d576a4c24545bb01c2ad375f733f4c82d98ab268
braney
  Mon Aug 3 12:17:04 2020 -0700
fix up dependency on kgXref

diff --git src/hg/visiGene/vgGetText/vgGetText.c src/hg/visiGene/vgGetText/vgGetText.c
index bc8c2c2..e404c49 100644
--- src/hg/visiGene/vgGetText/vgGetText.c
+++ src/hg/visiGene/vgGetText/vgGetText.c
@@ -1,30 +1,31 @@
 /* vgGetText - Get text for full text indexing for VisiGene.
  * This is just the kgRef.description for known genes associated
  * with the visiGene genes. */
 
 /* Copyright (C) 2013 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "localmem.h"
 #include "options.h"
 #include "jksql.h"
 #include "obscure.h"
 #include "visiGene.h"
+#include "hdb.h"
 
 
 char *db = "visiGene";
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "vgGetText - Get text for full text indexing for VisiGene\n"
   "usage:\n"
   "   vgGetText out.text genomeDb [genomeDb2 ...]\n"
   "Where the genomeDb is typically the latest human, the genomeDb2 is the latest mouse, and\n"
   "as more relevant organisms get added perhaps add genomeDb3 and so forth.\n"
   "options:\n"
   "   -db=xxx - Use another database (default visiGene)\n"
@@ -105,31 +106,32 @@
 }
 
 void makeKnownGeneHashes(int knownDbCount, char **knownDbs)
 /* Create hashes containing info on known genes. */
 {
 int i;
 knownTextHash = hashNew(18);
 uniProtToKnown = hashNew(18);
 refSeqToKnown = hashNew(18);
 aliasToKnown = hashNew(19);
 nameToKnown = hashNew(18);
 
 for (i=0; i<knownDbCount; i += 1)
     {
     char *gdb = knownDbs[i];
-    struct sqlConnection *conn = sqlConnect(gdb);
+    char *knownDatabase = hdbDefaultKnownDb(gdb);
+    struct sqlConnection *conn = sqlConnect(knownDatabase);
     struct sqlResult *sr;
     char **row;
 
 
     sr = sqlGetResult(conn, NOSQLINJ "select kgID,geneSymbol,spID,spDisplayID,refseq,description from kgXref");
     while ((row = sqlNextRow(sr)) != NULL)
         {
 	char *kgID = cloneString(row[0]);
 	touppers(kgID);
 	touppers(row[1]);
 	hashAdd(nameToKnown, row[1], kgID);
 	hashAdd(uniProtToKnown, row[2], kgID);
 	hashAdd(uniProtToKnown, row[3], kgID);
 	hashAdd(refSeqToKnown, row[4], kgID);
 	hashAdd(knownTextHash, kgID, cloneString(row[5]));