d96cce85869936e100269b1b5859acef8e1fec80
hiram
  Fri Feb 15 11:22:27 2019 -0800
now dumping contents of any database table refs #18869

diff --git src/hg/hubApi/hubApi.c src/hg/hubApi/hubApi.c
index 9657c6d..8df3375 100644
--- src/hg/hubApi/hubApi.c
+++ src/hg/hubApi/hubApi.c
@@ -1,702 +1,703 @@
 /* hubApi - access mechanism to hub data resources. */
 #include "dataApi.h"
 
 /*
 +------------------+------------------+------+-----+---------+-------+
 | Field            | Type             | Null | Key | Default | Extra |
 +------------------+------------------+------+-----+---------+-------+
 | hubUrl           | longblob         | NO   | PRI | NULL    |       |
 | shortLabel       | varchar(255)     | NO   |     | NULL    |       |
 | longLabel        | varchar(255)     | NO   |     | NULL    |       |
 | registrationTime | varchar(255)     | NO   |     | NULL    |       |
 | dbCount          | int(10) unsigned | NO   |     | NULL    |       |
 | dbList           | blob             | YES  |     | NULL    |       |
 | descriptionUrl   | longblob         | YES  |     | NULL    |       |
 +------------------+------------------+------+-----+---------+-------+
 */
 
 /* Global Variables */
 static struct cart *cart;             /* CGI and other variables */
 static struct hash *oldVars = NULL;
 static struct hash *trackCounter = NULL;
 static long totalTracks = 0;
 static boolean measureTiming = FALSE;	/* set by CGI parameters */
 static boolean allTrackSettings = FALSE;	/* checkbox setting */
 static char **shortLabels = NULL;	/* public hub short labels in array */
 // struct hubPublic *publicHubList = NULL;
 static int publicHubCount = 0;
 static char *defaultHub = "Plants";
 static char *defaultDb = "ce11";
 static long enteredMainTime = 0;	/* will become = clock1000() on entry */
 		/* to allow calculation of when to bail out, taking too long */
 static long timeOutSeconds = 100;
 static boolean timedOut = FALSE;
 
 static int publicHubCmpCase(const void *va, const void *vb)
 /* Compare two slNames, ignore case. */
 {
 const struct hubPublic *a = *((struct hubPublic **)va);
 const struct hubPublic *b = *((struct hubPublic **)vb);
 return strcasecmp(a->shortLabel, b->shortLabel);
 }
 
 static void publicHubSortCase(struct hubPublic **pList)
 /* Sort slName list, ignore case. */
 {
 slSort(pList, publicHubCmpCase);
 }
 
 static struct hubPublic *hubPublicLoad(char **row)
 /* Load a hubPublic from row fetched with select * from hubPublic
  * from database.  Dispose of this with hubPublicFree(). */
 {
 struct hubPublic *ret;
 
 AllocVar(ret);
 ret->hubUrl = cloneString(row[0]);
 ret->shortLabel = cloneString(row[1]);
 ret->longLabel = cloneString(row[2]);
 ret->registrationTime = cloneString(row[3]);
 ret->dbCount = sqlUnsigned(row[4]);
 ret->dbList = cloneString(row[5]);
 // if (row[6])
     ret->descriptionUrl = cloneString(row[6]);
 // else
 //     ret->descriptionUrl = cloneString("");
 return ret;
 }
 
 struct hubPublic *hubPublicLoadAll()
 {
 char query[1024];
 struct hubPublic *list = NULL;
 struct sqlConnection *conn = hConnectCentral();
 sqlSafef(query, sizeof(query), "select * from %s", hubPublicTableName());
 struct sqlResult *sr = sqlGetResult(conn, query);
 char **row;
 while ((row = sqlNextRow(sr)) != NULL)
     {
     struct hubPublic *el = hubPublicLoad(row);
     slAddHead(&list, el);
     }
 sqlFreeResult(&sr);
 hDisconnectCentral(&conn);
 publicHubSortCase(&list);
 int listSize = slCount(list);
 AllocArray(shortLabels, listSize);
 struct hubPublic *el = list;
 int i = 0;
 for ( ; el != NULL; el = el->next )
     {
     shortLabels[i++] = el->shortLabel;
     ++publicHubCount;
     }
 return list;
 }
 
 static boolean timeOutReached()
 {
 long nowTime = clock1000();
 timedOut = FALSE;
 if ((nowTime - enteredMainTime) > (1000 * timeOutSeconds))
     timedOut= TRUE;
 return timedOut;
 }
 
 static void trackSettings(struct trackDb *tdb)
 /* process the settingsHash for a track */
 {
 hPrintf("    <ul>\n");
 struct hashEl *hel;
 struct hashCookie hc = hashFirst(tdb->settingsHash);
 while ((hel = hashNext(&hc)) != NULL)
     {
     if (isEmpty((char *)hel->val))
 	hPrintf("    <li>%s : &lt;empty&gt;</li>\n", hel->name);
     else
 	hPrintf("    <li>%s : '%s'</li>\n", hel->name, (char *)hel->val);
     }
 hPrintf("    </ul>\n");
 }
 
 static int bbiBriefMeasure(char *type, char *bigDataUrl, char *bigDataIndex, long *chromCount, long *itemCount, struct dyString *errors)
 /* check a bigDataUrl to find chrom count and item count */
 {
 int retVal = 0;
 *chromCount = 0;
 *itemCount = 0;
 struct errCatch *errCatch = errCatchNew();
 if (errCatchStart(errCatch))
     {
     if (startsWithWord("bigNarrowPeak", type)
             || startsWithWord("bigBed", type)
             || startsWithWord("bigGenePred", type)
             || startsWithWord("bigPsl", type)
             || startsWithWord("bigChain", type)
             || startsWithWord("bigMaf", type)
             || startsWithWord("bigBarChart", type)
             || startsWithWord("bigInteract", type))
         {
         struct bbiFile *bbi = NULL;
         bbi = bigBedFileOpen(bigDataUrl);
         struct bbiChromInfo *chromList = bbiChromList(bbi);
         *chromCount = slCount(chromList);
         *itemCount = bigBedItemCount(bbi);
         bbiFileClose(&bbi);
         }
     else if (startsWithWord("bigWig", type))
         {
         struct bbiFile *bwf = bigWigFileOpen(bigDataUrl);
         struct bbiChromInfo *chromList = bbiChromList(bwf);
         struct bbiSummaryElement sum = bbiTotalSummary(bwf);
         *chromCount = slCount(chromList);
         *itemCount = sum.validCount;
         bbiFileClose(&bwf);
         }
     else if (startsWithWord("vcfTabix", type))
         {
         struct vcfFile *vcf = vcfTabixFileAndIndexMayOpen(bigDataUrl, bigDataIndex, NULL, 0, 0, 1, 1);
         if (vcf == NULL)
 	    {
 	    dyStringPrintf(errors, "Could not open %s and/or its tabix index (.tbi) file.  See http://genome.ucsc.edu/goldenPath/help/vcf.html", bigDataUrl);
             retVal = 1;
 	    }
         else
 	    vcfFileFree(&vcf);
         }
     else if (startsWithWord("bam", type))
         {
 	bamFileAndIndexMustExist(bigDataUrl, bigDataIndex);
         }
     else if (startsWithWord("longTabix", type))
         {
 	struct bedTabixFile *btf = bedTabixFileMayOpen(bigDataUrl, NULL, 0, 0);
 	if (btf == NULL)
 	    {
 	    dyStringPrintf(errors, "Couldn't open %s and/or its tabix index (.tbi) file.", bigDataUrl);
             retVal = 1;
 	    }
 	else
 	    bedTabixFileClose(&btf);
         }
 #ifdef USE_HAL
     else if (startsWithWord("halSnake", type))
         {
 	char *errString;
 	int handle = halOpenLOD(bigDataUrl, &errString);
 	if (handle < 0)
 	    {
 	    dyStringPrintf(errors, "HAL open error: %s", errString);
             retVal = 1;
 	    }
 	if (halClose(handle, &errString) < 0)
 	    {
 	    dyStringPrintf(errors, "HAL close error: %s", errString);
 	    retVal = 1;
 	    }
         }
 #endif
     else
         {
 	dyStringPrintf(errors, "unrecognized type %s", type);
         retVal = 1;
         }
 
     }
 errCatchEnd(errCatch);
 if (errCatch->gotError)
     {
     retVal = 1;
     dyStringPrintf(errors, "%s", errCatch->message->string);
     }
 errCatchFree(&errCatch);
 
 return retVal;
 }	/* static int bbiBriefMeasure() */
 
 #ifdef NOT
 static void cloneTdb(struct trackDb *source, struct trackDb *destination)
 /* TBD: is there a cloneTdb() function somewhere else ? */
 {
 destination->track = cloneString(source->track);
 destination->shortLabel = cloneString(source->shortLabel);
 destination->type = cloneString(source->type);
 destination->longLabel = cloneString(source->longLabel);
 destination->visibility = source->visibility;
 destination->priority = source->priority;
 destination->colorR = source->colorR;
 destination->colorG = source->colorG;
 destination->colorB = source->colorB;
 destination->altColorR = source->altColorR;
 destination->altColorG = source->altColorG;
 destination->altColorB = source->altColorB;
 destination->useScore = source->useScore;
 destination->private = source->private;
 destination->url = cloneString(source->url);
 destination->html = cloneString(source->html);
 destination->grp = cloneString(source->grp);
 destination->canPack = source->canPack;
 destination->settings = cloneString(source->settings);
 destination->settingsHash = source->settingsHash;
 }
 #endif
 
 static void hubTrackList(struct trackDb *tdb, struct trackHubGenome *genome)
 /* process the track list to show all tracks, return trackDb list */
 {
 if (tdb)
     {
     struct hash *countTracks = hashNew(0);
     hPrintf("    <ul>\n");
     struct trackDb *track = tdb;
     for ( ; track; track = track->next )
 	{
 	char *bigDataUrl = trackDbSetting(track, "bigDataUrl");
 	char *compositeTrack = trackDbSetting(track, "compositeTrack");
 	char *superTrack = trackDbSetting(track, "superTrack");
 	boolean depthSearch = cartUsualBoolean(cart, "depthSearch", FALSE);
 	if (compositeTrack)
 	    hashIncInt(countTracks, "composite container");
 	else if (superTrack)
 	    hashIncInt(countTracks, "superTrack container");
 	else if (isEmpty(track->type))
 	    hashIncInt(countTracks, "no type specified");
 	else
 	    hashIncInt(countTracks, track->type);
 	if (depthSearch && bigDataUrl)
 	    {
 	    char *bigDataIndex = NULL;
 	    char *relIdxUrl = trackDbSetting(tdb, "bigDataIndex");
 	    if (relIdxUrl != NULL)
 		bigDataIndex = trackHubRelativeUrl(genome->trackDbFile, relIdxUrl);
 
 	    long chromCount = 0;
 	    long itemCount = 0;
 	    struct dyString *errors = newDyString(1024);
 	    int retVal = bbiBriefMeasure(track->type, bigDataUrl, bigDataIndex, &chromCount, &itemCount, errors);
             if (retVal)
 		{
 		    hPrintf("    <li>%s : %s : <font color='red'>ERROR: %s</font></li>\n", track->track, track->type, errors->string);
 		}
 	    else
 		{
 		if (startsWithWord("bigBed", track->type))
 		    hPrintf("    <li>%s : %s : %ld chroms : %ld item count</li>\n", track->track, track->type, chromCount, itemCount);
 		else if (startsWithWord("bigWig", track->type))
 		    hPrintf("    <li>%s : %s : %ld chroms : %ld bases covered</li>\n", track->track, track->type, chromCount, itemCount);
 		else
 		    hPrintf("    <li>%s : %s : %ld chroms : %ld count</li>\n", track->track, track->type, chromCount, itemCount);
 		}
 	    }
 	else
 	    {
 	    if (compositeTrack)
 		hPrintf("    <li>%s : %s : composite track container</li>\n", track->track, track->type);
 	    else if (superTrack)
 		hPrintf("    <li>%s : %s : superTrack container</li>\n", track->track, track->type);
 	    else if (! depthSearch)
 		hPrintf("    <li>%s : %s : %s</li>\n", track->track, track->type, bigDataUrl);
             else
 		hPrintf("    <li>%s : %s</li>\n", track->track, track->type);
 	    }
         if (allTrackSettings)
             trackSettings(track); /* show all settings */
 	if (timeOutReached())
 	    break;
 	}	/*	for ( ; track; track = track->next )	*/
     hPrintf("    <li>%d different track types</li>\n", countTracks->elCount);
     if (countTracks->elCount)
 	{
         hPrintf("        <ul>\n");
         struct hashEl *hel;
         struct hashCookie hc = hashFirst(countTracks);
         while ((hel = hashNext(&hc)) != NULL)
 	    {
             int prevCount = ptToInt(hashFindVal(trackCounter, hel->name));
 	    totalTracks += ptToInt(hel->val);
 	    hashReplace(trackCounter, hel->name, intToPt(prevCount + ptToInt(hel->val)));
 	    hPrintf("        <li>%d - %s</li>\n", ptToInt(hel->val), hel->name);
 	    }
         hPrintf("        </ul>\n");
 	}
     hPrintf("    </ul>\n");
     }
 }	/*	static struct trackDb *hubTrackList()	*/
 
 static struct trackDb * assemblySettings(struct trackHubGenome *genome)
 /* display all the assembly 'settingsHash' */
 {
 struct trackDb *retTbd = NULL;
 hPrintf("    <ul>\n");
 struct hashEl *hel;
 struct hashCookie hc = hashFirst(genome->settingsHash);
 while ((hel = hashNext(&hc)) != NULL)
     {
     hPrintf("    <li>%s : %s</li>\n", hel->name, (char *)hel->val);
     if (sameWord("trackDb", hel->name))	/* examine the trackDb structure */
 	{
         struct trackDb *tdb = trackHubTracksForGenome(genome->trackHub, genome);
 	retTbd = tdb;
 	hubTrackList(tdb, genome);
         }
     if (timeOutReached())
 	break;
     }
 hPrintf("    </ul>\n");
 return retTbd;
 }
 
 struct slName *genomeList(struct trackHub *hubTop, struct trackDb **dbTrackList, char *selectGenome)
 /* follow the pointers from the trackHub to trackHubGenome and around
  * in a circle from one to the other to find all hub resources
  * return slName list of the genomes in this track hub
  * optionally, return the trackList from this hub for the specified genome
  */
 {
 struct slName *retList = NULL;
 
 long totalAssemblyCount = 0;
 struct trackHubGenome *genome = hubTop->genomeList;
 
 hPrintf("<h4>genome sequences (and tracks) present in this track hub</h4>\n");
 hPrintf("<ul>\n");
 long lastTime = clock1000();
 for ( ; genome; genome = genome->next )
     {
     if (selectGenome)	/* is only one genome requested ?	*/
 	{
 	if ( differentStringNullOk(selectGenome, genome->name) )
 	    continue;
 	}
     ++totalAssemblyCount;
     struct slName *el = slNameNew(genome->name);
     slAddHead(&retList, el);
     if (genome->organism)
 	{
 	hPrintf("<li>%s - %s - %s</li>\n", genome->organism, genome->name, genome->description);
 	}
     else
 	{	/* can there be a description when organism is empty ? */
 	hPrintf("<li>%s</li>\n", genome->name);
 	}
 	if (dbTrackList)
 	    *dbTrackList = assemblySettings(genome);
 	else
 	    (void) assemblySettings(genome);
     if (measureTiming)
 	{
 	long thisTime = clock1000();
 	hPrintf("<em>processing time %s: %ld millis</em><br>\n", genome->name, thisTime - lastTime);
 	}
     if (timeOutReached())
 	break;
     }
 if (trackCounter->elCount)
     {
     hPrintf("    <li>total genome assembly count: %ld</li>\n", totalAssemblyCount);
     hPrintf("    <li>%ld total tracks counted, %d different track types:</li>\n", totalTracks, trackCounter->elCount);
     hPrintf("    <ul>\n");
     struct hashEl *hel;
     struct hashCookie hc = hashFirst(trackCounter);
     while ((hel = hashNext(&hc)) != NULL)
 	{
 	hPrintf("    <li>%d - %s - total</li>\n", ptToInt(hel->val), hel->name);
 	}
     hPrintf("    </ul>\n");
     }
 hPrintf("</ul>\n");
 return retList;
 }	/*	static struct slName *genomeList ()	*/
 
 static char *urlFromShortLabel(char *shortLabel)
 /* this is not a fair way to get the URL since shortLabel's are not
  * necessarily unique.  This is temporary.  TBD: need to always use URL
  * and then get the shortLabel
  */
 {
 char hubUrl[1024];
 char query[1024];
 struct sqlConnection *conn = hConnectCentral();
 // Build a query to select the hubUrl for the given shortLabel
 sqlSafef(query, sizeof(query), "select hubUrl from %s where shortLabel='%s'",
       hubPublicTableName(), shortLabel);
 if (! sqlQuickQuery(conn, query, hubUrl, sizeof(hubUrl)))
     hubUrl[0] = 0;
 hDisconnectCentral(&conn);
 return cloneString(hubUrl);
 }
 
 static int dbDbCmpName(const void *va, const void *vb)
 /* Compare two dbDb elements: name, ignore case. */
 {
 const struct dbDb *a = *((struct dbDb **)va);
 const struct dbDb *b = *((struct dbDb **)vb);
 return strcasecmp(a->name, b->name);
 }
 
 struct dbDb *ucscDbDb()
 /* return the dbDb table as an slList */
 {
 char query[1024];
 struct sqlConnection *conn = hConnectCentral();
 sqlSafef(query, sizeof(query), "select * from dbDb");
 struct dbDb *dbList = NULL, *el = NULL;
 struct sqlResult *sr = sqlGetResult(conn, query);
 char **row;
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = dbDbLoad(row);
     slAddHead(&dbList, el);
     }
 sqlFreeResult(&sr);
 hDisconnectCentral(&conn);
 slSort(&dbList, dbDbCmpName);
 return dbList;
 }
 
 static struct hash *apiFunctionHash = NULL;
 
 static void setupFunctionHash()
 /* initialize the apiFunctionHash */
 {
 if (apiFunctionHash)
     return;	/* already done */
 
 apiFunctionHash = hashNew(0);
 hashAdd(apiFunctionHash, "list", &apiList);
 hashAdd(apiFunctionHash, "getData", &apiGetData);
 }
 
 static void apiFunctionSwitch(char *pathInfo)
 /* given a pathInfo string: /command/subCommand/etc...
  *  parse that and decide on which function to acll
  */
 {
 hPrintDisable();	/* turn off all normal HTML output, doing JSON output */
 
 /* the leading slash has been removed from the pathInfo, therefore, the
  * chop will have the first word in words[0]
  */
 char *words[MAX_PATH_INFO];/*expect no more than MAX_PATH_INFO number of words*/
 int wordCount = chopByChar(pathInfo, '/', words, ArraySize(words));
 if (wordCount < 2)
     apiErrAbort("unknown endpoint command: '/%s'", pathInfo);
 
 struct hashEl *hel = hashLookup(apiFunctionHash, words[0]);
 if (hel == NULL)
     apiErrAbort("no such command: '%s' for endpoint '/%s'", words[0], pathInfo);
 void (*apiFunction)(char **) = hel->val;
 // void (*apiFunction)(char **) = hashMustFindVal(apiFunctionHash, words[0]);
 
 (*apiFunction)(words);
 
 }	/*	static void apiFunctionSwitch(char *pathInfo)	*/
 
 static void tracksForUcscDb(char * ucscDb)
 {
 hPrintf("<p>Tracks in UCSC genome: '%s'<br>\n", ucscDb);
 struct trackDb *tdbList = hTrackDb(ucscDb);
 struct trackDb *track;
 hPrintf("<ul>\n");
 for (track = tdbList; track != NULL; track = track->next )
     {
     hPrintf("<li>%s</li>\n", track->track);
     if (allTrackSettings)
         trackSettings(track); /* show all settings */
     }
 hPrintf("</ul>\n");
 hPrintf("</p>\n");
 }
 
 static void showExamples(char *url, struct trackHubGenome *hubGenome, char *ucscDb)
 {
 
 hPrintf("<h2>Example URLs to return json data structures:</h2>\n");
 hPrintf("<ol>\n");
 hPrintf("<li><a href='/cgi-bin/hubApi/list/publicHubs' target=_blank>list public hubs</a> <em>/cgi-bin/hubApi/list/publicHubs</em></li>\n");
 hPrintf("<li><a href='/cgi-bin/hubApi/list/ucscGenomes' target=_blank>list database genomes</a> <em>/cgi-bin/hubApi/list/ucscGenomes</em></li>\n");
 hPrintf("<li><a href='/cgi-bin/hubApi/list/hubGenomes?hubUrl=%s' target=_blank>list genomes from specified hub</a> <em>/cgi-bin/hubApi/list/hubGenomes?hubUrl=%s</em></li>\n", url, url);
 hPrintf("<li><a href='/cgi-bin/hubApi/list/tracks?hubUrl=%s&genome=%s' target=_blank>list tracks from specified hub and genome</a> <em>/cgi-bin/hubApi/list/tracks?hubUrl=%s&genome=%s</em></li>\n", url, hubGenome->name, url, hubGenome->name);
 hPrintf("<li><a href='/cgi-bin/hubApi/list/tracks?db=%s' target=_blank>list tracks from specified UCSC database</a> <em>/cgi-bin/hubApi/list/tracks?db=%s</em></li>\n", ucscDb, ucscDb);
 hPrintf("<li><a href='/cgi-bin/hubApi/list/chromosomes?db=%s' target=_blank>list chromosomes from specified UCSC database</a> <em>/cgi-bin/hubApi/list/chromosomes?db=%s</em></li>\n", ucscDb, ucscDb);
 hPrintf("<li><a href='/cgi-bin/hubApi/list/chromosomes?db=%s&track=gap' target=_blank>list chromosomes from specified track from UCSC databaset</a> <em>/cgi-bin/hubApi/list/chromosomes?db=%s&track=gap</em></li>\n", ucscDb, ucscDb);
 hPrintf("<li><a href='/cgi-bin/hubApi/getData/sequence?db=%s&chrom=chrM' target=_blank>get sequence from specified database and chromosome</a> <em>/cgi-bin/hubApi/getData/sequence?db=%s&chrom=chrM</em></li>\n", ucscDb, ucscDb);
 hPrintf("<li><a href='/cgi-bin/hubApi/getData/sequence?db=%s&chrom=chrM&start=0&end=128' target=_blank>get sequence from specified database, chromosome with start,end coordinates</a> <em>/cgi-bin/hubApi/getData/sequence?db=%s&chrom=chrM&start=0&end=128</em></li>\n", ucscDb, ucscDb);
+hPrintf("<li><a href='/cgi-bin/hubApi/getData/track?db=%s&track=gold' target=_blank>get entire track data from specified database and track name (gold == Assembly)</a> <em>/cgi-bin/hubApi/getData/track?db=%s&track=gold</em></li>\n", ucscDb, ucscDb);
 hPrintf("<li><a href='/cgi-bin/hubApi/getData/track?db=%s&chrom=chrM&track=gold' target=_blank>get track data from specified database, chromosome and track name (gold == Assembly)</a> <em>/cgi-bin/hubApi/getData/track?db=%s&chrom=chrM&track=gold</em></li>\n", ucscDb, ucscDb);
-hPrintf("<li><a href='/cgi-bin/hubApi/getData/track?db=%s&chrom=chrM&track=gold&start=0&end=100' target=_blank>get track data from specified database, chromosome, track name, start and end coordinates</a> <em>/cgi-bin/hubApi/getData/track?db=%s&chrom=chrM&track=gold&start=0&end=100</em></li>\n", ucscDb, ucscDb);
+hPrintf("<li><a href='/cgi-bin/hubApi/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>/cgi-bin/hubApi/getData/track?db=%s&chrom=chr1&track=gold&start=107680&end=186148</em></li>\n", ucscDb, ucscDb);
 hPrintf("</ol>\n");
 }	/*	static void showExamples()	*/
 
 #ifdef NOT
 static void showCartDump()
 /* for information purposes only during development, will become obsolete */
 {
 hPrintf("<h4>cart dump</h4>");
 hPrintf("<pre>\n");
 cartDump(cart);
 hPrintf("</pre>\n");
 }
 #endif
 
 static void doMiddle(struct cart *theCart)
 /* Set up globals and make web page */
 {
 cart = theCart;
 measureTiming = hPrintStatus() && isNotEmpty(cartOptionalString(cart, "measureTiming"));
 measureTiming = TRUE;
 char *database = NULL;
 char *genome = NULL;
 
 getDbAndGenome(cart, &database, &genome, oldVars);
 initGenbankTableNames(database);
 
 char *docRoot = cfgOptionDefault("browser.documentRoot", DOCUMENT_ROOT);
 
 int timeout = cartUsualInt(cart, "udcTimeout", 300);
 if (udcCacheTimeout() < timeout)
     udcSetCacheTimeout(timeout);
 knetUdcInstall();
 
 char *pathInfo = getenv("PATH_INFO");
 
 if (isNotEmpty(pathInfo))
     {
     puts("Content-Type:application/json");
     puts("\n");
     /* skip the first leading slash to simplify chopByChar parsing */
     pathInfo += 1;
     setupFunctionHash();
     apiFunctionSwitch(pathInfo);
     return;
     }
 puts("Content-Type:text/html");
 puts("\n");
 
 (void) hubPublicLoadAll();
 
 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, "access mechanism to hub data resources");
 
 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;
 
 long lastTime = clock1000();
 struct trackHub *hub = trackHubOpen(urlInput, "");
 if (measureTiming)
     {
     long thisTime = clock1000();
     hPrintf("<em>hub open time: %ld millis</em><br>\n", thisTime - lastTime);
     }
 
 // hPrintf("<h3>ucscDb: '%s'</h2>\n", ucscDb);
 
 struct trackHubGenome *hubGenome = hub->genomeList;
 
 showExamples(urlInput, hubGenome, ucscDb);
 
 // showCartDump();
 
 hPrintf("<form action='%s' name='hubApiUrl' id='hubApiUrl' method='GET'>\n\n", "../cgi-bin/hubApi");
 
 hPrintf("<b>Select public hub:&nbsp;</b>");
 #define JBUFSIZE 2048
 #define SMALLBUF 256
 char javascript[JBUFSIZE];
 struct slPair *events = NULL;
 safef(javascript, sizeof(javascript), "this.lastIndex=this.selectedIndex;");
 slPairAdd(&events, "focus", cloneString(javascript));
 
 cgiMakeDropListClassWithIdStyleAndJavascript("publicHubs", "publicHubs",
     shortLabels, publicHubCount, hubDropDown, NULL, "width: 400px", events);
 
 hWrites("&nbsp;");
 hButton("goPublicHub", "go");
 
 hPrintf("<br>Or, enter a hub URL:&nbsp;");
 hPrintf("<input type='text' name='urlHub' id='urlHub' size='60' value='%s'>\n", urlInput);
 hWrites("&nbsp;");
 hButton("goOtherHub", "go");
 
 hPrintf("<br>Or, select a UCSC database name:&nbsp;");
 maxDbNameWidth *= 9;  // 9 should be font width here
 char widthPx[SMALLBUF];
 safef(widthPx, sizeof(widthPx), "width: %dpx", maxDbNameWidth);
 cgiMakeDropListClassWithIdStyleAndJavascript("ucscGenomes", "ucscGenomes",
     ucscDbList, ucscDataBaseCount, ucscDb, NULL, widthPx, events);
 hWrites("&nbsp;");
 hButton("goUcscDb", "go");
 
 boolean depthSearch = cartUsualBoolean(cart, "depthSearch", FALSE);
 hPrintf("<br>\n&nbsp;&nbsp;");
 hCheckBox("depthSearch", cartUsualBoolean(cart, "depthSearch", FALSE));
 hPrintf("&nbsp;perform full bbi file measurement : %s (will time out if taking longer than %ld seconds)<br>\n", depthSearch ? "TRUE" : "FALSE", timeOutSeconds);
 hPrintf("\n&nbsp;&nbsp;");
 allTrackSettings = cartUsualBoolean(cart, "allTrackSettings", FALSE);
 hCheckBox("allTrackSettings", allTrackSettings);
 hPrintf("&nbsp;display all track settings for each track : %s<br>\n", allTrackSettings ? "TRUE" : "FALSE");
 
 hPrintf("<br>\n</form>\n");
 
 if (sameWord("go", goUcscDb))	/* requested UCSC db track list */
     {
     tracksForUcscDb(ucscDb);
     }
 else
     {
     hPrintf("<p>URL: %s - %s<br>\n", urlInput, sameWord("go",goPublicHub) ? "public hub" : "other hub");
     hPrintf("name: %s<br>\n", hub->shortLabel);
     hPrintf("description: %s<br>\n", hub->longLabel);
     hPrintf("default db: '%s'<br>\n", isEmpty(hub->defaultDb) ? "(none available)" : hub->defaultDb);
     printf("docRoot:'%s'<br>\n", docRoot);
 
     if (hub->genomeList)
 	(void) genomeList(hub, NULL, NULL);	/* ignore returned list */
     hPrintf("</p>\n");
     }
 
 
 if (timedOut)
     hPrintf("<h1>Reached time out %ld seconds</h1>", timeOutSeconds);
 if (measureTiming)
     hPrintf("<em>Overall total time: %ld millis</em><br>\n", clock1000() - enteredMainTime);
 
 cartWebEnd();
 }	/*	void doMiddle(struct cart *theCart)	*/
 
 /* Null terminated list of CGI Variables we don't want to save
  * permanently. */
 char *excludeVars[] = {"Submit", "submit", NULL,};
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 enteredMainTime = clock1000();
 cgiSpoof(&argc, argv);
 measureTiming = TRUE;
 verboseTimeInit();
 trackCounter = hashNew(0);
 cartEmptyShellNoContent(doMiddle, hUserCookie(), excludeVars, oldVars);
 return 0;
 }