20d72f662e55fd7c611413dbb471a3a2714b9684
hiram
  Thu Oct 10 14:09:53 2019 -0700
newly supported type wigMaf refs #23589

diff --git src/hg/hubApi/hubApi.c src/hg/hubApi/hubApi.c
index e6ea63e..964ed6b 100644
--- src/hg/hubApi/hubApi.c
+++ src/hg/hubApi/hubApi.c
@@ -1,1589 +1,1591 @@
 /* hubApi - access mechanism to hub data resources. */
 #include "dataApi.h"
 #include "botDelay.h"
 #include "jsHelper.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 for all modules */
 
 static int maxItemLimit = 1000000;   /* maximum of 1,000,000 items returned */
 int maxItemsOutput = 1000000;   /* can be set in URL maxItemsOutput=N */
 boolean reachedMaxItems = FALSE;	/* during getData, signal to return */
 long long itemsReturned = 0;	/* for getData functions, number of items returned */
 /* for debugging purpose, current bot delay value */
 int botDelay = 0;
 boolean debug = FALSE;	/* can be set in URL debug=1, to turn off: debug=0 */
 #define delayFraction	0.03
 
 /* default is to list all trackDb entries, composite containers too.
  * This option will limit to only the actual track entries with data
  */
 boolean trackLeavesOnly = FALSE;  /* set by CGI parameter 'trackLeavesOnly' */
 /* this selects output type 'arrays', where the default type is: objects */
 boolean jsonOutputArrays = FALSE; /* set by CGI parameter 'jsonOutputArrays' */
 
 boolean measureTiming = FALSE;	/* set by CGI parameters */
 
 /* downloadUrl for use in error exits when reachedMaxItems */
 struct dyString *downloadUrl = NULL;
 
 /* valid argument listings to verify extraneous arguments */
 char *argListPublicHubs[] = { NULL };
 char *argListUcscGenomes[] = { NULL };
 char *argListHubGenomes[] = { argHubUrl, NULL };
 char *argListTracks[] = { argGenome, argHubUrl, argTrackLeavesOnly, NULL };
 char *argListChromosomes[] = { argGenome, argHubUrl, argTrack, NULL };
 char *argListSchema[] = { argGenome, argHubUrl, argTrack, NULL };
 char *argGetDataTrack[] = { argGenome, argHubUrl, argTrack, argChrom, argStart, argEnd, argMaxItemsOutput, argJsonOutputArrays, NULL };
 char *argGetDataSequence[] = { argGenome, argHubUrl, argTrack, argChrom, argStart, argEnd, NULL };
 
 /* Global only to this one source file */
 static struct cart *cart;             /* CGI and other variables */
 static struct hash *oldVars = NULL;
 static struct hash *trackCounter = NULL;
 static long totalTracks = 0;
 static boolean allTrackSettings = FALSE;	/* checkbox setting */
 static char **shortLabels = NULL;	/* public hub short labels in array */
 static int publicHubCount = 0;
 static char *defaultHub = "Plants";
 static char *defaultDb = "ce11";
 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 char *urlPrefix = "";	/* initalized to support self references */
 
 /* supportedTypes will be initialized to a known supported set */
 struct slName *supportedTypes = NULL;
 
 static void initSupportedTypes()
 /* initalize the list of supported track types */
 {
 struct slName *el = newSlName("bed");
 slAddHead(&supportedTypes, el);
 el = newSlName("wig");
 slAddHead(&supportedTypes, el);
+el = newSlName("wigMaf");
+slAddHead(&supportedTypes, el);
 el = newSlName("broadPeak");
 slAddHead(&supportedTypes, el);
 el = newSlName("narrowPeak");
 slAddHead(&supportedTypes, el);
 el = newSlName("bigBed");
 slAddHead(&supportedTypes, el);
 el = newSlName("bigWig");
 slAddHead(&supportedTypes, el);
 el = newSlName("bigNarrowPeak");
 slAddHead(&supportedTypes, el);
 el = newSlName("bigGenePred");
 slAddHead(&supportedTypes, el);
 el = newSlName("genePred");
 slAddHead(&supportedTypes, el);
 el = newSlName("psl");
 slAddHead(&supportedTypes, el);
 el = newSlName("rmsk");
 slAddHead(&supportedTypes, el);
 el = newSlName("bigPsl");
 slAddHead(&supportedTypes, el);
 el = newSlName("altGraphX");
 slAddHead(&supportedTypes, el);
 el = newSlName("barChart");
 slAddHead(&supportedTypes, el);
 el = newSlName("chain");
 slAddHead(&supportedTypes, el);
 el = newSlName("ctgPos");
 slAddHead(&supportedTypes, el);
 el = newSlName("expRatio");
 slAddHead(&supportedTypes, el);
 el = newSlName("factorSource");
 slAddHead(&supportedTypes, el);
 el = newSlName("gvf");
 slAddHead(&supportedTypes, el);
 el = newSlName("interact");
 slAddHead(&supportedTypes, el);
 el = newSlName("netAlign");
 slAddHead(&supportedTypes, el);
 el = newSlName("peptideMapping");
 slAddHead(&supportedTypes, el);
 el = newSlName("pgSnp");
 slAddHead(&supportedTypes, el);
 // el = newSlName("bigBarChart");
 // slAddHead(&supportedTypes, el);
 // el = newSlName("bigInteract");
 // slAddHead(&supportedTypes, el);
 // el = newSlName("bigMaf");
 // slAddHead(&supportedTypes, el);
 // el = newSlName("bigChain");
 // slAddHead(&supportedTypes, el);
 slNameSort(&supportedTypes);
 }	/*	static void initSupportedTypes()	*/
 
 static int publicHubCmpCase(const void *va, const void *vb)
 /* Compare two shortLabels, 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);
 }
 
 struct hubPublic *hubPublicDbLoadAll()
 /* read entire hubPublic table in hgcentral and return resulting list */
 {
 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()
 /* see if the timeout has been reached to determine if an exit
  *   is appropriate at this time
  */
 {
 long nowTime = clock1000();
 timedOut = FALSE;
 if ((nowTime - enteredMainTime) > (1000 * timeOutSeconds))
     timedOut= TRUE;
 return timedOut;
 }
 
 static void hashCountTrack(struct trackDb *tdb, struct hash *countTracks)
 /* this is counting up track types into the hash countTracks */
 {
 char *stripType = cloneString(tdb->type);
 if (startsWith("chain ", tdb->type))
     stripType = cloneString("chain");
 else if (startsWith("netAlign ", tdb->type))
     stripType = cloneString("netAlign");
 else if (startsWith("genePred ", tdb->type))
     stripType = cloneString("genePred");
 else if (startsWith("bigWig ", tdb->type))
     stripType = cloneString("bigWig");
 else if (startsWith("wigMaf ", tdb->type))
     stripType = cloneString("wigMaf");
 else if (startsWith("wig ", tdb->type))
     stripType = cloneString("wig");
 else
     stripType = cloneString(tdb->type);
 boolean compositeContainer = tdbIsComposite(tdb);
 boolean compositeView = tdbIsCompositeView(tdb);
 boolean superChild = tdbIsSuperTrackChild(tdb);
 if (compositeContainer)
     hashIncInt(countTracks, "composite container");
 else if (compositeView)
     hashIncInt(countTracks, "composite view");
 else if (superChild)
     {
     hashIncInt(countTracks, "superTrack child");
     hashIncInt(countTracks, stripType);
     hashIncInt(countTracks, "track count");
     }
 else if (isEmpty(tdb->type))
     hashIncInt(countTracks, "no type specified");
 else
     {
     hashIncInt(countTracks, stripType);
     hashIncInt(countTracks, "track count");
     }
 freeMem(stripType);
 }
 
 static void sampleUrl(struct trackHub *hub, char *db, struct trackDb *tdb, char *errorString)
 /* print out a sample getData URL */
 {
 char errorPrint[2048];
 errorPrint[0] = 0;
 
 if (isNotEmpty(errorString))
     {
     safef(errorPrint, sizeof(errorPrint), " <font color='red'>ERROR: %s</font>", errorString);
     }
 
 boolean superChild = tdbIsSuperTrackChild(tdb);
 char *genome = NULL;
 if (hub)
     genome = hub->genomeList->name;
 
 struct dyString *extraDyFlags = newDyString(128);
 if (debug)
     dyStringAppend(extraDyFlags, ";debug=1");
 if (jsonOutputArrays)
     dyStringAppend(extraDyFlags, ";jsonOutputArrays=1");
 char *extraFlags = dyStringCannibalize(&extraDyFlags);
 
 if (protectedTrack(tdb, tdb->track))
     hPrintf("<li>%s : %s &lt;protected data&gt;</li>\n", tdb->track, tdb->type);
 else if (db)
     {
     if (hub)
 	{
 	char urlReference[2048];
 	safef(urlReference,	sizeof(urlReference), " <a href='%s/getData/track?hubUrl=%s;genome=%s;track=%s;maxItemsOutput=5%s' target=_blank>(sample data)%s</a>\n", urlPrefix, hub->url, genome, tdb->track, extraFlags, errorPrint);
 
 	if (tdb->parent)
 	    hPrintf("<li><b>%s</b>: %s subtrack of parent: %s%s</li>\n", tdb->track, tdb->type, tdb->parent->track, urlReference);
 	else
 	    hPrintf("<li><b>%s</b>: %s%s</li>\n", tdb->track, tdb->type, urlReference);
 	}
     else
 	{
 	char urlReference[2048];
 	safef(urlReference, sizeof(urlReference), " <a href='%s/getData/track?genome=%s;track=%s;maxItemsOutput=5%s' target=_blank>(sample data)%s</a>\n", urlPrefix, db, tdb->track, extraFlags, errorPrint);
 
 	if (superChild)
 	    hPrintf("<li><b>%s</b>: %s superTrack child of parent: %s%s</li>\n", tdb->track, tdb->type, tdb->parent->track, urlReference);
 	else if (tdb->parent)
 	    hPrintf("<li><b>%s</b>: %s subtrack of parent: %s%s</li>\n", tdb->track, tdb->type, tdb->parent->track, urlReference);
 	else
 	    hPrintf("<li><b>%s</b>: %s%s</li>\n", tdb->track, tdb->type, urlReference );
 	}
     }
 else if (hub)
     {
     char urlReference[2048];
     safef(urlReference, sizeof(urlReference), " <a href='%s/getData/track?hubUrl=%s;genome=%s;track=%s;maxItemsOutput=5%s' target=_blank>(sample data)%s</a>\n", urlPrefix, hub->url, genome, tdb->track, extraFlags, errorPrint);
 
     if (tdb->parent)
 	hPrintf("<li><b>%s</b>: %s subtrack of parent: %s%s</li>\n", tdb->track, tdb->type, tdb->parent->track, urlReference);
     else
 	hPrintf("<li><b>%s</b>: %s%s</li>\n", tdb->track, tdb->type, urlReference);
     }
 else
     hPrintf("<li>%s : %s not db hub track ?</li>\n", tdb->track, tdb->type);
 }
 
 static void hubSampleUrl(struct trackHub *hub, struct trackDb *tdb,
     long chromCount, long itemCount, char *genome, char *errorString)
 {
 struct dyString *extraDyFlags = newDyString(128);
 if (debug)
     dyStringAppend(extraDyFlags, ";debug=1");
 if (jsonOutputArrays)
     dyStringAppend(extraDyFlags, ";jsonOutputArrays=1");
 char *extraFlags = dyStringCannibalize(&extraDyFlags);
 
 char errorPrint[2048];
 errorPrint[0] = 0;
 
 if (isNotEmpty(errorString))
     {
     safef(errorPrint, sizeof(errorPrint), " : <font color='red'>ERROR: %s</font>", errorString);
     }
 
 char countsMessage[512];
 countsMessage[0] = 0;
 if (chromCount > 0 || itemCount > 0)
     {
     if (allowedBigBedType(tdb->type))
         safef(countsMessage, sizeof(countsMessage), " : %ld chroms : %ld item count ", chromCount, itemCount);
     else if (startsWithWord("bigWig", tdb->type))
         safef(countsMessage, sizeof(countsMessage), " : %ld chroms : %ld bases covered ", chromCount, itemCount);
     else
         safef(countsMessage, sizeof(countsMessage), " : %ld chroms : %ld count ", chromCount, itemCount);
     }
 
 if (protectedTrack(tdb, tdb->track))
     hPrintf("    <li><b>%s</b>: %s protected data</li>\n", tdb->track, tdb->type);
 else if (isSupportedType(tdb->type))
     {
 	char urlReference[2048];
 	safef(urlReference, sizeof(urlReference), "<a href='%s/getData/track?hubUrl=%s;genome=%s;track=%s;maxItemsOutput=5%s' target=_blank>(sample data)%s</a>\n", urlPrefix, hub->url, genome, tdb->track, extraFlags, errorPrint);
 
 	if (allowedBigBedType(tdb->type))
             hPrintf("    <li><b>%s</b>: %s%s%s</li>\n", tdb->track, tdb->type, countsMessage, urlReference);
         else if (startsWithWord("bigWig", tdb->type))
             hPrintf("    <li><b>%s</b>: %s%s%s</li>\n", tdb->track, tdb->type, countsMessage, urlReference);
         else
             hPrintf("    <li><b>%s</b>: %s%s%s</li>\n", tdb->track, tdb->type, countsMessage, urlReference);
     }
 else
     {
         if (allowedBigBedType(tdb->type))
             hPrintf("    <li><b>%s</b>: %s%s</li>\n", tdb->track, tdb->type, countsMessage);
         else if (startsWithWord("bigWig", tdb->type))
             hPrintf("    <li><b>%s</b>: %s%s</li>\n", tdb->track, tdb->type, countsMessage);
         else
             hPrintf("    <li><b>%s</b>: %s%s</li>\n", tdb->track, tdb->type, countsMessage);
     }
 }	/* static void hubSampleUrl(struct trackHub *hub, struct trackDb *tdb,
 	 * long chromCount, long itemCount, char *genome)
 	 */
 
 static void bbiLargestChrom(struct bbiChromInfo *chromList, char **chromName,
     unsigned *chromSize)
 /* find largest chromosome name and size in the chromList */
 {
 if (chromName && chromSize)
     {
     *chromSize = 0;
     char *returnName = NULL;
     struct bbiChromInfo *el;
     for (el = chromList; el; el = el->next)
 	{
 	if (el->size > *chromSize)
 	    {
 	    *chromSize = el->size;
 	    returnName = el->name;
 	    }
 	}
     if (chromSize > 0)
 	*chromName = cloneString(returnName);
     }
 }
 
 static int bbiBriefMeasure(char *type, char *bigDataUrl, char *bigDataIndex, long *chromCount, long *itemCount, struct dyString *errors, char **chromName, unsigned *chromSize)
 /* check a bigDataUrl to find chrom count and item count, return
  *   name of largest chrom and its size
  */
 {
 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);
         bbiLargestChrom(chromList, chromName, chromSize);
         bbiChromInfoFreeList(&chromList);
         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;
         bbiLargestChrom(chromList, chromName, chromSize);
         bbiChromInfoFreeList(&chromList);
         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() */
 
 static void hubSubTracks(struct trackHub *hub, char *db, struct trackDb *tdb,
     struct hash *countTracks,  long chromCount, long itemCount,
     char *chromName, unsigned chromSize, char *genome, char *errorString)
 /* tdb has subtracks, show only subTracks, no details */
 {
 hPrintf("    <li><ul>\n");
 if (debug)
     {
     hPrintf("    <li>subtracks for '%s' db: '%s'</li>\n", tdb->track, db);
     hPrintf("    <li>chrom: '%s' size: %u</li>\n", chromName, chromSize);
     }
 if (tdb->subtracks)
     {
     struct trackDb *tdbEl = NULL;
     for (tdbEl = tdb->subtracks; tdbEl; tdbEl = tdbEl->next)
 	{
 	boolean compositeContainer = tdbIsComposite(tdbEl);
 	boolean compositeView = tdbIsCompositeView(tdbEl);
 	if (! (compositeContainer || compositeView) )
 	    {
             char *bigDataIndex = NULL;
             char *relIdxUrl = trackDbSetting(tdbEl, "bigDataIndex");
             if (relIdxUrl != NULL)
                 bigDataIndex = trackHubRelativeUrl(hub->genomeList->trackDbFile, relIdxUrl);
             char *bigDataUrl = trackDbSetting(tdbEl, "bigDataUrl");
             char *longName = NULL;
             unsigned longSize = 0;
             struct dyString *errors = newDyString(1024);
             (void) bbiBriefMeasure(tdbEl->type, bigDataUrl, bigDataIndex, &chromCount, &itemCount, errors, &longName, &longSize);
             chromSize = longSize;
             chromName = longName;
 	    }
         if (tdbIsCompositeView(tdbEl))
 	    hPrintf("<li><b>%s</b>: %s : composite view of parent: %s</li>\n", tdbEl->track, tdbEl->type, tdbEl->parent->track);
 	else
 	    {
 	    if (isSupportedType(tdbEl->type))
 		hubSampleUrl(hub, tdbEl, chromCount, itemCount, genome, errorString);
 	    else
 		hPrintf("<li><b>%s</b>: %s : subtrack of parent: %s</li>\n", tdbEl->track, tdbEl->type, tdbEl->parent->track);
 	    }
 	hashCountTrack(tdbEl, countTracks);
         if (tdbEl->subtracks)
 	    hubSubTracks(hub, db, tdbEl, countTracks, chromCount, itemCount, chromName, chromSize, genome, errorString);
 	}
     }
 hPrintf("    </ul></li>\n");
 }	/* hubSubTracks() */
 
 static void showSubTracks(struct trackHub *hub, char *db, struct trackDb *tdb, struct hash *countTracks,
     char *chromName, unsigned chromSize, char *errorString)
 /* tdb has subtracks, show only subTracks, no details */
 {
 hPrintf("    <li><ul>\n");
 if (debug)
     hPrintf("    <li>subtracks for '%s' db: '%s'</li>\n", tdb->track, db);
 if (tdb->subtracks)
     {
     struct trackDb *tdbEl = NULL;
     for (tdbEl = tdb->subtracks; tdbEl; tdbEl = tdbEl->next)
 	{
         if (tdbIsCompositeView(tdbEl))
 	    hPrintf("<li><b>%s</b>: %s : composite view of parent: %s</li>\n", tdbEl->track, tdbEl->type, tdbEl->parent->track);
 	else
 	    {
 	    if (isSupportedType(tdbEl->type))
 		sampleUrl(hub, db, tdbEl, errorString);
 	    else
 		hPrintf("<li><b>%s</b>: %s : subtrack of parent: %s</li>\n", tdbEl->track, tdbEl->type, tdbEl->parent->track);
 	    }
 	hashCountTrack(tdbEl, countTracks);
         if (tdbEl->subtracks)
 	    showSubTracks(hub, db, tdbEl, countTracks, chromName, chromSize, errorString);
 	}
     }
 hPrintf("    </ul></li>\n");
 }
 
 static void trackSettings(struct trackDb *tdb, struct hash *countTracks)
 /* process the settingsHash for a trackDb, recursive when subtracks */
 {
 hPrintf("    <li><ul>\n");
 boolean protectedData = protectedTrack(tdb, tdb->track);
 struct hashEl *hel;
 struct hashCookie hc = hashFirst(tdb->settingsHash);
 while ((hel = hashNext(&hc)) != NULL)
     {
     if (sameWord("track", hel->name))
 	continue;	// already output in header
     if (sameWord("tableBrowser", hel->name)
 		&& startsWithWord("off", (char*)hel->val))
 	hPrintf("    <li><b>protectedData</b>: 'true'</li>\n");
     else if (protectedData && sameWord("bigDataUrl", hel->name))
 	hPrintf("    <li><b>bigDataUrl</b>: &lt;protected data&gt;</li>\n");
     else if (isEmpty((char *)hel->val))
 	hPrintf("    <li><b>%s</b>: &lt;empty&gt;</li>\n", hel->name);
     else
 	hPrintf("    <li><b>%s</b>: '%s'</li>\n", hel->name, (char *)hel->val);
     }
 if (tdb->subtracks)
     {
     struct trackDb *tdbEl = NULL;
     if (debug)
 	hPrintf("   <li>has %d subtrack(s)</li>\n", slCount(tdb->subtracks));
     for (tdbEl = tdb->subtracks; tdbEl; tdbEl = tdbEl->next)
 	{
         hPrintf("<li>subtrack: %s of parent: %s : type: '%s' (TBD: sample data)</li>\n", tdbEl->track, tdbEl->parent->track, tdbEl->type);
 	hashCountTrack(tdbEl, countTracks);
 	trackSettings(tdbEl, countTracks);
 	}
     }
 hPrintf("    </ul></li>\n");
 }
 
 static void hubCountOneTdb(struct trackHub *hub, char *db, struct trackDb *tdb,
     char *bigDataIndex, struct hash *countTracks, char *chromName,
     unsigned chromSize, char *genome)
 {
 char *bigDataUrl = trackDbSetting(tdb, "bigDataUrl");
 boolean compositeContainer = tdbIsComposite(tdb);
 boolean compositeView = tdbIsCompositeView(tdb);
 boolean superChild = tdbIsSuperTrackChild(tdb);
 boolean depthSearch = cartUsualBoolean(cart, "depthSearch", FALSE);
 hashCountTrack(tdb, countTracks);
 
 long chromCount = 0;
 long itemCount = 0;
 
 struct dyString *errors = newDyString(1024);
 
 /* if given a chromSize, it belongs to a UCSC db and this is *not* an
  *   assembly hub, otherwise, look up a chrom and size in the bbi file
  */
 if (! (compositeContainer || compositeView) )
     {
     if (chromSize < 1 || depthSearch)
 	{
 	char *longName = NULL;
 	unsigned longSize = 0;
         (void) bbiBriefMeasure(tdb->type, bigDataUrl, bigDataIndex, &chromCount, &itemCount, errors, &longName, &longSize);
 	chromSize = longSize;
 	chromName = longName;
 	}
     }
 
 if (depthSearch && bigDataUrl)
     {
     if (isSupportedType(tdb->type))
 	    hubSampleUrl(hub, tdb, chromCount, itemCount, genome, errors->string);
     }
 else
     {
     if (compositeContainer)
         hPrintf("    <li><b>%s</b>: %s : composite track container has %d subtracks</li>\n", tdb->track, tdb->type, slCount(tdb->subtracks));
     else if (compositeView)
         hPrintf("    <li><b>%s</b>: %s : composite view of parent: %s</li>\n", tdb->track, tdb->type, tdb->parent->track);
     else if (superChild)
 	{
 	if (isSupportedType(tdb->type))
 	    hubSampleUrl(hub, tdb, chromCount, itemCount, genome,  errors->string);
 	else
 	    hPrintf("    <li><b>%s</b>: %s : superTrack child of parent: %s</li>\n", tdb->track, tdb->type, tdb->parent->track);
 	}
     else if (! depthSearch && bigDataUrl)
 	{
         if (isSupportedType(tdb->type))
 	    {
 	    hubSampleUrl(hub, tdb, chromCount, itemCount, genome, errors->string);
 	    }
 	}
     else
 	{
         if (isSupportedType(tdb->type))
 	    {
 	    hubSampleUrl(hub, tdb, chromCount, itemCount, genome, errors->string);
 	    }
 	else
 	    hPrintf("    <li><b>%s</b>: %s (what is this)</li>\n", tdb->track, tdb->type);
         }
     }
 if (allTrackSettings)
     {
     hPrintf("    <li><ul>\n");
     trackSettings(tdb, countTracks); /* show all settings */
     hPrintf("    </ul></li>\n");
     }
 else if (tdb->subtracks)
     {
     hubSubTracks(hub, db, tdb, countTracks, chromCount, itemCount, chromName, chromSize, genome, errors->string);
     }
 return;
 }	/*	static void hubCountOneTdb(char *db, struct trackDb *tdb,
 	 *	char *bigDataIndex, struct hash *countTracks,
 	 *	char *chromName, unsigned chromSize)
 	 */
 
 
 static void countOneTdb(char *db, struct trackDb *tdb,
     struct hash *countTracks, char *chromName, unsigned chromSize,
       char *errorString)
 /* for this tdb in this db, count it up and provide a sample */
 {
 char *bigDataUrl = trackDbSetting(tdb, "bigDataUrl");
 boolean compositeContainer = tdbIsComposite(tdb);
 boolean compositeView = tdbIsCompositeView(tdb);
 boolean superChild = tdbIsSuperTrackChild(tdb);
 boolean depthSearch = cartUsualBoolean(cart, "depthSearch", FALSE);
 boolean protectedData = protectedTrack(tdb, tdb->track);
 hashCountTrack(tdb, countTracks);
 
 if (compositeContainer)
     hPrintf("    <li><b>%s</b>: %s : composite track container has %d subtracks</li>\n", tdb->track, tdb->type, slCount(tdb->subtracks));
 else if (compositeView)
     hPrintf("    <li><b>%s</b>: %s : composite view of parent: %s</li>\n", tdb->track, tdb->type, tdb->parent->track);
 else if (superChild)
     {
     if (isSupportedType(tdb->type))
         sampleUrl(NULL, db, tdb, errorString);
     else
 	hPrintf("    <li><b>%s</b>: %s : superTrack child of parent: %s</li>\n", tdb->track, tdb->type, tdb->parent->track);
     }
 else if (! depthSearch && bigDataUrl)
     {
     if (protectedData)
 	hPrintf("    <li><b>%s</b>: %s : &lt;protected data&gt;</li>\n", tdb->track, tdb->type);
     else
 	hPrintf("    <li><b>%s</b>: %s : %s</li>\n", tdb->track, tdb->type, bigDataUrl);
     }
 else
     {
     if (isSupportedType(tdb->type))
         sampleUrl(NULL, db, tdb, errorString);
     else
         hPrintf("    <li><b>%s</b>: %s</li>\n", tdb->track, tdb->type);
     }
 
 if (allTrackSettings)
     {
     hPrintf("    <li><ul>\n");
     trackSettings(tdb, countTracks); /* show all settings */
     hPrintf("    </ul></li>\n");
     }
 else if (tdb->subtracks)
     {
     showSubTracks(NULL, db, tdb, countTracks, chromName, chromSize, NULL);
     }
 return;
 }	/*	static void countOneTdb(char *db, struct trackDb *tdb,
 	 *	struct hash *countTracks, char *chromName,
 	 *	unsigned chromSize)
 	 */
 
 static unsigned largestChrom(char *db, char **nameReturn, int *chromCount)
 /* return the length and get the chrom name for the largest chrom
  * from chromInfo table.  For use is sample getData URLs
  */
 {
 char query[1024];
 struct sqlConnection *conn = hAllocConn(db);
 sqlSafef(query, sizeof(query), "select chrom,size from chromInfo order by size desc limit 1");
 struct sqlResult *sr = sqlGetResult(conn, query);
 char **row = sqlNextRow(sr);
 unsigned length = 0;
 if (row)
    {
    *nameReturn = cloneString(row[0]);
    length = sqlLongLong(row[1]);
    }
 sqlFreeResult(&sr);
 if (chromCount)
     {
     sqlSafef(query, sizeof(query), "select count(*) from chromInfo");
     *chromCount = sqlQuickNum(conn, query);
     }
 hFreeConn(&conn);
 return length;
 }
 
 static void hubTrackList(struct trackHub *hub, struct trackDb *topTrackDb, struct trackHubGenome *genome)
 /* process the track list in a hub to show all tracks */
 {
 hPrintf("    <li><ul>\n");
 if (topTrackDb)
     {
     struct hash *countTracks = hashNew(0);
     struct trackDb *tdb = NULL;
     for ( tdb = topTrackDb; tdb; tdb = tdb->next )
 	{
 	char *bigDataIndex = NULL;
 	char *relIdxUrl = trackDbSetting(topTrackDb, "bigDataIndex");
 	if (relIdxUrl != NULL)
 	    bigDataIndex = trackHubRelativeUrl(genome->trackDbFile, relIdxUrl);
         char *defaultGenome = NULL;
         if (isNotEmpty(genome->name))
 	    defaultGenome = genome->name;
         char *chromName = NULL;
         unsigned chromSize = 0;
 	int chromCount = 0;
         if (isEmpty(genome->twoBitPath))
             chromSize = largestChrom(defaultGenome, &chromName, &chromCount);
 	hubCountOneTdb(hub, defaultGenome, tdb, bigDataIndex, countTracks, chromName, chromSize, defaultGenome);
 	if (timeOutReached())
 	    break;
 	}	/*	for ( tdb = topTrackDb; tdb; tdb = tdb->next )	*/
     hPrintf("    <li>%d different track types</li>\n",countTracks->elCount - 1);
     /* add this single genome count to the overall multi-genome counts */
     if (countTracks->elCount)
 	{
         hPrintf("        <li><ul>\n");
 	struct hashEl *hel, *helList = hashElListHash(countTracks);
 	slSort(&helList, hashElCmpIntValDesc);
 	for (hel = helList; hel; hel = hel->next)
 	    {
 	    if (sameOk("track count", hel->name))
 		continue;
             int prevCount = ptToInt(hashFindVal(trackCounter, hel->name));
 	    if (differentStringNullOk("track count", hel->name))
 		totalTracks += ptToInt(hel->val);
 	    hashReplace(trackCounter, hel->name, intToPt(prevCount + ptToInt(hel->val)));
 	    if (isSupportedType(hel->name))
 		hPrintf("        <li>%d - %s - supported</li>\n", ptToInt(hel->val), hel->name);
 	    else
 		hPrintf("        <li>%d - %s - not supported</li>\n", ptToInt(hel->val), hel->name);
 	    }
         hPrintf("        </ul></li>\n");
 	}
     }
 else
     hPrintf("    <li>no trackTopDb ?</li>\n");
 
 hPrintf("    </ul></li>\n");
 }	/*	static struct trackDb *hubTrackList()	*/
 
 static void hubAssemblySettings(struct trackHub *hub, struct trackHubGenome *genome)
 /* display all the assembly 'settingsHash' */
 {
 struct trackDb *tdb = obtainTdb(genome, NULL);
 
 hPrintf("    <li><ul>\n");
 struct hashEl *hel;
 struct hashCookie hc = hashFirst(genome->settingsHash);
 while ((hel = hashNext(&hc)) != NULL)
     {
     if (sameWord("description", hel->name) ||
 	sameWord("defaultPos", hel->name) ||
 	sameWord("organism", hel->name) ||
 	sameWord("groups", hel->name) ||
 	sameWord("twoBitPath", hel->name) ||
 	sameWord("genome", hel->name)
 	)
 	continue;	// already output in header
     if (sameWord("trackDb", hel->name))	/* examine the trackDb structure */
 	{
 	hubTrackList(hub, tdb, genome);
         }
     else
 	hPrintf("    <li><b>%s</b>: %s</li>\n", hel->name, (char *)hel->val);
     if (timeOutReached())
 	break;
     }
 hPrintf("    </ul></li>\n");
 }
 
 static unsigned largestChromInfo(struct chromInfo *ci, char **chromName)
 /* find largest chrom in this chromInfo, return name and size */
 {
 unsigned size = 0;
 char *name = NULL;
 struct chromInfo *el;
 for (el = ci; el; el = el->next)
     {
     if (el->size > size)
 	{
 	size = el->size;
 	name = el->chrom;
 	}
     }
 if (chromName)
     *chromName = name;
 return size;
 }
 
 static void hubInfo(char *tag, char *val)
 /* print one list element with the given tag and value, show <empty>
  * if not value present
  */
 {
 if (isNotEmpty(val))
     hPrintf("<li><b>%s</b>: '%s'</li>\n", tag, val);
 else
     hPrintf("<li><b>%s</b>: &lt;empty&gt;</li>\n", tag);
 }
 
 static void genomeList(struct trackHub *hubTop)
 /* follow the pointers from the trackHub to trackHubGenome and around
  * in a circle from one to the other to find all hub resources
  */
 {
 long totalAssemblyCount = 0;
 struct trackHubGenome *genome = hubTop->genomeList;
 
 hPrintf("<h4>genome sequences (and tracks) present in this track hub (<a href='%s/list/hubGenomes?hubUrl=%s' target=_blank>JSON example list hub genomes)</a></h4>\n", urlPrefix, hubTop->url);
 
 if (NULL == genome)
     {
     hPrintf("<h4>odd error, can not find a gnomeList ? at url: '%s'</h4>\n", hubTop->url);
     return;
     }
 
 hPrintf("<ul>\n");
 long lastTime = clock1000();
 for ( ; genome; genome = genome->next )
     {
     ++totalAssemblyCount;
     char urlReference[2048];
     if (isNotEmpty(genome->twoBitPath))
 	{
 	hPrintf("<li><b>Assembly genome</b> '%s' <b>twoBitPath</b>: '%s'</li>\n", genome->name, genome->twoBitPath);
 	char *chromName = NULL;
 	struct chromInfo *ci = trackHubAllChromInfo(genome->name);
         unsigned chromSize = largestChromInfo(ci, &chromName);
 	char sizeString[64];
 	sprintLongWithCommas(sizeString, chromSize);
 	hPrintf("<li><b>Sequence count</b> %d, <b>largest</b>: %s at %s bases</li>\n", slCount(ci), chromName, sizeString);
        safef(urlReference, sizeof(urlReference), " <a href='%s/getData/sequence?hubUrl=%s;genome=%s;chrom=%s;start=%u;end=%u' target=_blank>JSON example sequence output: %s:%u-%u</a>", urlPrefix, hubTop->url, genome->name, chromName, chromSize/4, (chromSize/4)+128, chromName, chromSize/4, (chromSize/4)+128);
         hPrintf("<li>%s</li>\n", urlReference);
 	}
     safef(urlReference, sizeof(urlReference), " <a href='%s/list/tracks?hubUrl=%s;genome=%s%s' target=_blank>JSON example list tracks output</a>", urlPrefix, hubTop->url, genome->name, trackLeavesOnly ? ";trackLeavesOnly=1" : "");
     hPrintf("<li>%s</li>\n", urlReference);
     hubInfo("organism", genome->organism);
     hubInfo("name", genome->name);
     hubInfo("description", genome->description);
     hubInfo("groups", genome->groups);
     hubInfo("defaultPos", genome->defaultPos);
     hubInfo("trackDbFile", genome->trackDbFile);
     hubAssemblySettings(hubTop, genome);
     if (measureTiming)
 	{
 	long thisTime = clock1000();
 	hPrintf("<li><em>processing time %s: %ld millis</em></li>\n", genome->name, thisTime - lastTime);
 	hPrintf("<hr>\n");
         }
     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("    <li><ul>\n");
     struct hashEl *hel, *helList = hashElListHash(trackCounter);
     slSort(&helList, hashElCmpIntValDesc);
     for (hel = helList; hel; hel = hel->next)
 	{
 	hPrintf("    <li>%d - %s - total</li>\n", ptToInt(hel->val), hel->name);
 	}
     hPrintf("    </ul></li>\n");
     }
 hPrintf("</ul>\n");
 }	/*	static void genomeList (hubTop)	*/
 
 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 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 struct hashEl *parsePathInfo(char *pathInfo, char *words[MAX_PATH_INFO])
 /* given a pathInfo string: /command/subCommand/etc...
  *  parse that and return a function pointer and the parsed words
  * Returns NULL if not recognized
  */
 {
 char *tmp = cloneString(pathInfo);
 /* skip the first leading slash to simplify chopByChar parsing */
 tmp += 1;
 int wordCount = chopByChar(tmp, '/', words, MAX_PATH_INFO);
 if (wordCount < 1 || wordCount > 2)
     return NULL;	/* only 2 words allowed */
 
 struct hashEl *hel = hashLookup(apiFunctionHash, words[0]);
 return hel;
 }
 
 static void tracksForUcscDb(char *db)
 /* scan the specified database for all tracks */
 {
 struct hash *countTracks = hashNew(0);
 char *chromName = NULL;
 int chromCount = 0;
 unsigned chromSize = largestChrom(db, &chromName, &chromCount);
 char countString[64];
 sprintLongWithCommas(countString, chromCount);
 char sizeString[64];
 sprintLongWithCommas(sizeString, chromSize);
 hPrintf("<h4>Tracks in UCSC genome: '%s', chrom count: %s, longest chrom: %s : %s</h4>\n", db, countString, chromName, sizeString);
 
 char urlReference[2048];
 safef(urlReference, sizeof(urlReference), " <a href='%s/list/tracks?genome=%s%s' target=_blank>JSON output: list tracks</a>", urlPrefix, db, trackLeavesOnly ? ";trackLeavesOnly=1" : "");
 hPrintf("<h4>%s</h4>\n", urlReference);
 
 struct trackDb *tdbList = obtainTdb(NULL, db);
 struct trackDb *tdb;
 hPrintf("<ul>\n");
 for (tdb = tdbList; tdb != NULL; tdb = tdb->next )
     {
     countOneTdb(db, tdb, countTracks, chromName, chromSize, NULL);
     if (timeOutReached())
 	break;
     }
 int trackCount = ptToInt(hashFindVal(countTracks, "track count"));
 /* elCount - 1 since the 'track count' element isn't a track */
 hPrintf("    <li>%d total tracks counted, %d different track types</li>\n", trackCount, countTracks->elCount - 1);
 if (countTracks->elCount)
     {
     hPrintf("        <ul>\n");
     struct hashEl *hel, *helList = hashElListHash(countTracks);
     slSort(&helList, hashElCmpIntValDesc);
     for (hel = helList; hel; hel = hel->next)
 	{
 	if (sameOk("track count", hel->name))
 	    continue;
 	if (isSupportedType(hel->name))
 	    hPrintf("        <li>%d - %s - supported</li>\n", ptToInt(hel->val), hel->name);
 	else
 	    hPrintf("        <li>%d - %s - not supported</li>\n", ptToInt(hel->val), hel->name);
 	}
     hPrintf("        </ul>\n");
     }
 hPrintf("</ul>\n");
 hPrintf("</p>\n");
 }	// static void tracksForUcscDb(char * db)
 
 static void initUrlPrefix()
 /* set up urlPrefix for self referenes */
 {
 char *httpHost = getenv("HTTP_HOST");
 
 if (isEmpty(httpHost))
     urlPrefix = "";
 else
     {
     if (! startsWith("hgwdev-api", httpHost))
 	{
 	if (startsWith("hgwdev",httpHost) || startsWith("genome-test", httpHost))
 	    {
 	    urlPrefix = "../cgi-bin/hubApi";
 	    }
 	}
     }
 }
 
 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");
 }
 
 static void sendJsonHogMessage(char *hogHost)
 {
 apiErrAbort(err429, err429Msg, "Your host, %s, has been sending too many requests lately and is "
        "unfairly loading our site, impacting performance for other users. "
        "Please contact genome@soe.ucsc.edu to ask that your site "
        "be reenabled.  Also, please consider downloading sequence and/or "
        "annotations in bulk -- see http://genome.ucsc.edu/downloads.html.",
        hogHost);
 }
 
 static void sendHogMessage(char *hogHost)
 {
 puts("Content-Type:text/html");
 hPrintf("Status: %d %s\n", err429, err429Msg);
 puts("Retry-After: 30");
 puts("\n");
 
 hPrintf("<!DOCTYPE HTML>\n");
 hPrintf("<html lang='en'>\n");
 hPrintf("<head>\n");
 hPrintf("<meta charset=\"utf-8\">\n");
 hPrintf("<title>Status %d %s</title></head>\n", err429, err429Msg);
 
 hPrintf("<body><h1>Status %d %s</h1><p>\n", err429, err429Msg);
 hPrintf("Your host, %s, has been sending too many requests lately and is "
        "unfairly loading our site, impacting performance for other users. "
        "Please contact genome@soe.ucsc.edu to ask that your site "
        "be reenabled.  Also, please consider downloading sequence and/or "
        "annotations in bulk -- see http://genome.ucsc.edu/downloads.html.",
        hogHost);
 hPrintf("</p></body></html>\n");
 cgiExitTime("hubApi hogExit", enteredMainTime);
 exit(0);
 }
 
 static void hogExit()
 /* bottleneck server requests exit */
 {
 char *hogHost = getenv("REMOTE_ADDR");
 char *pathInfo = getenv("PATH_INFO");
 /* nothing on incoming path, then display the WEB page instead */
 if (sameOk("/",pathInfo))
     pathInfo = NULL;
 if (isNotEmpty(pathInfo))
     {
     sendJsonHogMessage(hogHost);
     }
 else
     {
     sendHogMessage(hogHost);
     }
 }	/*	static void hogExit()	*/
 
 /* name of radio button group */
 #define RADIO_GROUP	"selectRadio"
 /* button functions */
 #define RADIO_PUBHUB	"pubHub"
 #define RADIO_OTHERHUB	"otherHub"
 #define RADIO_UCSCDB	"ucscDb"
 
 static void selectionForm()
 /* setup the selection pull-downs for source */
 {
 char *hubDropDown = cartUsualString(cart, "publicHubs", defaultHub);
 char *urlDropDown = urlFromShortLabel(hubDropDown);
 char *otherHubUrl = cartUsualString(cart, "urlHub", "");
 char *ucscDb = cartUsualString(cart, "ucscGenome", defaultDb);
 
 if (isEmpty(otherHubUrl))
     otherHubUrl = urlDropDown;
 
 char *radioOn = cartUsualString(cart, RADIO_GROUP, RADIO_PUBHUB);
 
 /* create border around table, but not inside the table with the data */
 hPrintf("<table border=4>\n");
 hPrintf("<tr><td><table border=0>\n");
 hPrintf("<tr><th colspan=3>Select one of these three sources, and display options:</th></tr>\n");
 
 int maxDbNameWidth = 0;
 struct dbDb *dbList = ucscDbDb();
 char **ucscDbList = NULL;
 int listSize = slCount(dbList);
 AllocArray(ucscDbList, listSize);
 struct dbDb *el = dbList;
 int ucscDataBaseCount = 0;
 for ( ; el != NULL; el = el->next )
     {
     ucscDbList[ucscDataBaseCount++] = el->name;
     if (strlen(el->name) > maxDbNameWidth)
 	maxDbNameWidth = strlen(el->name);
     }
 maxDbNameWidth += 1;
 
 hPrintf("<form action='%s' name='hubApiUrl' id='hubApiUrl' method='GET'>\n\n", urlPrefix);
 
 hWrites("<tr><td>");
 jsMakeTrackingRadioButton(RADIO_GROUP, "typeOneJs", RADIO_PUBHUB, radioOn);
 hWrites("</td><th>");
 hWrites("Select public hub:");
 hWrites("</th><td>");
 
 #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);
 
 jsOnEventById("change", "publicHubs", "document.getElementById('"RADIO_GROUP"_"RADIO_PUBHUB"').checked=true;");
 hWrites("</td></tr>\n");
 
 hWrites("<tr><td>");
 jsMakeTrackingRadioButton(RADIO_GROUP, "typeOneJs", RADIO_OTHERHUB, radioOn);
 hWrites("</td><th>");
 hWrites("enter a hub URL:");
 hWrites("</th><td>");
 hPrintf("<input type='text' name='urlHub' id='urlHub' size='60' value='%s'>\n", otherHubUrl);
 jsOnEventById("change", "urlHub", "document.getElementById('"RADIO_GROUP"_"RADIO_OTHERHUB"').checked=true;");
 hWrites("</td></tr>\n");
 
 hWrites("<tr><td>");
 jsMakeTrackingRadioButton(RADIO_GROUP, "typeOneJs", RADIO_UCSCDB, radioOn);
 hWrites("</td><th>");
 hWrites("select a UCSC database name:");
 hWrites("</th><td>");
 maxDbNameWidth *= 9;  // 9 should be font width here
 char widthPx[SMALLBUF];
 safef(widthPx, sizeof(widthPx), "width: %dpx", maxDbNameWidth);
 cgiMakeDropListClassWithIdStyleAndJavascript("ucscGenome", "ucscGenome",
     ucscDbList, ucscDataBaseCount, ucscDb, NULL, widthPx, events);
 jsOnEventById("change", "ucscGenome", "document.getElementById('"RADIO_GROUP"_"RADIO_UCSCDB"').checked=true;");
 hWrites("</td></tr>\n");
 
 allTrackSettings = cartUsualBoolean(cart, "allTrackSettings", FALSE);
 hWrites("<tr><td>&nbsp;</td><th>display control:</th><td>");
 hCheckBox("allTrackSettings", allTrackSettings);
 hWrites("&nbsp;display all track settings for each track");
 hWrites("</td></tr>\n");
 
 trackLeavesOnly = cartUsualBoolean(cart, "trackLeavesOnly", trackLeavesOnly);
 hWrites("<tr><td>&nbsp;</td><th>JSON list output:</th><td>");
 hCheckBox("trackLeavesOnly", trackLeavesOnly);
 hWrites("&nbsp;show only data tracks, do not show composite container information");
 hWrites("</td></tr>\n");
 
 jsonOutputArrays = cartUsualBoolean(cart, "jsonOutputArrays", jsonOutputArrays);
 hWrites("<tr><td>&nbsp;</td><th>JSON output type:</th><td>");
 hCheckBox("jsonOutputArrays", jsonOutputArrays);
 hWrites("&nbsp;more array data than objects (default: mostly object output)");
 hWrites("</td></tr>\n");
 
 /* go button at the bottom of the table */
 hWrites("<tr><td>&nbsp;</td><td align=center>");
 hButton("sourceSelected", "go");
 hWrites("</td><td>press 'go' after selections made</td></tr>\n");
 
 hPrintf("</form>\n");
 
 hPrintf("<tr><th colspan=3>(example JSON list output: <a href='/list/publicHubs' target=_blank>Public hubs</a>, and <a href='/list/ucscGenomes' target=_blank>UCSC database genomes</a>)</th></tr>\n");
 
 hPrintf("</table>\n");
 hPrintf("</td></tr></table>\n");
 
 /* how does debug carry forward ? */
 // if (debug)
 //    cgiMakeHiddenVar("debug", "1");
 }
 
 static void apiRequest(char *pathInfo)
 {
 hPrintDisable();
 /*expect no more than MAX_PATH_INFO number of words*/
 char *words[MAX_PATH_INFO];
 /* can immediately verify valid parameters right here right now */
 char *start = cgiOptionalString("start");
 char *end = cgiOptionalString("end");
 char *db = cgiOptionalString("genome");
 char *hubUrl = cgiOptionalString("hubUrl");
 struct dyString *errorMsg = newDyString(128);
 
 if (isEmpty(hubUrl) && isNotEmpty(db))
     {
     struct sqlConnection *conn = hAllocConnMaybe(db);
     if (NULL == conn)
         dyStringPrintf(errorMsg, "can not find genome genome='%s' for endpoint '%s'", db, pathInfo);
     else
         hFreeConn(&conn);
     }
 if (isNotEmpty(start) || isNotEmpty(end))
     {
     long long llStart = -1;
     long long llEnd = -1;
     struct errCatch *errCatch = errCatchNew();
     if (errCatchStart(errCatch))
         {
         if (isNotEmpty(start))
             llStart = sqlLongLong(start);
         if (isNotEmpty(end))
             llEnd = sqlLongLong(end);
         }
     errCatchEnd(errCatch);
     if (errCatch->gotError)
         {
         if (isNotEmpty(errorMsg->string))
             dyStringPrintf(errorMsg, ", ");
         dyStringPrintf(errorMsg, "%s", errCatch->message->string);
         if (isNotEmpty(start) && (-1 == llStart))
             dyStringPrintf(errorMsg, ", can not recognize start coordinate: '%s'", start);
         if (isNotEmpty(end) && (-1 == llEnd))
             dyStringPrintf(errorMsg, ", can not recognize end coordinate: '%s'", end);
         }
     else
         {
         if ( (llStart < 0) || (llEnd < 0) || (llEnd <= llStart) )
             {
             if (isNotEmpty(errorMsg->string))
                 dyStringPrintf(errorMsg, ", ");
             dyStringPrintf(errorMsg, "illegal start,end coordinates given: %s,%s, 'end' must be greater than 'start', and start greater than or equal to zero", start, end);
             }
         }
     errCatchFree(&errCatch);
     }
 
 if (isNotEmpty(errorMsg->string))
     apiErrAbort(err400, err400Msg, "%s", errorMsg->string);
 
 setupFunctionHash();
 struct hashEl *hel = parsePathInfo(pathInfo, words);
 /* verify valid API command */
 if (hel)	/* have valid command */
     {
     hPrintDisable();
     void (*apiFunction)(char **) = hel->val;
     (*apiFunction)(words);
     return;
     }
  else
     apiErrAbort(err400, err400Msg, "no such command: '/%s", pathInfo);
     /* due to Apache rewrite rules, will never be called with this error */
 }	/*	static void apiRequest(char *pathInfo)	*/
 
 static void doMiddle(struct cart *theCart)
 /* Set up globals and make web page */
 {
 cart = theCart;
 // measureTiming = isNotEmpty(cartOptionalString(cart, "measureTiming"));
 char *database = NULL;
 char *genome = NULL;
 
 if (measureTiming)
     startProcessTiming();
 
 cgiVarSet("ignoreCookie", "1");
 
 getDbAndGenome(cart, &database, &genome, oldVars);
 initGenbankTableNames(database);
 initUrlPrefix();
 
 trackLeavesOnly = cartUsualBoolean(cart, "trackLeavesOnly", trackLeavesOnly);
 jsonOutputArrays = cartUsualBoolean(cart, "jsonOutputArrays", jsonOutputArrays);
 
 char *pathInfo = getenv("PATH_INFO");
 /* nothing on incoming path, then display the WEB page instead */
 if (sameOk("/",pathInfo))
     pathInfo = NULL;
 
 (void) hubPublicDbLoadAll();
 
 webStartJWest(cart, database, "Genome Browser API");
 // webStartGbNoBanner(cart, database, "UCSC JSON API interface");
 // webStartGbOptionalBanner(cart, database, "UCSC JSON API interface", TRUE, FALSE);
 
 hPrintf("<div class='container-fluid gbPage'>\n");
 /* these style mentions need to go into custom css file */
 hPrintf("<div style='border:10px solid white'>\n");
 
 if (debug)
     {
     hPrintf("<ul>\n");
     hPrintf("<li>hgBotDelay: %d</li>\n", botDelay);
     char *envVar = getenv("BROWSER_HOST");
     hPrintf("<li>BROWSER_HOST:%s</li>\n", envVar);
     envVar = getenv("CONTEXT_DOCUMENT_ROOT");
     hPrintf("<li>CONTEXT_DOCUMENT_ROOT:%s</li>\n", envVar);
     envVar = getenv("CONTEXT_PREFIX");
     hPrintf("<li>CONTEXT_PREFIX:%s</li>\n", envVar);
     envVar = getenv("DOCUMENT_ROOT");
     hPrintf("<li>DOCUMENT_ROOT:%s</li>\n", envVar);
     envVar = getenv("HTTP_HOST");
     hPrintf("<li>HTTP_HOST:%s</li>\n", envVar);
     envVar = getenv("REQUEST_URI");
     hPrintf("<li>REQUEST_URI:%s</li>\n", envVar);
     envVar = getenv("SCRIPT_FILENAME");
     hPrintf("<li>SCRIPT_FILENAME:%s</li>\n", envVar);
     envVar = getenv("SCRIPT_NAME");
     hPrintf("<li>SCRIPT_NAME:%s</li>\n", envVar);
     envVar = getenv("SCRIPT_URI");
     hPrintf("<li>SCRIPT_URI:%s</li>\n", envVar);
     envVar = getenv("SCRIPT_URL");
     hPrintf("<li>SCRIPT_URL:%s</li>\n", envVar);
     envVar = getenv("SERVER_NAME");
     hPrintf("<li>SERVER_NAME:%s</li>\n", envVar);
     envVar = getenv("PATH_INFO");
     if (isNotEmpty(envVar))
        hPrintf("<li>PATH_INFO:'%s'</li>\n", envVar);
     else
        hPrintf("<li>PATH_INFO:&lt;empty&gt;</li>\n");
     hPrintf("</ul>\n");
     }
 
 char *otherHubUrl = cartUsualString(cart, "urlHub", "");
 char *hubDropDown = cartUsualString(cart, "publicHubs", defaultHub);
 char *urlDropDown = urlFromShortLabel(hubDropDown);
 char *ucscDb = cartUsualString(cart, "ucscGenome", defaultDb);
 char *selectRadio = cartUsualString(cart, RADIO_GROUP, RADIO_PUBHUB);
 char *urlInput = urlDropDown;	/* assume public hub */
 if (debug)
     {
     hPrintf("<ul>\n");
     hPrintf("<li>otherHubUrl: '%s'</li>\n", otherHubUrl);
     hPrintf("<li>hubDropDown: '%s'</li>\n", hubDropDown);
     hPrintf("<li>urlDropDown: '%s'</li>\n", urlDropDown);
     hPrintf("<li>ucscDb: '%s'</li>\n", ucscDb);
     hPrintf("<li>urlInput: '%s'</li>\n", urlInput);
     hPrintf("</ul>\n");
     }
 if (isEmpty(otherHubUrl))
     otherHubUrl = urlInput;
 
 if (sameWord(RADIO_OTHERHUB, selectRadio))	/* requested other hub URL */
     urlInput = otherHubUrl;
 
 long lastTime = clock1000();
 struct trackHub *hub = errCatchTrackHubOpen(urlInput);
 if (measureTiming)
     {
     long thisTime = clock1000();
     hPrintf("<em>hub open time: %ld millis</em><br>\n", thisTime - lastTime);
     }
 
 hPrintf("<h3>Documentation: <a href='../../goldenPath/help/api.html'>API definitions/help</a>, and <a href='../../goldenPath/help/trackDb/trackDbHub.html' target=_blank>Track definition document</a> for definitions of track settings.</h3>\n");
 
 if (debug)
     showCartDump();
 
 hPrintf("<h2>Explore hub or database assemblies and tracks</h2>\n");
 
 selectionForm();
 
 /* these style mentions need to go into custom css file */
 hPrintf("<div style='height:500px;overflow:scroll'>\n");
 
 if (sameWord(RADIO_UCSCDB, selectRadio))  /* requested UCSC db track list */
     {
     tracksForUcscDb(ucscDb);
     }
 else
     {
     hPrintf("<h3>%s url: <em>%s</em></h3>\n", sameWord(RADIO_PUBHUB,selectRadio) ? "Public hub" : "Other hub", urlInput);
     hPrintf("<ul>\n");
     hubInfo("hub name", hub->name);
     hubInfo("short label", hub->shortLabel);
     hubInfo("long label", hub->longLabel);
     hubInfo("genomes file", hub->genomesFile);
     hubInfo("default db", hub->defaultDb);
     hubInfo("description url", hub->descriptionUrl);
     hubInfo("email", hub->email);
     if (debug)
 	{
 	hubInfo("version", hub->version);	/* UCSC internal info */
 	hubInfo("level", hub->level);		/* UCSC internal info */
 	}
     hPrintf("</ul>\n");
 
     genomeList(hub);
     }
 
 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);
 
 hPrintf("</div> <!-- end of text analysis output -->\n");
 hPrintf("</div> <!-- end of surrounding border-->\n");
 hPrintf("</div> <!-- end this page contents -->\n");
 
 webIncludeFile("inc/jWestFooter.html");
 webEndJWest();
 // cartWebEnd();
 }	/*	void doMiddle(struct cart *theCart)	*/
 
 static void setGlobalCgiVars()
 /* check for legal CGI variables and set global flags */
 {
 /* count the arguments to see if any occur more than once */
 struct hash *varCounter = hashNew(0);
 struct cgiVar *varList = cgiVarList();
 struct cgiVar *el = varList;
 for ( ; el; el = el->next)
     {
     hashIncInt(varCounter, el->name);
     }
 struct hashCookie cookie = hashFirst(varCounter);
 struct hashEl *hel = NULL;
 for ( hel = hashNext(&cookie); hel; hel = hashNext(&cookie))
     {
     if (ptToInt(hel->val) > 1)
 	apiErrAbort(err400, err400Msg, "parameter '%s' found %d times, only one instance allowed", hel->name, ptToInt(hel->val));
     }
 
 char *trackLeaves = cgiOptionalString("trackLeavesOnly");
 if (isNotEmpty(trackLeaves))
     {
     if (sameString("1", trackLeaves))
 	trackLeavesOnly = TRUE;
     else if (sameString("0", trackLeaves))
 	trackLeavesOnly = FALSE;
     else
 	apiErrAbort(err400, err400Msg, "unrecognized 'trackLeavesOnly=%s' argument, can only be =1 or =0", trackLeaves);
     }
 
 char *jsonArray = cgiOptionalString("jsonOutputArrays");
 if (isNotEmpty(jsonArray))
     {
     if (sameString("1", jsonArray))
 	jsonOutputArrays = TRUE;
     else if (sameString("0", jsonArray))
 	jsonOutputArrays = FALSE;
     else
 	apiErrAbort(err400, err400Msg, "unrecognized 'jsonOutputArrays=%s' argument, can only be =1 or =0", jsonArray);
     }
 
 int maybeDebug = cgiOptionalInt("debug", 0);
 if (1 == maybeDebug)
     debug = TRUE;
 
 char *measTime = cgiOptionalString("measureTiming");
 if (isNotEmpty(measTime) && sameWord("1", measTime))
     measureTiming = TRUE;
 char *maxOut = cgiOptionalString("maxItemsOutput");
 if (isNotEmpty(maxOut))
     {
     long long n = -2;
     struct errCatch *errCatch = errCatchNew();
     if (errCatchStart(errCatch))
         {
 	n = sqlLongLong(maxOut);
         }
     errCatchEnd(errCatch);
     if (errCatch->gotError)
 	apiErrAbort(err400, err400Msg, "can not recognize maxItemsOutput '%s' as a number", maxOut);
     else
 	{
 	if (n == -1)	/* can use -1 to indicate as much as allowed */
 	    maxItemsOutput = maxItemLimit;
 	else if (n > maxItemLimit)	/* safety check */
 	    apiErrAbort(err400, err400Msg, "requested maxItemsOutput '%s' greater than maximum limit allowed: %d", maxOut, maxItemLimit);
 	else if (n < 1)
 	    apiErrAbort(err400, err400Msg, "requested maxItemsOutput '%s' can not be less than one", maxOut, maxItemLimit);
 	else
 	    maxItemsOutput = n;
 	}
     }
 }	/*	static void setGlobalCgiVars()	*/
 
 static void redirectToHelp()
 /* redirect to the help page */
 {
 puts("Content-Type:text/html");
 hPrintf("Status: %d %s\n", err301, err301Msg);
 hPrintf("Location: /goldenPath/help/api.html\n");
 puts("\n");
 
 hPrintf("<!DOCTYPE HTML>\n");
 hPrintf("<html lang='en'>\n");
 hPrintf("<head>\n");
 hPrintf("<meta http-equiv='Refresh' content='0; url=/goldenPath/help/api.html' />\n");
 hPrintf("</head>\n");
 }
 
 /* Null terminated list of CGI Variables we don't want to save
  * permanently. */
 static char *excludeVars[] = {"Submit", "submit", "sourceSelected", "selectRadio", "ucscGenome", "publicHubs", "clade", NULL,};
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 enteredMainTime = clock1000();
 cgiSpoof(&argc, argv);
 verboseTimeInit();
 /* similar delay system as in DAS server */
 botDelay = hgBotDelayTimeFrac(delayFraction);
 if (botDelay > 0)
     {
     if (botDelay > 2000)
         {
 	sleep1000(botDelay);
 	hogExit();
         return 0;
         }
     sleep1000(botDelay);
     }
 
 setGlobalCgiVars();
 
 int timeout = cgiOptionalInt("udcTimeout", 300);
 if (udcCacheTimeout() < timeout)
     udcSetCacheTimeout(timeout);
 knetUdcInstall();
 
 initSupportedTypes();
 
 char *pathInfo = getenv("PATH_INFO");
 if (isNotEmpty(pathInfo)) /* can get to this immediately, no cart needed */
     apiRequest(pathInfo);
 else
     {
     char *allowApiHtml = cfgOptionDefault("hubApi.allowHtml", "off");
     if (sameWord("on", allowApiHtml))
 	{
 	trackCounter = hashNew(0);
 	cartEmptyShellNoContent(doMiddle, hUserCookie(), excludeVars, oldVars);
 	}
     else
 	redirectToHelp();
     }
 cgiExitTime("hubApi", enteredMainTime);
 return 0;
 }