26f287e3c79aa9fa6c2a67487e2185e23e0f6dd0
braney
  Mon Aug 20 13:09:38 2012 -0700
more changes to support UCSC genes (#7045).   Added script to build new proteome database, fixed some utilities used in the building of that database, removed dependency on gdbPdb table in hgcentral (now it just uses the most recent proteome database rather than having a proteins database per assembly)
diff --git src/hg/lib/hdb.c src/hg/lib/hdb.c
index cfb4a38..d4067f3 100644
--- src/hg/lib/hdb.c
+++ src/hg/lib/hdb.c
@@ -2059,68 +2059,34 @@
 {
 struct slName *chromList = hChromList(db);
 struct slName *chrom;
 struct bed *list = NULL;
 for (chrom = chromList; chrom != NULL; chrom = chrom->next)
     {
     struct bed *bedList = hGetBedRange(db, table, chrom->name, 0, 0, NULL);
     list = slCat(list, bedList);
     }
 slFreeList(&chromList);
 return list;
 }
 
 char *hPdbFromGdb(char *genomeDb)
 /* Find proteome database name given genome database name */
+/* With the retirement of the proteome browser, we always use the most
+ * recent version of the database which is called "proteome" */
 {
-struct sqlConnection *conn = hConnectCentral();
-struct sqlResult *sr;
-char **row;
-char *ret = NULL;
-struct dyString *dy = newDyString(128);
-
-if (sqlTableExists(conn, "gdbPdb"))
-    {
-    if (genomeDb != NULL)
-	dyStringPrintf(dy, "select proteomeDb from gdbPdb where genomeDb = '%s';", genomeDb);
-    else
-	internalErr();
-    sr = sqlGetResult(conn, dy->string);
-    if ((row = sqlNextRow(sr)) != NULL)
-	{
-	ret = cloneString(row[0]);
-	}
-    else
-	{
-	// if a corresponding protein DB is not found, get the default one from the gdbPdb table
-        sqlFreeResult(&sr);
-    	sr = sqlGetResult(conn,  "select proteomeDb from gdbPdb where genomeDb = 'default';");
-    	if ((row = sqlNextRow(sr)) != NULL)
-	    {
-	    ret = cloneString(row[0]);
-	    }
-	else
-	    {
-	    errAbort("No protein database defined for %s.", genomeDb);
-	    }
-	}
-
-    sqlFreeResult(&sr);
-    }
-hDisconnectCentral(&conn);
-freeDyString(&dy);
-return(ret);
+return "proteome";
 }
 
 static char *hFreezeDbConversion(char *database, char *freeze)
 /* Find freeze given database or vice versa.  Pass in NULL
  * for parameter that is unknown and it will be returned
  * as a result.  This result can be freeMem'd when done. */
 {
 struct sqlConnection *conn = hConnectCentral();
 struct sqlResult *sr;
 char **row;
 char *ret = NULL;
 struct dyString *dy = newDyString(128);
 
 if (database != NULL)
     dyStringPrintf(dy, "select description from dbDb where name = '%s'", database);