4b3fe214cfd89ea4ff51f009bcd7b914bbf54f74
chmalee
  Mon Jul 22 13:44:16 2019 -0700
Change CGIs to use new omimGeneMap2 table

diff --git src/hg/hgTracks/simpleTracks.c src/hg/hgTracks/simpleTracks.c
index d545392..79d91567 100644
--- src/hg/hgTracks/simpleTracks.c
+++ src/hg/hgTracks/simpleTracks.c
@@ -12626,31 +12626,31 @@
 
 static char *omimGene2DisorderList(char *name)
 /* Return list of disorders associated with a OMIM entry.  Do not free result! */
 {
 static struct dyString *dy = NULL;
 struct sqlConnection *conn;
 char query[256];
 
 if (dy == NULL)
     dy = dyStringNew(0);
 dyStringClear(dy);
 
 // get gene symbol(s) first
 conn = hAllocConn(database);
 sqlSafef(query,sizeof(query),
-        "select geneSymbol from omimGeneMap where omimId =%s", name);
+        "select geneSymbol from omimGeneMap2 where omimId =%s", name);
 char buf[256];
 char *ret = sqlQuickQuery(conn, query, buf, sizeof(buf));
 if (isNotEmpty(ret))
     dyStringAppend(dy, ret);
 
 sqlSafef(query,sizeof(query),
         "select distinct description from omimPhenotype, omimGene2 where name='%s' and name=cast(omimId as char) order by description", name);
 char *disorders = collapseRowsFromQuery(query, "; ", 20);
 if (isNotEmpty(disorders))
     {
     dyStringAppend(dy, "; disorder(s): ");
     dyStringAppend(dy, disorders);
     }
 hFreeConn(&conn);
 return(dy->string);
@@ -12950,40 +12950,40 @@
     {
     omimId = strdup(el->name);
     if (omimId != NULL)
         {
         dyStringAppend(name, omimId);
         }
     labelStarted = TRUE;
     }
 
 if (useGeneSymbol)
     {
     if (labelStarted)
         dyStringAppendC(name, '/');
     else
         labelStarted = TRUE;
-    // get appoved gene symbol from omim2gene table first, if not available then get it from omimGeneMap table.
+    // get appoved gene symbol from omim2gene table first, if not available then get it from omimGeneMap2 table.
     char query[256];
     sqlSafef(query, sizeof(query), "select approvedGeneSymbol from omim2gene where omimId = %s", el->name);
     geneSymbol = sqlQuickString(conn, query);
     if (geneSymbol && differentString(geneSymbol, "-"))
         dyStringAppend(name, geneSymbol);
     else
         {
         char *chp;
-        sqlSafef(query, sizeof(query), "select geneSymbol from omimGeneMap where omimId = %s", el->name);
+        sqlSafef(query, sizeof(query), "select geneSymbol from omimGeneMap2 where omimId = %s", el->name);
         geneSymbol = sqlQuickString(conn, query);
         if (geneSymbol && differentString(geneSymbol, "0"))
             {
 	    // pick the first one, if multiple gene symbols exist
             chp = strstr(geneSymbol, ",");
 	    if (chp != NULL) *chp = '\0';
 	    dyStringAppend(name, geneSymbol);
 	    }
 	}
     }
 
 hFreeConn(&conn);
 return(name->string);
 }
 
@@ -13129,31 +13129,31 @@
 tg->nextPrevExon = simpleBedNextPrevEdge;
 }
 
 
 static char *omimLocationDescription(char *name)
 /* Return description of an OMIM entry */
 {
 static char omimLocationBuffer[512];
 struct sqlConnection *conn;
 char query[256];
 
 omimLocationBuffer[0] = '\0';
 
 conn = hAllocConn(database);
 sqlSafef(query,sizeof(query),
-        "select concat(title1, ' ', title2) from omimGeneMap where omimId=%s", name);
+        "select geneName from omimGeneMap2 where omimId=%s", name);
 (void)sqlQuickQuery(conn, query, omimLocationBuffer, sizeof(omimLocationBuffer));
 hFreeConn(&conn);
 return(omimLocationBuffer);
 }
 
 Color omimLocationColor(struct track *tg, void *item, struct hvGfx *hvg)
 /* set the color for omimLocation track items */
 {
 struct bed *el = item;
 char *phenClass;
 char query[256];
 struct sqlResult *sr;
 char **row;
 
 struct rgbColor *normal = &(tg->color);
@@ -13283,31 +13283,31 @@
 else
     {
     if (sameWord(omimGeneLabel, "UCSC gene symbol"))
         {
         /* get the gene symbol of the exact KG that matches not only ID but also genomic position */
         sqlSafef(query, sizeof(query),
               "select x.geneSymbol from kgXref x, omimToKnownCanonical c, knownGene k, omimGene o"
               " where c.omimId='%s' and c.kgId=x.kgId and k.name=x.kgId and o.name=c.omimId"
               " and o.chrom=k.chrom and k.txStart=%d and k.txEnd=%d",
               el->name, el->chromStart, el->chromEnd);
         geneLabel = sqlQuickString(conn, query);
         }
     else
         {
         sqlSafef(query, sizeof(query),
-	"select geneSymbol from omimGeneMap where omimId='%s'", el->name);
+	"select geneSymbol from omimGeneMap2 where omimId='%s'", el->name);
 	geneLabel = sqlQuickString(conn, query);
 	}
 
     if (geneLabel == NULL)
 	{
 	geneLabel = el->name;
 	}
     }
 hFreeConn(&conn);
 return(cloneString(geneLabel));
 }
 
 Color omimGeneColor(struct track *tg, void *item, struct hvGfx *hvg)
 /* set the color for omimGene track items */
 {