080a160c7b9595d516c9c70e83689a09b60839d0
galt
  Mon Jun 3 12:16:53 2013 -0700
fix SQL Injection
diff --git src/hg/lib/variome.c src/hg/lib/variome.c
index 03fb830..fed6085 100644
--- src/hg/lib/variome.c
+++ src/hg/lib/variome.c
@@ -111,80 +111,39 @@
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = variomeLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void variomeSaveToDb(struct sqlConnection *conn, struct variome *el, char *tableName, int updateSize)
 /* Save variome 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 variomeSaveToDbEscaped() */
+ * inserted as NULL. Strings are automatically escaped to allow insertion into the database. */
 {
 struct dyString *update = newDyString(updateSize);
-dyStringPrintf(update, "insert into %s values ( %u,'%s',%u,%u,'%s',%u,'%s','%s','%s','%s','%s','%s','%s','%s',%u,'%s')", 
+sqlDyStringPrintf(update, "insert into %s values ( %u,'%s',%u,%u,'%s',%u,'%s','%s','%s','%s','%s','%s','%s','%s',%u,'%s')", 
 	tableName,  el->bin,  el->chrom,  el->chromStart,  el->chromEnd,  el->name,  el->score,  el->strand,  el->db,  el->owner,  el->color,  el->class,  el->creationDate,  el->lastModifiedDate,  el->descriptionKey,  el->id,  el->geneSymbol);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 }
 
-void variomeSaveToDbEscaped(struct sqlConnection *conn, struct variome *el, char *tableName, int updateSize)
-/* Save variome 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 variomeSaveToDb().
- * For example automatically copies and converts: 
- * "autosql's features include" --> "autosql\'s features include" 
- * before inserting into database. */ 
-{
-struct dyString *update = newDyString(updateSize);
-char  *chrom, *name, *strand, *db, *owner, *color, *class, *creationDate, *lastModifiedDate, *descriptionKey, *geneSymbol;
-chrom = sqlEscapeString(el->chrom);
-name = sqlEscapeString(el->name);
-strand = sqlEscapeString(el->strand);
-db = sqlEscapeString(el->db);
-owner = sqlEscapeString(el->owner);
-color = sqlEscapeString(el->color);
-class = sqlEscapeString(el->class);
-creationDate = sqlEscapeString(el->creationDate);
-lastModifiedDate = sqlEscapeString(el->lastModifiedDate);
-descriptionKey = sqlEscapeString(el->descriptionKey);
-geneSymbol = sqlEscapeString(el->geneSymbol);
-
-dyStringPrintf(update, "insert into %s values ( %u,'%s',%u,%u,'%s',%u,'%s','%s','%s','%s','%s','%s','%s','%s',%u,'%s')", 
-	tableName,  el->bin,  chrom,  el->chromStart,  el->chromEnd,  name,  el->score,  strand,  db,  owner,  color,  class,  creationDate,  lastModifiedDate,  descriptionKey,  el->id,  geneSymbol);
-sqlUpdate(conn, update->string);
-freeDyString(&update);
-freez(&chrom);
-freez(&name);
-freez(&strand);
-freez(&db);
-freez(&owner);
-freez(&color);
-freez(&class);
-freez(&creationDate);
-freez(&lastModifiedDate);
-freez(&descriptionKey);
-freez(&geneSymbol);
-}
 
 struct variome *variomeCommaIn(char **pS, struct variome *ret)
 /* Create a variome out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new variome */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->bin = sqlUnsignedComma(&s);
 ret->chrom = sqlStringComma(&s);
 ret->chromStart = sqlUnsignedComma(&s);
 ret->chromEnd = sqlUnsignedComma(&s);
 ret->name = sqlStringComma(&s);
@@ -316,31 +275,31 @@
 
 char *variomeCoorList[] = {
     "exact coordinates",
     "estimated coordinates",
 };
 
 int variomeClassCnt = ArraySize(variomeClassList);
 
 struct variome *findVariomeItemId(char *db, char *wikiItemId)
 /* given a wikiItemId return the row from the table */
 {
 struct variome *item;
 char query[256];
 struct sqlConnection *conn = wikiConnect();
 
-safef(query, ArraySize(query), "SELECT * FROM variome WHERE id='%s' limit 1",
+sqlSafef(query, ArraySize(query), "SELECT * FROM variome WHERE id='%s' limit 1",
         wikiItemId);
 
 item = variomeLoadByQuery(conn, query);
 if (NULL == item)
     errAbort("display wiki item: failed to load item '%s'", wikiItemId);
 
 wikiDisconnect(&conn);
 return item;
 }
 
 /* use functions from lib/wikiTrack.c, lib/wikiLink.c for accessing wiki pages */
 
 int addVariomeItem(char *db, char *chrom, int start, int end,
     char *name, int score, char *strand, char *owner, char *class,
         char *color, char *category, char *geneSymbol, char *wikiKey)
@@ -359,65 +318,65 @@
     safef(newItem->strand, sizeof(newItem->strand), "%s", "+");
 else if (sameString(strand, "minus"))
     safef(newItem->strand, sizeof(newItem->strand), "%s", "-");
 else 
     safef(newItem->strand, sizeof(newItem->strand), "%s", " ");
 newItem->db = cloneString(db);
 newItem->owner = cloneString(owner);
 newItem->class = cloneString(class);
 newItem->color = cloneString(color);
 newItem->creationDate = cloneString("0");
 newItem->lastModifiedDate = cloneString("0");
 newItem->descriptionKey = cloneString("0");
 newItem->id = 0;
 newItem->geneSymbol = cloneString(geneSymbol);
 
-variomeSaveToDbEscaped(conn, newItem, "variome", 1024);
+variomeSaveToDb(conn, newItem, "variome", 1024);
 
 int id = sqlLastAutoId(conn);
 char descriptionKey[256];
 /* when wikiKey is NULL, assign the default key of category:db-id,
  *      else, it is the proper key
  */
 if (wikiKey)
     safef(descriptionKey,ArraySize(descriptionKey), "%s", wikiKey);
 else
     safef(descriptionKey,ArraySize(descriptionKey),
         "%s:%s-%d", category, db, id);
 
 variomeFree(&newItem);
 
 char query[1024];
-safef(query, ArraySize(query), "UPDATE %s set creationDate=now(),lastModifiedDate=now(),descriptionKey='%s' WHERE id='%d'",
+sqlSafef(query, ArraySize(query), "UPDATE %s set creationDate=now(),lastModifiedDate=now(),descriptionKey='%s' WHERE id='%d'",
     "variome", descriptionKey, id);
 
 sqlUpdate(conn,query);
 wikiDisconnect(&conn);
 return (id);
 }
 
 void updateVariomeLastModifiedDate(char *db, int id)
 /* set lastModifiedDate to now() */
 {
 char query[512];
 struct sqlConnection *conn = wikiConnect();
 
-safef(query, ArraySize(query),
+sqlSafef(query, ArraySize(query),
     "UPDATE %s set lastModifiedDate=now() WHERE id='%d'",
         "variome", id);
 sqlUpdate(conn,query);
 wikiDisconnect(&conn);
 }
 
 void deleteVariomeItem(char *db, int id)
 /* delete the item with specified id */
 {
 char query[512];
 struct sqlConnection *conn = wikiConnect();
-safef(query, ArraySize(query), "DELETE FROM %s WHERE id='%d'",
+sqlSafef(query, ArraySize(query), "DELETE FROM %s WHERE id='%d'",
         "variome", id);
 sqlUpdate(conn,query);
 wikiDisconnect(&conn);
 }
 
 /* prefixComments and addDescription used from wikiTrack.c */