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/kgAliasM/kgAliasM.c src/hg/protein/kgAliasM/kgAliasM.c
index aa61794..20061c5 100644
--- src/hg/protein/kgAliasM/kgAliasM.c
+++ src/hg/protein/kgAliasM/kgAliasM.c
@@ -1,150 +1,150 @@
 /* kgAliasM - generate alias list table (the mRNA part, there is another protein part) */
 
 /* 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(
   "kgAliasM - create gene alias (mRNA part) .tab files "
   "usage:\n"
   "   kgAliasM xxxx yyyy\n"
   "            xxxx is genome  database name\n"
   "            yyyy is protein database name \n"
   "example: kgAliasM hg15 proteins0405\n");
 }
 
 int main(int argc, char *argv[])
 {
 struct sqlConnection *conn;
 
 char query2[256];
 struct sqlResult *sr2;
 char **row2;
     
 char *chp0, *chp;
 char *kgID;
 FILE *o1, *o2;
 char cond_str[256];
 char *database;
 char *proteinDB;
 boolean doingAlias, bothDone;
 
 char *answer;
 char *symbol, *alias, *aliases;
 
 if (argc != 3) usage();
 database  = cloneString(argv[1]);
 proteinDB = cloneString(argv[2]);
 
 conn= hAllocConn(database);
 o1 = fopen("j.dat", "w");
 o2 = fopen("jj.dat", "w");
 
 doingAlias = TRUE;
 bothDone   = FALSE;
 
 while (!bothDone)
     {
     if (doingAlias)
 	{
     	sqlSafef(query2, sizeof query2, "select symbol, aliases from %s.hgnc;", proteinDB);
 	}
     else
 	{
         sqlSafef(query2, sizeof query2, "select symbol, prvSymbols from %s.hgnc;", proteinDB);
     	}
     
     sr2 = sqlMustGetResult(conn, query2);
     row2 = sqlNextRow(sr2);
     while (row2 != NULL)
 	{
 	symbol		= row2[0];
 	aliases		= row2[1];
 
 	if ( (symbol  != NULL) && (strlen(symbol) != 0) )
 	    {
-            sqlSafefFrag(cond_str, sizeof cond_str, "geneSymbol = '%s'", symbol);
+            sqlSafef(cond_str, sizeof cond_str, "geneSymbol = '%s'", symbol);
             answer = sqlGetField(database, "kgXref", "kgID", cond_str);
 	    if (answer != NULL)
 		{
 		kgID = strdup(answer);
 		fprintf(o2, "%s\t%s\n", kgID, symbol);
 		}
 	    if ( (aliases  != NULL) && (strlen(aliases) != 0) && (answer != NULL) )
 		{
 		kgID = strdup(answer);
     
 		chp0 = aliases; 
 	    	while (chp0 != NULL)
 		    {
 		    while (*chp0 == ' ') chp0++;
 		    chp = strstr(chp0, ",");
 		    if (chp == NULL)
 			{
 			alias = strdup(chp0);
 			
 			/* get rid of quote character in some aliases */
 			if (*alias == '"') 
 			    {
 			    *(alias + strlen(alias) - 1) = '\0';
 			    alias++;
 			    printf("%s\n", alias);fflush(stdout);
 			    }
 			chp0 = NULL;
 			}
 		    else
 			{
 			*chp = '\0';
 			
 			/* get rid of quote character in some aliases */
 			if (*chp0 == '"') 
 			    {
 			    *(chp0 + strlen(chp0) - 1) = '\0';
 			    chp0++;
 			    printf("%s\n", chp0);fflush(stdout);
 			    }
 			alias = strdup(chp0);
 			chp0 = chp+1;
 			}
 		    if (kgID != NULL)
 			{
 			fprintf(o1, "%s\t%s\t%s\n", kgID, symbol, alias);
 			fprintf(o2, "%s\t%s\n", kgID, alias);
 			}
 		    }
 		}
 	    }
 	row2 = sqlNextRow(sr2);
 	}
     sqlFreeResult(&sr2);
 
     if (doingAlias) 
 	{
 	doingAlias = FALSE;
 	}
     else
 	{
 	bothDone = TRUE;
 	}
     }
 fclose(o1);
 fclose(o2);
 
 /* geneAlias.tab has 3 columns, the 2nd is HUGO.symbol 
    and 3rd contains aliases and withdraws */
 
 mustSystem("cat  j.dat|sort|uniq  >geneAlias.tab");
 
 /*  kgAliasM.tab has 2 columns, all entries from HUGO.symbol, HUGO.aliass, 
     and HUGO.withdraws are listed in the 2nd column. */
 mustSystem("cat jj.dat|sort|uniq  >kgAliasM.tab");
 mustSystem("rm j.dat");
 mustSystem("rm jj.dat");
     
 return(0);
 }