81e8b9cb578ac40b8cdd16e3ffa306b5b167d66f
braney
  Sat Mar 18 12:30:15 2017 -0700
allow bigBed trix searches to work on GBDB by checking for hgdownload as
well as local files

diff --git src/hg/lib/bigBedFind.c src/hg/lib/bigBedFind.c
index 44b61a3..ebaaf30 100644
--- src/hg/lib/bigBedFind.c
+++ src/hg/lib/bigBedFind.c
@@ -1,156 +1,156 @@
 #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"
 
 static struct hgPos *bigBedIntervalListToHgPositions(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;
 
 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 = cloneString(term);
     hgPos->browserName = cloneString(term);
     hgPos->description = cloneString(description);
     }
 
 return posList;
 }
 
 static struct hgPos *getPosFromBigBed(char *bigDataUrl, char *indexField, char *term, char *description)
 /* Given a bigBed file with a search index, check for term. */
 {
 struct bbiFile *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);
 
 struct hgPos *posList = bigBedIntervalListToHgPositions(bbi, term, 
     intervalList, description);
 bbiFileClose(&bbi);
 return posList;
 }
 
 static struct hgPos *doTrixSearch(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(bigDataUrl, oneIndex->name, tsList->itemId, description);
 
 	posList = slCat(posList, posList2);
 	}
     }
 
 return posList;
 }
 
 
 boolean findBigBedPosInTdbList(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 */
 {
 struct trackDb *tdb;
 boolean found = FALSE;
 
 for(tdb=tdbList; tdb; tdb = tdb->next)
     {
     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)
 	{
 	char buf[2048];
 	char *description = NULL;
 	if (hfs && isNotEmpty(hfs->searchDescription))
 	    truncatef(buf, sizeof(buf), "%s", hfs->searchDescription);
 	else
 	    safef(buf, sizeof(buf), "%s", hfs->searchTable);
 	description = cloneString(buf);
-	posList1 = doTrixSearch(trixFile, indexList, fileName, term, description);
+	posList1 = doTrixSearch(hReplaceGbdb(trixFile), indexList, fileName, term, description);
 	}
 
     // now search for the raw id's
     struct slName *oneIndex=indexList;
     for (; oneIndex; oneIndex = oneIndex->next)
 	{
 	posList2 = getPosFromBigBed(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(tdb->table);
 	table->name = cloneString(tdb->table);
 
 	table->posList = posList1;
 	}
     }
 
 return found;
 }