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/makeDb/schema/dbFindFieldsWith/dbFindFieldsWith.c src/hg/makeDb/schema/dbFindFieldsWith/dbFindFieldsWith.c
index 9dddaed..7dd627b 100644
--- src/hg/makeDb/schema/dbFindFieldsWith/dbFindFieldsWith.c
+++ src/hg/makeDb/schema/dbFindFieldsWith/dbFindFieldsWith.c
@@ -1,113 +1,115 @@
 /* dbFindFieldsWith - Look through database and find fields that have elements matching a certain pattern in the first N rows.. */
 
 /* 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 <regex.h>
 #include "linefile.h"
 #include "jksql.h"
 #include "hash.h"
 #include "options.h"
 
 
 int maxRows = 100;
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "dbFindFieldsWith - Look through database and find fields that have elements matching a certain "
   "regular expression in the first N rows.\n"
   "usage:\n"
   "   dbFindFieldsWith db regExp outputFile\n"
   "options:\n"
   "   -maxRows=%d\n"
   "Example - to find tables in go that contain _exactly_ the word 'kinase'\n"
   "    dbFindFieldsWith go '^kinase$' outputFile\n"
   "Example - to find tables in hg18 that contain a known gene id\n"
   "    dbFindFieldsWith hg18 '^uc[0-9][0-9][0-9][a-z][a-z][a-z].[0-9]+$' output\n"
   , maxRows
   );
 }
 
 static struct optionSpec options[] = {
    {"maxRows", OPTION_INT},
    {NULL, 0},
 };
 
 char *sqlColumnName(struct sqlResult *sr, int colIx)
 /* REturn name of column of given index.  You can only use this once per result! */
 {
 int i;
 for (i=0; i<colIx; ++i)
     sqlFieldName(sr);
 return sqlFieldName(sr);
 }
 
 void dbFindFieldsWith(char *database, char *regExp, char *output)
 /* dbFindFieldsWith - Look through database and find fields that have elements matching a certain pattern in the first N rows.. */
 {
 regex_t re;
 int err = regcomp(&re, regExp, REG_NOSUB|REG_EXTENDED);
 if (err < 0)
    errAbort("regcomp failed code %d", err);
 struct sqlConnection *conn = sqlConnect(database);
-struct slName *table, *tableList = sqlQuickList(conn, NOSQLINJ "show tables");
+char query[1024];
+sqlSafef(query, sizeof query, "show tables");
+struct slName *table, *tableList = sqlQuickList(conn, query);
 FILE *f = mustOpen(output, "w");
 for (table = tableList; table != NULL; table = table->next)
     {
     char query[256];
     sqlSafef(query, sizeof(query), "select * from %s limit %d", table->name, maxRows);
     verbose(2, "%s.%s\n", database, table->name);
     struct sqlResult *sr = sqlGetResult(conn, query);
     if (sr != NULL)
 	{
 	int colCount = sqlCountColumns(sr);
 
 	/* Get labels for columns */
 	char **labels;
 	AllocArray(labels, colCount);
 	int i;
 	for (i=0; i<colCount; ++i)
 	    labels[i] = sqlFieldName(sr);
 
 	/* Get flags that say which fields we've reported. */
 	bool *flags;
 	AllocArray(flags, colCount);
 	char **row;
 	while ((row = sqlNextRow(sr)) != NULL)
 	    {
 	    int i;
 	    for (i=0; i<colCount; ++i)
 	         {
 		 char *field = row[i];
 		 if (field != NULL && field[0] != 0)
 		     {
 		     if (regexec(&re, row[i], 0, NULL, 0) == 0)
 			 {
 			 if (!flags[i])
 			     {
 			     flags[i] = TRUE;
 			     fprintf(f, "%s\t%s\t%s\n", table->name, labels[i], row[i]);
 			     }
 			 }
 		     }
 		 }
 	    }
 	sqlFreeResult(&sr);
 	freez(&flags);
 	freez(&labels);
 	}
     }
 carefulClose(&f);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 4)
     usage();
 dbFindFieldsWith(argv[1], argv[2], argv[3]);
 return 0;
 }