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/pdbSP/pdbSP.c src/hg/pdbSP/pdbSP.c
index a73b9e5..2fa6596 100644
--- src/hg/pdbSP/pdbSP.c
+++ src/hg/pdbSP/pdbSP.c
@@ -1,167 +1,167 @@
 /* pdbSP - create xref file for PDB and SWISS-PROT IDs */
 
 /* 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(
   "pdbSP - create xref file for PDB and SWISS-PROT IDs\n"
   "usage:\n"
   "   pdbSP xxxx\n"
   "            xxxx is protein database name \n"
   "example: pdbSP proteins072003\n");
 }
 
 int main(int argc, char *argv[])
 {
 FILE *inf;
 FILE *outf;
 struct sqlConnection *conn;
 char cond_str[256];
 char *proteinDB;
 char *displayID;
 char *chp0, *chp, *chp1, *chp9;
 char line[2000];
 int  len;
 char *pdb = NULL;
 char *date;
 char *spID;
 char *endPos = NULL;
 char *answer;
 
 if ((inf = fopen("pdbtosp.htm", "r")) == NULL)
     {		
     fprintf(stderr, "Can't open input file pdbtosp.htm.\n");
     exit(8);
     }
     
 if (argc != 2) usage();
 proteinDB = cloneString(argv[1]);
 conn = hAllocConn();
 
 /* First skip to the line contains "Number of Swiss-Prot entries" */
 while (fgets(line, 1000, inf) != NULL)
     {
     if (strstr(line, "Number of Swiss-Prot entries") != NULL) break;
     }
 
 /* Then skip to the line contains "________________________" */
 while (fgets(line, 1000, inf) != NULL)
     {
     if (strstr(line, "________________________") != NULL) break;
     }
 
 outf = fopen("pdbSP.tab", "w");	
 while (fgets(line, 1000, inf) != NULL)
     {
     /* an empty line signals end of data */
     if (strlen(line) < 3) break;
 		
     if (isdigit(line[0]))
 	{
 	endPos = line + strlen(line) - 1;
 
 	/* get pdb ID */
 	chp1 = line;
 	chp9 = strstr(line, " ");
 	*chp9 = '\0';
 	pdb = strdup(chp1);
 
 	/* get date */
 	/* New pdbtosp.txt does not have the date field any more, so skip the following lines */
 	/* 
 	chp = chp9 + 1;
 	chp1 = strstr(chp, "(");
 	chp1++;
 	chp9 = strstr(chp1, ")");
 	*chp9 = '\0';
 	date = strdup(chp1);
 	*/
 	
 	chp = chp9 + 1;
 
 	more:
 	chp1 = strstr(chp, "?");
 	if (chp1 != NULL)
 	    {
 	    /* get SWISS-PROT accesion */
 	    chp1++;
 	    chp9 = strstr(chp1, "\"");
 	    *chp9 = '\0';
 	    spID = strdup(chp1);
 	
 	    /* get corresponding display ID from spXref3 table	*/
-	    sqlSafefFrag(cond_str, "accession = '%s'", spID);
+	    sqlSafef(cond_str, "accession = '%s'", spID);
             answer = sqlGetField(conn, proteinDB, "spXref3", "displayID", cond_str);
             if (answer != NULL)
                 {
                 displayID = strdup(answer);
                 }
 	    else
 		{
 		displayID = NULL;
 		}
 
 	    fprintf(outf, "%s\t%s\n", pdb, displayID);fflush(stdout);
 
 	    chp9 ++;
 	    chp = strstr(chp9, ",");
 	
 	    /* if more, loop back */		
 	    if (chp != NULL)
 		{	
 		len = (int)(endPos - chp);		
 		    {
 		    if (len > 2) goto more;
 		    }
 		}
 	    }
 	}
     else
 	{
 	/* process the case of spill over lines */
 	
 	/* get accession number */
 	chp = line;
 	more2:
 	chp1 = strstr(chp, "?");
 	chp1++;
 	chp9 = strstr(chp1, "\"");
 	*chp9 = '\0';
 	spID = strdup(chp1);
 			
 	/* get display ID from spXref3 table */
-	sqlSafefFrag(cond_str, "accession = '%s'", spID);
+	sqlSafef(cond_str, "accession = '%s'", spID);
         answer = sqlGetField(conn, proteinDB, "spXref3", "displayID", cond_str);
         if (answer != NULL)
             {
             displayID = strdup(answer);
             }
 	else
 	    {
 	    displayID = NULL;
 	    }
 	fprintf(outf, "t%s\t%s\n", pdb,  displayID);fflush(stdout);
 
 	/* loop back if more */
 	chp9 ++;
 	chp = strstr(chp9, ",");
         if (chp != NULL)
             {
             len = (int)(endPos - chp);
             	{
                 if (len > 2) goto more2;
                 }
             }
 	}	
    }
 
 fclose(outf);
 return(0);
 }