3bbad1670f2e44ca41d06c657b8f8636abfce4fb
hiram
  Wed Mar 27 14:47:11 2019 -0700
provide list chrom function for hubs refs #18869

diff --git src/hg/hubApi/apiUtils.c src/hg/hubApi/apiUtils.c
index e304180..7b7936d 100644
--- src/hg/hubApi/apiUtils.c
+++ src/hg/hubApi/apiUtils.c
@@ -1,97 +1,150 @@
 /* utility functions for data API business */
 
 #include "dataApi.h"
 
 void apiErrAbort(char *format, ...)
 /* Issue an error message in json format, and exit(0) */
 {
 char errMsg[2048];
 va_list args;
 va_start(args, format);
 vsnprintf(errMsg, sizeof(errMsg), format, args);
 struct jsonWrite *jw = apiStartOutput();
 jsonWriteString(jw, "error", errMsg);
 jsonWriteObjectEnd(jw);
 fputs(jw->dy->string,stdout);
 exit(0);
 }
 
 struct jsonWrite *apiStartOutput()
 /* begin json output with standard header information for all requests */
 {
 time_t timeNow = time(NULL);
 // struct tm tm;
 // gmtime_r(&timeNow, &tm);
 struct jsonWrite *jw = jsonWriteNew();
 jsonWriteObjectStart(jw, NULL);
 // not recommended: jsonWriteString(jw, "apiVersion", "v"CGI_VERSION);
 // not needed jsonWriteString(jw, "source", "UCSantaCruz");
 jsonWriteDateFromUnix(jw, "downloadTime", (long long) timeNow);
 jsonWriteNumber(jw, "downloadTimeStamp", (long long) timeNow);
 if (debug)
     jsonWriteNumber(jw, "botDelay", (long long) botDelay);
 return jw;
 }
 
 int tableColumns(struct sqlConnection *conn, struct jsonWrite *jw, char *table,
    char ***nameReturn, char ***typeReturn)
 /* return the column names, and their MySQL data type, for the given table
  *  return number of columns (aka 'fields')
  */
 {
 // not needed jsonWriteListStart(jw, "columnNames");
 struct sqlFieldInfo *fi, *fiList = sqlFieldInfoGet(conn, table);
 int columnCount = slCount(fiList);
 char **namesReturn = NULL;
 char **typesReturn = NULL;
 AllocArray(namesReturn, columnCount);
 AllocArray(typesReturn, columnCount);
 int i = 0;
 for (fi = fiList; fi; fi = fi->next)
     {
     namesReturn[i] = cloneString(fi->field);
     typesReturn[i] = cloneString(fi->type);
     i++;
 // not needed     jsonWriteObjectStart(jw, NULL);
 // not needed     jsonWriteString(jw, fi->field, fi->type);
 // not needed     jsonWriteObjectEnd(jw);
     }
 // not needed jsonWriteListEnd(jw);
 *nameReturn = namesReturn;
 *typeReturn = namesReturn;
 return columnCount;
 }
 
 struct trackHub *errCatchTrackHubOpen(char *hubUrl)
 /* use errCatch around a trackHub open in case it fails */
 {
 struct trackHub *hub = NULL;
 struct errCatch *errCatch = errCatchNew();
 if (errCatchStart(errCatch))
     {
     hub = trackHubOpen(hubUrl, "");
     }
 errCatchEnd(errCatch);
 if (errCatch->gotError)
     {
     apiErrAbort("error opening hubUrl: '%s', '%s'", hubUrl,  errCatch->message->string);
     }
 errCatchFree(&errCatch);
 return hub;
 }
 
 struct trackDb *obtainTdb(struct trackHubGenome *genome, char *db)
 /* return a full trackDb fiven the hub genome pointer, or ucsc database name */
 {
 struct trackDb *tdb = NULL;
 if (db)
     tdb = hTrackDb(db);
 else
     {
     tdb = trackHubTracksForGenome(genome->trackHub, genome);
     tdb = trackDbLinkUpGenerations(tdb);
     tdb = trackDbPolishAfterLinkup(tdb, genome->name);
     slSort(&tdb, trackDbCmp);
     }
 return tdb;
 }
+
+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;
+}
+
+struct bbiFile *bigFileOpen(char *trackType, char *bigDataUrl)
+/* open bigDataUrl for correct trackType and error catch if failure */
+{
+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;
+}
+
+int chromInfoCmp(const void *va, const void *vb)
+/* Compare to sort based on size */
+{
+const struct chromInfo *a = *((struct chromInfo **)va);
+const struct chromInfo *b = *((struct chromInfo **)vb);
+int dif;
+dif = (long) a->size - (long) b->size;
+return dif;
+}