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/simpleRepeat.c src/hg/cgilib/simpleRepeat.c
index 6dacc92..153a8ff 100644
--- src/hg/cgilib/simpleRepeat.c
+++ src/hg/cgilib/simpleRepeat.c
@@ -1,204 +1,204 @@
 /* simpleRepeat.c was originally generated by the autoSql program, which also 
  * generated simpleRepeat.h and simpleRepeat.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 "simpleRepeat.h"
 
 
 void simpleRepeatStaticLoad(char **row, struct simpleRepeat *ret)
 /* Load a row from simpleRepeat 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->period = sqlUnsigned(row[4]);
 ret->copyNum = atof(row[5]);
 ret->consensusSize = sqlUnsigned(row[6]);
 ret->perMatch = sqlUnsigned(row[7]);
 ret->perIndel = sqlUnsigned(row[8]);
 ret->score = sqlUnsigned(row[9]);
 ret->A = sqlUnsigned(row[10]);
 ret->C = sqlUnsigned(row[11]);
 ret->G = sqlUnsigned(row[12]);
 ret->T = sqlUnsigned(row[13]);
 ret->entropy = atof(row[14]);
 ret->sequence = row[15];
 }
 
 struct simpleRepeat *simpleRepeatLoad(char **row)
 /* Load a simpleRepeat from row fetched with select * from simpleRepeat
  * from database.  Dispose of this with simpleRepeatFree(). */
 {
 struct simpleRepeat *ret;
 
 AllocVar(ret);
 ret->chrom = cloneString(row[0]);
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->name = cloneString(row[3]);
 ret->period = sqlUnsigned(row[4]);
 ret->copyNum = atof(row[5]);
 ret->consensusSize = sqlUnsigned(row[6]);
 ret->perMatch = sqlUnsigned(row[7]);
 ret->perIndel = sqlUnsigned(row[8]);
 ret->score = sqlUnsigned(row[9]);
 ret->A = sqlUnsigned(row[10]);
 ret->C = sqlUnsigned(row[11]);
 ret->G = sqlUnsigned(row[12]);
 ret->T = sqlUnsigned(row[13]);
 ret->entropy = atof(row[14]);
 ret->sequence = cloneString(row[15]);
 return ret;
 }
 
 struct simpleRepeat *simpleRepeatLoadAll(char *fileName) 
 /* Load all simpleRepeat from a tab-separated file.
  * Dispose of this with simpleRepeatFreeList(). */
 {
 struct simpleRepeat *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[16];
 
 while (lineFileRow(lf, row))
     {
     el = simpleRepeatLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct simpleRepeat *simpleRepeatLoadWhere(struct sqlConnection *conn, char *table, char *where)
 /* Load all simpleRepeat from table that satisfy where clause. The
  * where clause may be NULL in which case whole table is loaded
  * Dispose of this with simpleRepeatFreeList(). */
 {
 struct simpleRepeat *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 = simpleRepeatLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 dyStringFree(&query);
 return list;
 }
 
 struct simpleRepeat *simpleRepeatCommaIn(char **pS, struct simpleRepeat *ret)
 /* Create a simpleRepeat out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new simpleRepeat */
 {
 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->period = sqlUnsignedComma(&s);
 ret->copyNum = sqlFloatComma(&s);
 ret->consensusSize = sqlUnsignedComma(&s);
 ret->perMatch = sqlUnsignedComma(&s);
 ret->perIndel = sqlUnsignedComma(&s);
 ret->score = sqlUnsignedComma(&s);
 ret->A = sqlUnsignedComma(&s);
 ret->C = sqlUnsignedComma(&s);
 ret->G = sqlUnsignedComma(&s);
 ret->T = sqlUnsignedComma(&s);
 ret->entropy = sqlFloatComma(&s);
 ret->sequence = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void simpleRepeatFree(struct simpleRepeat **pEl)
 /* Free a single dynamically allocated simpleRepeat such as created
  * with simpleRepeatLoad(). */
 {
 struct simpleRepeat *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->sequence);
 freez(pEl);
 }
 
 void simpleRepeatFreeList(struct simpleRepeat **pList)
 /* Free a list of dynamically allocated simpleRepeat's */
 {
 struct simpleRepeat *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     simpleRepeatFree(&el);
     }
 *pList = NULL;
 }
 
 void simpleRepeatOutput(struct simpleRepeat *el, FILE *f, char sep, char lastSep) 
 /* Print out simpleRepeat.  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);
 fprintf(f, "%u", el->period);
 fputc(sep,f);
 fprintf(f, "%f", el->copyNum);
 fputc(sep,f);
 fprintf(f, "%u", el->consensusSize);
 fputc(sep,f);
 fprintf(f, "%u", el->perMatch);
 fputc(sep,f);
 fprintf(f, "%u", el->perIndel);
 fputc(sep,f);
 fprintf(f, "%u", el->score);
 fputc(sep,f);
 fprintf(f, "%u", el->A);
 fputc(sep,f);
 fprintf(f, "%u", el->C);
 fputc(sep,f);
 fprintf(f, "%u", el->G);
 fputc(sep,f);
 fprintf(f, "%u", el->T);
 fputc(sep,f);
 fprintf(f, "%f", el->entropy);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->sequence);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }