080a160c7b9595d516c9c70e83689a09b60839d0
galt
  Mon Jun 3 12:16:53 2013 -0700
fix SQL Injection
diff --git src/hg/lib/taxonName.c src/hg/lib/taxonName.c
index 5433309..76033ac 100644
--- src/hg/lib/taxonName.c
+++ src/hg/lib/taxonName.c
@@ -1,188 +1,165 @@
 /* taxonName.c was originally generated by the autoSql program, which also 
  * generated taxonName.h and taxonName.sql.  This module links the database and
  * the RAM representation of objects. */
 
 #include "common.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "jksql.h"
 #include "taxonName.h"
 
 
 void taxonNameStaticLoad(char **row, struct taxonName *ret)
 /* Load a row from taxonName table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->name = row[0];
 ret->taxon = sqlUnsigned(row[1]);
 ret->class = row[2];
 }
 
 struct taxonName *taxonNameLoad(char **row)
 /* Load a taxonName from row fetched with select * from taxonName
  * from database.  Dispose of this with taxonNameFree(). */
 {
 struct taxonName *ret;
 
 AllocVar(ret);
 ret->name = cloneString(row[0]);
 ret->taxon = sqlUnsigned(row[1]);
 ret->class = cloneString(row[2]);
 return ret;
 }
 
 struct taxonName *taxonNameLoadAll(char *fileName) 
 /* Load all taxonName from a whitespace-separated file.
  * Dispose of this with taxonNameFreeList(). */
 {
 struct taxonName *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[3];
 
 while (lineFileRow(lf, row))
     {
     el = taxonNameLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct taxonName *taxonNameLoadAllByChar(char *fileName, char chopper) 
 /* Load all taxonName from a chopper separated file.
  * Dispose of this with taxonNameFreeList(). */
 {
 struct taxonName *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[3];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = taxonNameLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct taxonName *taxonNameLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all taxonName 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 taxonNameFreeList(). */
 {
 struct taxonName *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = taxonNameLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void taxonNameSaveToDb(struct sqlConnection *conn, struct taxonName *el, char *tableName, int updateSize)
 /* Save taxonName 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. Note that strings must be escaped to allow insertion into the database.
- * For example "autosql's features include" --> "autosql\'s features include" 
- * If worried about this use taxonNameSaveToDbEscaped() */
+ * inserted as NULL. Strings are automatically escaped to allow insertion into the database. */
 {
 struct dyString *update = newDyString(updateSize);
-dyStringPrintf(update, "insert into %s values ( '%s',%u,'%s')", 
+sqlDyStringPrintf(update, "insert into %s values ( '%s',%u,'%s')", 
 	tableName,  el->name,  el->taxon,  el->class);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 }
 
-void taxonNameSaveToDbEscaped(struct sqlConnection *conn, struct taxonName *el, char *tableName, int updateSize)
-/* Save taxonName 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. Automatically 
- * escapes all simple strings (not arrays of string) but may be slower than taxonNameSaveToDb().
- * For example automatically copies and converts: 
- * "autosql's features include" --> "autosql\'s features include" 
- * before inserting into database. */ 
-{
-struct dyString *update = newDyString(updateSize);
-char  *name, *class;
-name = sqlEscapeString(el->name);
-class = sqlEscapeString(el->class);
-
-dyStringPrintf(update, "insert into %s values ( '%s',%u,'%s')", 
-	tableName,  name, el->taxon ,  class);
-sqlUpdate(conn, update->string);
-freeDyString(&update);
-freez(&name);
-freez(&class);
-}
 
 struct taxonName *taxonNameCommaIn(char **pS, struct taxonName *ret)
 /* Create a taxonName out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new taxonName */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->name = sqlStringComma(&s);
 ret->taxon = sqlUnsignedComma(&s);
 ret->class = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void taxonNameFree(struct taxonName **pEl)
 /* Free a single dynamically allocated taxonName such as created
  * with taxonNameLoad(). */
 {
 struct taxonName *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->name);
 freeMem(el->class);
 freez(pEl);
 }
 
 void taxonNameFreeList(struct taxonName **pList)
 /* Free a list of dynamically allocated taxonName's */
 {
 struct taxonName *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     taxonNameFree(&el);
     }
 *pList = NULL;
 }
 
 void taxonNameOutput(struct taxonName *el, FILE *f, char sep, char lastSep) 
 /* Print out taxonName.  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, "%u", el->taxon);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->class);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */