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/protein/rmKGPepMrna/rmKGPepMrna.c src/hg/protein/rmKGPepMrna/rmKGPepMrna.c
index a410ad5..cbef7e2 100644
--- src/hg/protein/rmKGPepMrna/rmKGPepMrna.c
+++ src/hg/protein/rmKGPepMrna/rmKGPepMrna.c
@@ -1,140 +1,140 @@
 /* rmKGPepMrna generates new .tab files with unused mRNA and protein sequences from known genes db tables removed. */
 
 /* Copyright (C) 2013 The Regents of the University of California 
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 #include "common.h"
 #include "hCommon.h"
 #include "hdb.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "rmKGPepMrna - generate new .tab files with unused mRNA and protein sequences from known genes db tables removed."
   "usage:\n"
   "   rmKGPepMrna xxxx yyyy\n"
   "      xxxx is the genome  database name\n"
   "      yyyy is the release date of the biosql and proteins DBs\n"
   "example: rmKGPepMrna hg15 0405\n");
 }
 
 int main(int argc, char *argv[])
 {
 struct sqlConnection *conn, *conn2;
 char query2[256];
 struct sqlResult *sr2;
 char **row2;
 
 char cond_str[256];
 char *kgID;
 char *proteinID;
 char *seq;
 char *acc;
  
 char protDbName[100];
 char spDbName[100];
 char *dbName;
 char *ro_dbName;
 
 FILE *o1, *o2;
 
 struct dnaSeq *kgSeq;
     
 if (argc != 4) usage();
 
 o1 = fopen("j.dat",  "w");
 o2 = fopen("jj.dat", "w");
     
 dbName = argv[1];
 ro_dbName = argv[3];
 sprintf(protDbName,   "proteins%s", argv[2]);
 sprintf(spDbName, "sp%s",   argv[2]);
 
 conn= hAllocConn(ro_dbName);
 conn2= hAllocConn(ro_dbName);
 sqlSafef(query2, sizeof query2, "select name from %s.knownGene;", dbName);
 sr2 = sqlMustGetResult(conn2, query2);
 row2 = sqlNextRow(sr2);
 while (row2 != NULL)
     {
     kgID    = row2[0];
     
-    sqlSafefFrag(cond_str, sizeof cond_str, "name = '%s';", kgID);
+    sqlSafef(cond_str, sizeof cond_str, "name = '%s';", kgID);
     seq = sqlGetField(dbName, "knownGenePep", "seq", cond_str);
     if (seq != NULL)
 	{
         fprintf(o1, "%s\t%s\n", kgID, seq);fflush(o1);
 	}
     else
 	{
-        sqlSafefFrag(cond_str, sizeof cond_str, "name = '%s';", kgID);
+        sqlSafef(cond_str, sizeof cond_str, "name = '%s';", kgID);
         proteinID=sqlGetField(dbName, "knownGene", "proteinID", cond_str);
 	if (proteinID != NULL)
 	    {
-            sqlSafefFrag(cond_str, sizeof cond_str, "val = '%s';", proteinID);
+            sqlSafef(cond_str, sizeof cond_str, "val = '%s';", proteinID);
             acc = sqlGetField(spDbName, "displayId", "acc", cond_str);
 	    if (acc == NULL)
 		{
 fprintf(stderr, "NO acc.displayId.%s: %s from name.knownGene.%s: %s\n", spDbName, proteinID, dbName, kgID);
 		fflush(stderr);
 		}
 	    else
 		{
-		sqlSafefFrag(cond_str, sizeof cond_str, "acc = '%s';", acc);
+		sqlSafef(cond_str, sizeof cond_str, "acc = '%s';", acc);
 		seq = sqlGetField(spDbName, "protein", "val", cond_str);
 		if (seq == NULL)
 		    {
 		    fprintf(stderr, "NO protein seq for %s\n", kgID);
 		    fprintf(stderr, "proteinID.knownGene.%s: %s, acc.displayID.%s: %s\n", dbName, proteinID, spDbName, acc);
 		    fflush(stderr);
 		    }
 		    else
 		    {
 		    fprintf(o1, "%s\t%s\n", kgID, seq);
 		    }
 		}
 	    } else {
 fprintf(stderr, "kgID: %s not in knownGenePep or knownGene\n", kgID);
 	    }
 	}
 
-    sqlSafefFrag(cond_str, sizeof cond_str, "name = '%s';", kgID);
+    sqlSafef(cond_str, sizeof cond_str, "name = '%s';", kgID);
         
     seq = sqlGetField(dbName, "knownGeneMrna", "seq", cond_str);
     if (seq != NULL)
     	{
         fprintf(o2, "%s\t%s\n", kgID, seq);fflush(o1);
         }
     else
         {
 	kgSeq = hGenBankGetMrna(dbName, kgID, NULL);
 	   
 	if (kgSeq != NULL)
 	    {
             fprintf(o2, "%s\t%s\n", kgID, kgSeq->dna);fflush(o1);
             }
 	else
 	    {
 	    fprintf(stderr, "NO mRNA seq for %s\n", kgID);fflush(stderr);
 	    }
 	}
     row2 = sqlNextRow(sr2);
     }
 
 sqlFreeResult(&sr2);
 hFreeConn(&conn);
 hFreeConn(&conn2);
 
 fclose(o1);
 fclose(o2);
     
 mustSystem("cat j.dat |sort|uniq > knownGenePep.tab");
 mustSystem("cat jj.dat|sort|uniq > knownGeneMrna.tab");
 mustSystem("rm j.dat");
 mustSystem("rm jj.dat");
 
 return(0);
 }