813ac14a66f960ceb9a2c8e56054664181c8d35b
hiram
  Sun Jan 27 21:20:09 2019 -0800
output valid json for public hub listing refs #18869

diff --git src/hg/hubApi/hubApi.c src/hg/hubApi/hubApi.c
index b3bc86e..b1c2bb2 100644
--- src/hg/hubApi/hubApi.c
+++ src/hg/hubApi/hubApi.c
@@ -1,476 +1,698 @@
 /* hubApi - access mechanism to hub data resources. */
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "jksql.h"
 #include "htmshell.h"
 #include "web.h"
 #include "cheapcgi.h"
 #include "cart.h"
 #include "hui.h"
 #include "udc.h"
 #include "knetUdc.h"
 #include "genbank.h"
 #include "trackHub.h"
 #include "hgConfig.h"
 #include "hCommon.h"
 #include "hPrint.h"
 #include "bigWig.h"
 #include "hubConnect.h"
 #include "obscure.h"
 #include "errCatch.h"
 #include "vcf.h"
 #include "bedTabix.h"
 #include "bamFile.h"
 
 #ifdef USE_HAL
 #include "halBlockViz.h"
 #endif
 
+/*
++------------------+------------------+------+-----+---------+-------+
+| 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    |       |
++------------------+------------------+------+-----+---------+-------+
+*/
+
+struct hubPublic
+/* Table of public track data hub connections. */
+    {
+    struct hubPublic *next;  /* Next in singly linked list. */
+    char *hubUrl;	/* URL to hub.ra file */
+    char *shortLabel;	/* Hub short label. */
+    char *longLabel;	/* Hub long label. */
+    char *registrationTime;	/* Time first registered */
+    unsigned dbCount;	/* Number of databases hub has data for. */
+    char *dbList;	/* Comma separated list of databases. */
+    char *descriptionUrl;	/* URL to description HTML */
+    };
+
 /* Global Variables */
 struct cart *cart;             /* CGI and other variables */
 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 struct slName *publicHubShortLabels = NULL;
 static char **shortLabels = NULL;	/* public hub short labels in array */
 static int publicHubCount = 0;
+static struct hubPublic *publicHubList = NULL;
 static char *defaultHub = "Plants";
 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 boolean jsonOutput = FALSE;	/* turns on when pathInfo present */
+
+/* ######################################################################### */
+
+/* json output needs to encode special characters in strings:
+  " - quotation mark
+  / - forward slash
+  \ - back slash
+  \n - new line
+  \r - carriage return
+  \t - tab
+*/
+
+static char* jsonEscape(char *jsonString)
+/* escape any of the special characters in the string for json output */
+{
+if (NULL == jsonString)
+    return NULL;
+/* going to alternate the result string between a and b so the returned
+ * string from replaceChars() can be freemem'ed
+ * returned result from here should also be freemem'ed
+ */
+static char *a = NULL;
+static char *b = NULL;
+/* replace back slash first since the other encodings will be adding
+ * the back slash
+ */
+a = replaceChars(jsonString, "\\", "\\\\");	/* \ -> \\ */
+b = replaceChars(a, "\"", "\\\"");	/* " -> \" */
+freeMem(a);
+a = replaceChars(b, "/", "\\/");	/* / -> \/ */
+freeMem(b);
+b = replaceChars(a, "\n", "\\\n");	/* \n -> \\n */
+freeMem(a);
+a = replaceChars(b, "\r", "\\\r");	/* \r -> \\r */
+freeMem(b);
+b = replaceChars(a, "\t", "\\\t");	/* \t -> \\t */
+return b;
+}
+
+static void hubPublicJsonOutput(struct hubPublic *el, FILE *f) 
+/* Print out hubPublic element in JSON format. */
+{
+fputc('{',f);
+fputc('"',f);
+fprintf(f,"hubUrl");
+fputc('"',f);
+fputc(':',f);
+fputc('"',f);
+char *a = jsonEscape(el->hubUrl);
+fprintf(f, "%s", a);
+freeMem(a);
+fputc('"',f);
+fputc(',',f);
+fputc('"',f);
+fprintf(f,"shortLabel");
+fputc('"',f);
+fputc(':',f);
+fputc('"',f);
+a = jsonEscape(el->shortLabel);
+fprintf(f, "%s", a);
+freeMem(a);
+fputc('"',f);
+fputc(',',f);
+fputc('"',f);
+fprintf(f,"longLabel");
+fputc('"',f);
+fputc(':',f);
+fputc('"',f);
+a = jsonEscape(el->longLabel);
+fprintf(f, "%s", a);
+freeMem(a);
+fputc('"',f);
+fputc(',',f);
+fputc('"',f);
+fprintf(f,"registrationTime");
+fputc('"',f);
+fputc(':',f);
+fputc('"',f);
+a = jsonEscape(el->registrationTime);
+fprintf(f, "%s", a);
+freeMem(a);
+fputc('"',f);
+fputc(',',f);
+fputc('"',f);
+fprintf(f,"dbCount");
+fputc('"',f);
+fputc(':',f);
+fprintf(f, "%u", el->dbCount);
+fputc(',',f);
+fputc('"',f);
+fprintf(f,"dbList");
+fputc('"',f);
+fputc(':',f);
+fputc('"',f);
+a = jsonEscape(el->dbList);
+fprintf(f, "%s", a);
+freeMem(a);
+fputc('"',f);
+fputc(',',f);
+fputc('"',f);
+fprintf(f,"descriptionUrl");
+fputc('"',f);
+fputc(':',f);
+a = jsonEscape(el->descriptionUrl);
+if (isEmpty(a))
+    fprintf(f, "%s", "null");
+else
+    {
+    fputc('"',f);
+    fprintf(f, "%s", a);
+    fputc('"',f);
+}
+freeMem(a);
+fputc('}',f);
+}
+
+static int publicHubCmpCase(const void *va, const void *vb)
+/* Compare two slNames, ignore case. */
+{
+const struct hubPublic *a = *((struct hubPublic **)va);
+const struct hubPublic *b = *((struct hubPublic **)vb);
+return strcasecmp(a->shortLabel, b->shortLabel);
+}
+
+static void publicHubSortCase(struct hubPublic **pList)
+/* Sort slName list, ignore case. */
+{
+slSort(pList, publicHubCmpCase);
+}
+
+static struct hubPublic *hubPublicLoad(char **row)
+/* Load a hubPublic from row fetched with select * from hubPublic
+ * from database.  Dispose of this with hubPublicFree(). */
+{
+struct hubPublic *ret;
+
+AllocVar(ret);
+ret->hubUrl = cloneString(row[0]);
+ret->shortLabel = cloneString(row[1]);
+ret->longLabel = cloneString(row[2]);
+ret->registrationTime = cloneString(row[3]);
+ret->dbCount = sqlUnsigned(row[4]);
+ret->dbList = cloneString(row[5]);
+// if (row[6])
+    ret->descriptionUrl = cloneString(row[6]);
+// else
+//     ret->descriptionUrl = cloneString("");
+return ret;
+}
+
+static struct hubPublic *hubPublicLoadAll()
+{
+struct hubPublic *list = NULL;
+struct sqlConnection *conn = hConnectCentral();
+// Build a query to find all public hub URL's
+struct dyString *query = sqlDyStringCreate("select * from %s",
+                                           hubPublicTableName());
+struct sqlResult *sr = sqlGetResult(conn, query->string);
+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;
+}
+
+#ifdef NOT
+static void startHtml(char *title)
+{
+printf ("<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01 Transitional//EN\" \"http://www.w3.org/TR/html4/loose.dtd\">\n<html>\n<head><title>%s</title></head><body>\n", title);
+}
+
+static void endHtml()
+{
+printf ("</body></html>\n");
+}
+#endif
 
 static boolean timeOutReached()
 {
 long nowTime = clock1000();
 timedOut = FALSE;
 if ((nowTime - enteredMainTime) > (1000 * timeOutSeconds))
     timedOut= TRUE;
 return timedOut;
 }
 
 static void trackSettings(struct trackDb *tdb)
 /* process the settingsHash for a track */
 {
 hPrintf("    <ul>\n");
 struct hashEl *hel;
 struct hashCookie hc = hashFirst(tdb->settingsHash);
 while ((hel = hashNext(&hc)) != NULL)
     {
     if (isEmpty((char *)hel->val))
 	hPrintf("    <li>%s : &lt;empty&gt;</li>\n", hel->name);
     else
 	hPrintf("    <li>%s : '%s'</li>\n", hel->name, (char *)hel->val);
     }
 hPrintf("    </ul>\n");
 }
 
 static int bbiBriefMeasure(char *type, char *bigDataUrl, char *bigDataIndex, long *chromCount, long *itemCount, struct dyString *errors)
 /* check a bigDataUrl to find chrom count and item count */
 {
 int retVal = 0;
 *chromCount = 0;
 *itemCount = 0;
 struct errCatch *errCatch = errCatchNew();
 if (errCatchStart(errCatch))
     {
     if (startsWithWord("bigNarrowPeak", type)
             || startsWithWord("bigBed", type)
             || startsWithWord("bigGenePred", type)
             || startsWithWord("bigPsl", type)
             || startsWithWord("bigChain", type)
             || startsWithWord("bigMaf", type)
             || startsWithWord("bigBarChart", type)
             || startsWithWord("bigInteract", type))
         {
         struct bbiFile *bbi = NULL;
         bbi = bigBedFileOpen(bigDataUrl);
         struct bbiChromInfo *chromList = bbiChromList(bbi);
         *chromCount = slCount(chromList);
         *itemCount = bigBedItemCount(bbi);
         bbiFileClose(&bbi);
         }
     else if (startsWithWord("bigWig", type))
         {
         struct bbiFile *bwf = bigWigFileOpen(bigDataUrl);
         struct bbiChromInfo *chromList = bbiChromList(bwf);
         struct bbiSummaryElement sum = bbiTotalSummary(bwf);
         *chromCount = slCount(chromList);
         *itemCount = sum.validCount;
         bbiFileClose(&bwf);
         }
     else if (startsWithWord("vcfTabix", type))
         {
         struct vcfFile *vcf = vcfTabixFileAndIndexMayOpen(bigDataUrl, bigDataIndex, NULL, 0, 0, 1, 1);
         if (vcf == NULL)
 	    {
 	    dyStringPrintf(errors, "Could not open %s and/or its tabix index (.tbi) file.  See http://genome.ucsc.edu/goldenPath/help/vcf.html", bigDataUrl);
             retVal = 1;
 	    }
         else
 	    vcfFileFree(&vcf);
         }
     else if (startsWithWord("bam", type))
         {
 	bamFileAndIndexMustExist(bigDataUrl, bigDataIndex);
         }
     else if (startsWithWord("longTabix", type))
         {
 	struct bedTabixFile *btf = bedTabixFileMayOpen(bigDataUrl, NULL, 0, 0);
 	if (btf == NULL)
 	    {
 	    dyStringPrintf(errors, "Couldn't open %s and/or its tabix index (.tbi) file.", bigDataUrl);
             retVal = 1;
 	    }
 	else
 	    bedTabixFileClose(&btf);
         }
 #ifdef USE_HAL
     else if (startsWithWord("halSnake", type))
         {
 	char *errString;
 	int handle = halOpenLOD(bigDataUrl, &errString);
 	if (handle < 0)
 	    {
 	    dyStringPrintf(errors, "HAL open error: %s", errString);
             retVal = 1;
 	    }
 	if (halClose(handle, &errString) < 0)
 	    {
 	    dyStringPrintf(errors, "HAL close error: %s", errString);
 	    retVal = 1;
 	    }
         }
 #endif
     else
         {
 	dyStringPrintf(errors, "unrecognized type %s", type);
         retVal = 1;
         }
 
     }
 errCatchEnd(errCatch);
 if (errCatch->gotError)
     {
     retVal = 1;
     dyStringPrintf(errors, "%s", errCatch->message->string);
     }
 errCatchFree(&errCatch);
 
 return retVal;
 }	/* static int bbiBriefMeasure() */
 
 static void trackList(struct trackDb *tdb, struct trackHubGenome *genome)
 /* process the track list to show all tracks */
 {
 if (tdb)
     {
     struct hash *countTracks = hashNew(0);
     hPrintf("    <ul>\n");
     struct trackDb *track = tdb;
     for ( ; track; track = track->next )
 	{
         char *bigDataUrl = hashFindVal(track->settingsHash, "bigDataUrl");
       char *compositeTrack = hashFindVal(track->settingsHash, "compositeTrack");
 	char *superTrack = hashFindVal(track->settingsHash, "superTrack");
         boolean depthSearch = cartUsualBoolean(cart, "depthSearch", FALSE);
         if (compositeTrack)
            hashIncInt(countTracks, "composite container");
         else if (superTrack)
            hashIncInt(countTracks, "superTrack container");
 	else if (isEmpty(track->type))
            hashIncInt(countTracks, "no type specified");
 	else
            hashIncInt(countTracks, track->type);
         if (depthSearch && bigDataUrl)
 	    {
 	    char *bigDataIndex = NULL;
 	    char *relIdxUrl = trackDbSetting(tdb, "bigDataIndex");
 	    if (relIdxUrl != NULL)
 		bigDataIndex = trackHubRelativeUrl(genome->trackDbFile, relIdxUrl);
 
 	    long chromCount = 0;
 	    long itemCount = 0;
 	    struct dyString *errors = newDyString(1024);
 	    int retVal = bbiBriefMeasure(track->type, bigDataUrl, bigDataIndex, &chromCount, &itemCount, errors);
             if (retVal)
 		{
 		    hPrintf("    <li>%s : %s : <font color='red'>ERROR: %s</font></li>\n", track->track, track->type, errors->string);
 		}
 	    else
 		{
 		if (startsWithWord("bigBed", track->type))
 		    hPrintf("    <li>%s : %s : %ld chroms : %ld item count</li>\n", track->track, track->type, chromCount, itemCount);
 		else if (startsWithWord("bigWig", track->type))
 		    hPrintf("    <li>%s : %s : %ld chroms : %ld bases covered</li>\n", track->track, track->type, chromCount, itemCount);
 		else
 		    hPrintf("    <li>%s : %s : %ld chroms : %ld count</li>\n", track->track, track->type, chromCount, itemCount);
 		}
 	    }
         else
 	    {
 	    if (compositeTrack)
 		hPrintf("    <li>%s : %s : composite track container</li>\n", track->track, track->type);
 	    else if (superTrack)
 		hPrintf("    <li>%s : %s : superTrack container</li>\n", track->track, track->type);
 	    else if (! depthSearch)
 		hPrintf("    <li>%s : %s : %s</li>\n", track->track, track->type, bigDataUrl);
             else
 		hPrintf("    <li>%s : %s</li>\n", track->track, track->type);
 	    }
         if (allTrackSettings)
             trackSettings(track); /* show all settings */
 	if (timeOutReached())
 	    break;
 	}	/*	for ( ; track; track = track->next )	*/
     hPrintf("    <li>%d different track types</li>\n", countTracks->elCount);
     if (countTracks->elCount)
 	{
         hPrintf("        <ul>\n");
         struct hashEl *hel;
         struct hashCookie hc = hashFirst(countTracks);
         while ((hel = hashNext(&hc)) != NULL)
 	    {
             int prevCount = ptToInt(hashFindVal(trackCounter, hel->name));
 	    totalTracks += ptToInt(hel->val);
 	    hashReplace(trackCounter, hel->name, intToPt(prevCount + ptToInt(hel->val)));
 	    hPrintf("        <li>%d - %s</li>\n", ptToInt(hel->val), hel->name);
 	    }
         hPrintf("        </ul>\n");
 	}
     hPrintf("    </ul>\n");
     }
 }	/*	static void trackList(struct trackDb *tdb)	*/
 
 static void assemblySettings(struct trackHubGenome *genome)
 /* display all the assembly 'settingsHash' */
 {
 hPrintf("    <ul>\n");
 struct hashEl *hel;
 struct hashCookie hc = hashFirst(genome->settingsHash);
 while ((hel = hashNext(&hc)) != NULL)
     {
     hPrintf("    <li>%s : %s</li>\n", hel->name, (char *)hel->val);
     if (sameWord("trackDb", hel->name))	/* examine the trackDb structure */
 	{
         struct trackDb *tdb = trackHubTracksForGenome(genome->trackHub, genome);
 	trackList(tdb, genome);
         }
     if (timeOutReached())
 	break;
     }
 hPrintf("    </ul>\n");
 }
 
 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</h4>\n");
 hPrintf("<ul>\n");
 long lastTime = clock1000();
 for ( ; genome; genome = genome->next )
     {
     ++totalAssemblyCount;
     if (genome->organism)
 	{
 	hPrintf("<li>%s - %s - %s</li>\n", genome->organism, genome->name, genome->description);
 	}
     else
 	{	/* can there be a description when organism is empty ? */
 	hPrintf("<li>%s</li>\n", genome->name);
 	}
     if (genome->settingsHash)
 	assemblySettings(genome);
     if (measureTiming)
 	{
 	long thisTime = clock1000();
 	hPrintf("<em>processing time %s: %ld millis</em><br>\n", genome->name, thisTime - lastTime);
 	}
     if (timeOutReached())
 	break;
     }
 if (trackCounter->elCount)
     {
     hPrintf("    <li>total assembly count: %ld</li>\n", totalAssemblyCount);
     hPrintf("    <li>%ld total tracks counted, %d different track types:</li>\n", totalTracks, trackCounter->elCount);
     hPrintf("    <ul>\n");
     struct hashEl *hel;
     struct hashCookie hc = hashFirst(trackCounter);
     while ((hel = hashNext(&hc)) != NULL)
 	{
 	hPrintf("    <li>%d - %s - total</li>\n", ptToInt(hel->val), hel->name);
 	}
     hPrintf("    </ul>\n");
     }
 hPrintf("</ul>\n");
 }
 
-static void getPublicHubList()
-/* obtain shortLabel from all public hubs */
-{
-struct sqlConnection *conn = hConnectCentral();
-// Build a query to find all public hub URL's
-struct dyString *query = sqlDyStringCreate("select shortLabel from %s",
-                                           hubPublicTableName());
-struct sqlResult *sr = sqlGetResult(conn, query->string);
-char **row;
-while ((row = sqlNextRow(sr)) != NULL)
-    {
-    slNameStore(&publicHubShortLabels, row[0]);
-    }
-sqlFreeResult(&sr);
-slNameSortCase(&publicHubShortLabels);
-int listSize = slCount(publicHubShortLabels);
-AllocArray(shortLabels, listSize);
-struct slName *el = publicHubShortLabels;
-int i = 0;
-for ( ; el != NULL; el = el->next )
-    {
-    shortLabels[i++] = el->name;
-    ++publicHubCount;
-    }
-}	/*	static void getPublicHubList()	*/
-
 static char *urlFromShortLabel(char *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);
 }
 
+void jsonPublicHubs()
+{
+struct hubPublic *el = publicHubList;
+hPrintf("{\"publicHubs\":[");
+for ( ; el != NULL; el = el->next )
+    {
+    hubPublicJsonOutput(el, stdout);
+    if (el->next)
+       hPrintf(",");
+    }
+hPrintf("]}\n");
+}
+
 void doMiddle(struct cart *theCart)
 /* Set up globals and make web page */
 {
-getPublicHubList();	/* populates slName publicHubShortLabels	*/
+// struct hubPublic *hubList = hubPublicLoadAll();
+publicHubList = hubPublicLoadAll();
 cart = theCart;
 measureTiming = hPrintStatus() && isNotEmpty(cartOptionalString(cart, "measureTiming"));
 measureTiming = TRUE;
 char *database = NULL;
 char *genome = NULL;
 
-
 getDbAndGenome(cart, &database, &genome, oldVars);
 initGenbankTableNames(database);
 
 char *docRoot = cfgOptionDefault("browser.documentRoot", DOCUMENT_ROOT);
 
 int timeout = cartUsualInt(cart, "udcTimeout", 300);
 if (udcCacheTimeout() < timeout)
     udcSetCacheTimeout(timeout);
 knetUdcInstall();
 
 char *pathInfo = getenv("PATH_INFO");
 
-if ((NULL == pathInfo) || strlen(pathInfo) < 1) {
+if ((NULL == pathInfo) || strlen(pathInfo) < 1)
+    {
     pathInfo = cloneString("noPathInfo");
     }
+else
+    {
+    jsonOutput = TRUE;
+    }
 
+if (jsonOutput)
+    {
+//    startHtml("json output example");
+//    hPrintf("<br><a href='http://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi'>return to hubApi</a><br><br>\n");
+    jsonPublicHubs();
+//    endHtml();
+    return;
+    }
 cartWebStart(cart, database, "access mechanism to hub data resources");
 
 char *goOtherHub = cartUsualString(cart, "goOtherHub", defaultHub);
 char *otherHubUrl = cartUsualString(cart, "urlHub", defaultHub);
 char *goPublicHub = cartUsualString(cart, "goPublicHub", defaultHub);
 char *hubDropDown = cartUsualString(cart, "publicHubs", defaultHub);
 char *urlDropDown = urlFromShortLabel(hubDropDown);
 char *urlInput = urlDropDown;	/* assume public hub */
 if (sameWord("go", goOtherHub))	/* requested other hub URL */
     urlInput = otherHubUrl;
 
+hPrintf("<h2>Example URLs to return json data structures:</h2>\n");
+hPrintf("<ul>\n");
+hPrintf("<li><a href='/cgi-bin/hubApi/list/publicHubs'>list public hubs</a> <em>/cgi-bin/hubApi/list/publicHubs</em></li>\n");
+hPrintf("</ul>\n");
 long lastTime = clock1000();
 struct trackHub *hub = trackHubOpen(urlInput, "");
 if (measureTiming)
     {
     long thisTime = clock1000();
     hPrintf("<em>hub open time: %ld millis</em><br>\n", thisTime - lastTime);
     }
 
-hPrintf("<h2>cart dump</h2>");
+hPrintf("<h4>cart dump</h4>");
 hPrintf("<pre>\n");
 cartDump(cart);
 hPrintf("</pre>\n");
 
 hPrintf("<form action='%s' name='hubApiUrl' id='hubApiUrl' method='GET'>\n\n", "../cgi-bin/hubApi");
 
 hPrintf("<b>Select public hub:&nbsp;</b>");
 #define JBUFSIZE 2048
 char javascript[JBUFSIZE];
 struct slPair *events = NULL;
 safef(javascript, sizeof(javascript), "this.lastIndex=this.selectedIndex;");
 slPairAdd(&events, "focus", cloneString(javascript));
 #define SMALLBUF 256
 // char class[SMALLBUF];
 // safef(class, sizeof(class), "viewDD normalText %s", "class");
 
 cgiMakeDropListClassWithIdStyleAndJavascript("publicHubs", "publicHubs",
     shortLabels, publicHubCount, hubDropDown, NULL, "width: 400px", events);
 
 hWrites("&nbsp;");
 hButton("goPublicHub", "go");
 
 hPrintf("<br>Or, enter a hub URL:&nbsp;");
 hPrintf("<input type='text' name='urlHub' id='urlHub' size='60' value='%s'>\n", urlInput);
 hWrites("&nbsp;");
 hButton("goOtherHub", "go");
 
 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>URL: %s - %s<br>\n", urlInput, sameWord("go",goPublicHub) ? "public hub" : "other hub");
 hPrintf("name: %s<br>\n", hub->shortLabel);
 hPrintf("description: %s<br>\n", hub->longLabel);
 hPrintf("default db: '%s'<br>\n", isEmpty(hub->defaultDb) ? "(none available)" : hub->defaultDb);
 printf("pathInfo:'%s'<br>\ndocRoot:'%s'<br>\n", pathInfo, docRoot);
 
 if (hub->genomeList)
     genomeList(hub);
 
 hPrintf("</p>\n");
 
 if (timedOut)
     hPrintf("<h1>Reached time out %ld seconds</h1>", timeOutSeconds);
 if (measureTiming)
     hPrintf("<em>Overall total time: %ld millis</em><br>\n", clock1000() - enteredMainTime);
 
 cartWebEnd();
 }	/*	void doMiddle(struct cart *theCart)	*/
 
 /* Null terminated list of CGI Variables we don't want to save
  * permanently. */
 char *excludeVars[] = {"Submit", "submit", NULL,};
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 enteredMainTime = clock1000();
 cgiSpoof(&argc, argv);
 measureTiming = TRUE;
 verboseTimeInit();
 trackCounter = hashNew(0);
 cartEmptyShell(doMiddle, hUserCookie(), excludeVars, oldVars);
 return 0;
 }