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/cgilib/synteny100000.c src/hg/cgilib/synteny100000.c
index 9be9d07..7280336 100644
--- src/hg/cgilib/synteny100000.c
+++ src/hg/cgilib/synteny100000.c
@@ -1,153 +1,153 @@
 /* synteny100000.c was originally generated by the autoSql program, which also 
  * generated synteny100000.h and synteny100000.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 "synteny100000.h"
 
 
 void synteny100000StaticLoad(char **row, struct synteny100000 *ret)
 /* Load a row from synteny100000 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->mouseChrom = row[3];
 ret->score = sqlUnsigned(row[4]);
 strcpy(ret->strand, row[5]);
 }
 
 struct synteny100000 *synteny100000Load(char **row)
 /* Load a synteny100000 from row fetched with select * from synteny100000
  * from database.  Dispose of this with synteny100000Free(). */
 {
 struct synteny100000 *ret;
 
 AllocVar(ret);
 ret->chrom = cloneString(row[0]);
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->mouseChrom = cloneString(row[3]);
 ret->score = sqlUnsigned(row[4]);
 strcpy(ret->strand, row[5]);
 return ret;
 }
 
 struct synteny100000 *synteny100000LoadAll(char *fileName) 
 /* Load all synteny100000 from a tab-separated file.
  * Dispose of this with synteny100000FreeList(). */
 {
 struct synteny100000 *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[6];
 
 while (lineFileRow(lf, row))
     {
     el = synteny100000Load(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct synteny100000 *synteny100000LoadWhere(struct sqlConnection *conn, char *table, char *where)
 /* Load all synteny100000 from table that satisfy where clause. The
  * where clause may be NULL in which case whole table is loaded
  * Dispose of this with synteny100000FreeList(). */
 {
 struct synteny100000 *list = NULL, *el;
 struct dyString *query = dyStringNew(256);
 struct sqlResult *sr;
 char **row;
 
 sqlDyStringPrintf(query, "select * from %s", table);
 if (where != NULL)
-    dyStringPrintf(query, " where %s", where);
+    sqlDyStringPrintf(query, " where %-s", where);
 sr = sqlGetResult(conn, query->string);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = synteny100000Load(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 dyStringFree(&query);
 return list;
 }
 
 struct synteny100000 *synteny100000CommaIn(char **pS, struct synteny100000 *ret)
 /* Create a synteny100000 out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new synteny100000 */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->chrom = sqlStringComma(&s);
 ret->chromStart = sqlUnsignedComma(&s);
 ret->chromEnd = sqlUnsignedComma(&s);
 ret->mouseChrom = sqlStringComma(&s);
 ret->score = sqlUnsignedComma(&s);
 sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
 *pS = s;
 return ret;
 }
 
 void synteny100000Free(struct synteny100000 **pEl)
 /* Free a single dynamically allocated synteny100000 such as created
  * with synteny100000Load(). */
 {
 struct synteny100000 *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->mouseChrom);
 freez(pEl);
 }
 
 void synteny100000FreeList(struct synteny100000 **pList)
 /* Free a list of dynamically allocated synteny100000's */
 {
 struct synteny100000 *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     synteny100000Free(&el);
     }
 *pList = NULL;
 }
 
 void synteny100000Output(struct synteny100000 *el, FILE *f, char sep, char lastSep) 
 /* Print out synteny100000.  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->mouseChrom);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->score);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->strand);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }