44ccfacbe3a3d4b300f80d48651c77837a4b571e
galt
  Tue Apr 26 11:12:02 2022 -0700
SQL INJECTION Prevention Version 2 - this improves our methods by making subclauses of SQL that get passed around be both easy and correct to use. The way that was achieved was by getting rid of the obscure and not well used functions sqlSafefFrag and sqlDyStringPrintfFrag and replacing them with the plain versions of those functions, since these are not needed anymore. The new version checks for NOSQLINJ in unquoted %-s which is used to include SQL clauses, and will give an error the NOSQLINJ clause is not present, and this will automatically require the correct behavior by developers. sqlDyStringPrint is a very useful function, however because it was not enforced, users could use various other dyString functions and they operated without any awareness or checking for SQL correct use. Now those dyString functions are prohibited and it will produce an error if you try to use a dyString function on a SQL string, which is simply detected by the presence of the NOSQLINJ prefix.

diff --git src/hg/featureBits/featureBits.c src/hg/featureBits/featureBits.c
index 363ec5c..b658645 100644
--- src/hg/featureBits/featureBits.c
+++ src/hg/featureBits/featureBits.c
@@ -138,31 +138,35 @@
   "providing all tables as files or directories.\n"
   );
 }
 
 static struct chromInfo *fbCreateChromInfoList(char *name, char *database)
 /* Load up all chromosome infos. */
 {
 struct sqlConnection *conn = sqlConnect(database);
 struct sqlResult *sr = NULL;
 char **row;
 int loaded=0;
 struct chromInfo *ret = NULL;
 unsigned totalSize = 0;
 
 if (sameWord(name, "all"))
-    sr = sqlGetResult(conn, NOSQLINJ "select * from chromInfo");
+    {
+    char query[1024];
+    sqlSafef(query, sizeof query, "select * from chromInfo");
+    sr = sqlGetResult(conn, query);
+    }
 else
     {
     char select[256];
     sqlSafef(select, ArraySize(select), "select * from chromInfo where chrom='%s'",
 	name);
     sr = sqlGetResult(conn, select);
     }
 
 while ((row = sqlNextRow(sr)) != NULL)
     {
     struct chromInfo *el;
     struct chromInfo *ci;
     AllocVar(ci);
 
     el = chromInfoLoad(row);
@@ -680,32 +684,33 @@
 struct chromInfo *cInfo;
 struct sqlResult *sr;
 char **row;
 struct hash *ret;
 int totalGapSize = 0;
 int gapCount = 0;
 
 ret = newHash(0);
 
 /*	If not split, read in whole gulp, create per-chrom hash of sizes */
 if (hTableExists(db, "gap"))
     {
     char *prevChrom = NULL;
     int totalGapsThisChrom = 0;
 
-    sr = sqlGetResult(conn,
-	NOSQLINJ "select chrom,chromStart,chromEnd from gap order by chrom");
+    char query[1024];
+    sqlSafef(query, sizeof query, "select chrom,chromStart,chromEnd from gap order by chrom");
+    sr = sqlGetResult(conn, query);
     while ((row = sqlNextRow(sr)) != NULL)
 	{
 	int gapSize = sqlUnsigned(row[2]) - sqlUnsigned(row[1]);
 	++gapCount;
 	if (prevChrom && sameWord(prevChrom,row[0]))
 	    {
 	    totalGapsThisChrom += gapSize;
 	    totalGapSize += gapSize;
 	    }
 	else
 	    {
 	    if (prevChrom)
 		{
 		hashAddInt(ret, prevChrom, totalGapsThisChrom);
 		freeMem(prevChrom);