3c3c42b1f7491b065fe19858f24d91fd93524fe5 hiram Mon Apr 8 14:37:27 2019 -0700 added support for PSL types and remove reference to top-level explore tools refs #18869 diff --git src/hg/htdocs/goldenPath/help/api.html src/hg/htdocs/goldenPath/help/api.html index 65231a9..f566a89 100755 --- src/hg/htdocs/goldenPath/help/api.html +++ src/hg/htdocs/goldenPath/help/api.html @@ -21,44 +21,36 @@ <h6><a href="#Error examples">Error return examples</a></h6> <!-- ========== What is JSON data ? ============================== --> <a name="Intro"></a> <h2>What is JSON data ?</h2> <p> JSON data is a data transfer syntax from a data provider to a data consumer. See also: <a href="https://www.w3schools.com/js/js_json_intro.asp" target=_blank>JSON Introduction</a> </p> <!-- ========== What is the access URL ? ============================== --> <a name="Access"></a> <h2>What is the access URL ?</h2> <p> -The gateway html page to the interface is available at -<a href="https://api-test.gi.ucsc.edu/" -target=_blank>api-test.gi.ucsc.edu</a>. This page can be used -to explore track hubs, assembly hubs, and UCSC browser data resources. -Example URL links for JSON output are provided on that page for track -types that are currently supported for data output. Work is underway -to provide access to additional data track types. -</p> -<p> This access url: <b>https://api-test.gi.ucsc.edu/</b> is used to access the endpoint functions. For example: <pre> wget -O- 'https://api-test.gi.ucsc.edu/list/publicHubs' </pre> +</p> <!-- ========== What type of data can be accessed ? ===================== --> <a name="Return"></a> <h2>What type of data can be accessed ?</h2> <p> The following data sets can be accessed at this time: <ul> <li>Listing of available public hubs</li> <li>Listing of available UCSC browser genome assemblies</li> <li>List genomes from a specified assembly or track hub</li> <li>List available data tracks from a specified hub or UCSC browser genome assembly (see also: <a href='trackDb/trackDbHub.html' target=_blank>track definition help</a>)</li> <li>List of chromosomes contained in an assembly hub or UCSC browser genome assembly. <li>List of chromosomes contained in a specific track of an assembly or track hub or UCSC browser genome assembly. <li>Return DNA sequence from an assembly hub 2bit file, or UCSC genome browser assembly</li> <li>Return track data from a specified assembly or track hub or UCSC genome browser assembly</li> @@ -145,30 +137,31 @@ <!-- ========== 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 <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='/FAQ/FAQformat.html#format9' target=_blank>genePred</a></li> <li><a href='/FAQ/FAQformat.html#format9.5' target=_blank>narrowPeak</a></li> +<li><a href='/FAQ/FAQformat.html#format2' target=_blank>psl</a></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>