4d72ed9554069edb885ff2f793add75e422a5459
hiram
  Thu Mar 21 15:58:39 2019 -0700
error catch aroung bbi file open and better sample getData links refs #18869

diff --git src/hg/hubApi/hubApi.c src/hg/hubApi/hubApi.c
index e03035b..410a905 100644
--- src/hg/hubApi/hubApi.c
+++ src/hg/hubApi/hubApi.c
@@ -192,93 +192,101 @@
     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(struct trackHub *hub, char *db, struct trackDb *tdb, char *chrom, long long chromSize)
+static void sampleUrl(struct trackHub *hub, char *db, struct trackDb *tdb, char *chrom, long long chromSize, char *errorString)
 /* print out a sample getData URL */
 {
+char errorPrint[2048];
+errorPrint[0] = 0;
+
+if (isNotEmpty(errorString))
+    {
+    safef(errorPrint, sizeof(errorPrint), " <font color='red'>ERROR: %s</font>", errorString);
+    }
+
 unsigned start = chromSize / 4;
 unsigned end = start + 10000;
 if (end > chromSize)
     end = chromSize;
 char *genome = NULL;
 if (hub)
     genome = hub->genomeList->name;
 
 if (db)
     {
     if (hub)
 	{
 	if (tdb->parent)
-	    hPrintf("<li>%s : %s subtrack of parent: %s <a href='%s/getData/track?hubUrl=%s&amp;genome=%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, hub->url, genome, chrom, tdb->track, start, end );
+	    hPrintf("<li>%s : %s subtrack of parent: %s <a href='%s/getData/track?hubUrl=%s&amp;genome=%s&amp;chrom=%s&amp;track=%s&amp;start=%u&amp;end=%u' target=_blank>(sample getData)%s</a></li>\n", tdb->track, tdb->type, tdb->parent->track, urlPrefix, hub->url, genome, chrom, tdb->track, start, end, errorPrint);
 	else
-	    hPrintf("<li>%s : %s <a href='%s/getData/track?hubUrl=%s&amp;genome=%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, hub->url, genome, chrom, tdb->track, start, end );
+	    hPrintf("<li>%s : %s <a href='%s/getData/track?hubUrl=%s&amp;genome=%s&amp;chrom=%s&amp;track=%s&amp;start=%u&amp;end=%u' target=_blank>(sample getData)%s</a></li>\n", tdb->track, tdb->type, urlPrefix, hub->url, genome, chrom, tdb->track, start, end, errorPrint);
 	}
     else
 	{
 	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=%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 );
+	    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)%s</a></li>\n", tdb->track, tdb->type, tdb->parent->track, urlPrefix, db, chrom, tdb->track, start, end, errorPrint);
 	else
-	    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 );
+	    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)%s</a></li>\n", tdb->track, tdb->type, urlPrefix, db, chrom, tdb->track, start, end, errorPrint);
 	}
     }
 else if (hub)
     {
     if (tdb->parent)
-	hPrintf("<li>%s : %s subtrack of parent: %s <a href='%s/getData/track?hubUrl=%s&amp;genome=%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, hub->url, genome, chrom, tdb->track, start, end );
+	hPrintf("<li>%s : %s subtrack of parent: %s <a href='%s/getData/track?hubUrl=%s&amp;genome=%s&amp;chrom=%s&amp;track=%s&amp;start=%u&amp;end=%u' target=_blank>(sample getData)%s</a></li>\n", tdb->track, tdb->type, tdb->parent->track, urlPrefix, hub->url, genome, chrom, tdb->track, start, end, errorPrint);
     else
-	hPrintf("<li>%s : %s <a href='%s/getData/track?hubUrl=%s&amp;genome=%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, hub->url, genome, chrom, tdb->track, start, end );
+	hPrintf("<li>%s : %s <a href='%s/getData/track?hubUrl=%s&amp;genome=%s&amp;chrom=%s&amp;track=%s&amp;start=%u&amp;end=%u' target=_blank>(sample getData)%s</a></li>\n", tdb->track, tdb->type, urlPrefix, hub->url, genome, chrom, tdb->track, start, end, errorPrint);
     }
 else
     hPrintf("<li>%s : %s not db hub track ?</li>\n", tdb->track, tdb->type);
 }
 
 static void showSubTracks(struct trackHub *hub, char *db, struct trackDb *tdb, struct hash *countTracks,
-    char *chromName, long long chromSize)
+    char *chromName, long long chromSize, char *errorString)
 /* tdb has subtracks, show only subTracks, no details */
 {
 hPrintf("    <li><ul>\n");
 if (debug)
     hPrintf("    <li>subtracks for '%s' db: '%s'</li>\n", tdb->track, db);
 if (tdb->subtracks)
     {
     struct trackDb *tdbEl = NULL;
     for (tdbEl = tdb->subtracks; tdbEl; tdbEl = tdbEl->next)
 	{
         if (tdbIsCompositeView(tdbEl))
 	    hPrintf("<li>%s : %s : composite view of parent: %s</li>\n", tdbEl->track, tdbEl->type, tdbEl->parent->track);
 	else
 	    {
 	    if (isSupportedType(tdbEl->type))
-		sampleUrl(hub, db, tdbEl, chromName, chromSize);
+		sampleUrl(hub, db, tdbEl, chromName, chromSize, errorString);
 	    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(hub, db, tdbEl, countTracks, chromName, chromSize);
+	    showSubTracks(hub, db, tdbEl, countTracks, chromName, chromSize, errorString);
 	}
     }
 hPrintf("    </ul></li>\n");
 }
 
 static void trackSettings(struct trackDb *tdb, struct hash *countTracks)
 /* process the settingsHash for a trackDb, recursive when subtracks */
 {
 hPrintf("    <li><ul>\n");
 // 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);
@@ -419,171 +427,189 @@
 
     }
 errCatchEnd(errCatch);
 if (errCatch->gotError)
     {
     retVal = 1;
     dyStringPrintf(errors, "%s", errCatch->message->string);
     }
 errCatchFree(&errCatch);
 
 return retVal;
 }	/* static int bbiBriefMeasure() */
 
 static void hubSampleUrl(struct trackHub *hub, struct trackDb *tdb,
     long chromCount, long itemCount, char *chromName, unsigned chromSize,
-      char *genome)
+      char *genome, char *errorString)
 {
 unsigned start = chromSize / 4;
 unsigned end = start + 10000;
 if (end > chromSize)
     end = chromSize;
 
+char errorPrint[2048];
+errorPrint[0] = 0;
+
+if (isNotEmpty(errorString))
+    {
+    safef(errorPrint, sizeof(errorPrint), " : <font color='red'>ERROR: %s</font>", errorString);
+    }
+
 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>(Xsample getData)</a></li>\n", tdb->track, tdb->type, chromCount, itemCount, urlPrefix, hub->url, genome, tdb->track, chromName, start, end);
+            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)%s</a></li>\n", tdb->track, tdb->type, chromCount, itemCount, urlPrefix, hub->url, genome, tdb->track, chromName, start, end, errorPrint);
         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>(Xsample getData)</a></li>\n", tdb->track, tdb->type, chromCount, itemCount, urlPrefix, hub->url, genome, tdb->track, chromName, start, end);
+            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)%s</a></li>\n", tdb->track, tdb->type, chromCount, itemCount, urlPrefix, hub->url, genome, tdb->track, chromName, start, end, errorPrint);
         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>(Xsample getData)</a></li>\n", tdb->track, tdb->type, chromCount, itemCount, urlPrefix, hub->url, genome, tdb->track, chromName, start, end);
+            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)%s</a></li>\n", tdb->track, tdb->type, chromCount, itemCount, urlPrefix, hub->url, genome, tdb->track, chromName, start, end, errorPrint);
     }
 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 hubSampleUrl(struct trackHub *hub, struct trackDb *tdb,
+	 * long chromCount, long itemCount, char *chromName, unsigned chromSize,
+	 *   char *genome)
+	 */
 
 static void hubCountOneTdb(struct trackHub *hub, char *db, struct trackDb *tdb,
     char *bigDataIndex, struct hash *countTracks, char *chromName,
     unsigned chromSize, char *genome)
 {
 char *bigDataUrl = trackDbSetting(tdb, "bigDataUrl");
 // 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);
 
 char *longName = NULL;
 unsigned longSize = 0;
 long chromCount = 0;
 long itemCount = 0;
 
-if (! (compositeContainer || compositeView) )
-    {
 struct dyString *errors = newDyString(1024);
-    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);
-    }
+
+if (! (compositeContainer || compositeView) )
+    (void) bbiBriefMeasure(tdb->type, bigDataUrl, bigDataIndex, &chromCount, &itemCount, errors, &longName, &longSize);
 
 if (depthSearch && bigDataUrl)
     {
     if (isSupportedType(tdb->type))
 	{
 	if (chromSize > 0)
-	    hubSampleUrl(hub, tdb, chromCount, itemCount, chromName, chromSize, genome);
+	    hubSampleUrl(hub, tdb, chromCount, itemCount, chromName, chromSize, genome, errors->string);
 	else
-	    hubSampleUrl(hub, tdb, chromCount, itemCount, longName, longSize, genome);
+	    hubSampleUrl(hub, tdb, chromCount, itemCount, longName, longSize, genome, errors->string);
 	}
     }
 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 (sample getData)</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);
+	{
+        if (isSupportedType(tdb->type))
+	    {
+	    if (chromSize > 0)
+		hubSampleUrl(hub, tdb, chromCount, itemCount, chromName, chromSize, genome, errors->string);
+	    else
+		hubSampleUrl(hub, tdb, chromCount, itemCount, longName, longSize, genome, errors->string);
+	    }
+        // hPrintf("    <li>%s : %s : %s (maybe sample ?)</li>\n", tdb->track, tdb->type, bigDataUrl);
+	}
     else
 	{
         if (isSupportedType(tdb->type))
 	    {
 	    if (chromSize > 0)
-		hubSampleUrl(hub, tdb, chromCount, itemCount, chromName, chromSize, genome);
+		hubSampleUrl(hub, tdb, chromCount, itemCount, chromName, chromSize, genome, errors->string);
 	    else
-		hubSampleUrl(hub, tdb, chromCount, itemCount, longName, longSize, genome);
+		hubSampleUrl(hub, tdb, chromCount, itemCount, longName, longSize, genome, errors->string);
 	    }
 	else
-	    hPrintf("    <li>%s : %s</li>\n", tdb->track, tdb->type);
+	    hPrintf("    <li>%s : %s (what is this)</li>\n", tdb->track, tdb->type);
         }
     }
 if (allTrackSettings)
     {
     hPrintf("    <li><ul>\n");
     trackSettings(tdb, countTracks); /* show all settings */
     hPrintf("    </ul></li>\n");
     }
 else if (tdb->subtracks)
     {
-    showSubTracks(hub, db, tdb, countTracks, chromName, chromSize);
+    showSubTracks(hub, db, tdb, countTracks, chromName, chromSize, errors->string);
     }
 return;
 }	/*	static void hubCountOneTdb(char *db, struct trackDb *tdb,
 	 *	char *bigDataIndex, struct hash *countTracks,
 	 *	char *chromName, long long chromSize)
 	 */
 
 
 static void countOneTdb(char *db, struct trackDb *tdb,
-    struct hash *countTracks, char *chromName, unsigned chromSize)
+    struct hash *countTracks, char *chromName, unsigned chromSize,
+      char *errorString)
 /* for this tdb in this db, count it up and provide a sample */
 {
 char *bigDataUrl = trackDbSetting(tdb, "bigDataUrl");
 // 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 (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(NULL, db, tdb, chromName, chromSize);
+        sampleUrl(NULL, db, tdb, chromName, chromSize, errorString);
     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(NULL, db, tdb, countTracks, chromName, chromSize);
+    showSubTracks(NULL, db, tdb, countTracks, chromName, chromSize, NULL);
     }
 return;
 }	/*	static void countOneTdb(char *db, struct trackDb *tdb,
 	 *	struct hash *countTracks, char *chromName,
 	 *	unsigned chromSize)
 	 */
 
 static unsigned largestChrom(char *db, char **nameReturn)
 /* return the length and get the chrom name for the largest chrom
  * from chromInfo table.  For use is sample getData URLs
  */
 {
 char query[1024];
 struct sqlConnection *conn = hAllocConn(db);
 sqlSafef(query, sizeof(query), "select chrom,size from chromInfo order by size desc limit 1");
@@ -819,31 +845,31 @@
 }
 
 static void tracksForUcscDb(char *db)
 /* scan the specified database for all tracks */
 {
 struct hash *countTracks = hashNew(0);
 char *chromName = NULL;
 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:%u</li>\n", chromName, chromSize);
 for (tdb = tdbList; tdb != NULL; tdb = tdb->next )
     {
-    countOneTdb(db, tdb, countTracks, chromName, chromSize);
+    countOneTdb(db, tdb, countTracks, chromName, chromSize, NULL);
     if (timeOutReached())
 	break;
     }
 int trackCount = ptToInt(hashFindVal(countTracks, "track count"));
 /* elCount - 1 since the 'track count' element isn't a track */
 hPrintf("    <li>%d total tracks counted, %d different track types</li>\n", trackCount, countTracks->elCount - 1);
 if (countTracks->elCount)
     {
     hPrintf("        <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;