daab58830afaaff9af3cd658fc0c544b2f151e7f hiram Tue May 7 10:55:03 2019 -0700 update to api.genome.ucsc.edu reference refs #18869 diff --git src/hg/htdocs/goldenPath/help/api.html src/hg/htdocs/goldenPath/help/api.html index 2f7f451..5111363 100755 --- src/hg/htdocs/goldenPath/help/api.html +++ src/hg/htdocs/goldenPath/help/api.html @@ -21,65 +21,65 @@ <h6><a href="#Error_examples">Error return examples</a></h6> <!-- ========== What is JSON data ? ============================== --> <a id="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 id="Access"></a> <h2>What is the access URL ?</h2> <p> -This access url: <b>https://api-test.gi.ucsc.edu/</b> is used to access +This access url: <b>https://api.genome.ucsc.edu/</b> is used to access the endpoint functions. For example: <pre> - wget -O- 'https://api-test.gi.ucsc.edu/list/publicHubs' + wget -O- 'https://api.genome.ucsc.edu/list/publicHubs' </pre> </p> <!-- ========== What type of data can be accessed ? ===================== --> <a id="Return"></a> <h2>What type of data can be accessed ?</h2> <p> The following data sets can be accessed at this time: <ul> <li>List of available public hubs</li> <li>List of available UCSC Genome 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 Genome 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 Genome Browser genome assembly <li>List of chromosomes contained in a specific track of an assembly or track hub, or UCSC Genome 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> </ul> </p> <!-- ========== Endpoint functions ======================= --> <a id="Endpoint"></a> <h2>Endpoint functions to return data</h2> <p> -The url <b>https://api-test.gi.ucsc.edu/</b> is used to access +The url <b>https://api.genome.ucsc.edu/</b> is used to access the endpoint functions. For example: <pre> - wget -O- 'https://api-test.gi.ucsc.edu/list/publicHubs' + wget -O- 'https://api.genome.ucsc.edu/list/publicHubs' </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/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> @@ -103,31 +103,31 @@ 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?genome=ce11;chrom=chrM +https://api.genome.ucsc.edu/getData/sequence?genome=ce11;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/hubGenomes</th><td>hubUrl</td><td>(none)</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 @@ -164,30 +164,37 @@ --> <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='http://hgdownload.cse.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 under way to support additional track types)</li> </ul> </p> <!-- ========== Example data access ======================= --> <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='/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?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> -