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/rikenBest.c src/hg/lib/rikenBest.c
index dd726f6..e74dc52 100644
--- src/hg/lib/rikenBest.c
+++ src/hg/lib/rikenBest.c
@@ -1,171 +1,171 @@
 /* rikenBest.c was originally generated by the autoSql program, which also 
  * generated rikenBest.h and rikenBest.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 "rikenBest.h"
 
 
 void rikenBestStaticLoad(char **row, struct rikenBest *ret)
 /* Load a row from rikenBest table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->name = row[0];
 ret->orfScore = atof(row[1]);
 strcpy(ret->orfStrand, row[2]);
 ret->intronOrientation = sqlSigned(row[3]);
 ret->position = row[4];
 ret->rikenCount = sqlSigned(row[5]);
 ret->genBankCount = sqlSigned(row[6]);
 ret->refSeqCount = sqlSigned(row[7]);
 ret->clusterId = row[8];
 }
 
 struct rikenBest *rikenBestLoad(char **row)
 /* Load a rikenBest from row fetched with select * from rikenBest
  * from database.  Dispose of this with rikenBestFree(). */
 {
 struct rikenBest *ret;
 
 AllocVar(ret);
 ret->name = cloneString(row[0]);
 ret->orfScore = atof(row[1]);
 strcpy(ret->orfStrand, row[2]);
 ret->intronOrientation = sqlSigned(row[3]);
 ret->position = cloneString(row[4]);
 ret->rikenCount = sqlSigned(row[5]);
 ret->genBankCount = sqlSigned(row[6]);
 ret->refSeqCount = sqlSigned(row[7]);
 ret->clusterId = cloneString(row[8]);
 return ret;
 }
 
 struct rikenBest *rikenBestLoadAll(char *fileName) 
 /* Load all rikenBest from a tab-separated file.
  * Dispose of this with rikenBestFreeList(). */
 {
 struct rikenBest *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[9];
 
 while (lineFileRow(lf, row))
     {
     el = rikenBestLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct rikenBest *rikenBestLoadWhere(struct sqlConnection *conn, char *table, char *where)
 /* Load all rikenBest from table that satisfy where clause. The
  * where clause may be NULL in which case whole table is loaded
  * Dispose of this with rikenBestFreeList(). */
 {
 struct rikenBest *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 = rikenBestLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 dyStringFree(&query);
 return list;
 }
 
 struct rikenBest *rikenBestCommaIn(char **pS, struct rikenBest *ret)
 /* Create a rikenBest out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new rikenBest */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->name = sqlStringComma(&s);
 ret->orfScore = sqlFloatComma(&s);
 sqlFixedStringComma(&s, ret->orfStrand, sizeof(ret->orfStrand));
 ret->intronOrientation = sqlSignedComma(&s);
 ret->position = sqlStringComma(&s);
 ret->rikenCount = sqlSignedComma(&s);
 ret->genBankCount = sqlSignedComma(&s);
 ret->refSeqCount = sqlSignedComma(&s);
 ret->clusterId = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void rikenBestFree(struct rikenBest **pEl)
 /* Free a single dynamically allocated rikenBest such as created
  * with rikenBestLoad(). */
 {
 struct rikenBest *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->name);
 freeMem(el->position);
 freeMem(el->clusterId);
 freez(pEl);
 }
 
 void rikenBestFreeList(struct rikenBest **pList)
 /* Free a list of dynamically allocated rikenBest's */
 {
 struct rikenBest *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     rikenBestFree(&el);
     }
 *pList = NULL;
 }
 
 void rikenBestOutput(struct rikenBest *el, FILE *f, char sep, char lastSep) 
 /* Print out rikenBest.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->name);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%f", el->orfScore);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->orfStrand);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%d", el->intronOrientation);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->position);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%d", el->rikenCount);
 fputc(sep,f);
 fprintf(f, "%d", el->genBankCount);
 fputc(sep,f);
 fprintf(f, "%d", el->refSeqCount);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->clusterId);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }