5194786c88bd4ab5e802eec79089897461389fe9
hiram
  Fri Mar 22 14:52:22 2019 -0700
getting a little bit better refs #18869

diff --git src/hg/hubApi/getData.c src/hg/hubApi/getData.c
index 6a90351..ae734ce 100644
--- src/hg/hubApi/getData.c
+++ src/hg/hubApi/getData.c
@@ -1,526 +1,544 @@
 /* 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 tableDataOutput(char *db, struct trackDb *tdb,
     struct sqlConnection *conn, struct jsonWrite *jw, char *table,
     char *chrom, unsigned start, unsigned end)
 /* output the table data from the specified query string */
 {
 char query[4096];
 /* no chrom specified, return entire table */
 if (isEmpty(chrom))
     sqlSafef(query, sizeof(query), "select * from %s", table);
 else if (0 == (start + end))	/* have chrom, no start,end == full chr */
     {
     /* need to extend the chrom column check to allow tName also */
     if (! sqlColumnExists(conn, table, "chrom"))
 	apiErrAbort("track '%s' is not a position track, request track without chrom specification, genome: '%s'", table, db);
     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 chrom='%s'", table, chrom);
     }
 else	/* fully specified chrom:start-end */
     {
     if (! sqlColumnExists(conn, table, "chrom"))
 	apiErrAbort("track '%s' is not a position track, request track without chrom specification, genome: '%s'", table, db);
     jsonWriteNumber(jw, "start", (long long)start);
     jsonWriteNumber(jw, "end", (long long)end);
     if (startsWith("wig", tdb->type))
 	{
         wigTableDataOutput(jw, db, table, chrom, start, end);
         return;	/* DONE */
 	}
     else
 	{
 	sqlSafef(query, sizeof(query), "select * from %s where chrom='%s' AND chromEnd > %u AND chromStart < %u", table, chrom, start, end);
 	}
     }
 
 /* continuing, not a wiggle output */
 char **columnNames = NULL;
 char **columnTypes = NULL;
 int columnCount = tableColumns(conn, jw, table, &columnNames, &columnTypes);
 jsonWriteListStart(jw, table);
 struct sqlResult *sr = sqlGetResult(conn, query);
 char **row = NULL;
 unsigned itemCount = 0;
 while (itemCount < maxItemsOutput && (row = sqlNextRow(sr)) != NULL)
     {
     jsonWriteObjectStart(jw, NULL);
     int i = 0;
     for (i = 0; i < columnCount; ++i)
 	jsonWriteString(jw, columnNames[i], row[i]);
     jsonWriteObjectEnd(jw);
     ++itemCount;
     }
 sqlFreeResult(&sr);
 jsonWriteListEnd(jw);
 }
 
 static struct bbiFile *bigFileOpen(char *trackType, char *bigDataUrl)
 {
 struct bbiFile *bbi = NULL;
 struct errCatch *errCatch = errCatchNew();
 if (errCatchStart(errCatch))
     {
 if (startsWith("bigBed", trackType))
     bbi = bigBedFileOpen(bigDataUrl);
 else if (startsWith("bigWig", trackType))
     bbi = bigWigFileOpen(bigDataUrl);
     }
 errCatchEnd(errCatch);
 if (errCatch->gotError)
     {
     apiErrAbort("error opening bigFile URL: '%s', '%s'", bigDataUrl,  errCatch->message->string);
     }
 errCatchFree(&errCatch);
 return bbi;
 }
 
 /* from hgTables.h */
 struct sqlFieldType
 /* List field names and types */
     {
     struct sqlFieldType *next;
     char *name;         /* Name of field. */
     char *type;         /* Type of field (MySQL notion) */
     }; 
 
 /* from hgTables.c */
 static struct sqlFieldType *sqlFieldTypeNew(char *name, char *type)
 /* Create a new sqlFieldType */
 {
 struct sqlFieldType *ft;
 AllocVar(ft);
 ft->name = cloneString(name);
 ft->type = cloneString(type);
 return ft;
 }
 
 /* from hgTables.c */
 static struct sqlFieldType *sqlFieldTypesFromAs(struct asObject *as)
 /* Convert asObject to list of sqlFieldTypes */
 {
 struct sqlFieldType *ft, *list = NULL;
 struct asColumn *col;
 for (col = as->columnList; col != NULL; col = col->next)
     {
     struct dyString *type = asColumnToSqlType(col);
     ft = sqlFieldTypeNew(col->name, type->string);
     slAddHead(&list, ft);
     dyStringFree(&type);
     }
 slReverse(&list);
 return list;
 }
 
 static void bedDataOutput(struct jsonWrite *jw, struct bbiFile *bbi,
     char *chrom, unsigned start, unsigned end, struct sqlFieldType *fiList)
 /* output bed data for one chrom in the given bbi file */
 {
 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);
     jsonWriteObjectStart(jw, NULL);
     int i;
     struct sqlFieldType *fi = fiList;
     for (i = 0; i < bbi->fieldCount; ++i)
         {
         jsonWriteString(jw, fi->name, row[i]);
         fi = fi->next;
         }
     jsonWriteObjectEnd(jw);
     ++itemCount;
     }
 lmCleanup(&bbLm);
 }
 
 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 struct trackDb *findTrackDb(char *track, struct trackDb *tdb)
+/* search tdb structure for specific track, recursion on subtracks */
+{
+struct trackDb *trackFound = NULL;
+
+for (trackFound = tdb; trackFound; trackFound = trackFound->next)
+    {
+    if (trackFound->subtracks)
+	{
+        struct trackDb *subTrack = findTrackDb(track, trackFound->subtracks);
+	if (subTrack)
+	    {
+	    if (sameOk(subTrack->track, track))
+		trackFound = subTrack;
+	    }
+	}
+    if (sameOk(trackFound->track, track))
+	break;
+    }
+return trackFound;
+}
+
 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("missing genome=<name> for endpoint '/getdata/track'  given hubUrl='%s'", hubUrl);
 if (isEmpty(track))
     apiErrAbort("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("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("failed to find a track hub definition in genome=%s for endpoint '/getdata/track'  given hubUrl='%s'", genome, hubUrl);
 
-struct trackDb *thisTrack = NULL;
-for (thisTrack = tdb; thisTrack; thisTrack = thisTrack->next)
-    {
-    if (sameWord(thisTrack->track, track))
-	break;
-    }
+struct trackDb *thisTrack = findTrackDb(track, tdb);
+
 if (NULL == thisTrack)
     apiErrAbort("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("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("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 (startsWith("bigBed", thisTrack->type))
     {
     struct asObject *as = bigBedAsOrDefault(bbi);
     struct sqlFieldType *fiList = sqlFieldTypesFromAs(as);
     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);
 	    }
 	}
     else
 	bedDataOutput(jw, bbi, chrom, uStart, uEnd, fiList);
     jsonWriteListEnd(jw);
     }
 else if (startsWith("bigWig", thisTrack->type))
     {
     jsonWriteObjectStart(jw, track);
     wigData(jw, bbi, chrom, uStart, uEnd);
     jsonWriteObjectEnd(jw);
     }
 bbiFileClose(&bbi);
 jsonWriteObjectEnd(jw);
 fputs(jw->dy->string,stdout);
 }	/*	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("given start coordinate %u is greater than given end coordinate", uStart, uEnd);
     }
 
 if (isEmpty(db))
     apiErrAbort("missing URL variable db=<ucscDb> name for endpoint '/getData/track");
 if (isEmpty(track))
     apiErrAbort("missing URL variable track=<trackName> name for endpoint '/getData/track");
 
 struct trackDb *thisTrack = hTrackDbForTrackAndAncestors(db, track);
 if (NULL == thisTrack)
     apiErrAbort("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("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);
     }
 jsonWriteString(jw, "trackType", thisTrack->type);
 
 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("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("can not find specified chrom=%s in bigWig file URL %s", chrom, bigDataUrl);
 	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 (startsWith("bigBed", thisTrack->type))
     {
     struct asObject *as = bigBedAsOrDefault(bbi);
     struct sqlFieldType *fiList = sqlFieldTypesFromAs(as);
     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);
 	    }
 	}
     else
 	bedDataOutput(jw, bbi, chrom, uStart, uEnd, fiList);
     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);
 
 jsonWriteObjectEnd(jw);	/* closing the overall global object */
 fputs(jw->dy->string,stdout);
 hFreeConn(&conn);
 }
 
 static void getSequenceData()
 /* return DNA sequence, given at least a db=name and chrom=chr,
    optionally start and end  */
 {
 char *db = cgiOptionalString("db");
 char *chrom = cgiOptionalString("chrom");
 char *start = cgiOptionalString("start");
 char *end = cgiOptionalString("end");
 
 if (isEmpty(db))
     apiErrAbort("missing URL db=<ucscDb> name for endpoint '/getData/sequence");
 if (isEmpty(chrom))
     apiErrAbort("missing URL chrom=<name> for endpoint '/getData/sequence?db=%s", db);
 if (chromSeqFileExists(db, chrom))
     {
     struct chromInfo *ci = hGetChromInfo(db, chrom);
     struct dnaSeq *seq = NULL;
     if (isEmpty(start) || isEmpty(end))
 	seq = hChromSeqMixed(db, chrom, 0, 0);
     else
 	seq = hChromSeqMixed(db, chrom, sqlSigned(start), sqlSigned(end));
     if (NULL == seq)
         apiErrAbort("can not find sequence for chrom=%s for endpoint '/getData/sequence?db=%s&chrom=%s", chrom, db, chrom);
     struct jsonWrite *jw = apiStartOutput();
     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);
     jsonWriteObjectEnd(jw);
     fputs(jw->dy->string,stdout);
     freeDnaSeq(&seq);
     }
 else
     apiErrAbort("can not find specified chrom=%s in sequence for endpoint '/getData/sequence?db=%s&chrom=%s", chrom, db, chrom);
 }
 
 void apiGetData(char *words[MAX_PATH_INFO])
 /* 'getData' function, words[1] is the subCommand */
 {
 if (sameWord("track", words[1]))
     {
     char *hubUrl = cgiOptionalString("hubUrl");
     if (isNotEmpty(hubUrl))
 	getHubTrackData(hubUrl);
     else
 	getTrackData();
     }
 else if (sameWord("sequence", words[1]))
     getSequenceData();
 else
     apiErrAbort("do not recognize endpoint function: '/%s/%s'", words[0], words[1]);
 }