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/liftOverChain.c src/hg/lib/liftOverChain.c
index a9078b5..c422877 100644
--- src/hg/lib/liftOverChain.c
+++ src/hg/lib/liftOverChain.c
@@ -1,226 +1,226 @@
 /* liftOverChain.c was originally generated by the autoSql program, which also 
  * generated liftOverChain.h and liftOverChain.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 "liftOverChain.h"
 
 
 void liftOverChainStaticLoad(char **row, struct liftOverChain *ret)
 /* Load a row from liftOverChain table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->fromDb = row[0];
 ret->toDb = row[1];
 ret->path = row[2];
 ret->minMatch = atof(row[3]);
 ret->minChainT = sqlUnsigned(row[4]);
 ret->minSizeQ = sqlUnsigned(row[5]);
 strcpy(ret->multiple, row[6]);
 ret->minBlocks = atof(row[7]);
 strcpy(ret->fudgeThick, row[8]);
 }
 
 struct liftOverChain *liftOverChainLoad(char **row)
 /* Load a liftOverChain from row fetched with select * from liftOverChain
  * from database.  Dispose of this with liftOverChainFree(). */
 {
 struct liftOverChain *ret;
 
 AllocVar(ret);
 ret->fromDb = cloneString(row[0]);
 ret->toDb = cloneString(row[1]);
 ret->path = cloneString(row[2]);
 ret->minMatch = atof(row[3]);
 ret->minChainT = sqlUnsigned(row[4]);
 ret->minSizeQ = sqlUnsigned(row[5]);
 strcpy(ret->multiple, row[6]);
 ret->minBlocks = atof(row[7]);
 strcpy(ret->fudgeThick, row[8]);
 return ret;
 }
 
 struct liftOverChain *liftOverChainLoadAll(char *fileName) 
 /* Load all liftOverChain from a whitespace-separated file.
  * Dispose of this with liftOverChainFreeList(). */
 {
 struct liftOverChain *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[9];
 
 while (lineFileRow(lf, row))
     {
     el = liftOverChainLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct liftOverChain *liftOverChainLoadAllByChar(char *fileName, char chopper) 
 /* Load all liftOverChain from a chopper separated file.
  * Dispose of this with liftOverChainFreeList(). */
 {
 struct liftOverChain *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[9];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = liftOverChainLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct liftOverChain *liftOverChainLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all liftOverChain from table that satisfy the query given.  
  * Where query is of the form 'select * from example where something=something'
  * or 'select example.* from example, anotherTable where example.something = 
  * anotherTable.something'.
  * Dispose of this with liftOverChainFreeList(). */
 {
 struct liftOverChain *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = liftOverChainLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void liftOverChainSaveToDb(struct sqlConnection *conn, struct liftOverChain *el, char *tableName, int updateSize)
 /* Save liftOverChain as a row to the table specified by tableName. 
  * As blob fields may be arbitrary size updateSize specifies the approx size
  * of a string that would contain the entire query. Arrays of native types are
  * converted to comma separated strings and loaded as such, User defined types are
  * inserted as NULL. Strings are automatically escaped to allow insertion into the database. */
 {
-struct dyString *update = newDyString(updateSize);
+struct dyString *update = dyStringNew(updateSize);
 sqlDyStringPrintf(update, "insert into %s values ( '%s','%s','%s',%g,%u,%u,'%s',%g,'%s')", 
 	tableName,  el->fromDb,  el->toDb,  el->path,  el->minMatch,  el->minChainT,  el->minSizeQ,  el->multiple,  el->minBlocks,  el->fudgeThick);
 sqlUpdate(conn, update->string);
-freeDyString(&update);
+dyStringFree(&update);
 }
 
 
 struct liftOverChain *liftOverChainCommaIn(char **pS, struct liftOverChain *ret)
 /* Create a liftOverChain out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new liftOverChain */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->fromDb = sqlStringComma(&s);
 ret->toDb = sqlStringComma(&s);
 ret->path = sqlStringComma(&s);
 ret->minMatch = sqlFloatComma(&s);
 ret->minChainT = sqlUnsignedComma(&s);
 ret->minSizeQ = sqlUnsignedComma(&s);
 sqlFixedStringComma(&s, ret->multiple, sizeof(ret->multiple));
 ret->minBlocks = sqlFloatComma(&s);
 sqlFixedStringComma(&s, ret->fudgeThick, sizeof(ret->fudgeThick));
 *pS = s;
 return ret;
 }
 
 void liftOverChainFree(struct liftOverChain **pEl)
 /* Free a single dynamically allocated liftOverChain such as created
  * with liftOverChainLoad(). */
 {
 struct liftOverChain *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->fromDb);
 freeMem(el->toDb);
 freeMem(el->path);
 freez(pEl);
 }
 
 void liftOverChainFreeList(struct liftOverChain **pList)
 /* Free a list of dynamically allocated liftOverChain's */
 {
 struct liftOverChain *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     liftOverChainFree(&el);
     }
 *pList = NULL;
 }
 
 void liftOverChainOutput(struct liftOverChain *el, FILE *f, char sep, char lastSep) 
 /* Print out liftOverChain.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->fromDb);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->toDb);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->path);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%g", el->minMatch);
 fputc(sep,f);
 fprintf(f, "%u", el->minChainT);
 fputc(sep,f);
 fprintf(f, "%u", el->minSizeQ);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->multiple);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%g", el->minBlocks);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->fudgeThick);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 boolean liftOverChainExists(struct sqlConnection *conn, char *tableName,
                                 char *fromDb, char *toDb)
 /* Return TRUE if row where fromDb and toDb match */
 {
 char query[256];
 sqlSafef(query, sizeof(query), 
         "select count(*) from %s where fromDb = '%s' and toDb = '%s'",
 	        tableName, fromDb, toDb);
 return sqlQuickNum(conn, query) > 0;
 }
 
 void liftOverChainRemove(struct sqlConnection *conn, char *tableName,
                                 char *fromDb, char *toDb)
 /* Remove rows where fromDb and toDb match */
 {
 char query[256];
 sqlSafef(query, sizeof(query), 
         "delete from %s where fromDb = '%s' and toDb = '%s'",
 	        tableName, fromDb, toDb);
 sqlUpdate(conn, query);
 }