50d394c587526db4622320a27d85f1e1ef8b9e4f lrnassar Thu May 16 11:12:37 2019 -0700 Adding an additional section with longer examples to api.html #18869 diff --git src/hg/htdocs/goldenPath/help/api.html src/hg/htdocs/goldenPath/help/api.html index b8dc50c..10eddad 100755 --- src/hg/htdocs/goldenPath/help/api.html +++ src/hg/htdocs/goldenPath/help/api.html @@ -1,278 +1,322 @@ <!DOCTYPE html> <!--#set var="TITLE" value="JSON API data interface" --> <!--#set var="ROOT" value="../.." --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <h1>JSON API data interface</h1> <h2>Contents</h2> <h6><a href="#Intro">What is JSON data ?</a></h6> <h6><a href="#Access">What is the access URL ?</a></h6> <h6><a href="#Return">What type of data can be accessed ?</a></h6> <h6><a href="#Endpoint">Endpoint functions</a></h6> <h6><a href="#Parameters">Parameters to endpoint functions</a></h6> <h6><a href="#Parameter_use">Required and optional parameters</a></h6> <h6><a href="#Track_types">Supported track types</a></h6> <h6><a href="#list_examples">Example data access, list functions</a></h6> <h6><a href="#getData_examples">Example data access, getData functions</a></h6> <h6><a href="#Error_examples">Error return examples</a></h6> +<h6><a href="#Practical_examples">Practical 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.genome.ucsc.edu/</b> is used to access the endpoint functions. For example: <pre> 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.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/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 id="Parameters"></a> <h2>Parameters to endpoint functions</h2> <p> <ul> <li>hubUrl=<url> - specify track hub or assembly hub URL</li> <li>genome=<name> - specify genome assembly in UCSC Genome Browser or track/assembly hub</li> <li>track=<trackName> - specify data track in track/assembly hub or UCSC database genome assembly</li> <li>chrom=<chrN> - specify chromosome name for sequence or track data</li> <li>start=<123> - specify start coordinate (0 relative) for data from track or sequence retrieval (start and end required together). 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>end=<456> - specify end coordinate (1 relative) for data from track or sequence retrieval (start and end required together). 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.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/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 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. Specify <b>genome</b> without a <b>hubUrl</b> to refer to a UCSC Genome Browser assembly. </p> <p> Using the <b>chrom=<name></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> <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, 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='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='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/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> - <br><b>api.genome.ucsc.edu/list/chromosomes?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ</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;track=assembly' target=_blank>list chromosomes from specified track in assembly hub genome</a> - <br><b>api.genome.ucsc.edu/list/chromosomes?hubUrl=hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ;track=assembly</b></li> </ol> <a id="getData_examples"></a> <h3>getData functions</h3> <ol> <li><a href='https://api.genome.ucsc.edu/getData/sequence?genome=hg38;chrom=chrM' target=_blank>Get DNA sequence from specified chromosome in UCSC database genome</a> - <br><b>api.genome.ucsc.edu/getData/sequence?genome=hg38;chrom=chrM</b></li> <li><a href='https://api.genome.ucsc.edu/getData/sequence?genome=hg38;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=hg38;chrom=chrM;start=4321;end=5678</b></li> <li><a href='https://api.genome.ucsc.edu/getData/sequence?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=mm10;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://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=mm10;chrom=chrM;start=4321;end=5678</b></li> <li><a href='https://api.genome.ucsc.edu/getData/sequence?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ;chrom=chr1;start=4321;end=5678' target=_blank>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://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ;chrom=chr1;start=4321;end=5678</b></li> <li><a href='https://api.genome.ucsc.edu/getData/track?genome=hg38;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=hg38;track=gold;maxItemsOutput=100</b></li> <li><a href='https://api.genome.ucsc.edu/getData/track?genome=hg38;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=hg38;track=gold;chrom=chrM</b></li> <li><a href='https://api.genome.ucsc.edu/getData/track?genome=hg38;track=gold;chrom=chr1;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=hg38;track=gold;chrom=chr1;start=47000;end=48000</b></li> <li><a href='https://api.genome.ucsc.edu/getData/track?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ;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://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ;track=assembly</b></li> <li><a href='https://api.genome.ucsc.edu/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://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ;track=assembly;chrom=chr1</b></li> <li><a href='https://api.genome.ucsc.edu/getData/track?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ;track=ensGene' target=_blank>Get track data for specified track in a track hub</a> - <br><b>api.genome.ucsc.edu/getData/track?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ;track=ensGene</b></li> <li><a href='https://api.genome.ucsc.edu/getData/track?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ;track=ensGene;chrom=chr1' 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://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ;track=ensGene;chrom=chr1</b></li> <li><a href='https://api.genome.ucsc.edu/getData/track?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ;track=gc5Base;chrom=chr1;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=hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ;track=gc5Base;chrom=chr1;start=4321;end=5678</b></li> <li><a href='https://api.genome.ucsc.edu/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='https://api.genome.ucsc.edu/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 id="Error_examples"></a> <h3>Error return examples</h3> <p> <ol> <li><a href='https://api.genome.ucsc.edu/getData/track?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ;track=assembly;chrom=chrI;start=43521;end=54321' 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://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ;track=assembly;chrom=chrI;start=43521;end=54321</b></li> <li><a href='https://api.genome.ucsc.edu/getData/track?genome=hg19;track=knownGene' target=_blank>Request track data with over 1M items, return first 1M and flag maxItemsLimit:true</a> - <br><b>api.genome.ucsc.edu/getData/track?genome=hg19;track=knownGene</b></li> <li><a href='https://api.genome.ucsc.edu/getData/track?genome=hg19;track=decipherSnvs' target=_blank>Request track data from a restricted track</a>. See <a href='../../FAQ/FAQdownloads.html#download40' target=_blank>FAQ</a> - <br><b>api.genome.ucsc.edu/getData/track?genome=hg19;track=decipherSnvs</b></li> </ol> </p> +<!-- ========== Practical Examples ======================= --> + +<a id="Practical_examples"></a> +<h2>Practical examples</h2> + +<h3>Looking up the schema of a specific track</h3> + +<p> +When querying track data with the <b>/getData/track</b> function, the <b>jsonOutputArrays</b> +can be used in conjunction to see the track schema. This includes a description of each field +present in the track. The data will also be returned in JSON array type.</p> + +<p> +<a href='https://api.genome.ucsc.edu/getData/track?genome=hg38;track=gold;chrom=chrM;jsonOutputArrays=1' +target=_blank>Request data from hg38 gold track in array type</a> - +<br><b>api.genome.ucsc.edu/getData/track?genome=hg38;track=gold;chrom=chrM;jsonOutputArrays=1</b></p> + +<h3>Hide track container information with trackLeavesOnly parameter</h3> + +<p> +When using the <b>/list/tracks</b> function to see the available tracks in an assembly, it can +be useful to return all tracks in the same hierarchical level. By default, composite and +supertracks will have the subtracks nested below, however, the <b>trackLeavesOnly=1</b> parameter +can be passed to hide the container information, and display all tracks and subtracks at the +same level.</p> + +<p> +In the following example, the first link does not include the trackLeavesOnly parameter. The +output can be compared to the second link to see the difference. This can be observed in the +conservation track. In the first link, the multiz20way track is nested within the cons20way +track. In the second link, however, the multiz20way subtrack is seen at an equivelant level +with all other tracks, and the container, cons20way, is not present in the list.</p> + +<p> +<a href='https://api.genome.ucsc.edu/list/tracks?genome=rn6' +target=_blank>Request available tracks in the rn6 genome</a> - +<br><b>api.genome.ucsc.edu/list/tracks?genome=rn6</b></p> + +<p> +<a href='https://api.genome.ucsc.edu/list/tracks?genome=rn6;trackLeavesOnly=1' +target=_blank>Request available tracks in the rn6 genome, hiding container information</a> - +<br><b>api.genome.ucsc.edu/list/tracks?genome=rn6;trackLeavesOnly=1</b></p> + <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->