a9c9cf2828c124535a1562f709bd4437b1bf60a2
braney
  Mon Jun 22 16:41:31 2020 -0700
starting on making hgGene use and external database for the know* tables

diff --git src/hg/hgGene/pathways.c src/hg/hgGene/pathways.c
index 27ef8ec..03e4492 100644
--- src/hg/hgGene/pathways.c
+++ src/hg/hgGene/pathways.c
@@ -288,56 +288,56 @@
 char condStr[256];
 char *origSpID;
 /* check the existence of kgXref table first */
 if (!isRgdGene(conn))
     {
     if (!sqlTableExists(conn, "kgXref")) return(0);
     }
 else
     {
     if (!sqlTableExists(conn, "rgdGene2Xref")) return(0);
     }
 
 if (isRgdGene(conn))
     {
     sqlSafefFrag(condStr, sizeof(condStr), "name='%s'", geneId);
-    spID = sqlGetField(database, "rgdGene2ToUniProt", "value", condStr);
+    spID = sqlGetField(sqlGetDatabase(conn), "rgdGene2ToUniProt", "value", condStr);
     }
 else
     {
     sqlSafefFrag(condStr, sizeof(condStr), "kgID='%s'", geneId);
-    spID = sqlGetField(database, "kgXref", "spID", condStr);
+    spID = sqlGetField(sqlGetDatabase(conn), "kgXref", "spID", condStr);
     }
 
 if (spID != NULL)
     {
     origSpID = cloneString(spID);
     /* convert splice variant UniProt ID to its main root ID */
     chp = strstr(spID, "-");
     if (chp != NULL) *chp = '\0';
 
     if (!isRgdGene(conn))
         {
         sqlSafef(query, sizeof(query), 
 	  "select count(*) from %s.spReactomeEvent, %s.spVariant, %s.kgXref where kgID='%s' and kgXref.spID=variant and variant = '%s' and spReactomeEvent.spID=parent", 
-	  PROTEOME_DB_NAME, PROTEOME_DB_NAME, database, geneId, origSpID);
+	  PROTEOME_DB_NAME, PROTEOME_DB_NAME, sqlGetDatabase(conn), geneId, origSpID);
 	}
     else
     	{
         sqlSafef(query, sizeof(query), 
 	  "select count(*) from %s.spReactomeEvent, %s.spVariant, %s.rgdGene2ToUniProt where name='%s' and value=variant and variant = '%s' and spReactomeEvent.spID=parent", 
-	  PROTEOME_DB_NAME, PROTEOME_DB_NAME, database, geneId, origSpID);
+	  PROTEOME_DB_NAME, PROTEOME_DB_NAME, sqlGetDatabase(conn), geneId, origSpID);
 	}
 
     ret = sqlQuickNum(conn, query);
     }
 return ret;
 }
 
 struct pathwayLink pathwayLinks[] =
 {
    { "kegg", "KEGG", "KEGG - Kyoto Encyclopedia of Genes and Genomes", 
    	"keggPathway keggMapDesc", 
 	keggCount, keggLink},
    { "bioCyc", "BioCyc", "BioCyc Knowledge Library",
         "bioCycPathway bioCycMapDesc", 
 	bioCycCount, bioCycLink},