15c2acbbf16454d91d9079216f21427fdd33a609
hiram
  Tue Apr 16 13:45:20 2019 -0700
beginning to allow the array output time to function refs #18869

diff --git src/hg/hubApi/getData.c src/hg/hubApi/getData.c
index ab5e0ab..e0e455a 100644
--- src/hg/hubApi/getData.c
+++ src/hg/hubApi/getData.c
@@ -1,670 +1,694 @@
 /* manage endpoint /getData/ functions */
 
 #include "dataApi.h"
 
 static void wigTableDataOutput(struct jsonWrite *jw, char *database, char *table, char *chrom, int start, int end)
 /* output wiggle data from the given table and specified chrom:start-end */
 {
 struct wiggleDataStream *wds = wiggleDataStreamNew();
 wds->setMaxOutput(wds, maxItemsOutput);
 wds->setChromConstraint(wds, chrom);
 wds->setPositionConstraint(wds, start, end);
 int operations = wigFetchAscii;
 long long valuesMatched = wds->getData(wds, database, table, operations);
 jsonWriteNumber(jw, "valuesMatched", valuesMatched);
 struct wigAsciiData *el;
 jsonWriteListStart(jw, chrom);
 unsigned itemCount = 0;
 for (el = wds->ascii; itemCount < maxItemsOutput && el; el = el->next)
     {
     jsonWriteObjectStart(jw, NULL);
     int s = el->data->chromStart;
     int e = s + el->span;
     double val = el->data->value;
     jsonWriteNumber(jw, "start", (long long)s);
     jsonWriteNumber(jw, "end", (long long)e);
     jsonWriteDouble(jw, "value", val);
     jsonWriteObjectEnd(jw);
     ++itemCount;
     }
 jsonWriteListEnd(jw);
 }
 
 static void jsonDatumOut(struct jsonWrite *jw, char *name, char *val,
     int jsonType)
 /* output a json item, determine type, appropriate output */
 {
 if (JSON_DOUBLE == jsonType)
     jsonWriteDouble(jw, name, sqlDouble(val));
 else if (JSON_NUMBER == jsonType)
     jsonWriteNumber(jw, name, sqlLongLong(val));
 else
     jsonWriteString(jw, name, val);
 }
 
 static void tableDataOutput(char *db, struct trackDb *tdb,
     struct sqlConnection *conn, struct jsonWrite *jw, char *track,
     char *chrom, unsigned start, unsigned end)
 /* output the SQL table data for given track */
 {
 char query[4096];
 
 /* for MySQL select statements, name for 'chrom' 'start' 'end' to use
  *     for a table which has different names than that
  */
 char chromName[256];
 char startName[256];
 char endName[256];
 
 /* defaults, normal stuff */
 safef(chromName, sizeof(chromName), "chrom");
 safef(startName, sizeof(startName), "chromStart");
 safef(endName, sizeof(endName), "chromEnd");
 
 /* might have a specific table defined instead of the track name */
 char *sqlTable = cloneString(track);
 char *tableName = trackDbSetting(tdb, "table");
 if (isNotEmpty(tableName))
     {
     freeMem(sqlTable);
     sqlTable = cloneString(tableName);
     jsonWriteString(jw, "sqlTable", sqlTable);
     }
 
 /* determine name for 'chrom' in table select */
 if (! sqlColumnExists(conn, sqlTable, "chrom"))
     {
     if (sqlColumnExists(conn, sqlTable, "tName"))	// track type psl
 	{
 	safef(chromName, sizeof(chromName), "tName");
 	safef(startName, sizeof(startName), "tStart");
 	safef(endName, sizeof(endName), "tEnd");
 	}
     else if (sqlColumnExists(conn, sqlTable, "genoName"))// track type rmsk
 	{
 	safef(chromName, sizeof(chromName), "genoName");
 	safef(startName, sizeof(startName), "genoStart");
 	safef(endName, sizeof(endName), "genoEnd");
 	}
     }
 
 if (sqlColumnExists(conn, sqlTable, "txStart"))	// track type genePred
     {
     safef(startName, sizeof(startName), "txStart");
     safef(endName, sizeof(endName), "txEnd");
     }
 
 /* no chrom specified, return entire table */
 if (isEmpty(chrom))
     sqlSafef(query, sizeof(query), "select * from %s", sqlTable);
 else if (0 == (start + end))	/* have chrom, no start,end == full chr */
     {
-//    boolean useTname = FALSE;
-    /* need to extend the chrom column check to allow tName also */
     if (! sqlColumnExists(conn, sqlTable, chromName))
 	apiErrAbort(err400, err400Msg, "track '%s' is not a position track, request track without chrom specification, genome: '%s'", track, db);
 
     jsonWriteString(jw, "chrom", chrom);
     struct chromInfo *ci = hGetChromInfo(db, chrom);
     jsonWriteNumber(jw, "start", (long long)0);
     jsonWriteNumber(jw, "end", (long long)ci->size);
     sqlSafef(query, sizeof(query), "select * from %s where %s='%s'", sqlTable, chromName, chrom);
     }
 else	/* fully specified chrom:start-end */
     {
     jsonWriteString(jw, "chrom", chrom);
     jsonWriteNumber(jw, "start", (long long)start);
     jsonWriteNumber(jw, "end", (long long)end);
     if (startsWith("wig", tdb->type))
 	{
         wigTableDataOutput(jw, db, sqlTable, chrom, start, end);
         return;	/* DONE */
 	}
     else
 	{
 	sqlSafef(query, sizeof(query), "select * from %s where %s='%s' AND %s > %u AND %s < %u", sqlTable, chromName, chrom, endName, start, startName, end);
 	}
     }
 
 if (debug)
     jsonWriteString(jw, "select", query);
 
 /* continuing, not a wiggle output */
 char **columnNames = NULL;
 char **columnTypes = NULL;
 int *jsonTypes = NULL;
 int columnCount = tableColumns(conn, jw, sqlTable, &columnNames, &columnTypes, &jsonTypes);
-if (debug)
+if (jsonOutputArrays || debug)
     {
     jsonWriteObjectStart(jw, "columnTypes");
     int i = 0;
     for (i = 0; i < columnCount; ++i)
 	{
 	char bothTypes[1024];
 	safef(bothTypes, sizeof(bothTypes), "%s - %s", columnTypes[i], jsonTypeStrings[jsonTypes[i]]);
 	jsonWriteString(jw, columnNames[i], bothTypes);
 	}
     jsonWriteObjectEnd(jw);
     }
 jsonWriteListStart(jw, track);
 struct sqlResult *sr = sqlGetResult(conn, query);
 char **row = NULL;
 unsigned itemCount = 0;
 while (itemCount < maxItemsOutput && (row = sqlNextRow(sr)) != NULL)
     {
+    if (jsonOutputArrays)
+	jsonWriteListStart(jw, NULL);
+    else
 	jsonWriteObjectStart(jw, NULL);
     int i = 0;
     for (i = 0; i < columnCount; ++i)
 	{
+	if (jsonOutputArrays)
+	    jsonDatumOut(jw, NULL, row[i], jsonTypes[i]);
+	else
 	    jsonDatumOut(jw, columnNames[i], row[i], jsonTypes[i]);
 	}
+    if (jsonOutputArrays)
+	jsonWriteListEnd(jw);
+    else
 	jsonWriteObjectEnd(jw);
     ++itemCount;
     }
 sqlFreeResult(&sr);
 jsonWriteListEnd(jw);
 }	/*  static void tableDataOutput(char *db, struct trackDb *tdb, ... ) */
 
 static void bedDataOutput(struct jsonWrite *jw, struct bbiFile *bbi,
     char *chrom, unsigned start, unsigned end, struct sqlFieldType *fiList,
      struct trackDb *tdb)
 /* output bed data for one chrom in the given bbi file */
 {
 char *itemRgb = trackDbSetting(tdb, "itemRgb");
 int *jsonTypes = NULL;
 int columnCount = slCount(fiList);
 AllocArray(jsonTypes, columnCount);
 int i = 0;
 struct sqlFieldType *fi;
 for ( fi = fiList; fi; fi = fi->next)
     {
     if (itemRgb)
 	{
 	if (8 == i && sameWord("on", itemRgb))
 	    jsonTypes[i++] = JSON_STRING;
 	else
 	    jsonTypes[i++] = autoSqlToJsonType(fi->type);
 	}
     else
 	jsonTypes[i++] = autoSqlToJsonType(fi->type);
     }
 struct lm *bbLm = lmInit(0);
 struct bigBedInterval *iv, *ivList = NULL;
 ivList = bigBedIntervalQuery(bbi,chrom, start, end, 0, bbLm);
 char *row[bbi->fieldCount];
 unsigned itemCount = 0;
 for (iv = ivList; itemCount < maxItemsOutput && iv; iv = iv->next)
     {
     char startBuf[16], endBuf[16];
     bigBedIntervalToRow(iv, chrom, startBuf, endBuf, row, bbi->fieldCount);
+    if (jsonOutputArrays)
+	jsonWriteListStart(jw, NULL);
+    else
 	jsonWriteObjectStart(jw, NULL);
     int i;
     struct sqlFieldType *fi = fiList;
     for (i = 0; i < bbi->fieldCount; ++i)
         {
+	if (jsonOutputArrays)
+	    jsonDatumOut(jw, NULL, row[i], jsonTypes[i]);
+	else
 	    jsonDatumOut(jw, fi->name, row[i], jsonTypes[i]);
         fi = fi->next;
         }
+    if (jsonOutputArrays)
+	jsonWriteListEnd(jw);
+    else
 	jsonWriteObjectEnd(jw);
     ++itemCount;
     }
 lmCleanup(&bbLm);
-}
+}	/* static void bedDataOutput(struct jsonWrite *jw, . . . ) */
 
 static void wigDataOutput(struct jsonWrite *jw, struct bbiFile *bwf,
     char *chrom, unsigned start, unsigned end)
 /* output wig data for one chrom in the given bwf file */
 {
 struct lm *lm = lmInit(0);
 struct bbiInterval *iv, *ivList = bigWigIntervalQuery(bwf, chrom, start, end, lm);
 if (NULL == ivList)
     return;
 
 unsigned itemCount = 0;
 
 jsonWriteListStart(jw, chrom);
 for (iv = ivList; iv && itemCount < maxItemsOutput; iv = iv->next)
     {
     jsonWriteObjectStart(jw, NULL);
     int s = max(iv->start, start);
     int e = min(iv->end, end);
     double val = iv->val;
     jsonWriteNumber(jw, "start", (long long)s);
     jsonWriteNumber(jw, "end", (long long)e);
     jsonWriteDouble(jw, "value", val);
     jsonWriteObjectEnd(jw);
     ++itemCount;
     }
 jsonWriteListEnd(jw);
 }
 
 static void wigData(struct jsonWrite *jw, struct bbiFile *bwf, char *chrom,
     unsigned start, unsigned end)
 /* output the data for a bigWig bbi file */
 {
 struct bbiChromInfo *chromList = NULL;
 // struct bbiSummaryElement sum = bbiTotalSummary(bwf);
 if (isEmpty(chrom))
     {
     chromList = bbiChromList(bwf);
     struct bbiChromInfo *bci;
     for (bci = chromList; bci; bci = bci->next)
 	{
 	wigDataOutput(jw, bwf, bci->name, 0, bci->size);
 	}
     }
     else
 	wigDataOutput(jw, bwf, chrom, start, end);
 }
 
 static void bigColumnTypes(struct jsonWrite *jw, struct sqlFieldType *fiList)
 /* show the column types from a big file autoSql definitions */
 {
 jsonWriteObjectStart(jw, "columnTypes");
 struct sqlFieldType *fi = fiList;
 for ( ; fi; fi = fi->next)
     {
     char bothTypes[1024];
     int jsonType = autoSqlToJsonType(fi->type);
     safef(bothTypes, sizeof(bothTypes), "%s - %s", fi->type, jsonTypeStrings[jsonType]);
     jsonWriteString(jw, fi->name, bothTypes);
     }
 jsonWriteObjectEnd(jw);
 }
 
 static void getHubTrackData(char *hubUrl)
 /* return data from a hub track, optionally just one chrom data,
  *  optionally just one section of that chrom data
  */
 {
 char *genome = cgiOptionalString("genome");
 char *track = cgiOptionalString("track");
 char *chrom = cgiOptionalString("chrom");
 char *start = cgiOptionalString("start");
 char *end = cgiOptionalString("end");
 
 if (isEmpty(genome))
     apiErrAbort(err400, err400Msg, "missing genome=<name> for endpoint '/getData/track'  given hubUrl='%s'", hubUrl);
 if (isEmpty(track))
     apiErrAbort(err400, err400Msg, "missing track=<name> for endpoint '/getData/track'  given hubUrl='%s'", hubUrl);
 
 struct trackHub *hub = errCatchTrackHubOpen(hubUrl);
 struct trackHubGenome *hubGenome = NULL;
 for (hubGenome = hub->genomeList; hubGenome; hubGenome = hubGenome->next)
     {
     if (sameString(genome, hubGenome->name))
 	break;
     }
 if (NULL == hubGenome)
     apiErrAbort(err400, err400Msg, "failed to find specified genome=%s for endpoint '/getData/track'  given hubUrl '%s'", genome, hubUrl);
 
 struct trackDb *tdb = obtainTdb(hubGenome, NULL);
 
 if (NULL == tdb)
     apiErrAbort(err400, err400Msg, "failed to find a track hub definition in genome=%s for endpoint '/getData/track'  given hubUrl='%s'", genome, hubUrl);
 
 struct trackDb *thisTrack = findTrackDb(track, tdb);
 
 if (NULL == thisTrack)
     apiErrAbort(err400, err400Msg, "failed to find specified track=%s in genome=%s for endpoint '/getData/track'  given hubUrl='%s'", track, genome, hubUrl);
 
 char *bigDataUrl = trackDbSetting(thisTrack, "bigDataUrl");
 struct bbiFile *bbi = bigFileOpen(thisTrack->type, bigDataUrl);
 if (NULL == bbi)
     apiErrAbort(err400, err400Msg, "track type %s management not implemented yet TBD track=%s in genome=%s for endpoint '/getData/track'  given hubUrl='%s'", track, genome, hubUrl);
 
 struct jsonWrite *jw = apiStartOutput();
 jsonWriteString(jw, "hubUrl", hubUrl);
 jsonWriteString(jw, "genome", genome);
 // jsonWriteString(jw, "track", track);
 unsigned chromSize = 0;
 struct bbiChromInfo *chromList = NULL;
 if (isNotEmpty(chrom))
     {
 //    jsonWriteString(jw, "chrom", chrom);
     chromSize = bbiChromSize(bbi, chrom);
     if (0 == chromSize)
 	apiErrAbort(err400, err400Msg, "can not find specified chrom=%s in bigBed file URL %s", chrom, bigDataUrl);
     jsonWriteNumber(jw, "chromSize", (long long)chromSize);
     }
 else
     {
     chromList = bbiChromList(bbi);
     jsonWriteNumber(jw, "chromCount", (long long)slCount(chromList));
     }
 
 unsigned uStart = 0;
 unsigned uEnd = chromSize;
 if ( ! (isEmpty(start) || isEmpty(end)) )
     {
     uStart = sqlUnsigned(start);
     uEnd = sqlUnsigned(end);
     jsonWriteNumber(jw, "start", uStart);
     jsonWriteNumber(jw, "end", uEnd);
     }
 
 jsonWriteString(jw, "bigDataUrl", bigDataUrl);
 jsonWriteString(jw, "trackType", thisTrack->type);
+if (debug)
+    jsonWriteString(jw, "jsonOutputArrays", jsonOutputArrays ? "TRUE":"FALSE");
 
 if (allowedBigBedType(thisTrack->type))
     {
     struct asObject *as = bigBedAsOrDefault(bbi);
     struct sqlFieldType *fiList = sqlFieldTypesFromAs(as);
     if (debug)
         bigColumnTypes(jw, fiList);
 
     jsonWriteListStart(jw, track);
     if (isEmpty(chrom))
 	{
 	struct bbiChromInfo *bci;
 	for (bci = chromList; bci; bci = bci->next)
 	    {
 	    bedDataOutput(jw, bbi, bci->name, 0, bci->size, fiList, thisTrack);
 	    }
 	}
     else
 	bedDataOutput(jw, bbi, chrom, uStart, uEnd, fiList, thisTrack);
     jsonWriteListEnd(jw);
     }
 else if (startsWith("bigWig", thisTrack->type))
     {
     jsonWriteObjectStart(jw, track);
     wigData(jw, bbi, chrom, uStart, uEnd);
     jsonWriteObjectEnd(jw);
     }
 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("db");
 char *chrom = cgiOptionalString("chrom");
 char *start = cgiOptionalString("start");
 char *end = cgiOptionalString("end");
 /* 'track' name in trackDb refers to a SQL 'table' */
 char *track = cgiOptionalString("track");
 char *sqlTable = cloneString(track);
 
 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 db=<ucscDb> name for endpoint '/getData/track");
 if (isEmpty(track))
     apiErrAbort(err400, err400Msg, "missing URL variable track=<trackName> name for endpoint '/getData/track");
 
 struct trackDb *thisTrack = hTrackDbForTrackAndAncestors(db, track);
 if (NULL == thisTrack)
     apiErrAbort(err400, err400Msg, "can not find track=%s name for endpoint '/getData/track", track);
 
 
 /* might be a big* track with no table */
 char *bigDataUrl = trackDbSetting(thisTrack, "bigDataUrl");
 boolean tableTrack = TRUE;
 
 /* might have a specific table defined instead of the track name */
 char *tableName = trackDbSetting(thisTrack, "table");
 if (isNotEmpty(tableName))
     {
     freeMem(sqlTable);
     sqlTable = cloneString(tableName);
     }
 
 struct sqlConnection *conn = hAllocConn(db);
 if (! sqlTableExists(conn, sqlTable))
     {
     if (! bigDataUrl)
 	apiErrAbort(err400, err400Msg, "can not find specified 'track=%s' for endpoint: /getData/track?db=%s;track=%s", track, db, track);
     else
 	tableTrack = FALSE;
     }
 
 struct jsonWrite *jw = apiStartOutput();
 jsonWriteString(jw, "db", db);
 if (tableTrack)
     {
     char *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);
     }
 jsonWriteString(jw, "trackType", thisTrack->type);
 jsonWriteString(jw, "track", track);
+if (debug)
+    jsonWriteString(jw, "jsonOutputArrays", jsonOutputArrays ? "TRUE":"FALSE");
 
 char query[4096];
 struct bbiFile *bbi = NULL;
 struct bbiChromInfo *chromList = NULL;
 
 if (startsWith("big", thisTrack->type))
     {
     if (bigDataUrl)
 	bbi = bigFileOpen(thisTrack->type, bigDataUrl);
     else
 	{
 	char quickReturn[2048];
         sqlSafef(query, sizeof(query), "select fileName from %s", sqlTable);
         if (sqlQuickQuery(conn, query, quickReturn, sizeof(quickReturn)))
 	    {
 	    bigDataUrl = cloneString(quickReturn);
 	    bbi = bigFileOpen(thisTrack->type, bigDataUrl);
 	    }
 	}
     if (NULL == bbi)
 	apiErrAbort(err400, err400Msg, "failed to find bigDataUrl=%s for track=%s in database=%s for endpoint '/getData/track'", bigDataUrl, track, db);
     if (isNotEmpty(chrom))
 	{
 	jsonWriteString(jw, "chrom", chrom);
 	chromSize = bbiChromSize(bbi, chrom);
 	if (0 == chromSize)
 	    apiErrAbort(err400, err400Msg, "can not find specified chrom=%s in bigWig file URL %s", chrom, bigDataUrl);
 	if (uEnd < 1)
 	    uEnd = chromSize;
 	jsonWriteNumber(jw, "chromSize", (long long)chromSize);
 	}
 else
 	{
 	chromList = bbiChromList(bbi);
 	jsonWriteNumber(jw, "chromCount", (long long)slCount(chromList));
 	}
      jsonWriteString(jw, "bigDataUrl", bigDataUrl);
     }
 
 /* when start, end given, show them */
 if ( uEnd > uStart )
     {
     jsonWriteNumber(jw, "start", uStart);
     jsonWriteNumber(jw, "end", uEnd);
     }
 
 if (allowedBigBedType(thisTrack->type))
     {
     struct asObject *as = bigBedAsOrDefault(bbi);
     struct sqlFieldType *fiList = sqlFieldTypesFromAs(as);
     if (debug)
         bigColumnTypes(jw, fiList);
 
     jsonWriteListStart(jw, track);
     if (isEmpty(chrom))
 	{
 	struct bbiChromInfo *bci;
 	for (bci = chromList; bci; bci = bci->next)
 	    {
 	    bedDataOutput(jw, bbi, bci->name, 0, bci->size, fiList, thisTrack);
 	    }
 	}
     else
 	bedDataOutput(jw, bbi, chrom, uStart, uEnd, fiList, thisTrack);
     jsonWriteListEnd(jw);
     }
 else if (startsWith("bigWig", thisTrack->type))
     {
     jsonWriteObjectStart(jw, track);
     wigData(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 getSequenceData(char *db, char *hubUrl)
 /* return DNA sequence, given at least a db=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");
 
 if (isEmpty(chrom))
     apiErrAbort(err400, err400Msg, "missing URL chrom=<name> for endpoint '/getData/sequence?db=%s'", db);
 if (chromSeqFileExists(db, chrom))
     {
     struct chromInfo *ci = hGetChromInfo(db, chrom);
     unsigned chromSize = ci->size;
     struct dnaSeq *seq = NULL;
     if (isEmpty(start) || isEmpty(end))
 	if (chromSize > MAX_DNA_LENGTH)
 	    apiErrAbort(err400, err400Msg, "DNA sequence request %d too large, limit: %u for endpoint '/getData/sequence?db=%s;chrom=%s'", chromSize, MAX_DNA_LENGTH, db, chrom);
 	else
 	    seq = hChromSeqMixed(db, chrom, 0, 0);
     else
 	if ( (sqlSigned(end) - sqlSigned(start)) > MAX_DNA_LENGTH)
 	    apiErrAbort(err400, err400Msg, "DNA sequence request %d too large, limit: %u for endpoint '/getData/sequence?db=%s;chrom=%s;start=%s;end=%s'", sqlSigned(end) - sqlSigned(start), MAX_DNA_LENGTH, db, chrom, start, end);
 	else
 	    seq = hChromSeqMixed(db, chrom, sqlSigned(start), sqlSigned(end));
     if (NULL == seq)
         apiErrAbort(err400, err400Msg, "can not find sequence for chrom=%s for endpoint '/getData/sequence?db=%s;chrom=%s'", chrom, db, chrom);
     struct jsonWrite *jw = apiStartOutput();
     if (isNotEmpty(hubUrl))
 	jsonWriteString(jw, "hubUrl", hubUrl);
     jsonWriteString(jw, "db", db);
     jsonWriteString(jw, "chrom", chrom);
     if (isEmpty(start) || isEmpty(end))
 	{
         jsonWriteNumber(jw, "start", (long long)0);
         jsonWriteNumber(jw, "end", (long long)ci->size);
 	}
     else
 	{
         jsonWriteNumber(jw, "start", (long long)sqlSigned(start));
         jsonWriteNumber(jw, "end", (long long)sqlSigned(end));
 	}
     jsonWriteString(jw, "dna", seq->dna);
     apiFinishOutput(0, NULL, jw);
     freeDnaSeq(&seq);
     }
 else
     apiErrAbort(err400, err400Msg, "can not find specified chrom=%s in sequence for endpoint '/getData/sequence?db=%s;chrom=%s", chrom, db, chrom);
 }	/*	static void getSequenceData(char *db, char *hubUrl)	*/
 
 static void getHubSequenceData(char *hubUrl)
 /* return DNA sequence, given at least a genome=name and chrom=chr,
    optionally start and end  */
 {
 char *genome = cgiOptionalString("genome");
 char *chrom = cgiOptionalString("chrom");
 char *start = cgiOptionalString("start");
 char *end = cgiOptionalString("end");
 
 if (isEmpty(genome))
     apiErrAbort(err400, err400Msg, "missing genome=<name> for endpoint '/getData/sequence'  given hubUrl='%s'", hubUrl);
 if (isEmpty(chrom))
     apiErrAbort(err400, err400Msg, "missing chrom=<name> for endpoint '/getData/sequence?genome=%s' given hubUrl='%s'", genome, hubUrl);
 
 struct trackHub *hub = errCatchTrackHubOpen(hubUrl);
 struct trackHubGenome *hubGenome = NULL;
 for (hubGenome = hub->genomeList; hubGenome; hubGenome = hubGenome->next)
     {
     if (sameString(genome, hubGenome->name))
 	break;
     }
 if (NULL == hubGenome)
     apiErrAbort(err400, err400Msg, "failed to find specified genome=%s for endpoint '/getData/sequence'  given hubUrl '%s'", genome, hubUrl);
 
 /* might be a UCSC database track hub, where hubGenome=name is the database */
 if (isEmpty(hubGenome->twoBitPath))
     {
     getSequenceData(hubGenome->name, hubUrl);
     return;
     }
 
 /* this MaybeChromInfo will open the twoBit file, if not already done */
 struct chromInfo *ci = trackHubMaybeChromInfo(hubGenome->name, chrom);
 if (NULL == ci)
     apiErrAbort(err400, err400Msg, "can not find sequence for chrom=%s for endpoint '/getData/sequence?genome=%s;chrom=%s' given hubUrl='%s'", chrom, genome, chrom, hubUrl);
 
 struct jsonWrite *jw = apiStartOutput();
 jsonWriteString(jw, "hubUrl", hubUrl);
 jsonWriteString(jw, "genome", genome);
 jsonWriteString(jw, "chrom", chrom);
 int fragStart = 0;
 int fragEnd = 0;
 if (isNotEmpty(start) && isNotEmpty(end))
     {
     fragStart = sqlSigned(start);
     fragEnd = sqlSigned(end);
+    if ((fragEnd - fragStart) > MAX_DNA_LENGTH)
+	apiErrAbort(err400, err400Msg, "DNA sequence request %d too large, limit: %u for endpoint '/getData/sequence?genome=%s;chrom=%s;start=%d;end=%d' given hubUrl='%s'", fragEnd-fragEnd, MAX_DNA_LENGTH, genome, chrom, fragStart, fragEnd, hubUrl);
     jsonWriteNumber(jw, "start", (long long)fragStart);
     jsonWriteNumber(jw, "end", (long long)fragEnd);
     }
 else
     {
+    if (ci->size > MAX_DNA_LENGTH)
+	apiErrAbort(err400, err400Msg, "DNA sequence request %d too large, limit: %u for endpoint '/getData/sequence?genome=%s;chrom=%s' given hubUrl='%s'", ci->size, MAX_DNA_LENGTH, genome, chrom, hubUrl);
     jsonWriteNumber(jw, "start", (long long)0);
     jsonWriteNumber(jw, "end", (long long)ci->size);
     }
 struct dnaSeq *seq = twoBitReadSeqFrag(hubGenome->tbf, chrom, fragStart, fragEnd);
 if (NULL == seq)
     {
     if (fragEnd > fragStart)
 	apiErrAbort(err400, err400Msg, "can not find sequence for chrom=%s;start=%s;end=%s for endpoint '/getData/sequence?genome=%s;chrom=%s;start=%s;end=%s' give hubUrl='%s'", chrom, start, end, genome, chrom, start, end, hubUrl);
     else
 	apiErrAbort(err400, err400Msg, "can not find sequence for chrom=%s for endpoint '/getData/sequence?genome=%s;chrom=%s' give hubUrl='%s'", chrom, genome, chrom, hubUrl);
     }
 jsonWriteString(jw, "dna", seq->dna);
 apiFinishOutput(0, NULL, jw);
 }
 
 void apiGetData(char *words[MAX_PATH_INFO])
 /* 'getData' function, words[1] is the subCommand */
 {
 char *hubUrl = cgiOptionalString("hubUrl");
 if (sameWord("track", words[1]))
     {
     if (isNotEmpty(hubUrl))
 	getHubTrackData(hubUrl);
     else
 	getTrackData();
     }
 else if (sameWord("sequence", words[1]))
     {
     if (isNotEmpty(hubUrl))
 	getHubSequenceData(hubUrl);
     else
 	{
 	char *db = cgiOptionalString("db");
 	if (isEmpty(db))
 	    apiErrAbort(err400, err400Msg, "missing URL db=<ucscDb> name for endpoint '/getData/sequence");
 	getSequenceData(db, NULL);
 	}
     }
 else
     apiErrAbort(err400, err400Msg, "do not recognize endpoint function: '/%s/%s'", words[0], words[1]);
 }