3ef1589ee01ec67a7cfd1ddfb050f606c3a03ccb
braney
  Thu Jun 27 11:23:38 2019 -0700
make sure bigBed gets closed even if it's asked for an index it doesn't
have

diff --git src/hg/lib/bigBedFind.c src/hg/lib/bigBedFind.c
index 23b8603..f991e81 100644
--- src/hg/lib/bigBedFind.c
+++ src/hg/lib/bigBedFind.c
@@ -1,184 +1,188 @@
 #include "common.h"
 #include "bPlusTree.h"
 #include "bbiFile.h"
 #include "bigBed.h"
 #include "hgFind.h"
 #include "trix.h"
 #include "trackHub.h"
 #include "hubConnect.h"
 #include "hdb.h"
 #include "errCatch.h"
 #include "bigBedLabel.h"
 #include "bigBedFind.h"
 
 static struct hgPos *bigBedIntervalListToHgPositions(struct cart *cart, struct trackDb *tdb,  struct bbiFile *bbi, char *term, struct bigBedInterval *intervalList, char *description)
 /* Given an open bigBed file, and an interval list, return a pointer to a list of hgPos structures. */
 {
 struct hgPos *posList = NULL;
 char chromName[bbi->chromBpt->keySize+1];
 int lastChromId = -1;
 struct bigBedInterval *interval;
 struct slInt *labelColumns = NULL;
 
 bigBedLabelCalculateFields(cart, tdb, bbi,  &labelColumns );
 for (interval = intervalList; interval != NULL; interval = interval->next)
     {
     struct hgPos *hgPos;
     AllocVar(hgPos);
     slAddHead(&posList, hgPos);
 
     bbiCachedChromLookup(bbi, interval->chromId, lastChromId, chromName, sizeof(chromName));
     lastChromId = interval->chromId;
 
     hgPos->chrom = cloneString(chromName);
     hgPos->chromStart = interval->start;
     hgPos->chromEnd = interval->end;
     hgPos->name = bigBedMakeLabel(tdb, labelColumns, interval, chromName);
     hgPos->browserName = cloneString(term);
     hgPos->description = cloneString(description);
     }
 
 return posList;
 }
 
 static struct hgPos *getPosFromBigBed(struct cart * cart, struct trackDb *tdb, char *bigDataUrl, char *indexField, char *term, char *description)
 /* Given a bigBed file with a search index, check for term. */
 {
 struct errCatch *errCatch = errCatchNew();
 struct hgPos *posList = NULL;
+struct bbiFile *bbi = NULL;
 if (errCatchStart(errCatch))
     {
-    struct bbiFile *bbi = bigBedFileOpen(bigDataUrl);
+    bbi = bigBedFileOpen(bigDataUrl);
     int fieldIx;
     struct bptFile *bpt = bigBedOpenExtraIndex(bbi, indexField, &fieldIx);
     struct lm *lm = lmInit(0);
     struct bigBedInterval *intervalList;
     intervalList = bigBedNameQuery(bbi, bpt, fieldIx, term, lm);
 
     posList = bigBedIntervalListToHgPositions(cart, tdb,  bbi, term, 
         intervalList, description);
     bbiFileClose(&bbi);
     }
 errCatchEnd(errCatch);
 if (errCatch->gotError) 
+    {
+    bbiFileClose(&bbi);
     // we fail silently if bigBed is missing
     return NULL;
+    }
 
 return posList;
 }
 
 static struct hgPos *doTrixSearch(struct cart *cart, struct trackDb *tdb, char *trixFile, struct slName  *indices, char *bigDataUrl, char *term, char *description)
 /* search a trix file in the "searchTrix" field of a bigBed trackDb */
 {
 struct trix *trix = trixOpen(trixFile);
 int trixWordCount = 0;
 char *tmp = cloneString(term);
 char *val = nextWord(&tmp);
 char *trixWords[128];
 
 while (val != NULL)
     {
     trixWords[trixWordCount] = strLower(val);
     trixWordCount++;
     if (trixWordCount == sizeof(trixWords)/sizeof(char*))
 	errAbort("exhausted space for trixWords");
 
     val = nextWord(&tmp);        
     }
 
 if (trixWordCount == 0)
     return NULL;
 
 struct trixSearchResult *tsList = trixSearch(trix, trixWordCount, trixWords, tsmExpand);
 struct hgPos *posList = NULL;
 for ( ; tsList != NULL; tsList = tsList->next)
     {
     struct slName *oneIndex = indices;
     for (; oneIndex; oneIndex = oneIndex->next)
 	{
 	struct hgPos *posList2 = getPosFromBigBed(cart, tdb, bigDataUrl, oneIndex->name, tsList->itemId, description);
 
 	posList = slCat(posList, posList2);
 	}
     }
 
 return posList;
 }
 
 
 boolean findBigBedPosInTdbList(struct cart *cart, char *db, struct trackDb *tdbList, char *term, struct hgPositions *hgp, struct hgFindSpec *hfs)
 /* Given a list of trackDb entries, check each of them for a searchIndex */
 {
 char *description = NULL;
 if (hfs)
     {
     char buf[2048];
     if (isNotEmpty(hfs->searchDescription))
         truncatef(buf, sizeof(buf), "%s", hfs->searchDescription);
     else
         safef(buf, sizeof(buf), "%s", hfs->searchTable);
     description = cloneString(buf);
     }
 struct trackDb *tdb;
 boolean found = FALSE;
 for(tdb=tdbList; tdb; tdb = tdb->next)
     {
     if (tdb->subtracks)
         found = findBigBedPosInTdbList(cart, db, tdbList->subtracks, term, hgp, hfs) || found;
 
     char *indexField = trackDbSetting(tdb, "searchIndex");
     char *fileName = NULL;
 
     if (isHubTrack(tdb->table))
 	fileName = trackDbSetting(tdb, "bigDataUrl");
     else
 	{
 	struct sqlConnection *conn = hAllocConnTrack(db, tdb);
 	fileName = bbiNameFromSettingOrTable(tdb, conn, tdb->table);
 	hFreeConn(&conn);
 	}
 
     if (!(indexField && fileName))
 	continue;
 
     struct slName *indexList = slNameListFromString(indexField, ',');
     struct hgPos *posList1 = NULL, *posList2 = NULL;
     char *trixFile = trackDbSetting(tdb, "searchTrix");
     // if there is a trix file, use it to search for the term
     if (trixFile != NULL)
 	{
         struct errCatch *errCatch = errCatchNew();
         if (errCatchStart(errCatch))
             {
             posList1 = doTrixSearch(cart, tdb, hReplaceGbdb(trixFile), indexList, fileName, term, NULL);
             }
         errCatchEnd(errCatch);
         if (errCatch->gotError)
             warn("trix search failure for %s: %s", tdb->table, dyStringContents(errCatch->message));
         errCatchFree(&errCatch);
 	}
 
     // now search for the raw id's
     struct slName *oneIndex=indexList;
     for (; oneIndex; oneIndex = oneIndex->next)
 	{
 	posList2 = getPosFromBigBed(cart, tdb, fileName, oneIndex->name, term, NULL);
 	posList1 = slCat(posList1, posList2);
 	}
 
     if (posList1 != NULL)
 	{
 	struct hgPosTable *table;
 
 	found = TRUE;
 	AllocVar(table);
 	slAddHead(&hgp->tableList, table);
 	table->description = cloneString(description ? description : tdb->longLabel);
 	table->name = cloneString(tdb->table);
 
 	table->posList = posList1;
 	}
     }
 freeMem(description);
 return found;
 }