eda78578a5c610db7acf00034b8823d6e9b96383
hiram
  Tue Feb 19 14:39:21 2019 -0800
returning any and all data from bigBed track refs #18869

diff --git src/hg/hubApi/getData.c src/hg/hubApi/getData.c
index 7188b0b..7a7b0b8 100644
--- src/hg/hubApi/getData.c
+++ src/hg/hubApi/getData.c
@@ -1,293 +1,329 @@
 /* manage endpoint /getData/ functions */
 
 #include "dataApi.h"
 
 static void tableDataOutput(struct sqlConnection *conn, struct jsonWrite *jw, char *query, char *table)
 /* output the table data from the specified query string */
 {
 int columnCount = tableColumns(conn, jw, table);
 jsonWriteListStart(jw, "trackData");
 struct sqlResult *sr = sqlGetResult(conn, query);
 char **row = NULL;
 while ((row = sqlNextRow(sr)) != NULL)
     {
     jsonWriteListStart(jw, NULL);
     int i = 0;
     for (i = 0; i < columnCount; ++i)
 	jsonWriteString(jw, NULL, row[i]);
     jsonWriteListEnd(jw);
     }
 jsonWriteListEnd(jw);
 }
 
 static struct bbiFile *bigFileOpen(char *trackType, char *bigDataUrl)
 {
 struct bbiFile *bbi = NULL;
 if (startsWith("bigBed", trackType))
     bbi = bigBedFileOpen(bigDataUrl);
 else if (startsWith("bigWig", trackType))
     bbi = bigWigFileOpen(bigDataUrl);
 
 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, unsigned maxItems)
+/* output the 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];
+for (iv = ivList; iv; iv = iv->next)
+    {
+    char startBuf[16], endBuf[16];
+    bigBedIntervalToRow(iv, chrom, startBuf, endBuf, row, bbi->fieldCount);
+    jsonWriteListStart(jw, NULL);
+    int i;
+    for (i = 0; i < bbi->fieldCount; ++i)
+        {
+        jsonWriteString(jw, NULL, row[i]);
+        }
+    jsonWriteListEnd(jw);
+    }
+lmCleanup(&bbLm);
+}
+
 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 = trackHubTracksForGenome(hubGenome->trackHub, hubGenome);
 
 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;
     }
 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)) )
     {
-    jsonWriteString(jw, "start", start);
-    jsonWriteString(jw, "end", end);
+    uStart = sqlUnsigned(start);
+    uEnd = sqlUnsigned(end);
+    jsonWriteNumber(jw, "start", uStart);
+    jsonWriteNumber(jw, "end", uEnd);
     }
-char *bigDataUrl = trackDbSetting(thisTrack, "bigDataUrl");
+
 jsonWriteString(jw, "bigDataUrl", bigDataUrl);
 jsonWriteString(jw, "type", thisTrack->type);
-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);
+
 if (startsWith("bigBed", thisTrack->type))
     {
     struct asObject *as = bigBedAsOrDefault(bbi);
     struct sqlFieldType *fi, *fiList = sqlFieldTypesFromAs(as);
     jsonWriteListStart(jw, "columnNames");
+    unsigned maxItems = 0;	/* TBD will use this later for paging */
 //    int columnCount = slCount(fiList);
     for (fi = fiList; fi; fi = fi->next)
 	{
 	jsonWriteObjectStart(jw, NULL);
 	jsonWriteString(jw, fi->name, fi->type);
 	jsonWriteObjectEnd(jw);
 	}
     jsonWriteListEnd(jw);
-    struct lm *bbLm = lmInit(0);
-    unsigned uStart = sqlUnsigned(start);
-    unsigned uEnd = sqlUnsigned(end);
-    struct bigBedInterval *iv, *ivList = NULL;
-    ivList = bigBedIntervalQuery(bbi,chrom, uStart, uEnd, 0, bbLm);
-    char *row[bbi->fieldCount];
     jsonWriteListStart(jw, "trackData");
-    for (iv = ivList; iv; iv = iv->next)
+    if (isEmpty(chrom))
 	{
-	char startBuf[16], endBuf[16];
-	bigBedIntervalToRow(iv, chrom, startBuf, endBuf, row, bbi->fieldCount);
-	jsonWriteListStart(jw, NULL);
-        int i;
-        for (i = 0; i < bbi->fieldCount; ++i)
+	struct bbiChromInfo *bci;
+	for (bci = chromList; bci; bci = bci->next)
 	    {
-	    jsonWriteString(jw, NULL, row[i]);
+	    bedDataOutput(jw, bbi, bci->name, 0, bci->size, maxItems);
 	    }
-	jsonWriteListEnd(jw);
 	}
+    else
+	bedDataOutput(jw, bbi, chrom, uStart, uEnd, maxItems);
     jsonWriteListEnd(jw);
-    lmCleanup(&bbLm);
     }
 else if (startsWith("bigWig", thisTrack->type))
     {
     }
 bbiFileClose(&bbi);
 jsonWriteObjectEnd(jw);
 fputs(jw->dy->string,stdout);
 }
 
 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");
 char *table = cgiOptionalString("track");
 /* 'track' name in trackDb refers to a SQL 'table' */
 
 if (isEmpty(db))
     apiErrAbort("missing URL db=<ucscDb> name for endpoint '/getData/track");
 if (isEmpty(table))
     apiErrAbort("missing URL track=<trackName> name for endpoint '/getData/track");
 struct sqlConnection *conn = hAllocConn(db);
 if (! sqlTableExists(conn, table))
     apiErrAbort("can not find specified 'track=%s' for endpoint: /getData/track?db=%s&track=%s", table, db, table);
 
 struct jsonWrite *jw = apiStartOutput();
 jsonWriteString(jw, "db", db);
 jsonWriteString(jw, "track", table);
 char *dataTime = sqlTableUpdate(conn, table);
 time_t dataTimeStamp = sqlDateToUnixTime(dataTime);
 replaceChar(dataTime, ' ', 'T');	/*	ISO 8601	*/
 jsonWriteString(jw, "dataTime", dataTime);
 jsonWriteNumber(jw, "dataTimeStamp", (long long)dataTimeStamp);
 
 char query[4096];
 /* no chrom specified, return entire table */
 if (isEmpty(chrom))
     {
     sqlSafef(query, sizeof(query), "select * from %s", table);
     tableDataOutput(conn, jw, query, table);
     }
 else if (isEmpty(start) || isEmpty(end))
     {
     if (! sqlColumnExists(conn, table, "chrom"))
 	apiErrAbort("track '%s' is not a position track, request track without chrom specification, genome: '%s'", table, 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 chrom='%s'", table, chrom);
     tableDataOutput(conn, jw, query, table);
     }
 else
     {
     if (! sqlColumnExists(conn, table, "chrom"))
 	apiErrAbort("track '%s' is not a position track, request track without chrom specification, genome: '%s'", table, db);
     jsonWriteString(jw, "chrom", chrom);
     jsonWriteNumber(jw, "start", (long long)sqlSigned(start));
     jsonWriteNumber(jw, "end", (long long)sqlSigned(end));
     sqlSafef(query, sizeof(query), "select * from %s where chrom='%s' AND chromEnd > %d AND chromStart < %d", table, chrom, sqlSigned(start), sqlSigned(end));
     tableDataOutput(conn, jw, query, table);
     }
 jsonWriteObjectEnd(jw);
 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]);
 }