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/lib/snp125Exceptions.c src/hg/lib/snp125Exceptions.c
index cb6b379..3702ebb 100644
--- src/hg/lib/snp125Exceptions.c
+++ src/hg/lib/snp125Exceptions.c
@@ -1,160 +1,160 @@
 /* snp125Exceptions.c was originally generated by the autoSql program, which also 
  * generated snp125Exceptions.h and snp125Exceptions.sql.  This module links the database and
  * the RAM representation of objects. */
 
 /* Copyright (C) 2014 The Regents of the University of California 
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 #include "common.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "jksql.h"
 #include "snp125Exceptions.h"
 
 
 void snp125ExceptionsStaticLoad(char **row, struct snp125Exceptions *ret)
 /* Load a row from snp125Exceptions table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->chrom = row[0];
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->name = row[3];
 ret->exception = row[4];
 }
 
 struct snp125Exceptions *snp125ExceptionsLoad(char **row)
 /* Load a snp125Exceptions from row fetched with select * from snp125Exceptions
  * from database.  Dispose of this with snp125ExceptionsFree(). */
 {
 struct snp125Exceptions *ret;
 
 AllocVar(ret);
 ret->chrom = cloneString(row[0]);
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->name = cloneString(row[3]);
 ret->exception = cloneString(row[4]);
 return ret;
 }
 
 struct snp125Exceptions *snp125ExceptionsLoadAll(char *fileName) 
 /* Load all snp125Exceptions from a whitespace-separated file.
  * Dispose of this with snp125ExceptionsFreeList(). */
 {
 struct snp125Exceptions *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[5];
 
 while (lineFileRow(lf, row))
     {
     el = snp125ExceptionsLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct snp125Exceptions *snp125ExceptionsLoadAllByChar(char *fileName, char chopper) 
 /* Load all snp125Exceptions from a chopper separated file.
  * Dispose of this with snp125ExceptionsFreeList(). */
 {
 struct snp125Exceptions *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[5];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = snp125ExceptionsLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct snp125Exceptions *snp125ExceptionsCommaIn(char **pS, struct snp125Exceptions *ret)
 /* Create a snp125Exceptions out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new snp125Exceptions */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->chrom = sqlStringComma(&s);
 ret->chromStart = sqlUnsignedComma(&s);
 ret->chromEnd = sqlUnsignedComma(&s);
 ret->name = sqlStringComma(&s);
 ret->exception = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void snp125ExceptionsFree(struct snp125Exceptions **pEl)
 /* Free a single dynamically allocated snp125Exceptions such as created
  * with snp125ExceptionsLoad(). */
 {
 struct snp125Exceptions *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->exception);
 freez(pEl);
 }
 
 void snp125ExceptionsFreeList(struct snp125Exceptions **pList)
 /* Free a list of dynamically allocated snp125Exceptions's */
 {
 struct snp125Exceptions *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     snp125ExceptionsFree(&el);
     }
 *pList = NULL;
 }
 
 void snp125ExceptionsOutput(struct snp125Exceptions *el, FILE *f, char sep, char lastSep) 
 /* Print out snp125Exceptions.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->chrom);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->chromStart);
 fputc(sep,f);
 fprintf(f, "%u", el->chromEnd);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->name);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->exception);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 
 void snp125ExceptionsTableCreate(struct sqlConnection *conn)
 /* create a snp125Exceptions table */
 {
-char *createString =
-NOSQLINJ "CREATE TABLE snp125Exceptions (\n"
+char query[1024];
+sqlSafef(query, sizeof query, 
+"CREATE TABLE snp125Exceptions (\n"
 "    chrom varchar(15) not null,\n"
 "    chromStart int(10) unsigned not null,\n"
 "    chromEnd int(10) unsigned not null,\n"
 "    name varchar(15) not null,\n"
 "    exception varchar(64) not null \n"
+")\n");
 
-")\n";
-
-sqlRemakeTable(conn, "snp125Exceptions", createString);
+sqlRemakeTable(conn, "snp125Exceptions", query);
 }