4de18188ae5bb1336c3f49ad155358ee8f94db00 hiram Wed May 3 10:20:58 2023 -0700 adding new endpoint /list/files definitions and examples refs #23589 diff --git src/hg/htdocs/goldenPath/help/api.html src/hg/htdocs/goldenPath/help/api.html index 54923a2..5f76c3f 100755 --- src/hg/htdocs/goldenPath/help/api.html +++ src/hg/htdocs/goldenPath/help/api.html @@ -49,59 +49,61 @@ 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 of files available for download for UCSC Browser genome assemblies</li> <li>List of genomes from a specified assembly or track hub</li> <li>List of 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> <li>List of chromosomes contained in a specific track of an assembly or track hub, or UCSC Genome Browser genome assembly</li> <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> <b>Note:</b> BLAT also supports programmatic URL queries which return in JSON format. See our <a href="/FAQ/FAQblat.html#blat14">BLAT FAQ</a> for more info. </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/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> </ul> </p> <!-- ========== Parameters to endpoint functions ======================= --> <a id="Parameters"></a> <h2>Parameters to endpoint functions</h2> <p> <ul> @@ -112,72 +114,79 @@ <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</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> </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/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 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> +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='/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> @@ -243,30 +252,36 @@ <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=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ;track=assembly</b></li> <li><a href='https://api.genome.ucsc.edu/list/schema?genome=hg38;track=knownGene' target=_blank>list schema from specified track in UCSC database genome</a> - <br><b>api.genome.ucsc.edu/list/schema?genome=hg38;track=knownGene</b></li> +<li><a href='https://api.genome.ucsc.edu/list/files?genome=GCF_000955945.1;maxItemsOutput=5' +target=_blank>list download files for UCSC GenArk genome 'GCF_000955945.1' in JSON format limit 5 items output</a> - +<br><b>api.genome.ucsc.edu/list/files?genome=GCF_000955945.1;maxItemsOutput=5</b></li> +<li><a href='https://api.genome.ucsc.edu/list/files?genome=hs1;format=text;maxItemsOutput=5' +target=_blank>list download files for UCSC genome 'hs1' in plain text format limit 5 items output</a> - +<br><b>api.genome.ucsc.edu/list/files?genome=hs1;format=text;maxItemsOutput=5</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> -