>(Work is under way to support additional track types)</li>
 </ul>
 </p>
 
 <!-- ========== Example data access ======================= -->
 <a name="list examples"></a>
 <h2>Example data access</h2>
 <h3>Listing functions</h3>
 <ol>
 <li><a href='/list/publicHubs' target=_blank>list public hubs</a> - <b>api.genome.ucsc.edu/list/publicHubs</b></li>
 <li><a href='/list/ucscGenomes' target=_blank>list UCSC database genomes</a> - <b>api.genome.ucsc.edu/list/ucscGenomes</b></li>
 <li><a href='/list/hubGenomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt' target=_blank>list genomes from specified hub</a> - <b>api.genome.ucsc.edu/list/hubGenomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt</b></li>
 <li><a href='/list/tracks?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1' target=_blank>list tracks from specified hub and genome</a> - <b>api.genome.ucsc.edu/list/tracks?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1</b></li>
-<li><a href='/list/tracks?db=ce11' target=_blank>list tracks from UCSC database genome</a> - <b>api.genome.ucsc.edu/list/tracks?db=ce11</b></li>
-<li><a href='/list/chromosomes?db=ce11' target=_blank>list chromosomes from UCSC database genome</a> - <b>api.genome.ucsc.edu/list/chromosomes?db=ce11</b></li>
-<li><a href='/list/chromosomes?db=ce11;track=gold' target=_blank>list chromosomes from specified track in UCSC database genome</a> - <b>api.genome.ucsc.edu/list/chromosomes?db=ce11;track=gold</b></li>
+<li><a href='/list/tracks?genome=ce11' target=_blank>list tracks from UCSC database genome</a> - <b>api.genome.ucsc.edu/list/tracks?genome=ce11</b></li>
+<li><a href='/list/chromosomes?genome=ce11' target=_blank>list chromosomes from UCSC database genome</a> - <b>api.genome.ucsc.edu/list/chromosomes?genome=ce11</b></li>
+<li><a href='/list/chromosomes?genome=ce11;track=gold' target=_blank>list chromosomes from specified track in UCSC database genome</a> - <b>api.genome.ucsc.edu/list/chromosomes?genome=ce11;track=gold</b></li>
 <li><a href='/list/chromosomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1' target=_blank>list chromosomes from assembly hub genome</a> -<br><b>api.genome.ucsc.edu/list/chromosomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1</b></li>
 <li><a href='/list/chromosomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1;track=assembly_' target=_blank>list chromosomes from specified track in assembly hub genome</a> -<br><b>api.genome.ucsc.edu/list/chromosomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1;track=assembly_</b></li>
 </ol>
 <a name="getData examples"></a>
 <h3>getData functions</h3>
 <ol>
-<li><a href='/getData/sequence?db=ce11;chrom=chrM' target=_blank>Get DNA sequence from specified chromosome in UCSC database genome</a> -<br><b>api.genome.ucsc.edu/getData/sequence?db=ce11;chrom=chrM</b></li>
-<li><a href='/getData/sequence?db=ce11;chrom=chrM;start=4321;end=5678' target=_blank>Get DNA sequence from specified chromosome and start,end coordinates in UCSC database genome</a> -<br><b>api.genome.ucsc.edu/getData/sequence?db=ce11;chrom=chrM;start=4321;end=5678</b></li>
+<li><a href='/getData/sequence?genome=ce11;chrom=chrM' target=_blank>Get DNA sequence from specified chromosome in UCSC database genome</a> -<br><b>api.genome.ucsc.edu/getData/sequence?genome=ce11;chrom=chrM</b></li>
+<li><a href='/getData/sequence?genome=ce11;chrom=chrM;start=4321;end=5678' target=_blank>Get DNA sequence from specified chromosome and start,end coordinates in UCSC database genome</a> -<br><b>api.genome.ucsc.edu/getData/sequence?genome=ce11;chrom=chrM;start=4321;end=5678</b></li>
 <li><a href='/getData/sequence?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt;genome=hg19;chrom=chrM;start=4321;end=5678' target=_blank>Get DNA sequence from a track hub where 'genome' is a UCSC database</a> -<br><b>api.genome.ucsc.edu/getData/sequence?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt;genome=hg19;chrom=chrM;start=4321;end=5678</b></li>
 <li><a href='/getData/sequence?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1;chrom=chrCp;start=4321;end=5678' target=_blank><b></b> Get DNA sequence from specified chromosome and start,end coordinates in an assembly hub genome</a> -<br><b>api.genome.ucsc.edu/getData/sequence?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1;chrom=chrCp;start=4321;end=5678</b></li>
-<li><a href='/getData/track?db=ce11;track=gold;maxItemsOutput=100' target=_blank>Get track data for specified track in UCSC database genome</a> -<br><b>api.genome.ucsc.edu/getData/track?db=ce11;track=gold;maxItemsOutput=100</b></li>
-<li><a href='/getData/track?db=ce11;track=gold;chrom=chrM' target=_blank>Get track data for specified track and chromosome in UCSC database genome</a> -<br><b>api.genome.ucsc.edu/getData/track?db=ce11;track=gold;chrom=chrM</b></li>
-<li><a href='/getData/track?db=ce11;track=gold;chrom=chrI;start=47000;end=48000' target=_blank>Get track data for specified track, chromosome and start,end coordinates in UCSC database genome</a> -<br><b>api.genome.ucsc.edu/getData/track?db=ce11;track=gold;chrom=chrI;start=47000;end=48000</b></li>
+<li><a href='/getData/track?genome=ce11;track=gold;maxItemsOutput=100' target=_blank>Get track data for specified track in UCSC database genome</a> -<br><b>api.genome.ucsc.edu/getData/track?genome=ce11;track=gold;maxItemsOutput=100</b></li>
+<li><a href='/getData/track?genome=ce11;track=gold;chrom=chrM' target=_blank>Get track data for specified track and chromosome in UCSC database genome</a> -<br><b>api.genome.ucsc.edu/getData/track?genome=ce11;track=gold;chrom=chrM</b></li>
+<li><a href='/getData/track?genome=ce11;track=gold;chrom=chrI;start=47000;end=48000' target=_blank>Get track data for specified track, chromosome and start,end coordinates in UCSC database genome</a> -<br><b>api.genome.ucsc.edu/getData/track?genome=ce11;track=gold;chrom=chrI;start=47000;end=48000</b></li>
 <li><a href='/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1;track=assembly_' target=_blank>Get track data for specified track in an assembly hub genome</a> -<br><b>api.genome.ucsc.edu/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1;track=assembly_</b></li>
 <li><a href='/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1;track=assembly_;chrom=chrCp' target=_blank>Get track data for specified track and chromosome in an assembly hub genome</a> -<br><b>api.genome.ucsc.edu/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1;track=assembly_;chrom=chrCp</b></li>
 <li><a href='/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt;genome=hg19;track=ultraConserved' target=_blank>Get track data for specified track in a track hub</a> -<br><b>api.genome.ucsc.edu/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt;genome=hg19;track=ultraConserved</b></li>
 <li><a href='/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt;genome=hg19;track=ultraConserved;chrom=chr8' target=_blank>Get track data for specified track and chromosome in a track hub</a> -<br><b>api.genome.ucsc.edu/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt;genome=hg19;track=ultraConserved;chrom=chr8</b></li>
 <li><a href='/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1;track=gc5Base_;chrom=chrCp;start=4321;end=5678' target=_blank>Wiggle track data for specified track, chromosome with start and end limits in an assembly hub genome</a> -<br><b>api.genome.ucsc.edu/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1;track=assembly_;chrom=chrCp;start=4321;end=5678</b></li>
-<li><a href='/getData/track?db=galGal6;track=gc5BaseBw;maxItemsOutput=100' target=_blank>Wiggle track data for specified track in a UCSC database genome</a> -<br><b>api.genome.ucsc.edu/getData/track?genome=galGal6;track=gc5BaseBw;maxItemsOutput=100</b></li>
-<li><a href='/getData/track?db=galGal6;track=ncbiRefSeqOther;chrom=chr1;start=750000;end=55700000' target=_blank>bigBed data from a UCSC database, chrom and start,end limits</a> -<br><b>api.genome.ucsc.edu/getData/track?genome=galGal6;track=ncbiRefSeqOther;chrom=chr1;start=750000;end=55700000</b></li>
+<li><a href='/getData/track?genome=galGal6;track=gc5BaseBw;maxItemsOutput=100' target=_blank>Wiggle track data for specified track in a UCSC database genome</a> -<br><b>api.genome.ucsc.edu/getData/track?genome=galGal6;track=gc5BaseBw;maxItemsOutput=100</b></li>
+<li><a href='/getData/track?genome=galGal6;track=ncbiRefSeqOther;chrom=chr1;start=750000;end=55700000' target=_blank>bigBed data from a UCSC database, chrom and start,end limits</a> -<br><b>api.genome.ucsc.edu/getData/track?genome=galGal6;track=ncbiRefSeqOther;chrom=chr1;start=750000;end=55700000</b></li>
 </ol>
 <p>
 </p>
 
 <a name="Error examples"></a>
 <h3>Error return examples</h3>
 <p>
 <ol>
 <li><a href='/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1;track=gc5Base_;chrom=chrI;start=4321;end=5678' target=_blank>Request track data for non-existent chromosome in an assembly hub genome</a> -<br><b>api.genome.ucsc.edu/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1;track=assembly_;chrom=chrI;start=43521;end=54321</b></li>
 </ol>
 </p>
 
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