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/omimCheckAv/omimCheckAv.c src/hg/protein/omimCheckAv/omimCheckAv.c
index dd020d5..9f4f811 100644
--- src/hg/protein/omimCheckAv/omimCheckAv.c
+++ src/hg/protein/omimCheckAv/omimCheckAv.c
@@ -1,155 +1,155 @@
 /* omimCheckAv - validate AV positions against protein sequences */
 
 /* 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"
 #include "spDb.h"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "omimCheckAv - validate AV positions against protein sequences\n"
   "usage:\n"
   "   omimCheckAv gdb outfile\n"
   "      gdb is the geneome DB\n"
   "      outFile is the validated AV positions"
   "example: omimCheckAv hg17 omimAvPosValidated.tab\n");
 }
 
 int main(int argc, char *argv[])
 {
 struct sqlConnection *conn2, *conn3, *conn4;
  
 char query2[256], query3[256];
 struct sqlResult *sr2, *sr3;
 char **row2, **row3;
 
 char *accession;
 char *extDB;
 char *extAC;
 char condStr[255];
 
 char *id, *subId, *avStr, *pos;
 char *baseAAStr, *subsAAStr;
 char baseAA, subsAA;
 
 char *genomeDb;
 char *aaSeq;
 char ch;
 
 int  aaPos, aaLen;
 int nTotal = 0;
 int nOK    = 0;
 int nBase  = 0;
 int nErr   = 0;
 int nSubs  = 0;
 boolean gotAMatch = FALSE;
 
 FILE   *outf;
 
 if (argc != 3) usage();
 genomeDb = argv[1];
    
 outf = fopen(argv[2], "w");
 conn2= hAllocConn();
 conn3= hAllocConn();
 conn4= hAllocConn();
 	
 /* loop thru all recordd in the omimAvPos table */
 sqlSafef(query2, sizeof query2, "select * from %s.omimAvPos", genomeDb);
 sr2 = sqlMustGetResult(conn2, query2);
 row2 = sqlNextRow(sr2);
 while (row2 != NULL)
     {
     id 		= row2[0];
     subId 	= row2[1];
     avStr	= row2[2];
     pos 	= row2[3];
     baseAAStr	= row2[4];
     subsAAStr	= row2[5]; 
     
     baseAA	= *baseAAStr;
     subsAA	= *subsAAStr;
     aaPos 	= atoi(pos);
     
     /* find corresponding protein for each OMIM record */
     sqlSafef(query3, sizeof query3,  
         "select distinct accession, extDB, extAC from %s.spXref2 where extAC='%s' and extDB='MIM';",
     	    PROTEOME_DB_NAME, id);
 
     sr3 = sqlMustGetResult(conn3, query3);
     row3 = sqlNextRow(sr3);
 
     while (row3 != NULL)
 	{
    	accession = row3[0];
 	extDB	  = row3[1];     
 	extAC	  = row3[2];
 
 	nTotal++;
         
 	gotAMatch = FALSE;
 	
 	/* get protein sequence */
-	sqlSafefFrag(condStr, sizeof condStr, "acc='%s'", accession);
+	sqlSafef(condStr, sizeof condStr, "acc='%s'", accession);
 	aaSeq = sqlGetField(UNIPROT_DB_NAME, "protein", "val", condStr);
 	aaLen = strlen(aaSeq);
 
 	/* check AA (both base and substitition) of the AV entry against 
 	   AA in the protein sequence */
 	if (aaPos <= aaLen)
 	    {
 	    ch = *(aaSeq+aaPos-1);
 	    if (ch == baseAA)
 	    	{
 		gotAMatch = TRUE;
 		nOK++;
 		nBase++;
 		}
 	    else
 	    	{
 	    	if (ch == subsAA)
 	    	    {
 		    gotAMatch = TRUE;
 		    nOK++;
 		    nSubs++;
 		    }
 		}
 	    
 	    if (gotAMatch) 
 	    	{
 	        fprintf(outf, "%s\t%s\t%s\t%s\n", id, subId, accession, pos);
 	    	}
 	    else 
 	    	{
 		nErr++;
 		}
 	    }
 	else
 	    {
 	    nErr++;
 	    }
 	
 	row3 = sqlNextRow(sr3);
 	}
     sqlFreeResult(&sr3);
     row2 = sqlNextRow(sr2);
     }
 sqlFreeResult(&sr2);
 
 hFreeConn(&conn2);
 hFreeConn(&conn3);
 fclose(outf);
 
 fprintf(stderr, "nTotal\t= %6d\n", nTotal);
 fprintf(stderr, "nOk\t= %6d\n", nOK);
 fprintf(stderr, "nBase\t= %6d\n", nBase);
 fprintf(stderr, "nSub\t= %6d\n", nSubs);
 fprintf(stderr, "nErr\t= %6d\n", nErr);
 
 return(0);
 }