2770a53d1e8e0e5773020965d19c2499439481ca
chmalee
  Tue Feb 7 13:33:08 2023 -0800
Make hubApi return data from multiple tracks at once. Get trackDb tableBrowser setting working correctly in the api

diff --git src/hg/hubApi/hubApi.c src/hg/hubApi/hubApi.c
index 73cf62c..ae8d8d1 100644
--- src/hg/hubApi/hubApi.c
+++ src/hg/hubApi/hubApi.c
@@ -245,31 +245,31 @@
     safef(errorPrint, sizeof(errorPrint), " <font color='red'>ERROR: %s</font>", errorString);
     }
 
 boolean superChild = tdbIsSuperTrackChild(tdb);
 char *genome = NULL;
 if (hub)
     genome = hub->genomeList->name;
 
 struct dyString *extraDyFlags = dyStringNew(128);
 if (debug)
     dyStringAppend(extraDyFlags, ";debug=1");
 if (jsonOutputArrays)
     dyStringAppend(extraDyFlags, ";jsonOutputArrays=1");
 char *extraFlags = dyStringCannibalize(&extraDyFlags);
 
-if (protectedTrack(tdb, tdb->track))
+if (protectedTrack(db, tdb, tdb->track))
     hPrintf("<li>%s : %s &lt;protected data&gt;</li>\n", tdb->track, tdb->type);
 else if (db)
     {
     if (hub)
 	{
 	char urlReference[2048];
 	safef(urlReference,	sizeof(urlReference), " <a href='%s/getData/track?hubUrl=%s;genome=%s;track=%s;maxItemsOutput=5%s' target=_blank>(sample data)%s</a>\n", urlPrefix, hub->url, genome, tdb->track, extraFlags, errorPrint);
 
 	if (tdb->parent)
 	    hPrintf("<li><b>%s</b>: %s subtrack of parent: %s%s</li>\n", tdb->track, tdb->type, tdb->parent->track, urlReference);
 	else
 	    hPrintf("<li><b>%s</b>: %s%s</li>\n", tdb->track, tdb->type, urlReference);
 	}
     else
 	{
@@ -286,61 +286,61 @@
     }
 else if (hub)
     {
     char urlReference[2048];
     safef(urlReference, sizeof(urlReference), " <a href='%s/getData/track?hubUrl=%s;genome=%s;track=%s;maxItemsOutput=5%s' target=_blank>(sample data)%s</a>\n", urlPrefix, hub->url, genome, tdb->track, extraFlags, errorPrint);
 
     if (tdb->parent)
 	hPrintf("<li><b>%s</b>: %s subtrack of parent: %s%s</li>\n", tdb->track, tdb->type, tdb->parent->track, urlReference);
     else
 	hPrintf("<li><b>%s</b>: %s%s</li>\n", tdb->track, tdb->type, urlReference);
     }
 else
     hPrintf("<li>%s : %s not db hub track ?</li>\n", tdb->track, tdb->type);
 }
 
-static void hubSampleUrl(struct trackHub *hub, struct trackDb *tdb,
+static void hubSampleUrl(struct trackHub *hub, char *db, struct trackDb *tdb,
     long chromCount, long itemCount, char *genome, char *errorString)
 {
 struct dyString *extraDyFlags = dyStringNew(128);
 if (debug)
     dyStringAppend(extraDyFlags, ";debug=1");
 if (jsonOutputArrays)
     dyStringAppend(extraDyFlags, ";jsonOutputArrays=1");
 char *extraFlags = dyStringCannibalize(&extraDyFlags);
 
 char errorPrint[2048];
 errorPrint[0] = 0;
 
 if (isNotEmpty(errorString))
     {
     safef(errorPrint, sizeof(errorPrint), " : <font color='red'>ERROR: %s</font>", errorString);
     }
 
 char countsMessage[512];
 countsMessage[0] = 0;
 if (chromCount > 0 || itemCount > 0)
     {
     if (allowedBigBedType(tdb->type))
         safef(countsMessage, sizeof(countsMessage), " : %ld chroms : %ld item count ", chromCount, itemCount);
     else if (startsWithWord("bigWig", tdb->type))
         safef(countsMessage, sizeof(countsMessage), " : %ld chroms : %ld bases covered ", chromCount, itemCount);
     else
         safef(countsMessage, sizeof(countsMessage), " : %ld chroms : %ld count ", chromCount, itemCount);
     }
 
-if (protectedTrack(tdb, tdb->track))
+if (protectedTrack(db, tdb, tdb->track))
     hPrintf("    <li><b>%s</b>: %s protected data</li>\n", tdb->track, tdb->type);
 else if (isSupportedType(tdb->type))
     {
 	char urlReference[2048];
 	safef(urlReference, sizeof(urlReference), "<a href='%s/getData/track?hubUrl=%s;genome=%s;track=%s;maxItemsOutput=5%s' target=_blank>(sample data)%s</a>\n", urlPrefix, hub->url, genome, tdb->track, extraFlags, errorPrint);
 
 	if (allowedBigBedType(tdb->type))
             hPrintf("    <li><b>%s</b>: %s%s%s</li>\n", tdb->track, tdb->type, countsMessage, urlReference);
         else if (startsWithWord("bigWig", tdb->type))
             hPrintf("    <li><b>%s</b>: %s%s%s</li>\n", tdb->track, tdb->type, countsMessage, urlReference);
         else
             hPrintf("    <li><b>%s</b>: %s%s%s</li>\n", tdb->track, tdb->type, countsMessage, urlReference);
     }
 else
     {
@@ -503,31 +503,31 @@
             if (relIdxUrl != NULL)
                 bigDataIndex = trackHubRelativeUrl(hub->genomeList->trackDbFile, relIdxUrl);
             char *bigDataUrl = trackDbSetting(tdbEl, "bigDataUrl");
             char *longName = NULL;
             unsigned longSize = 0;
             struct dyString *errors = dyStringNew(1024);
             (void) bbiBriefMeasure(tdbEl->type, bigDataUrl, bigDataIndex, &chromCount, &itemCount, errors, &longName, &longSize);
             chromSize = longSize;
             chromName = longName;
 	    }
         if (tdbIsCompositeView(tdbEl))
 	    hPrintf("<li><b>%s</b>: %s : composite view of parent: %s</li>\n", tdbEl->track, tdbEl->type, tdbEl->parent->track);
 	else
 	    {
 	    if (isSupportedType(tdbEl->type))
-		hubSampleUrl(hub, tdbEl, chromCount, itemCount, genome, errorString);
+		hubSampleUrl(hub, db, tdbEl, chromCount, itemCount, genome, errorString);
 	    else
 		hPrintf("<li><b>%s</b>: %s : subtrack of parent: %s</li>\n", tdbEl->track, tdbEl->type, tdbEl->parent->track);
 	    }
 	hashCountTrack(tdbEl, countTracks);
         if (tdbEl->subtracks)
 	    hubSubTracks(hub, db, tdbEl, countTracks, chromCount, itemCount, chromName, chromSize, genome, errorString);
 	}
     }
 hPrintf("    </ul></li>\n");
 }	/* hubSubTracks() */
 
 static void showSubTracks(struct trackHub *hub, char *db, struct trackDb *tdb, struct hash *countTracks,
     char *chromName, unsigned chromSize, char *errorString)
 /* tdb has subtracks, show only subTracks, no details */
 {
@@ -544,61 +544,61 @@
 	else
 	    {
 	    if (isSupportedType(tdbEl->type))
 		sampleUrl(hub, db, tdbEl, errorString);
 	    else
 		hPrintf("<li><b>%s</b>: %s : subtrack of parent: %s</li>\n", tdbEl->track, tdbEl->type, tdbEl->parent->track);
 	    }
 	hashCountTrack(tdbEl, countTracks);
         if (tdbEl->subtracks)
 	    showSubTracks(hub, db, tdbEl, countTracks, chromName, chromSize, errorString);
 	}
     }
 hPrintf("    </ul></li>\n");
 }
 
-static void trackSettings(struct trackDb *tdb, struct hash *countTracks)
+static void trackSettings(char *db, struct trackDb *tdb, struct hash *countTracks)
 /* process the settingsHash for a trackDb, recursive when subtracks */
 {
 hPrintf("    <li><ul>\n");
-boolean protectedData = protectedTrack(tdb, tdb->track);
+boolean protectedData = protectedTrack(db, tdb, tdb->track);
 struct hashEl *hel;
 struct hashCookie hc = hashFirst(tdb->settingsHash);
 while ((hel = hashNext(&hc)) != NULL)
     {
     if (sameWord("track", hel->name))
 	continue;	// already output in header
     if (sameWord("tableBrowser", hel->name)
 		&& startsWithWord("off", (char*)hel->val))
 	hPrintf("    <li><b>protectedData</b>: 'true'</li>\n");
     else if (protectedData && sameWord("bigDataUrl", hel->name))
 	hPrintf("    <li><b>bigDataUrl</b>: &lt;protected data&gt;</li>\n");
     else if (isEmpty((char *)hel->val))
 	hPrintf("    <li><b>%s</b>: &lt;empty&gt;</li>\n", hel->name);
     else
 	hPrintf("    <li><b>%s</b>: '%s'</li>\n", hel->name, (char *)hel->val);
     }
 if (tdb->subtracks)
     {
     struct trackDb *tdbEl = NULL;
     if (debug)
 	hPrintf("   <li>has %d subtrack(s)</li>\n", slCount(tdb->subtracks));
     for (tdbEl = tdb->subtracks; tdbEl; tdbEl = tdbEl->next)
 	{
         hPrintf("<li>subtrack: %s of parent: %s : type: '%s' (TBD: sample data)</li>\n", tdbEl->track, tdbEl->parent->track, tdbEl->type);
 	hashCountTrack(tdbEl, countTracks);
-	trackSettings(tdbEl, countTracks);
+	trackSettings(db, tdbEl, countTracks);
 	}
     }
 hPrintf("    </ul></li>\n");
 }
 
 static void hubCountOneTdb(struct trackHub *hub, char *db, struct trackDb *tdb,
     char *bigDataIndex, struct hash *countTracks, char *chromName,
     unsigned chromSize, char *genome)
 {
 char *bigDataUrl = trackDbSetting(tdb, "bigDataUrl");
 boolean compositeContainer = tdbIsComposite(tdb);
 boolean compositeView = tdbIsCompositeView(tdb);
 boolean superChild = tdbIsSuperTrackChild(tdb);
 boolean depthSearch = cartUsualBoolean(cart, "depthSearch", FALSE);
 hashCountTrack(tdb, countTracks);
@@ -614,90 +614,90 @@
 if (! (compositeContainer || compositeView) )
     {
     if (chromSize < 1 || depthSearch)
 	{
 	char *longName = NULL;
 	unsigned longSize = 0;
         (void) bbiBriefMeasure(tdb->type, bigDataUrl, bigDataIndex, &chromCount, &itemCount, errors, &longName, &longSize);
 	chromSize = longSize;
 	chromName = longName;
 	}
     }
 
 if (depthSearch && bigDataUrl)
     {
     if (isSupportedType(tdb->type))
-	    hubSampleUrl(hub, tdb, chromCount, itemCount, genome, errors->string);
+	    hubSampleUrl(hub, db, tdb, chromCount, itemCount, genome, errors->string);
     }
 else
     {
     if (compositeContainer)
         hPrintf("    <li><b>%s</b>: %s : composite track container has %d subtracks</li>\n", tdb->track, tdb->type, slCount(tdb->subtracks));
     else if (compositeView)
         hPrintf("    <li><b>%s</b>: %s : composite view of parent: %s</li>\n", tdb->track, tdb->type, tdb->parent->track);
     else if (superChild)
 	{
 	if (isSupportedType(tdb->type))
-	    hubSampleUrl(hub, tdb, chromCount, itemCount, genome,  errors->string);
+	    hubSampleUrl(hub, db, tdb, chromCount, itemCount, genome,  errors->string);
 	else
 	    hPrintf("    <li><b>%s</b>: %s : superTrack child of parent: %s</li>\n", tdb->track, tdb->type, tdb->parent->track);
 	}
     else if (! depthSearch && bigDataUrl)
 	{
         if (isSupportedType(tdb->type))
 	    {
-	    hubSampleUrl(hub, tdb, chromCount, itemCount, genome, errors->string);
+	    hubSampleUrl(hub, db, tdb, chromCount, itemCount, genome, errors->string);
 	    }
 	}
     else
 	{
         if (isSupportedType(tdb->type))
 	    {
-	    hubSampleUrl(hub, tdb, chromCount, itemCount, genome, errors->string);
+	    hubSampleUrl(hub, db, tdb, chromCount, itemCount, genome, errors->string);
 	    }
 	else
 	    hPrintf("    <li><b>%s</b>: %s (what is this)</li>\n", tdb->track, tdb->type);
         }
     }
 if (allTrackSettings)
     {
     hPrintf("    <li><ul>\n");
-    trackSettings(tdb, countTracks); /* show all settings */
+    trackSettings(db, tdb, countTracks); /* show all settings */
     hPrintf("    </ul></li>\n");
     }
 else if (tdb->subtracks)
     {
     hubSubTracks(hub, db, tdb, countTracks, chromCount, itemCount, chromName, chromSize, genome, errors->string);
     }
 return;
 }	/*	static void hubCountOneTdb(char *db, struct trackDb *tdb,
 	 *	char *bigDataIndex, struct hash *countTracks,
 	 *	char *chromName, unsigned chromSize)
 	 */
 
 
 static void countOneTdb(char *db, struct trackDb *tdb,
     struct hash *countTracks, char *chromName, unsigned chromSize,
       char *errorString)
 /* for this tdb in this db, count it up and provide a sample */
 {
 char *bigDataUrl = trackDbSetting(tdb, "bigDataUrl");
 boolean compositeContainer = tdbIsComposite(tdb);
 boolean compositeView = tdbIsCompositeView(tdb);
 boolean superChild = tdbIsSuperTrackChild(tdb);
 boolean depthSearch = cartUsualBoolean(cart, "depthSearch", FALSE);
-boolean protectedData = protectedTrack(tdb, tdb->track);
+boolean protectedData = protectedTrack(db, tdb, tdb->track);
 hashCountTrack(tdb, countTracks);
 
 if (compositeContainer)
     hPrintf("    <li><b>%s</b>: %s : composite track container has %d subtracks</li>\n", tdb->track, tdb->type, slCount(tdb->subtracks));
 else if (compositeView)
     hPrintf("    <li><b>%s</b>: %s : composite view of parent: %s</li>\n", tdb->track, tdb->type, tdb->parent->track);
 else if (superChild)
     {
     if (isSupportedType(tdb->type))
         sampleUrl(NULL, db, tdb, errorString);
     else
 	hPrintf("    <li><b>%s</b>: %s : superTrack child of parent: %s</li>\n", tdb->track, tdb->type, tdb->parent->track);
     }
 else if (! depthSearch && bigDataUrl)
     {
@@ -705,31 +705,31 @@
 	hPrintf("    <li><b>%s</b>: %s : &lt;protected data&gt;</li>\n", tdb->track, tdb->type);
     else
 	hPrintf("    <li><b>%s</b>: %s : %s</li>\n", tdb->track, tdb->type, bigDataUrl);
     }
 else
     {
     if (isSupportedType(tdb->type))
         sampleUrl(NULL, db, tdb, errorString);
     else
         hPrintf("    <li><b>%s</b>: %s</li>\n", tdb->track, tdb->type);
     }
 
 if (allTrackSettings)
     {
     hPrintf("    <li><ul>\n");
-    trackSettings(tdb, countTracks); /* show all settings */
+    trackSettings(db, tdb, countTracks); /* show all settings */
     hPrintf("    </ul></li>\n");
     }
 else if (tdb->subtracks)
     {
     showSubTracks(NULL, db, tdb, countTracks, chromName, chromSize, NULL);
     }
 return;
 }	/*	static void countOneTdb(char *db, struct trackDb *tdb,
 	 *	struct hash *countTracks, char *chromName,
 	 *	unsigned chromSize)
 	 */
 
 static unsigned largestChrom(char *db, char **nameReturn, int *chromCount)
 /* return the length and get the chrom name for the largest chrom
  * from chromInfo table.  For use is sample getData URLs