5e4c5867d5a5b041bbaaa72dea9236c7bbb0fbf8
jnavarr5
  Tue Feb 19 14:20:38 2019 -0800
Accidentally inserted the ENCODE section after the anniversary title section, refs #20314

diff --git src/hg/hubApi/getData.c src/hg/hubApi/getData.c
index 6f40d0a..7188b0b 100644
--- src/hg/hubApi/getData.c
+++ src/hg/hubApi/getData.c
@@ -8,30 +8,178 @@
 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 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);
+
+struct jsonWrite *jw = apiStartOutput();
+jsonWriteString(jw, "hubUrl", hubUrl);
+jsonWriteString(jw, "genome", genome);
+jsonWriteString(jw, "track", track);
+if (isNotEmpty(chrom))
+    jsonWriteString(jw, "chrom", chrom);
+if ( ! (isEmpty(start) || isEmpty(end)) )
+    {
+    jsonWriteString(jw, "start", start);
+    jsonWriteString(jw, "end", end);
+    }
+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");
+//    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)
+	{
+	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);
+	}
+    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))
@@ -119,21 +267,27 @@
         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]);
 }