f6772f5e8a7399f1430561d708c3dcf033241cc8 hiram Wed Mar 20 15:27:49 2019 -0700 consolidate the tableDataOutput functions refs #18869 diff --git src/hg/hubApi/hubApi.c src/hg/hubApi/hubApi.c index d85ec80..c74b1f7 100644 --- src/hg/hubApi/hubApi.c +++ src/hg/hubApi/hubApi.c @@ -786,31 +786,31 @@ } } static void showExamples(char *url, struct trackHubGenome *hubGenome, char *ucscDb) { hPrintf("<h2>Example URLs to return json data structures:</h2>\n"); hPrintf("<h3>listing functions</h3>\n"); hPrintf("<ol>\n"); hPrintf("<li><a href='%s/list/publicHubs' target=_blank>list public hubs</a> <em>%s/list/publicHubs</em></li>\n", urlPrefix, urlPrefix); hPrintf("<li><a href='%s/list/ucscGenomes' target=_blank>list database genomes</a> <em>%s/list/ucscGenomes</em></li>\n", urlPrefix, urlPrefix); hPrintf("<li><a href='%s/list/hubGenomes?hubUrl=%s' target=_blank>list genomes from specified hub</a> <em>%s/list/hubGenomes?hubUrl=%s</em></li>\n", urlPrefix, url, urlPrefix, url); hPrintf("<li><a href='%s/list/tracks?hubUrl=%s&genome=%s' target=_blank>list tracks from specified hub and genome</a> <em>%s/list/tracks?hubUrl=%s&genome=%s</em></li>\n", urlPrefix, url, hubGenome->name, urlPrefix, url, hubGenome->name); hPrintf("<li><a href='%s/list/tracks?db=%s' target=_blank>list tracks from specified UCSC database</a> <em>%s/list/tracks?db=%s</em></li>\n", urlPrefix, ucscDb, urlPrefix, ucscDb); hPrintf("<li><a href='%s/list/chromosomes?db=%s' target=_blank>list chromosomes from specified UCSC database</a> <em>%s/list/chromosomes?db=%s</em></li>\n", urlPrefix, ucscDb, urlPrefix, ucscDb); -hPrintf("<li><a href='%s/list/chromosomes?db=%s&track=gap' target=_blank>list chromosomes from specified track from UCSC databaset</a> <em>%s/list/chromosomes?db=%s&track=gap</em></li>\n", urlPrefix, ucscDb, urlPrefix, ucscDb); +hPrintf("<li><a href='%s/list/chromosomes?db=%s&track=gold' target=_blank>list chromosomes from specified track from UCSC databaset</a> <em>%s/list/chromosomes?db=%s&track=gold</em></li>\n", urlPrefix, ucscDb, urlPrefix, ucscDb); hPrintf("</ol>\n"); hPrintf("<h3>getData functions</h3>\n"); hPrintf("<ol>\n"); hPrintf("<li><a href='%s/getData/sequence?db=%s&chrom=chrM' target=_blank>get sequence from specified database and chromosome</a> <em>%s/getData/sequence?db=%s&chrom=chrM</em></li>\n", urlPrefix, ucscDb, urlPrefix, ucscDb); hPrintf("<li><a href='%s/getData/sequence?db=%s&chrom=chrM&start=0&end=128' target=_blank>get sequence from specified database, chromosome with start,end coordinates</a> <em>%s/getData/sequence?db=%s&chrom=chrM&start=0&end=128</em></li>\n", urlPrefix, ucscDb, urlPrefix, ucscDb); hPrintf("<li><a href='%s/getData/track?db=%s&track=gold' target=_blank>get entire track data from specified database and track name (gold == Assembly)</a> <em>%s/getData/track?db=%s&track=gold</em></li>\n", urlPrefix, ucscDb, urlPrefix, ucscDb); hPrintf("<li><a href='%s/getData/track?db=%s&chrom=chrM&track=gold' target=_blank>get track data from specified database, chromosome and track name (gold == Assembly)</a> <em>%s/getData/track?db=%s&chrom=chrM&track=gold</em></li>\n", urlPrefix, ucscDb, urlPrefix, ucscDb); hPrintf("<li><a href='%s/getData/track?db=%s&chrom=chrI&track=gold&start=107680&end=186148' target=_blank>get track data from specified database, chromosome, track name, start and end coordinates</a> <em>%s/getData/track?db=%s&chrom=chrI&track=gold&start=107680&end=186148</em></li>\n", urlPrefix, defaultDb, urlPrefix, defaultDb); hPrintf("<li><a href='%s/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt&genome=hg19&track=ultraConserved' target=_blank>get entire track data from specified hub and track name</a> <em>%s/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt&genome=hg19&track=ultraConserved</em></li>\n", urlPrefix, urlPrefix); hPrintf("<li><a href='%s/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt&genome=_araTha1&chrom=chrCp&track=assembly_' target=_blank>get track data from specified hub, chromosome and track name (full chromosome)</a> <em>%s/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt&genome=_araTha1&chrom=chrCp&track=assembly_</em></li>\n", urlPrefix, urlPrefix); hPrintf("<li><a href='%s/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt&genome=_araTha1&chrom=chr1&track=assembly_&start=0&end=14309681' target=_blank>get track data from specified hub, chromosome, track name, start and end coordinates</a> <em>%s/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt&genome=_araTha1&chrom=chr1&track=assembly_&start=0&end=14309681</em></li>\n", urlPrefix, urlPrefix); hPrintf("<li><a href='%s/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt&genome=_araTha1&track=gc5Base_' target=_blank>get all track data from specified hub and track name</a> <em>%s/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt&genome=_araTha1&track=gc5Base</em></li>\n", urlPrefix, urlPrefix); hPrintf("<li><a href='%s/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt&genome=_araTha1&chrom=chrMt&track=gc5Base_&start=143600&end=143685' target=_blank>get track data from specified hub, chromosome, track name, start and end coordinates</a> <em>%s/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt&genome=_araTha1&chrom=chrMt&track=gc5Base&start=143600&end=143685</em></li>\n", urlPrefix, urlPrefix); hPrintf("<li><a href='%s/getData/track?db=%s&chrom=chrI&track=gc5BaseBw&start=107680&end=186148' target=_blank>get bigWig track data from specified database, chromosome, track name, start and end coordinates</a> <em>%s/getData/track?db=%s&chrom=chrI&track=gc5BaseBw&start=107680&end=186148</em></li>\n", urlPrefix, defaultDb, urlPrefix, defaultDb); @@ -839,30 +839,31 @@ /* Set up globals and make web page */ { cart = theCart; measureTiming = hPrintStatus() && isNotEmpty(cartOptionalString(cart, "measureTiming")); measureTiming = TRUE; char *database = NULL; char *genome = NULL; cgiVarSet("ignoreCookie", "1"); getDbAndGenome(cart, &database, &genome, oldVars); initGenbankTableNames(database); initSupportedTypes(); initUrlPrefix(); +debug = cartUsualBoolean(cart, "debug", debug); int timeout = cartUsualInt(cart, "udcTimeout", 300); if (udcCacheTimeout() < timeout) udcSetCacheTimeout(timeout); knetUdcInstall(); char *pathInfo = getenv("PATH_INFO"); /* nothing on incoming path, then display the WEB page instead */ if (sameOk("/",pathInfo)) pathInfo = NULL; boolean commandError = FALSE; /*expect no more than MAX_PATH_INFO number of words*/ char *words[MAX_PATH_INFO]; if (isNotEmpty(pathInfo)) @@ -892,59 +893,60 @@ struct dbDb *dbList = ucscDbDb(); char **ucscDbList = NULL; int listSize = slCount(dbList); AllocArray(ucscDbList, listSize); struct dbDb *el = dbList; int ucscDataBaseCount = 0; int maxDbNameWidth = 0; for ( ; el != NULL; el = el->next ) { ucscDbList[ucscDataBaseCount++] = el->name; if (strlen(el->name) > maxDbNameWidth) maxDbNameWidth = strlen(el->name); } maxDbNameWidth += 1; -cartWebStart(cart, database, "UCSC API v"CGI_VERSION); +cartWebStart(cart, database, "UCSC JSON API interface"); if (debug) { char *envVar = getenv("BROWSER_HOST"); - hPrintf("<h4>BROWSER_HOST:%s</h4>\n", envVar); + hPrintf("<ul>\n"); + hPrintf("<li>BROWSER_HOST:%s</li>\n", envVar); envVar = getenv("CONTEXT_DOCUMENT_ROOT"); - hPrintf("<h4>CONTEXT_DOCUMENT_ROOT:%s</h4>\n", envVar); + hPrintf("<li>CONTEXT_DOCUMENT_ROOT:%s</li>\n", envVar); envVar = getenv("CONTEXT_PREFIX"); - hPrintf("<h4>CONTEXT_PREFIX:%s</h4>\n", envVar); + hPrintf("<li>CONTEXT_PREFIX:%s</li>\n", envVar); envVar = getenv("DOCUMENT_ROOT"); - hPrintf("<h4>DOCUMENT_ROOT:%s</h4>\n", envVar); + hPrintf("<li>DOCUMENT_ROOT:%s</li>\n", envVar); envVar = getenv("HTTP_HOST"); - hPrintf("<h4>HTTP_HOST:%s</h4>\n", envVar); + hPrintf("<li>HTTP_HOST:%s</li>\n", envVar); envVar = getenv("REQUEST_URI"); - hPrintf("<h4>REQUEST_URI:%s</h4>\n", envVar); + hPrintf("<li>REQUEST_URI:%s</li>\n", envVar); envVar = getenv("SCRIPT_FILENAME"); - hPrintf("<h4>SCRIPT_FILENAME:%s</h4>\n", envVar); + hPrintf("<li>SCRIPT_FILENAME:%s</li>\n", envVar); envVar = getenv("SCRIPT_NAME"); - hPrintf("<h4>SCRIPT_NAME:%s</h4>\n", envVar); + hPrintf("<li>SCRIPT_NAME:%s</li>\n", envVar); envVar = getenv("SCRIPT_URI"); - hPrintf("<h4>SCRIPT_URI:%s</h4>\n", envVar); + hPrintf("<li>SCRIPT_URI:%s</li>\n", envVar); envVar = getenv("SCRIPT_URL"); - hPrintf("<h4>SCRIPT_URL:%s</h4>\n", envVar); + hPrintf("<li>SCRIPT_URL:%s</li>\n", envVar); envVar = getenv("SERVER_NAME"); - hPrintf("<h4>SERVER_NAME:%s</h4>\n", envVar); + hPrintf("<li>SERVER_NAME:%s</li>\n", envVar); + hPrintf("</ul>\n"); } - char *goOtherHub = cartUsualString(cart, "goOtherHub", defaultHub); char *goUcscDb = cartUsualString(cart, "goUcscDb", ""); char *otherHubUrl = cartUsualString(cart, "urlHub", defaultHub); char *goPublicHub = cartUsualString(cart, "goPublicHub", defaultHub); char *hubDropDown = cartUsualString(cart, "publicHubs", defaultHub); char *urlDropDown = urlFromShortLabel(hubDropDown); char *ucscDb = cartUsualString(cart, "ucscGenomes", defaultDb); char *urlInput = urlDropDown; /* assume public hub */ if (sameWord("go", goOtherHub)) /* requested other hub URL */ urlInput = otherHubUrl; else if (isEmpty(otherHubUrl)) otherHubUrl = urlInput; if (commandError) {