6eacdcdb29afdeefa7ba7a5ec1e52e13e86680f9
hiram
  Wed Apr 10 14:45:45 2019 -0700
better layout for selection menus and now returning errors properly refs #18869

diff --git src/hg/hubApi/getData.c src/hg/hubApi/getData.c
index da90de0..11a7513 100644
--- src/hg/hubApi/getData.c
+++ src/hg/hubApi/getData.c
@@ -90,31 +90,31 @@
 
 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("track '%s' is not a position track, request track without chrom specification, genome: '%s'", track, db);
+	apiErrAbort(400, "Bad Request", "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);
@@ -272,71 +272,71 @@
 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("missing genome=<name> for endpoint '/getData/track'  given hubUrl='%s'", hubUrl);
+    apiErrAbort(400, "Bad Request", "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);
+    apiErrAbort(400, "Bad Request", "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);
+    apiErrAbort(400, "Bad Request", "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);
+    apiErrAbort(400, "Bad Request", "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("failed to find specified track=%s in genome=%s for endpoint '/getData/track'  given hubUrl='%s'", track, genome, hubUrl);
+    apiErrAbort(400, "Bad Request", "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);
+    apiErrAbort(400, "Bad Request", "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);
+	apiErrAbort(400, "Bad Request", "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);
@@ -361,82 +361,84 @@
 	    {
 	    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);
-jsonWriteObjectEnd(jw);
-fputs(jw->dy->string,stdout);
+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("given start coordinate %u is greater than given end coordinate", uStart, uEnd);
+	apiErrAbort(400, "Bad Request", "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");
+    apiErrAbort(400, "Bad Request", "missing URL variable db=<ucscDb> name for endpoint '/getData/track");
 if (isEmpty(track))
-    apiErrAbort("missing URL variable track=<trackName> name for endpoint '/getData/track");
+    apiErrAbort(400, "Bad Request", "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);
+    apiErrAbort(400, "Bad Request", "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);
+	apiErrAbort(400, "Bad Request", "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);
@@ -451,37 +453,37 @@
 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);
+	apiErrAbort(400, "Bad Request", "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);
+	    apiErrAbort(400, "Bad Request", "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 )
     {
@@ -507,157 +509,155 @@
 	}
     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);
 
-jsonWriteObjectEnd(jw);	/* closing the overall global object */
-fputs(jw->dy->string,stdout);
+
+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("missing URL chrom=<name> for endpoint '/getData/sequence?db=%s'", db);
+    apiErrAbort(400, "Bad Request", "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);
+        apiErrAbort(400, "Bad Request", "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);
-    jsonWriteObjectEnd(jw);
-    fputs(jw->dy->string,stdout);
+    apiFinishOutput(0, NULL, jw);
     freeDnaSeq(&seq);
     }
 else
-    apiErrAbort("can not find specified chrom=%s in sequence for endpoint '/getData/sequence?db=%s&chrom=%s", chrom, db, chrom);
+    apiErrAbort(400, "Bad Request", "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("missing genome=<name> for endpoint '/getData/sequence'  given hubUrl='%s'", hubUrl);
+    apiErrAbort(400, "Bad Request", "missing genome=<name> for endpoint '/getData/sequence'  given hubUrl='%s'", hubUrl);
 if (isEmpty(chrom))
-    apiErrAbort("missing chrom=<name> for endpoint '/getData/sequence?genome=%s' given hubUrl='%s'", genome, hubUrl);
+    apiErrAbort(400, "Bad Request", "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("failed to find specified genome=%s for endpoint '/getData/sequence'  given hubUrl '%s'", genome, hubUrl);
+    apiErrAbort(400, "Bad Request", "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("can not find sequence for chrom=%s for endpoint '/getData/sequence?genome=%s&chrom=%s' given hubUrl='%s'", chrom, genome, chrom, hubUrl);
+    apiErrAbort(400, "Bad Request", "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);
     jsonWriteNumber(jw, "start", (long long)fragStart);
     jsonWriteNumber(jw, "end", (long long)fragEnd);
     }
 else
     {
     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("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);
+	apiErrAbort(400, "Bad Request", "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("can not find sequence for chrom=%s for endpoint '/getData/sequence?genome=%s&chrom=%s' give hubUrl='%s'", chrom, genome, chrom, hubUrl);
+	apiErrAbort(400, "Bad Request", "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);
-jsonWriteObjectEnd(jw);	/* closing the overall global object */
-fputs(jw->dy->string,stdout);
+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("missing URL db=<ucscDb> name for endpoint '/getData/sequence");
+	    apiErrAbort(400, "Bad Request", "missing URL db=<ucscDb> name for endpoint '/getData/sequence");
 	getSequenceData(db, NULL);
 	}
     }
 else
-    apiErrAbort("do not recognize endpoint function: '/%s/%s'", words[0], words[1]);
+    apiErrAbort(400, "Bad Request", "do not recognize endpoint function: '/%s/%s'", words[0], words[1]);
 }