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/rikenCluster.c src/hg/lib/rikenCluster.c
index fa21ffe..869e4ac 100644
--- src/hg/lib/rikenCluster.c
+++ src/hg/lib/rikenCluster.c
@@ -1,227 +1,227 @@
 /* rikenCluster.c was originally generated by the autoSql program, which also 
  * generated rikenCluster.h and rikenCluster.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 "rikenCluster.h"
 
 
 struct rikenUcscCluster *rikenUcscClusterLoad(char **row)
 /* Load a rikenUcscCluster from row fetched with select * from rikenUcscCluster
  * from database.  Dispose of this with rikenUcscClusterFree(). */
 {
 struct rikenUcscCluster *ret;
 int sizeOne;
 
 AllocVar(ret);
 ret->refSeqCount = sqlUnsigned(row[6]);
 ret->genBankCount = sqlUnsigned(row[8]);
 ret->rikenCount = sqlUnsigned(row[10]);
 ret->chrom = cloneString(row[0]);
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->name = cloneString(row[3]);
 ret->score = sqlUnsigned(row[4]);
 strcpy(ret->strand, row[5]);
 sqlStringDynamicArray(row[7], &ret->refSeqs, &sizeOne);
 assert(sizeOne == ret->refSeqCount);
 sqlStringDynamicArray(row[9], &ret->genBanks, &sizeOne);
 assert(sizeOne == ret->genBankCount);
 sqlStringDynamicArray(row[11], &ret->rikens, &sizeOne);
 assert(sizeOne == ret->rikenCount);
 return ret;
 }
 
 struct rikenUcscCluster *rikenUcscClusterLoadAll(char *fileName) 
 /* Load all rikenUcscCluster from a tab-separated file.
  * Dispose of this with rikenUcscClusterFreeList(). */
 {
 struct rikenUcscCluster *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[12];
 
 while (lineFileRow(lf, row))
     {
     el = rikenUcscClusterLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct rikenUcscCluster *rikenUcscClusterLoadWhere(struct sqlConnection *conn, char *table, char *where)
 /* Load all rikenUcscCluster from table that satisfy where clause. The
  * where clause may be NULL in which case whole table is loaded
  * Dispose of this with rikenUcscClusterFreeList(). */
 {
 struct rikenUcscCluster *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 = rikenUcscClusterLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 dyStringFree(&query);
 return list;
 }
 
 struct rikenUcscCluster *rikenUcscClusterCommaIn(char **pS, struct rikenUcscCluster *ret)
 /* Create a rikenUcscCluster out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new rikenUcscCluster */
 {
 char *s = *pS;
 int i;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->chrom = sqlStringComma(&s);
 ret->chromStart = sqlUnsignedComma(&s);
 ret->chromEnd = sqlUnsignedComma(&s);
 ret->name = sqlStringComma(&s);
 ret->score = sqlUnsignedComma(&s);
 sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
 ret->refSeqCount = sqlUnsignedComma(&s);
 s = sqlEatChar(s, '{');
 AllocArray(ret->refSeqs, ret->refSeqCount);
 for (i=0; i<ret->refSeqCount; ++i)
     {
     ret->refSeqs[i] = sqlStringComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 ret->genBankCount = sqlUnsignedComma(&s);
 s = sqlEatChar(s, '{');
 AllocArray(ret->genBanks, ret->genBankCount);
 for (i=0; i<ret->genBankCount; ++i)
     {
     ret->genBanks[i] = sqlStringComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 ret->rikenCount = sqlUnsignedComma(&s);
 s = sqlEatChar(s, '{');
 AllocArray(ret->rikens, ret->rikenCount);
 for (i=0; i<ret->rikenCount; ++i)
     {
     ret->rikens[i] = sqlStringComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 *pS = s;
 return ret;
 }
 
 void rikenUcscClusterFree(struct rikenUcscCluster **pEl)
 /* Free a single dynamically allocated rikenUcscCluster such as created
  * with rikenUcscClusterLoad(). */
 {
 struct rikenUcscCluster *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 /* All strings in refSeqs are allocated at once, so only need to free first. */
 if (el->refSeqs != NULL)
     freeMem(el->refSeqs[0]);
 freeMem(el->refSeqs);
 /* All strings in genBanks are allocated at once, so only need to free first. */
 if (el->genBanks != NULL)
     freeMem(el->genBanks[0]);
 freeMem(el->genBanks);
 /* All strings in rikens are allocated at once, so only need to free first. */
 if (el->rikens != NULL)
     freeMem(el->rikens[0]);
 freeMem(el->rikens);
 freez(pEl);
 }
 
 void rikenUcscClusterFreeList(struct rikenUcscCluster **pList)
 /* Free a list of dynamically allocated rikenUcscCluster's */
 {
 struct rikenUcscCluster *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     rikenUcscClusterFree(&el);
     }
 *pList = NULL;
 }
 
 void rikenUcscClusterOutput(struct rikenUcscCluster *el, FILE *f, char sep, char lastSep) 
 /* Print out rikenUcscCluster.  Separate fields with sep. Follow last field with lastSep. */
 {
 int i;
 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->score);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->strand);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->refSeqCount);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->refSeqCount; ++i)
     {
     if (sep == ',') fputc('"',f);
     fprintf(f, "%s", el->refSeqs[i]);
     if (sep == ',') fputc('"',f);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(sep,f);
 fprintf(f, "%u", el->genBankCount);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->genBankCount; ++i)
     {
     if (sep == ',') fputc('"',f);
     fprintf(f, "%s", el->genBanks[i]);
     if (sep == ',') fputc('"',f);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(sep,f);
 fprintf(f, "%u", el->rikenCount);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->rikenCount; ++i)
     {
     if (sep == ',') fputc('"',f);
     fprintf(f, "%s", el->rikens[i]);
     if (sep == ',') fputc('"',f);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(lastSep,f);
 }