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/plasEndPairs.c src/hg/lib/plasEndPairs.c
index 5f21759..f5b9797 100644
--- src/hg/lib/plasEndPairs.c
+++ src/hg/lib/plasEndPairs.c
@@ -1,220 +1,220 @@
 /* plasEndPairs.c was originally generated by the autoSql program, which also 
  * generated plasEndPairs.h and plasEndPairs.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 "plasEndPairs.h"
 
 
 struct plasEndPairs *plasEndPairsLoad(char **row)
 /* Load a plasEndPairs from row fetched with select * from plasEndPairs
  * from database.  Dispose of this with plasEndPairsFree(). */
 {
 struct plasEndPairs *ret;
 int sizeOne;
 
 AllocVar(ret);
 ret->lfCount = sqlUnsigned(row[8]);
 ret->bin = sqlSigned(row[0]);
 ret->chrom = cloneString(row[1]);
 ret->chromStart = sqlUnsigned(row[2]);
 ret->chromEnd = sqlUnsigned(row[3]);
 ret->name = cloneString(row[4]);
 ret->score = sqlUnsigned(row[5]);
 strcpy(ret->strand, row[6]);
 ret->pslTable = cloneString(row[7]);
 sqlUnsignedDynamicArray(row[9], &ret->lfStarts, &sizeOne);
 assert(sizeOne == ret->lfCount);
 sqlUnsignedDynamicArray(row[10], &ret->lfSizes, &sizeOne);
 assert(sizeOne == ret->lfCount);
 sqlStringDynamicArray(row[11], &ret->lfNames, &sizeOne);
 assert(sizeOne == ret->lfCount);
 return ret;
 }
 
 struct plasEndPairs *plasEndPairsLoadAll(char *fileName) 
 /* Load all plasEndPairs from a tab-separated file.
  * Dispose of this with plasEndPairsFreeList(). */
 {
 struct plasEndPairs *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[12];
 
 while (lineFileRow(lf, row))
     {
     el = plasEndPairsLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct plasEndPairs *plasEndPairsLoadWhere(struct sqlConnection *conn, char *table, char *where)
 /* Load all plasEndPairs from table that satisfy where clause. The
  * where clause may be NULL in which case whole table is loaded
  * Dispose of this with plasEndPairsFreeList(). */
 {
 struct plasEndPairs *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 = plasEndPairsLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 dyStringFree(&query);
 return list;
 }
 
 struct plasEndPairs *plasEndPairsCommaIn(char **pS, struct plasEndPairs *ret)
 /* Create a plasEndPairs out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new plasEndPairs */
 {
 char *s = *pS;
 int i;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->bin = sqlSignedComma(&s);
 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->pslTable = sqlStringComma(&s);
 ret->lfCount = sqlUnsignedComma(&s);
 s = sqlEatChar(s, '{');
 AllocArray(ret->lfStarts, ret->lfCount);
 for (i=0; i<ret->lfCount; ++i)
     {
     ret->lfStarts[i] = sqlUnsignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 s = sqlEatChar(s, '{');
 AllocArray(ret->lfSizes, ret->lfCount);
 for (i=0; i<ret->lfCount; ++i)
     {
     ret->lfSizes[i] = sqlUnsignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 s = sqlEatChar(s, '{');
 AllocArray(ret->lfNames, ret->lfCount);
 for (i=0; i<ret->lfCount; ++i)
     {
     ret->lfNames[i] = sqlStringComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 *pS = s;
 return ret;
 }
 
 void plasEndPairsFree(struct plasEndPairs **pEl)
 /* Free a single dynamically allocated plasEndPairs such as created
  * with plasEndPairsLoad(). */
 {
 struct plasEndPairs *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->pslTable);
 freeMem(el->lfStarts);
 freeMem(el->lfSizes);
 /* All strings in lfNames are allocated at once, so only need to free first. */
 if (el->lfNames != NULL)
     freeMem(el->lfNames[0]);
 freeMem(el->lfNames);
 freez(pEl);
 }
 
 void plasEndPairsFreeList(struct plasEndPairs **pList)
 /* Free a list of dynamically allocated plasEndPairs's */
 {
 struct plasEndPairs *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     plasEndPairsFree(&el);
     }
 *pList = NULL;
 }
 
 void plasEndPairsOutput(struct plasEndPairs *el, FILE *f, char sep, char lastSep) 
 /* Print out plasEndPairs.  Separate fields with sep. Follow last field with lastSep. */
 {
 int i;
 fprintf(f, "%d", el->bin);
 fputc(sep,f);
 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);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->pslTable);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->lfCount);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->lfCount; ++i)
     {
     fprintf(f, "%u", el->lfStarts[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->lfCount; ++i)
     {
     fprintf(f, "%u", el->lfSizes[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->lfCount; ++i)
     {
     if (sep == ',') fputc('"',f);
     fprintf(f, "%s", el->lfNames[i]);
     if (sep == ',') fputc('"',f);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(lastSep,f);
 }