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/utils/subColumn/subColumn.c src/utils/subColumn/subColumn.c
index 832c872..ee4c5ca 100644
--- src/utils/subColumn/subColumn.c
+++ src/utils/subColumn/subColumn.c
@@ -1,169 +1,169 @@
 /* subColumn - Substitute one column in a tab-separated file.. */
 
 /* Copyright (C) 2011 The Regents of the University of California 
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 #include "common.h"
 #include "localmem.h"
 #include "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "dystring.h"
 #include "obscure.h"
 
 
 boolean isList = FALSE;
 boolean skipMiss = FALSE;
 FILE *fMiss = NULL;
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "subColumn - Substitute one column in a tab-separated file.\n"
   "usage:\n"
   "   subColumn column in.tab sub.tab out.tab\n"
   "Where:\n"
   "    column is the column number (starting with 1)\n"
   "    in.tab is a tab-separated file\n"
   "    sub.tab is a where first column is old values, second new\n"
   "    out.tab is the substituted output\n"
   "options:\n"
   "   -list - Column is a comma-separated list.  Substitute all elements in list\n"
   "   -miss=fileName - Print misses to this file instead of aborting\n"
   "   -skipMiss -- skip missing id's instead of outputting them\n"
   );
 }
 
 static struct optionSpec options[] = {
    {"list", OPTION_BOOLEAN},
    {"miss", OPTION_STRING},
    {"skipMiss", OPTION_BOOLEAN},
    {NULL, 0},
 };
 
 char *subCommaList(struct hash *subHash, char *in)
 /* In is a comma-separated list.  Return the list with
  * substitution done.  This routine not reentrant. */
 {
 static struct dyString *dy;
 if (dy == NULL)
     dy = dyStringNew(0);
 else
     dyStringClear(dy);
 while (in != NULL && in[0] != 0)
     {
     char *e = strchr(in, ',');
     if (e != NULL)
         *e++ = 0;
     char *s = hashMustFindVal(subHash, in);
     dyStringPrintf(dy, "%s,", s);
     in = e;
     }
 return dy->string;
 }
 
 int missCount = 0;
 
 struct hash *hashTwoColumnTsv(char *fileName)
 /* Given a two column file (key, value) return a hash. */
 {
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 struct hash *hash = hashNew(16);
 char *row[3];
 int fields = 0;
 while ((fields = lineFileChopTab(lf, row)) != 0)
     {
     lineFileExpectWords(lf, 2, fields);
     char *name = row[0];
     char *value = lmCloneString(hash->lm, row[1]);
     hashAdd(hash, name, value);
     }
 lineFileClose(&lf);
 return hash;
 }
 
 
 void subColumn(char *asciiColumn, char *inFile, char *subFile, char *outFile)
 /* subColumn - Substitute one column in a tab-separated file.. */
 {
 struct hash *subHash = hashTwoColumnTsv(subFile);
 int column = atoi(asciiColumn);
 if (column == 0)
     usage();
 else
     column -= 1;
 char *row[1024*4];
 struct lineFile *lf = lineFileOpen(inFile, TRUE);
-struct dyString *dy = newDyString(1024);
+struct dyString *dy = dyStringNew(1024);
 FILE *f = mustOpen(outFile, "w");
 int rowCount;
 while ((rowCount = lineFileChopNextTab(lf, row, ArraySize(row))) > 0)
     {
     if (rowCount == ArraySize(row))
         errAbort("Too many columns (%d) line %d of  %s.", rowCount, lf->lineIx, lf->fileName);
     if (column >= rowCount)
         errAbort("Not enough columns (%d) line %d of  %s.", rowCount, lf->lineIx, lf->fileName);
     int i;
     for (i=0; i<rowCount; ++i)
 	{
 	char *s = row[i];
 	if (i == column)
 	    {
 	    if (isList)
 	        {
 		s = subCommaList(subHash, s);
 		}
 	    else
 		{
 		char *sub = hashFindVal(subHash, s);
 		if (sub == NULL)
 		    {
 		    if (fMiss || skipMiss)
 			{
                         if (fMiss)
                             {
                             fprintf(fMiss, "%s\n", s);
                             ++missCount;
                             }
                         if (skipMiss)
                             goto out;
 			}
 		    else
 			errAbort("%s not in %s line %d of %s", s, subFile, lf->lineIx, lf->fileName);
 		    }
 		else
 		    s = sub;
 		}
 	    }
         dyStringAppend(dy, s);
 	if (i == rowCount-1)
             dyStringAppendC(dy, '\n');
 	else
             dyStringAppendC(dy, '\t');
 	}
     fputs(dy->string, f);
 out:
     dyStringResize(dy, 0);
     }
 carefulClose(&f);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 5)
     usage();
 isList = optionExists("list");
 char *fileName = optionVal("miss", NULL);
 if (fileName != NULL)
     fMiss = mustOpen(fileName, "w");
 skipMiss = optionExists("skipMiss");
 subColumn(argv[1], argv[2], argv[3], argv[4]);
 if (fMiss != NULL)
     {
     carefulClose(&fMiss);
     warn("missed %d\n", missCount);
     }
 return 0;
 }