aa487ff67c04e2961d0ff4b5ba1d4568fa1d6f17
hiram
  Fri Mar 15 15:51:40 2019 -0700
now using source tree version tag and alpha install rule to cgi-bin-api and cleaned up html errors refs #18869

diff --git src/hg/hubApi/hubApi.c src/hg/hubApi/hubApi.c
index 6f40732..4cbfffb 100644
--- src/hg/hubApi/hubApi.c
+++ src/hg/hubApi/hubApi.c
@@ -4,30 +4,31 @@
 /*
 +------------------+------------------+------+-----+---------+-------+
 | 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 = TRUE;
 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;
@@ -97,36 +98,36 @@
  *   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("        <ul>\n");
+    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>\n");
+    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))
@@ -154,58 +155,58 @@
     }
 else if (isEmpty(tdb->type))
     hashIncInt(countTracks, "no type specified");
 else
     {
     hashIncInt(countTracks, stripType);
     hashIncInt(countTracks, "track count");
     }
 freeMem(stripType);
 // showCounts(countTracks);
 }
 
 static void trackSettings(struct trackDb *tdb, struct hash *countTracks)
 /* process the settingsHash for a trackDb, recursive when subtracks */
 {
-hPrintf("    <ul>\n");
+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;
     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>\n");
+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 */
 {
 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)
@@ -326,99 +327,100 @@
 else
     {
     if (compositeContainer)
         hPrintf("    <li>%s : %s : composite track container</li>\n", tdb->track, tdb->type);
     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)
         hPrintf("    <li>%s : %s : %s</li>\n", tdb->track, tdb->type, bigDataUrl);
     else
         hPrintf("    <li>%s : %s</li>\n", tdb->track, tdb->type);
     }
 if (allTrackSettings)
     {
-    hPrintf("    <ul>\n");
+    hPrintf("    <li><ul>\n");
     trackSettings(tdb, countTracks); /* show all settings */
-    hPrintf("    </ul>\n");
+    hPrintf("    </ul></li>\n");
     }
 return;
 }	/*	static void countOneTdb(struct trackDb *tdb,
 	 *	    char *bigDataIndex, struct hash *countTracks)
 	 */
 
 static void hubTrackList(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);
-    hPrintf("    <ul>\n");
     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(tdb, bigDataIndex, countTracks);
 	if (timeOutReached())
 	    break;
 	}	/*	for ( tdb = topTrackDb; tdb; tdb = tdb->next )	*/
     hPrintf("    <li>%d different track types</li>\n", countTracks->elCount);
     /* add this single genome count to the overall multi-genome counts */
     if (countTracks->elCount)
 	{
-        hPrintf("        <ol>\n");
+        hPrintf("        <li><ol>\n");
 	struct hashEl *hel, *helList = hashElListHash(countTracks);
 	slSort(&helList, hashElCmpIntValDesc);
 	for (hel = helList; hel; hel = hel->next)
 	    {
             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)));
 	    hPrintf("        <li>%d - %s</li>\n", ptToInt(hel->val), hel->name);
 	    }
-        hPrintf("        </ol>\n");
+        hPrintf("        </ol></li>\n");
 	}
-    hPrintf("    </ul>\n");
     }
 else
     hPrintf("    <li>no trackTopDb</li>\n");
+
+hPrintf("    </ul><li>\n");
 }	/*	static struct trackDb *hubTrackList()	*/
 
 static struct trackDb *assemblySettings(struct trackHubGenome *genome)
 /* display all the assembly 'settingsHash' */
 {
 struct trackDb *tdb = obtainTdb(genome, NULL);
 
-hPrintf("    <ul>\n");
+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);
         }
     if (timeOutReached())
 	break;
     }
-hPrintf("    </ul>\n");
+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;
 
@@ -437,47 +439,47 @@
     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);
     if (dbTrackList)
 	*dbTrackList = tdb;
     if (measureTiming)
 	{
 	long thisTime = clock1000();
-	hPrintf("<em>processing time %s: %ld millis</em><br>\n", genome->name, thisTime - lastTime);
+	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("    <ol>\n");
+    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>\n");
+    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
@@ -518,54 +520,75 @@
 }
 
 static struct hash *apiFunctionHash = NULL;
 
 static void setupFunctionHash()
 /* initialize the apiFunctionHash */
 {
 if (apiFunctionHash)
     return;	/* already done */
 
 apiFunctionHash = hashNew(0);
 hashAdd(apiFunctionHash, "list", &apiList);
 hashAdd(apiFunctionHash, "getData", &apiGetData);
 }
 
-static void apiFunctionSwitch(char *pathInfo)
+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;
+}
+
+#ifdef NOT
+static void apiFunctionSwitch(struct hashEl *hel, char *words[MAX_PATH_INFO])
 /* given a pathInfo string: /command/subCommand/etc...
  *  parse that and decide on which function to acll
  */
 {
 hPrintDisable();	/* turn off all normal HTML output, doing JSON output */
 
 /* the leading slash has been removed from the pathInfo, therefore, the
  * chop will have the first word in words[0]
  */
+#ifdef NOT
 char *words[MAX_PATH_INFO];/*expect no more than MAX_PATH_INFO number of words*/
 int wordCount = chopByChar(pathInfo, '/', words, ArraySize(words));
 if (wordCount < 2)
     apiErrAbort("unknown endpoint command: '/%s'", pathInfo);
 
 struct hashEl *hel = hashLookup(apiFunctionHash, words[0]);
 if (hel == NULL)
     apiErrAbort("no such command: '%s' for endpoint '/%s'", words[0], pathInfo);
+#endif
 void (*apiFunction)(char **) = hel->val;
 // void (*apiFunction)(char **) = hashMustFindVal(apiFunctionHash, words[0]);
 
 (*apiFunction)(words);
 
 }	/*	static void apiFunctionSwitch(char *pathInfo)	*/
+#endif
 
 static void tracksForUcscDb(char *db)
 /* scan the specified database for all tracks */
 {
 struct hash *countTracks = hashNew(0);
 hPrintf("<p>Tracks in UCSC genome: '%s'<br>\n", db);
 struct trackDb *tdbList = obtainTdb(NULL, db);
 struct trackDb *tdb;
 hPrintf("<ul>\n");
 for (tdb = tdbList; tdb != NULL; tdb = tdb->next )
     {
     countOneTdb(tdb, NULL, countTracks);
     if (timeOutReached())
 	break;
     }
@@ -581,59 +604,61 @@
 	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 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='/cgi-bin/hubApi/list/publicHubs' target=_blank>list public hubs</a> <em>/cgi-bin/hubApi/list/publicHubs</em></li>\n");
-hPrintf("<li><a href='/cgi-bin/hubApi/list/ucscGenomes' target=_blank>list database genomes</a> <em>/cgi-bin/hubApi/list/ucscGenomes</em></li>\n");
-hPrintf("<li><a href='/cgi-bin/hubApi/list/hubGenomes?hubUrl=%s' target=_blank>list genomes from specified hub</a> <em>/cgi-bin/hubApi/list/hubGenomes?hubUrl=%s</em></li>\n", url, url);
-hPrintf("<li><a href='/cgi-bin/hubApi/list/tracks?hubUrl=%s&hubUrl=%s&genome=%s' target=_blank>list tracks from specified hub and genome</a> <em>/cgi-bin/hubApi/list/tracks?hubUrl=%s&genome=%s</em></li>\n", url, url, hubGenome->name, url, hubGenome->name);
-hPrintf("<li><a href='/cgi-bin/hubApi/list/tracks?db=%s' target=_blank>list tracks from specified UCSC database</a> <em>/cgi-bin/hubApi/list/tracks?db=%s</em></li>\n", ucscDb, ucscDb);
-hPrintf("<li><a href='/cgi-bin/hubApi/list/chromosomes?db=%s' target=_blank>list chromosomes from specified UCSC database</a> <em>/cgi-bin/hubApi/list/chromosomes?db=%s</em></li>\n", ucscDb, ucscDb);
-hPrintf("<li><a href='/cgi-bin/hubApi/list/chromosomes?db=%s&track=gap' target=_blank>list chromosomes from specified track from UCSC databaset</a> <em>/cgi-bin/hubApi/list/chromosomes?db=%s&track=gap</em></li>\n", ucscDb, ucscDb);
+hPrintf("<li><a href='/list/publicHubs' target=_blank>list public hubs</a> <em>/list/publicHubs</em></li>\n");
+hPrintf("<li><a href='/list/ucscGenomes' target=_blank>list database genomes</a> <em>/list/ucscGenomes</em></li>\n");
+hPrintf("<li><a href='/list/hubGenomes?hubUrl=%s' target=_blank>list genomes from specified hub</a> <em>/list/hubGenomes?hubUrl=%s</em></li>\n", url, url);
+hPrintf("<li><a href='/list/tracks?hubUrl=%s&amp;hubUrl=%s&amp;genome=%s' target=_blank>list tracks from specified hub and genome</a> <em>/list/tracks?hubUrl=%s&amp;genome=%s</em></li>\n", url, url, hubGenome->name, url, hubGenome->name);
+hPrintf("<li><a href='/list/tracks?db=%s' target=_blank>list tracks from specified UCSC database</a> <em>/list/tracks?db=%s</em></li>\n", ucscDb, ucscDb);
+hPrintf("<li><a href='/list/chromosomes?db=%s' target=_blank>list chromosomes from specified UCSC database</a> <em>/list/chromosomes?db=%s</em></li>\n", ucscDb, ucscDb);
+hPrintf("<li><a href='/list/chromosomes?db=%s&amp;track=gap' target=_blank>list chromosomes from specified track from UCSC databaset</a> <em>/list/chromosomes?db=%s&amp;track=gap</em></li>\n", ucscDb, ucscDb);
 hPrintf("</ol>\n");
 
 hPrintf("<h3>getData functions</h3>\n");
 hPrintf("<ol>\n");
-hPrintf("<li><a href='/cgi-bin/hubApi/getData/sequence?db=%s&chrom=chrM' target=_blank>get sequence from specified database and chromosome</a> <em>/cgi-bin/hubApi/getData/sequence?db=%s&chrom=chrM</em></li>\n", ucscDb, ucscDb);
-hPrintf("<li><a href='/cgi-bin/hubApi/getData/sequence?db=%s&chrom=chrM&start=0&end=128' target=_blank>get sequence from specified database, chromosome with start,end coordinates</a> <em>/cgi-bin/hubApi/getData/sequence?db=%s&chrom=chrM&start=0&end=128</em></li>\n", ucscDb, ucscDb);
-hPrintf("<li><a href='/cgi-bin/hubApi/getData/track?db=%s&track=gold' target=_blank>get entire track data from specified database and track name (gold == Assembly)</a> <em>/cgi-bin/hubApi/getData/track?db=%s&track=gold</em></li>\n", ucscDb, ucscDb);
-hPrintf("<li><a href='/cgi-bin/hubApi/getData/track?db=%s&chrom=chrM&track=gold' target=_blank>get track data from specified database, chromosome and track name (gold == Assembly)</a> <em>/cgi-bin/hubApi/getData/track?db=%s&chrom=chrM&track=gold</em></li>\n", ucscDb, ucscDb);
-hPrintf("<li><a href='/cgi-bin/hubApi/getData/track?db=%s&chrom=chrI&track=gold&start=107680&end=186148' target=_blank>get track data from specified database, chromosome, track name, start and end coordinates</a> <em>/cgi-bin/hubApi/getData/track?db=%s&chrom=chrI&track=gold&start=107680&end=186148</em></li>\n", defaultDb, defaultDb);
-hPrintf("<li><a href='/cgi-bin/hubApi/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt&genome=hg19&track=ultraConserved' target=_blank>get entire track data from specified hub and track name</a> <em>/cgi-bin/hubApi/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt&genome=hg19&track=ultraConserved</em></li>\n");
-hPrintf("<li><a href='/cgi-bin/hubApi/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt&genome=_araTha1&chrom=chrCp&track=assembly_' target=_blank>get track data from specified hub, chromosome and track name (full chromosome)</a> <em>/cgi-bin/hubApi/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt&genome=_araTha1&chrom=chrCp&track=assembly_</em></li>\n");
-hPrintf("<li><a href='/cgi-bin/hubApi/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt&genome=_araTha1&chrom=chr1&track=assembly_&start=0&end=14309681' target=_blank>get track data from specified hub, chromosome, track name, start and end coordinates</a> <em>/cgi-bin/hubApi/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt&genome=_araTha1&chrom=chr1&track=assembly_&start=0&end=14309681</em></li>\n");
-hPrintf("<li><a href='/cgi-bin/hubApi/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt&genome=_araTha1&track=gc5Base_' target=_blank>get all track data from specified hub and track name</a> <em>/cgi-bin/hubApi/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt&genome=_araTha1&track=gc5Base</em></li>\n");
-hPrintf("<li><a href='/cgi-bin/hubApi/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt&genome=_araTha1&chrom=chrMt&track=gc5Base_&start=143600&end=143685' target=_blank>get track data from specified hub, chromosome, track name, start and end coordinates</a> <em>/cgi-bin/hubApi/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt&genome=_araTha1&chrom=chrMt&track=gc5Base&start=143600&end=143685</em></li>\n");
-hPrintf("<li><a href='/cgi-bin/hubApi/getData/track?db=%s&chrom=chrI&track=gc5BaseBw&start=107680&end=186148' target=_blank>get bigWig track data from specified database, chromosome, track name, start and end coordinates</a> <em>/cgi-bin/hubApi/getData/track?db=%s&chrom=chrI&track=gc5BaseBw&start=107680&end=186148</em></li>\n", defaultDb, defaultDb);
-hPrintf("<li><a href='/cgi-bin/hubApi/getData/track?db=%s&chrom=chrII&track=ncbiRefSeqOther&start=14334626&end=14979625' target=_blank>get bigBed track data from specified database, chromosome, track name, start and end coordinates</a> <em>/cgi-bin/hubApi/getData/track?db=%s&chrom=chrII&track=ncbiRefSeqOther&start=14334626&end=14979625</em></li>\n", defaultDb, defaultDb);
+hPrintf("<li><a href='/getData/sequence?db=%s&amp;chrom=chrM' target=_blank>get sequence from specified database and chromosome</a> <em>/getData/sequence?db=%s&amp;chrom=chrM</em></li>\n", ucscDb, ucscDb);
+hPrintf("<li><a href='/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>/getData/sequence?db=%s&amp;chrom=chrM&amp;start=0&amp;end=128</em></li>\n", ucscDb, ucscDb);
+hPrintf("<li><a href='/getData/track?db=%s&amp;track=gold' target=_blank>get entire track data from specified database and track name (gold == Assembly)</a> <em>/getData/track?db=%s&amp;track=gold</em></li>\n", ucscDb, ucscDb);
+hPrintf("<li><a href='/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>/getData/track?db=%s&amp;chrom=chrM&amp;track=gold</em></li>\n", ucscDb, ucscDb);
+hPrintf("<li><a href='/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>/getData/track?db=%s&amp;chrom=chrI&amp;track=gold&amp;start=107680&amp;end=186148</em></li>\n", defaultDb, defaultDb);
+hPrintf("<li><a href='/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>/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt&amp;genome=hg19&amp;track=ultraConserved</em></li>\n");
+hPrintf("<li><a href='/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>/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");
+hPrintf("<li><a href='/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>/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");
+hPrintf("<li><a href='/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>/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt&amp;genome=_araTha1&amp;track=gc5Base</em></li>\n");
+hPrintf("<li><a href='/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>/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");
+hPrintf("<li><a href='/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>/getData/track?db=%s&amp;chrom=chrI&amp;track=gc5BaseBw&amp;start=107680&amp;end=186148</em></li>\n", defaultDb, defaultDb);
+hPrintf("<li><a href='/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>/getData/track?db=%s&amp;chrom=chrII&amp;track=ncbiRefSeqOther&amp;start=14334626&amp;end=14979625</em></li>\n", defaultDb, defaultDb);
+hPrintf("<li><a href='/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>/getData/track?db=%s&amp;chrom=chr1&amp;track=wgEncodeAwgDnaseDuke8988tUniPk&amp;start=14334626&amp;end=14979625</em></li>\n", "hg19", "hg19");
+hPrintf("<li><a href='/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>/getData/track?db=%s&amp;chrom=chr1&amp;track=wgEncodeBroadHistoneOsteoP300kat3bPk&amp;start=14334626&amp;end=14979625</em></li>\n", "hg19", "hg19");
 
 hPrintf("</ol>\n");
 
 hPrintf("<h2>Example URLs to generate errors:</h2>\n");
-hPrintf("<li><a href='/cgi-bin/hubApi/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt&genome=_araTha1&chrom=chrI&track=assembly_&start=0&end=14309681' target=_blank>get track data from specified hub, chromosome, track name, start and end coordinates</a> <em>/cgi-bin/hubApi/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt&genome=_araTha1&chrom=chrI&track=assembly_&start=0&end=14309681</em></li>\n");
 hPrintf("<ol>\n");
+hPrintf("<li><a href='/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>/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");
 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 */
 {
@@ -644,88 +669,112 @@
 char *genome = NULL;
 
 cgiVarSet("ignoreCookie", "1");
 
 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");
+/* nothing on incoming path, then display the WEB page instead */
+if (sameOk("/",pathInfo))
+    pathInfo = NULL;
+
+boolean commandError = FALSE;
+char *words[MAX_PATH_INFO];
 
 if (isNotEmpty(pathInfo))
     {
+    setupFunctionHash();
+    /*expect no more than MAX_PATH_INFO number of words*/
+    struct hashEl *hel = parsePathInfo(pathInfo, words);
+    /* verify valid API command */
+
+    if (hel)	/* have valid command */
+	{
 	puts("Content-Type:application/json");
 	puts("\n");
 	/* skip the first leading slash to simplify chopByChar parsing */
-    pathInfo += 1;
-    setupFunctionHash();
-    apiFunctionSwitch(pathInfo);
+//	pathInfo += 1;
+//	apiFunctionSwitch(hel, words);
+        void (*apiFunction)(char **) = hel->val;
+        (*apiFunction)(words);
 	return;
 	}
+     else
+	commandError = TRUE;
+    }
+
 puts("Content-Type:text/html");
 puts("\n");
 
 (void) hubPublicLoadAll();
 
 struct dbDb *dbList = ucscDbDb();
 char **ucscDbList = NULL;
 int listSize = slCount(dbList);
 AllocArray(ucscDbList, listSize);
 struct dbDb *el = dbList;
 int ucscDataBaseCount = 0;
 int maxDbNameWidth = 0;
 for ( ; el != NULL; el = el->next )
     {
     ucscDbList[ucscDataBaseCount++] = el->name;
     if (strlen(el->name) > maxDbNameWidth)
 	maxDbNameWidth = strlen(el->name);
     }
 maxDbNameWidth += 1;
 
-cartWebStart(cart, database, "access mechanism to hub data resources");
+cartWebStart(cart, database, "UCSC API v"CGI_VERSION);
 
 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;
 
+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();
     hPrintf("<em>hub open time: %ld millis</em><br>\n", thisTime - lastTime);
     }
 
 // hPrintf("<h3>ucscDb: '%s'</h2>\n", ucscDb);
 
 struct trackHubGenome *hubGenome = hub->genomeList;
 
 showExamples(urlInput, hubGenome, ucscDb);
 
+if (debug)
     showCartDump();
 
 hPrintf("<form action='%s' name='hubApiUrl' id='hubApiUrl' method='GET'>\n\n", "../cgi-bin/hubApi");
 
 hPrintf("<b>Select public hub:&nbsp;</b>");
 #define JBUFSIZE 2048
 #define SMALLBUF 256
 char javascript[JBUFSIZE];
 struct slPair *events = NULL;
 safef(javascript, sizeof(javascript), "this.lastIndex=this.selectedIndex;");
 slPairAdd(&events, "focus", cloneString(javascript));
 
 cgiMakeDropListClassWithIdStyleAndJavascript("publicHubs", "publicHubs",
     shortLabels, publicHubCount, hubDropDown, NULL, "width: 400px", events);