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/getData.c src/hg/hubApi/getData.c
index 9a7541f..14fce17 100644
--- src/hg/hubApi/getData.c
+++ src/hg/hubApi/getData.c
@@ -545,58 +545,72 @@
     }
 bbiFileClose(&bbi);
 apiFinishOutput(0, NULL, jw);
 }	/*	static void getHubTrackData(char *hubUrl)	*/
 
 static void getTrackData()
 /* return data from a track, optionally just one chrom data,
  *  optionally just one section of that chrom data
  */
 {
 char *db = cgiOptionalString("genome");
 char *chrom = cgiOptionalString("chrom");
 char *start = cgiOptionalString("start");
 char *end = cgiOptionalString("end");
 /* 'track' name in trackDb often refers to a SQL 'table' */
-char *track = cgiOptionalString("track");
-char *sqlTable = cloneString(track); /* might be something else */
+char *trackArg = cgiOptionalString("track");
+char *sqlTable = cloneString(trackArg); /* might be something else */
      /* depends upon 'table' setting in track db, or split table business */
 
 unsigned chromSize = 0;	/* maybe set later */
 unsigned uStart = 0;
 unsigned uEnd = chromSize;	/* maybe set later */
 if ( ! (isEmpty(start) || isEmpty(end)) )
     {
     uStart = sqlUnsigned(start);
     uEnd = sqlUnsigned(end);
     if (uEnd < uStart)
 	apiErrAbort(err400, err400Msg, "given start coordinate %u is greater than given end coordinate", uStart, uEnd);
     }
 
 if (isEmpty(db))
     apiErrAbort(err400, err400Msg, "missing URL variable genome=<ucscDb> name for endpoint '/getData/track");
-if (isEmpty(track))
+if (isEmpty(trackArg))
     apiErrAbort(err400, err400Msg, "missing URL variable track=<trackName> name for endpoint '/getData/track");
 
 /* database existence has already been checked before now, might
  * have disappeared in the mean time (well, not really . . .)
  */
 struct sqlConnection *conn = hAllocConnMaybe(db);
 if (NULL == conn)
     apiErrAbort(err400, err400Msg, "can not find genome 'genome=%s' for endpoint '/getData/track", db);
 
-struct trackDb *thisTrack = hTrackDbForTrack(db, track);
+struct jsonWrite *jw = apiStartOutput();
+
+// load the tracks
+struct trackDb *tdbList = NULL;
+cartTrackDbInitForApi(NULL, db, &tdbList, NULL, FALSE);
+
+// allow optional comma sep list of tracks
+char *tracks[100];
+int numTracks = chopByChar(trackArg, ',', tracks, sizeof(tracks));
+int i = 0;
+for (i = 0; i < numTracks; i++)
+    {
+    char *track = cloneString(tracks[i]);
+    char *sqlTable = cloneString(track);
+    struct trackDb *thisTrack = tdbForTrack(db, track, &tdbList);
 
     if (NULL == thisTrack)
         {
         if (! sqlTableExists(conn, track))
             apiErrAbort(err400, err400Msg, "can not find track=%s name for endpoint '/getData/track", track);
         }
     if (thisTrack && ! isSupportedType(thisTrack->type))
         apiErrAbort(err415, err415Msg, "track type '%s' for track=%s not supported at this time", thisTrack->type, track);
     if (trackHasNoData(thisTrack))
         apiErrAbort(err400, err400Msg, "container track '%s' does not contain data, use the children of this container", track);
 
     /* might be a big* track with no table */
     char *bigDataUrl = NULL;
     boolean tableTrack = TRUE;
 
@@ -606,31 +620,31 @@
 
         /* might have a specific table defined instead of the track name */
         char *tableName = trackDbSetting(thisTrack, "table");
         if (isNotEmpty(tableName))
             {
             freeMem(sqlTable);
             sqlTable = cloneString(tableName);
             }
         }
     else
         {
         freeMem(sqlTable);
         sqlTable = cloneString(track);
         }
 
-if (protectedTrack(thisTrack, sqlTable))
+    if (protectedTrack(db, thisTrack, sqlTable) && !(chrom && start && end))
             apiErrAbort(err403, err403Msg, "this data request: 'db=%s;track=%s' is protected data, see also: https://genome.ucsc.edu/FAQ/FAQdownloads.html#download40", db, track);
 
     struct hTableInfo *hti = hFindTableInfoWithConn(conn, NULL, sqlTable);
 
     char *splitSqlTable = NULL;
 
     if (hti && hti->isSplit)
         {
         if (isNotEmpty(chrom))
             {
             char fullTableName[256];
             safef(fullTableName, sizeof(fullTableName), "%s_%s", chrom, hti->rootName);
             splitSqlTable = cloneString(fullTableName);
             }
         else
@@ -638,31 +652,30 @@
             char *defaultChrom = hDefaultChrom(db);
             char fullTableName[256];
             safef(fullTableName, sizeof(fullTableName), "%s_%s", defaultChrom, hti->rootName);
             splitSqlTable = cloneString(fullTableName);
             }
         }
 
     if (! hTableOrSplitExists(db, sqlTable))
         {
         if (! bigDataUrl)
             apiErrAbort(err400, err400Msg, "can not find specified 'track=%s' for endpoint: /getData/track?genome=%s;track=%s", track, db, track);
         else
             tableTrack = FALSE;
         }
 
-struct jsonWrite *jw = apiStartOutput();
     jsonWriteString(jw, "genome", db);
     if (tableTrack)
         {
         char *dataTime = NULL;
         if (hti && hti->isSplit)
             dataTime = sqlTableUpdate(conn, splitSqlTable);
         else
             dataTime = sqlTableUpdate(conn, sqlTable);
         time_t dataTimeStamp = sqlDateToUnixTime(dataTime);
         replaceChar(dataTime, ' ', 'T');	/*	ISO 8601	*/
         jsonWriteString(jw, "dataTime", dataTime);
         jsonWriteNumber(jw, "dataTimeStamp", (long long)dataTimeStamp);
         if (differentStringNullOk(sqlTable,track))
             jsonWriteString(jw, "sqlTable", sqlTable);
         }
@@ -746,30 +759,31 @@
         itemsReturned += itemsDone;
         jsonWriteListEnd(jw);
         }
     else if (thisTrack && startsWith("bigWig", thisTrack->type))
         {
         if (jsonOutputArrays || debug)
             wigColumnTypes(jw);
 
         jsonWriteObjectStart(jw, track);
         bigWigData(jw, bbi, chrom, uStart, uEnd);
         jsonWriteObjectEnd(jw);
         bbiFileClose(&bbi);
         }
     else
         tableDataOutput(db, thisTrack, conn, jw, track, chrom, uStart, uEnd);
+    }
 
 apiFinishOutput(0, NULL, jw);
 hFreeConn(&conn);
 }	/*	static void getTrackData()	*/
 
 static void getSequenceData(char *db, char *hubUrl)
 /* return DNA sequence, given at least a genome=name and chrom=chr,
    optionally start and end, might be a track hub for UCSC database  */
 {
 char *chrom = cgiOptionalString("chrom");
 char *start = cgiOptionalString("start");
 char *end = cgiOptionalString("end");
 
 long timeStart = clock1000();