b7749ec648f88880da646bca0bba1a14f288639c
hiram
  Wed Mar 20 18:13:15 2019 -0700
adding hubPublic.c and .h to library refs #18869

diff --git src/hg/hubApi/hubApi.c src/hg/hubApi/hubApi.c
index c74b1f7..6897631 100644
--- src/hg/hubApi/hubApi.c
+++ src/hg/hubApi/hubApi.c
@@ -1,1073 +1,1111 @@
 /* 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 boolean debug = FALSE;
+static boolean debug = FALSE;	/* can be set in URL debug=1 */
 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 char *urlPrefix = "";	/* initalized to support self references */
 static struct slName *supportedTypes = NULL;
 	/* will be initialized to a known supported set */
 
 static void initSupportedTypes()
-/* initalize the list of supported track types,
- */
+/* initalize the list of supported track types */
 {
 struct slName *el = newSlName("bed");
 slAddHead(&supportedTypes, el);
 el = newSlName("wig");
 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("bigPsl");
 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 boolean isSupportedType(char *type)
 /* is given type in the supportedTypes list ? */
 {
 boolean ret = FALSE;
-if (startsWith("wigMaf", type))
+if (startsWith("wigMaf", type))	/* not wigMaf at this time */
     return ret;
 struct slName *el;
 for (el = supportedTypes; el; el = el->next)
     {
     if (startsWith(el->name, type))
 	{
 	ret = TRUE;
 	break;
 	}
     }
 return ret;
 }
 
 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);
 }
 
-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]);
-ret->descriptionUrl = cloneString(row[6]);
-return ret;
-}
-
-struct hubPublic *hubPublicLoadAll()
+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;
 }
 
 #ifdef NOT
 static void showCounts(struct hash *countTracks)
 {
 if (countTracks->elCount)
     {
     hPrintf("        <li><ul>\n");
     struct hashEl *hel;
     struct hashCookie hc = hashFirst(countTracks);
     while ((hel = hashNext(&hc)) != NULL)
         hPrintf("        <li>%d - %s</li>\n", ptToInt(hel->val), hel->name);
     hPrintf("        </ul></li>\n");
     }
 }
 #endif
 
 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);
 // char *compositeTrack = trackDbLocalSetting(tdb, "compositeTrack");
 boolean compositeContainer = tdbIsComposite(tdb);
 boolean compositeView = tdbIsCompositeView(tdb);
 // char *superTrack = trackDbLocalSetting(tdb, "superTrack");
 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);
 // showCounts(countTracks);
 }
 
 static void sampleUrl(char *db, struct trackDb *tdb, char *chrom, long long chromSize)
 /* print out a sample getData URL */
 {
-long long start = chromSize / 4;
-long long end = start + 10000;
+unsigned start = chromSize / 4;
+unsigned end = start + 10000;
 if (end > chromSize)
     end = chromSize;
 
 if (db)
     {
     if (tdb->parent)
-	hPrintf("<li>%s : %s subtrack of parent: %s <a href='%s/getData/track?db=%s&amp;chrom=%s&amp;track=%s&amp;start=%lld&amp;end=%lld' target=_blank>(sample getData)</a></li>\n", tdb->track, tdb->type, tdb->parent->track, urlPrefix, db, chrom, tdb->track, start, end );
+	hPrintf("<li>%s : %s subtrack of parent: %s <a href='%s/getData/track?db=%s&amp;chrom=%s&amp;track=%s&amp;start=%u&amp;end=%u' target=_blank>(sample getData)</a></li>\n", tdb->track, tdb->type, tdb->parent->track, urlPrefix, db, chrom, tdb->track, start, end );
     else
-	hPrintf("<li>%s : %s <a href='%s/getData/track?db=%s&amp;chrom=%s&amp;track=%s&amp;start=%lld&amp;end=%lld' target=_blank>(sample getData)</a></li>\n", tdb->track, tdb->type, urlPrefix, db, chrom, tdb->track, start, end );
+	hPrintf("<li>%s : %s <a href='%s/getData/track?db=%s&amp;chrom=%s&amp;track=%s&amp;start=%u&amp;end=%u' target=_blank>(sample getData)</a></li>\n", tdb->track, tdb->type, urlPrefix, db, chrom, tdb->track, start, end );
     }
 }
 
 static void showSubTracks(char *db, struct trackDb *tdb, struct hash *countTracks,
     char *chromName, long long chromSize)
 /* tdb has subtracks, show only subTracks, no details */
 {
 hPrintf("    <li><ul>\n");
 if (tdb->subtracks)
     {
     struct trackDb *tdbEl = NULL;
     for (tdbEl = tdb->subtracks; tdbEl; tdbEl = tdbEl->next)
 	{
         if (tdbIsCompositeView(tdbEl))
 	    hPrintf("<li>%s : %s : composite view of parent: %s</li>\n", tdbEl->track, tdbEl->type, tdbEl->parent->track);
 	else
 	    {
         if (isSupportedType(tdbEl->type))
 	    {
             sampleUrl(db, tdbEl, chromName, chromSize);
 //            hPrintf("<li>%s : %s : subtrack of parent: %s (with sample)</li>\n", tdbEl->track, tdbEl->type, tdbEl->parent->track, getData);
 	    }
 	else
             hPrintf("<li>%s : %s : subtrack of parent: %s</li>\n", tdbEl->track, tdbEl->type, tdbEl->parent->track);
 	    }
 	hashCountTrack(tdbEl, countTracks);
         if (tdbEl->subtracks)
 	    showSubTracks(db, tdbEl, countTracks, chromName, chromSize);
 	}
     }
 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");
 // if (tdb->children)  haven't yet seen a track with children ?
 //   hPrintf("    <li>%s: has children</li>\n", tdb->track);
 // else
 //   hPrintf("    <li>%s: NO children</li>\n", 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 (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);
     }
 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'</li>\n", tdbEl->track, tdbEl->parent->track, tdbEl->type);
 	hashCountTrack(tdbEl, countTracks);
 	trackSettings(tdbEl, countTracks);
 	}
     }
 hPrintf("    </ul></li>\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 */
+static void bbiBiggestChrom(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);
+        bbiBiggestChrom(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;
+        bbiBiggestChrom(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 countOneTdb(char *db, struct trackDb *tdb, char *bigDataIndex,
-    struct hash *countTracks, char *chromName, long long chromSize)
+static void hubSampleUrl(struct trackHub *hub, struct trackDb *tdb,
+    long chromCount, long itemCount, char *chromName, unsigned chromSize,
+      char *genome)
+{
+unsigned start = chromSize / 4;
+unsigned end = start + 10000;
+if (end > chromSize)
+    end = chromSize;
+
+if (isSupportedType(tdb->type))
+    {
+        if (startsWithWord("bigBed", tdb->type))
+            hPrintf("    <li>%s : %s : %ld chroms : %ld item count <a href='%s/getData/track?hubUrl=%s&amp;genome=%s&amp;track=%s&amp;chrom=%s&amp;start=%u&amp;end=%u' target=_blank>(sample getData)</a></li>\n", tdb->track, tdb->type, chromCount, itemCount, urlPrefix, hub->url, genome, tdb->track, chromName, start, end);
+        else if (startsWithWord("bigWig", tdb->type))
+            hPrintf("    <li>%s : %s : %ld chroms : %ld bases covered <a href='%s/getData/track?hubUrl=%s&amp;genome=%s&amp;track=%s&amp;chrom=%s&amp;start=%u&amp;end=%u' target=_blank>(sample getData)</a></li>\n", tdb->track, tdb->type, chromCount, itemCount, urlPrefix, hub->url, genome, tdb->track, chromName, start, end);
+        else
+            hPrintf("    <li>%s : %s : %ld chroms : %ld count <<a href='%s/getData/track?hubUrl=%s&amp;genome=%s&amp;track=%s&amp;chrom=%s&amp;start=%u&amp;end=%u' target=_blank>(sample getData)</a></li>\n", tdb->track, tdb->type, chromCount, itemCount, urlPrefix, hub->url, genome, tdb->track, chromName, start, end);
+    }
+else
+    {
+        if (startsWithWord("bigBed", tdb->type))
+            hPrintf("    <li>%s : %s : %ld chroms : %ld item count</li>\n", tdb->track, tdb->type, chromCount, itemCount);
+        else if (startsWithWord("bigWig", tdb->type))
+            hPrintf("    <li>%s : %s : %ld chroms : %ld bases covered</li>\n", tdb->track, tdb->type, chromCount, itemCount);
+        else
+            hPrintf("    <li>%s : %s : %ld chroms : %ld count</li>\n", tdb->track, tdb->type, chromCount, itemCount);
+    }
+}
+
+static void countOneTdb(struct trackHub *hub, char *db, struct trackDb *tdb,
+    char *bigDataIndex, struct hash *countTracks, char *chromName,
+    unsigned chromSize, char *genome)
 {
 char *bigDataUrl = trackDbSetting(tdb, "bigDataUrl");
 // char *compositeTrack = trackDbSetting(tdb, "compositeTrack");
 boolean compositeContainer = tdbIsComposite(tdb);
 boolean compositeView = tdbIsCompositeView(tdb);
 // char *superTrack = trackDbSetting(tdb, "superTrack");
 boolean superChild = tdbIsSuperTrackChild(tdb);
 boolean depthSearch = cartUsualBoolean(cart, "depthSearch", FALSE);
 hashCountTrack(tdb, countTracks);
 
 if (depthSearch && bigDataUrl)
     {
+    char *longName = NULL;
+    unsigned longSize = 0;
     long chromCount = 0;
     long itemCount = 0;
     struct dyString *errors = newDyString(1024);
-    int retVal = bbiBriefMeasure(tdb->type, bigDataUrl, bigDataIndex, &chromCount, &itemCount, errors);
+    int retVal = bbiBriefMeasure(tdb->type, bigDataUrl, bigDataIndex, &chromCount, &itemCount, errors, &longName, &longSize);
     if (retVal)
         {
             hPrintf("    <li>%s : %s : <font color='red'>ERROR: %s</font></li>\n", tdb->track, tdb->type, errors->string);
         }
     else
-        {
-        if (startsWithWord("bigBed", tdb->type))
-            hPrintf("    <li>%s : %s : %ld chroms : %ld item count</li>\n", tdb->track, tdb->type, chromCount, itemCount);
-        else if (startsWithWord("bigWig", tdb->type))
-            hPrintf("    <li>%s : %s : %ld chroms : %ld bases covered</li>\n", tdb->track, tdb->type, chromCount, itemCount);
-        else
-            hPrintf("    <li>%s : %s : %ld chroms : %ld count</li>\n", tdb->track, tdb->type, chromCount, itemCount);
-        }
+	hubSampleUrl(hub, tdb, chromCount, itemCount, longName, longSize, genome);
     }
 else
     {
     if (compositeContainer)
         hPrintf("    <li>%s : %s : composite track container has %d subtracks</li>\n", tdb->track, tdb->type, slCount(tdb->subtracks));
     else if (compositeView)
         hPrintf("    <li>%s : %s : composite view of parent: %s</li>\n", tdb->track, tdb->type, tdb->parent->track);
     else if (superChild)
         hPrintf("    <li>%s : %s : superTrack child of parent: %s</li>\n", tdb->track, tdb->type, tdb->parent->track);
     else if (! depthSearch && bigDataUrl)
         hPrintf("    <li>%s : %s : %s</li>\n", tdb->track, tdb->type, bigDataUrl);
     else
 	{
         if (isSupportedType(tdb->type))
             sampleUrl(db, tdb, chromName, chromSize);
 	else
 	    hPrintf("    <li>%s : %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(db, tdb, countTracks, chromName, chromSize);
     }
 return;
 }	/*	static void countOneTdb(char *db, struct trackDb *tdb,
 	 *	char *bigDataIndex, struct hash *countTracks,
 	 *	char *chromName, long long chromSize)
 	 */
 
-static void hubTrackList(struct trackDb *topTrackDb, struct trackHubGenome *genome)
+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);
-	countOneTdb(NULL, tdb, bigDataIndex, countTracks, NULL, 0);
+        char *defaultGenome = NULL;
+        if (isNotEmpty(genome->name))
+	    defaultGenome = genome->name;
+	countOneTdb(hub, NULL, tdb, bigDataIndex, countTracks, NULL, 0, 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><ol>\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</li>\n", ptToInt(hel->val), hel->name);
 	    }
         hPrintf("        </ol></li>\n");
 	}
     }
 else
     hPrintf("    <li>no trackTopDb</li>\n");
 
 hPrintf("    </ul><li>\n");
 }	/*	static struct trackDb *hubTrackList()	*/
 
-static struct trackDb *assemblySettings(struct trackHubGenome *genome)
+static struct trackDb *assemblySettings(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)
     {
     hPrintf("    <li>%s : %s</li>\n", hel->name, (char *)hel->val);
     if (sameWord("trackDb", hel->name))	/* examine the trackDb structure */
 	{
-	hubTrackList(tdb, genome);
+	hubTrackList(hub, tdb, genome);
         }
     if (timeOutReached())
 	break;
     }
 hPrintf("    </ul></li>\n");
 return tdb;
 }
 
 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);
 	}
-    struct trackDb *tdb = assemblySettings(genome);
+    struct trackDb *tdb = assemblySettings(hubTop, genome);
     if (dbTrackList)
 	*dbTrackList = tdb;
     if (measureTiming)
 	{
 	long thisTime = clock1000();
 	hPrintf("<li><em>processing time %s: %ld millis</em></li>\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("    <li><ol>\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("    </ol></li>\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 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)
     return NULL;
 
 struct hashEl *hel = hashLookup(apiFunctionHash, words[0]);
 return hel;
 }
 
-static long long largestChrom(char *db, char **nameReturn)
+static unsigned largestChrom(char *db, char **nameReturn)
 /* 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);
 // Build a query to select the hubUrl for the given shortLabel
 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);
-long long length = 0;
+unsigned length = 0;
 if (row)
    {
    *nameReturn = cloneString(row[0]);
    length = sqlLongLong(row[1]);
    }
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 return length;
 }
 
 static void tracksForUcscDb(char *db)
 /* scan the specified database for all tracks */
 {
 struct hash *countTracks = hashNew(0);
 char *chromName = NULL;
-long long chromSize = largestChrom(db, &chromName);
-hPrintf("<h4>Tracks in UCSC genome: '%s', longest chrom: %s:%lld</h4>\n", db, chromName, chromSize);
+unsigned chromSize = largestChrom(db, &chromName);
+hPrintf("<h4>Tracks in UCSC genome: '%s', longest chrom: %s:%u</h4>\n", db, chromName, chromSize);
 struct trackDb *tdbList = obtainTdb(NULL, db);
 struct trackDb *tdb;
 hPrintf("<ul>\n");
-hPrintf("<li>%s:%lld</li>\n", chromName, chromSize);
+hPrintf("<li>%s:%u</li>\n", chromName, chromSize);
 for (tdb = tdbList; tdb != NULL; tdb = tdb->next )
     {
-    countOneTdb(db, tdb, NULL, countTracks, chromName, chromSize);
+    countOneTdb(NULL, db, tdb, NULL, 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("        <ol>\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</li>\n", ptToInt(hel->val), hel->name);
 	}
     hPrintf("        </ol>\n");
     }
 hPrintf("</ul>\n");
 hPrintf("</p>\n");
 }	// static void tracksForUcscDb(char * db)
 
 static void introductionText()
 /* output explanation text */
 {
 char *scriptUri = getenv("SCRIPT_URI");
 
 hPrintf("<h1>JSON data API interface to U.C. Santa Cruz genome browser data</h1>\n");
 hPrintf("<h2>Data access URL: <em>%s</em></h2>\n", scriptUri);
 hPrintf("<h3>Endpoint functions:</h3>\n");
 hPrintf("<ul>\n");
 hPrintf("<li>/list/...</li>\n");
 hPrintf("<li><ol>\n");
 hPrintf("<li>/list/publicHubs - list public hubs</li>\n");
 hPrintf("<li>/list/ucscGenomes - list UCSC database genomes</li>\n");
 hPrintf("<li>/list/hubGenomes - list genomes from specified hub</li>\n");
 hPrintf("<li>/list/tracks - list data tracks available in specified hub or database genome</li>\n");
 hPrintf("<li>/list/chromosomes - list chromosomes from specified data track in specified hub or database genome</li>\n");
 hPrintf("</ol></li>\n");
 hPrintf("<li>/getData/...</li>\n");
 hPrintf("<li><ol>\n");
 hPrintf("<li>/getData/sequence - return sequence from specified hub or database genome</li>\n");
 hPrintf("<li>/getData/track - return data from specified track in hub or database genome</li>\n");
 hPrintf("</ol></li>\n");
 hPrintf("</ul>\n");
 hPrintf("<h3>Parameters to endpoint functions:</h3>\n");
 hPrintf("<ul>\n");
 hPrintf("<li>hubUrl=&lt;url&gt; - specify track hub or assembly hub URL</li>\n");
 hPrintf("<li>genome=&lt;name&gt; - specify genome assemby in track or assembly hub</li>\n");
 hPrintf("<li>db=&lt;ucscDb&gt; - specify database (aka genome assembly) in UCSC genome browser</li>\n");
 hPrintf("<li>track=&lt;trackName&gt; - specify data track in hub or UCSC database genome assembly</li>\n");
 hPrintf("<li>chrom=&lt;chrN&gt; - specify chromosome name for sequence or track data</li>\n");
 hPrintf("<li>start=&lt;123&gt; - specify start coordinate (0 relative) for data from track or sequence retrieval</li>\n");
 hPrintf("<li>end=&lt;456&gt; - specify end coordinate (1 relative) for data from track or sequence retrieval</li>\n");
 hPrintf("<li>(see also: <a href='http://genome.ucsc.edu/blog/the-ucsc-genome-browser-coordinate-counting-systems/' target=_blank>UCSC browser coordinate counting systems)</a></li>");
 hPrintf("</ul>\n");
 hPrintf("<h3>Supported track types, at this time, for getData functions:</h3>\n");
 hPrintf("<ul>\n");
 static struct slName *el;
 for (el = supportedTypes; el; el = el->next)
     {
     hPrintf("<li>%s</li>\n", el->name);
     }
 hPrintf("</ul>\n");
 }
 
 static void initUrlPrefix()
 /* set up urlPrefix for self referenes */
 {
 char *httpHost = getenv("HTTP_HOST");
 
 if (! startsWith("hgwdev-api", httpHost))
     {
     if (startsWith("hgwdev",httpHost) || startsWith("genome-test", httpHost))
 	{
 	urlPrefix = "../cgi-bin/hubApi";
 	}
     }
 }
 
 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&amp;genome=%s' target=_blank>list tracks from specified hub and genome</a> <em>%s/list/tracks?hubUrl=%s&amp;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&amp;track=gold' target=_blank>list chromosomes from specified track from UCSC databaset</a> <em>%s/list/chromosomes?db=%s&amp;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&amp;chrom=chrM' target=_blank>get sequence from specified database and chromosome</a> <em>%s/getData/sequence?db=%s&amp;chrom=chrM</em></li>\n", urlPrefix, ucscDb, urlPrefix, ucscDb);
 hPrintf("<li><a href='%s/getData/sequence?db=%s&amp;chrom=chrM&amp;start=0&amp;end=128' target=_blank>get sequence from specified database, chromosome with start,end coordinates</a> <em>%s/getData/sequence?db=%s&amp;chrom=chrM&amp;start=0&amp;end=128</em></li>\n", urlPrefix, ucscDb, urlPrefix, ucscDb);
 hPrintf("<li><a href='%s/getData/track?db=%s&amp;track=gold' target=_blank>get entire track data from specified database and track name (gold == Assembly)</a> <em>%s/getData/track?db=%s&amp;track=gold</em></li>\n", urlPrefix, ucscDb, urlPrefix, ucscDb);
 hPrintf("<li><a href='%s/getData/track?db=%s&amp;chrom=chrM&amp;track=gold' target=_blank>get track data from specified database, chromosome and track name (gold == Assembly)</a> <em>%s/getData/track?db=%s&amp;chrom=chrM&amp;track=gold</em></li>\n", urlPrefix, ucscDb, urlPrefix, ucscDb);
 hPrintf("<li><a href='%s/getData/track?db=%s&amp;chrom=chrI&amp;track=gold&amp;start=107680&amp;end=186148' target=_blank>get track data from specified database, chromosome, track name, start and end coordinates</a> <em>%s/getData/track?db=%s&amp;chrom=chrI&amp;track=gold&amp;start=107680&amp;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&amp;genome=hg19&amp;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&amp;genome=hg19&amp;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&amp;genome=_araTha1&amp;chrom=chrCp&amp;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&amp;genome=_araTha1&amp;chrom=chrCp&amp;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&amp;genome=_araTha1&amp;chrom=chr1&amp;track=assembly_&amp;start=0&amp;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&amp;genome=_araTha1&amp;chrom=chr1&amp;track=assembly_&amp;start=0&amp;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&amp;genome=_araTha1&amp;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&amp;genome=_araTha1&amp;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&amp;genome=_araTha1&amp;chrom=chrMt&amp;track=gc5Base_&amp;start=143600&amp;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&amp;genome=_araTha1&amp;chrom=chrMt&amp;track=gc5Base&amp;start=143600&amp;end=143685</em></li>\n", urlPrefix, urlPrefix);
 hPrintf("<li><a href='%s/getData/track?db=%s&amp;chrom=chrI&amp;track=gc5BaseBw&amp;start=107680&amp;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&amp;chrom=chrI&amp;track=gc5BaseBw&amp;start=107680&amp;end=186148</em></li>\n", urlPrefix, defaultDb, urlPrefix, defaultDb);
 hPrintf("<li><a href='%s/getData/track?db=%s&amp;chrom=chrII&amp;track=ncbiRefSeqOther&amp;start=14334626&amp;end=14979625' target=_blank>get bigBed track data from specified database, chromosome, track name, start and end coordinates</a> <em>%s/getData/track?db=%s&amp;chrom=chrII&amp;track=ncbiRefSeqOther&amp;start=14334626&amp;end=14979625</em></li>\n", urlPrefix, defaultDb, urlPrefix, defaultDb);
 hPrintf("<li><a href='%s/getData/track?db=%s&amp;chrom=chr1&amp;track=wgEncodeAwgDnaseDuke8988tUniPk&amp;start=14334626&amp;end=14979625' target=_blank>get narrowPeak track data from specified database, chromosome, track name, start and end coordinates</a> <em>%s/getData/track?db=%s&amp;chrom=chr1&amp;track=wgEncodeAwgDnaseDuke8988tUniPk&amp;start=14334626&amp;end=14979625</em></li>\n", urlPrefix, "hg19", urlPrefix, "hg19");
 hPrintf("<li><a href='%s/getData/track?db=%s&amp;chrom=chr1&amp;track=wgEncodeBroadHistoneOsteoP300kat3bPk&amp;start=14334626&amp;end=14979625' target=_blank>get broadPeak track data from specified database, chromosome, track name, start and end coordinates</a> <em>%s/getData/track?db=%s&amp;chrom=chr1&amp;track=wgEncodeBroadHistoneOsteoP300kat3bPk&amp;start=14334626&amp;end=14979625</em></li>\n", urlPrefix, "hg19", urlPrefix, "hg19");
 
 hPrintf("</ol>\n");
 
 hPrintf("<h2>Example URLs to generate errors:</h2>\n");
 hPrintf("<ol>\n");
 hPrintf("<li><a href='%s/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt&amp;genome=_araTha1&amp;chrom=chrI&amp;track=assembly_&amp;start=0&amp;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&amp;genome=_araTha1&amp;chrom=chrI&amp;track=assembly_&amp;start=0&amp;end=14309681</em></li>\n", urlPrefix, urlPrefix);
 hPrintf("</ol>\n");
 }	/*	static void showExamples()	*/
 
 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 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;
 
 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))
     {
     setupFunctionHash();
     struct hashEl *hel = parsePathInfo(pathInfo, words);
     /* verify valid API command */
 
     if (hel)	/* have valid command */
 	{
         hPrintDisable();
 	puts("Content-Type:application/json");
 	puts("\n");
         void (*apiFunction)(char **) = hel->val;
         (*apiFunction)(words);
 	return;
 	}
      else
 	commandError = TRUE;
     }
 
 puts("Content-Type:text/html");
 puts("\n");
 
-(void) hubPublicLoadAll();
+(void) hubPublicDbLoadAll();
 
 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 JSON API interface");
 
 if (debug)
     {
     char *envVar = getenv("BROWSER_HOST");
     hPrintf("<ul>\n");
     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);
     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)
   {
   hPrintf("<h3>ERROR: no such command: '%s/%s' for endpoint '%s'</h3>", words[0], words[1], pathInfo);
   }
 
 long lastTime = clock1000();
 struct trackHub *hub = errCatchTrackHubOpen(urlInput);
 if (measureTiming)
     {
     long thisTime = clock1000();
     if (debug)
        hPrintf("<em>hub open time: %ld millis</em><br>\n", thisTime - lastTime);
     }
 
 // hPrintf("<h3>ucscDb: '%s'</h2>\n", ucscDb);
 
 struct trackHubGenome *hubGenome = hub->genomeList;
 
 introductionText();
 
 showExamples(urlInput, hubGenome, ucscDb);
 
 if (debug)
     showCartDump();
 
 hPrintf("<h2>Explore hub or database assemblies and tracks</h2>\n");
 
 // hPrintf("<form action='%s' name='hubApiUrl' id='hubApiUrl' method='GET'>\n\n", "../cgi-bin/hubApi");
 hPrintf("<form action='%s' name='hubApiUrl' id='hubApiUrl' method='GET'>\n\n", urlPrefix);
 
 #ifdef NOT
 if (isEmpty(urlPrefix))
     {
     char *scriptUri = getenv("SCRIPT_URI");
     hPrintf("<form action='%s' name='hubApiUrl' id='hubApiUrl' method='GET'>\n\n", scriptUri);
     }
 else
     hPrintf("<form action='%s' name='hubApiUrl' id='hubApiUrl' method='GET'>\n\n", urlPrefix);
 #endif
 
 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", otherHubUrl);
 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");
 
 hPrintf("<p>\n");
 if (sameWord("go", goUcscDb))	/* requested UCSC db track list */
     {
     tracksForUcscDb(ucscDb);
     }
 else
     {
     hPrintf("<h4>Examine %s at: %s</h4>\n", sameWord("go",goPublicHub) ? "public hub" : "other hub", urlInput);
     hPrintf("<ul>\n");
     hPrintf("<li>%s</li>\n", hub->shortLabel);
     hPrintf("<li>%s</li>\n", hub->longLabel);
     if (isNotEmpty(hub->defaultDb))
         hPrintf("<li>%s - default database</li>\n", hub->defaultDb);
     hPrintf("</ul>\n");
 
     if (hub->genomeList)
 	(void) genomeList(hub, NULL, NULL);	/* ignore returned list */
     }
 
 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("</p>\n");
 
 cartWebEnd();
 }	/*	void doMiddle(struct cart *theCart)	*/
 
 /* Null terminated list of CGI Variables we don't want to save
  * permanently. */
 static char *excludeVars[] = {"Submit", "submit", "goOtherHub", "goPublicHub", "goUcscDb", "ucscGenomes", "publicHubs", 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;
 }