[svn-r22056] - fix several bugs in id management

- update test cases that get the H5F_t struct to use H5I_object_verify instead of H5I_object because of the higher user level ID that is introduced
- add some workarounds to take into consideration that the high level ID is not used everywhere at the moment
- add a routine that translates from low level ids to high level ids

7 files changed, 192 insertions, 106 deletions

diff --git a/src/H5F.c b/src/H5F.c
index 459dbd8..2c16c65 100644
--- a/src/H5F.c
+++ b/src/H5F.c
@@ -323,7 +323,7 @@ H5F_get_access_plist(H5F_t *f, hbool_t app_ref)
         HGOTO_ERROR(H5E_FILE, H5E_CANTINC, FAIL, "unable to increment ref count on VFL driver")
     if(H5P_set(new_plist, H5F_ACS_FILE_DRV_ID_NAME, &(f->shared->lf->driver_id)) < 0)
         HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set file driver ID")
-#if 0
+#if 1
     /* Increment the reference count on the VOL ID and insert it into the property list */
     if(H5I_inc_ref(f->vol_id, FALSE) < 0)
         HGOTO_ERROR(H5E_FILE, H5E_CANTINC, FAIL, "unable to increment ref count on VOL")
@@ -1337,6 +1337,10 @@ H5F_open(const char *name, unsigned flags, hid_t fcpl_id, hid_t fapl_id,
     if(NULL == (a_plist = (H5P_genplist_t *)H5I_object(fapl_id)))
         HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "not file access property list")
 
+    /* Store the VOL id in the file struct */
+    if(H5P_get(a_plist, H5F_ACS_VOL_ID_NAME, &(file->vol_id)) < 0)
+        HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't get vol plugin ID")
+
     /*
      * Decide the file close degree.  If it's the first time to open the
      * file, set the degree to access property list value; if it's the
@@ -1440,15 +1444,6 @@ H5Fcreate(const char *filename, unsigned flags, hid_t fcpl_id, hid_t fapl_id)
             HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not file access property list")
 
     /*
-     * Adjust bit flags by turning on the creation bit and making sure that
-     * the EXCL or TRUNC bit is set.  All newly-created files are opened for
-     * reading and writing.
-     */
-    if (0==(flags & (H5F_ACC_EXCL|H5F_ACC_TRUNC)))
-	flags |= H5F_ACC_EXCL;	 /*default*/
-    flags |= H5F_ACC_RDWR | H5F_ACC_CREAT;
-
-    /*
      * Create a new file or truncate an existing file.
      */
     if((ret_value = H5VL_create(filename, flags, fcpl_id, fapl_id)) < 0)
@@ -2022,13 +2017,26 @@ H5F_get_id(H5F_t *file, hbool_t app_ref)
     HDassert(file);
 
     if(file->file_id == -1) {
+        H5I_t               *uid_info;                /* user id structure */
         /* Get an atom for the file */
         if((file->file_id = H5I_register(H5I_FILE, file, app_ref)) < 0)
 	    HGOTO_ERROR(H5E_ATOM, H5E_CANTREGISTER, FAIL, "unable to atomize file")
+
+        /* Create a new id that points to a struct that holds the file id and the VOL id */
+        if(NULL == (uid_info = H5FL_MALLOC(H5I_t)))
+            HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed")
+        uid_info->obj_id = file->file_id;
+        uid_info->vol_id = file->vol_id;
+        if((H5I_register(H5I_UID, uid_info, TRUE)) < 0)
+            HGOTO_ERROR(H5E_ATOM, H5E_CANTREGISTER, FAIL, "unable to atomize file handle")
     } else {
         /* Increment reference count on atom. */
         if(H5I_inc_ref(file->file_id, app_ref) < 0)
             HGOTO_ERROR(H5E_ATOM, H5E_CANTSET, FAIL, "incrementing file ID failed")
+
+        /* Increment reference count on upper level ID. */
+        if(H5I_inc_ref_uid(file->file_id, app_ref) < 0)
+            HGOTO_ERROR(H5E_ATOM, H5E_CANTSET, FAIL, "incrementing user ID failed")
     } /* end else */
 
     ret_value = file->file_id;
@@ -2671,11 +2679,44 @@ H5Fget_name(hid_t uid, char *name/*out*/, size_t size)
     FUNC_ENTER_API(FAIL)
     H5TRACE3("Zs", "ixz", uid, name, size);
 
-    argv[0] = &ret_value;
-    argv[1] = &size;
-    if(H5VL_get(uid, H5F_GET_NAME, (void *)name, 2, argv) < 0)
-        HGOTO_ERROR(H5E_INTERNAL, H5E_CANTGET, FAIL, "unable to get file name")
+    /* MSC - temp fix to handle later when all user level ids are of type UID */
+    if (H5I_UID == H5I_get_type(uid)) {
+        argv[0] = &ret_value;
+        argv[1] = &size;
+        if(H5VL_get(uid, H5F_GET_NAME, (void *)name, 2, argv) < 0)
+            HGOTO_ERROR(H5E_INTERNAL, H5E_CANTGET, FAIL, "unable to get file name")
+    }
+    else {
+        H5F_t         *f;           /* Top file in mount hierarchy */
+        size_t        len;
+        /* For file IDs, get the file object directly */
+        /* (This prevents the H5G_loc() call from returning the file pointer for
+         * the top file in a mount hierarchy)
+         */
+        if(H5I_get_type(uid) == H5I_FILE ) {
+            if(NULL == (f = (H5F_t *)H5I_object(uid)))
+                HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a file")
+        } /* end if */
+        else {
+            H5G_loc_t     loc;        /* Object location */
+
+            /* Get symbol table entry */
+            if(H5G_loc(uid, &loc) < 0)
+                HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "not a valid object ID")
+            f = loc.oloc->file;
+        } /* end else */
 
+        len = HDstrlen(H5F_OPEN_NAME(f));
+
+        if(name) {
+            HDstrncpy(name, H5F_OPEN_NAME(f), MIN(len + 1,size));
+            if(len >= size)
+                name[size-1]='\0';
+        } /* end if */
+
+        /* Set return value */
+        ret_value = (ssize_t)len;
+    }
 done:
     FUNC_LEAVE_API(ret_value)
 } /* end H5Fget_name() */
diff --git a/src/H5Fpkg.h b/src/H5Fpkg.h
index 5c6223b..bb6cc4e 100644
--- a/src/H5Fpkg.h
+++ b/src/H5Fpkg.h
@@ -274,7 +274,7 @@ struct H5F_t {
     hbool_t             closing;        /* File is in the process of being closed */
     struct H5F_t        *parent;        /* Parent file that this file is mounted to */
     unsigned            nmounts;        /* Number of children mounted to this file */
-    //hid_t               vol_id;         /* id of the vol plugin used to open the file */
+    hid_t               vol_id;         /* id of the vol plugin used to open the file */
     //H5VL_class_t       vol_cls;        /* class of the VOL plugin */
 };
 
diff --git a/src/H5I.c b/src/H5I.c
index 3f6c2fd..ffdb21e 100644
--- a/src/H5I.c
+++ b/src/H5I.c
@@ -978,18 +978,13 @@ done:
  *-------------------------------------------------------------------------
  */
 void *
-H5Iobject_verify(hid_t uid, H5I_type_t id_type)
+H5Iobject_verify(hid_t id, H5I_type_t id_type)
 {
-    H5I_t *uid_info;                    /* user id structure */
-    hid_t id;
     void * ret_value;                      /* Return value */
 
     FUNC_ENTER_API(NULL)
 
-    /* Check arguments */
-    if(uid < 0)
-	HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL, "invalid ID")
-
+#if 0
     if (H5I_UID == H5I_get_type(uid)) {
         if(NULL == (uid_info = (H5I_t *)H5I_object(uid)))
             HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid user identifier")
@@ -998,6 +993,7 @@ H5Iobject_verify(hid_t uid, H5I_type_t id_type)
     else {
         id = uid;
     }
+#endif
 
     if(H5I_IS_LIB_TYPE(id_type))
         HGOTO_ERROR(H5E_ATOM, H5E_BADGROUP, NULL, "cannot call public function on library type")
@@ -1031,12 +1027,19 @@ void *
 H5I_object_verify(hid_t id, H5I_type_t id_type)
 {
     H5I_id_info_t	*id_ptr = NULL;		/*ptr to the new atom	*/
+    H5I_t               *uid_info;              /* user id structure */
     void		*ret_value = NULL;	/*return value		*/
 
     FUNC_ENTER_NOAPI(NULL)
 
     HDassert(id_type >= 1 && id_type < H5I_next_type);
 
+    if (H5I_UID == H5I_get_type(id) && H5I_UID != id_type) {
+        if(NULL == (uid_info = (H5I_t *)H5I_object(id)))
+            HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid user identifier")
+        id = uid_info->obj_id;       
+    }
+
     /* Verify that the type of the ID is correct & lookup the ID */
     if(id_type == H5I_TYPE(id) && NULL != (id_ptr = H5I_find_id(id))) {
         /* Get the object pointer to return */
@@ -1148,18 +1151,13 @@ done:
  *-------------------------------------------------------------------------
  */
 void *
-H5Iremove_verify(hid_t uid, H5I_type_t id_type)
+H5Iremove_verify(hid_t id, H5I_type_t id_type)
 {
-    H5I_t *uid_info;                    /* user id structure */
-    hid_t id;
     void * ret_value;                      /* Return value */
 
     FUNC_ENTER_API(NULL)
 
-    /* Check arguments */
-    if(uid < 0)
-	HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL, "invalid ID")
-
+#if 0
     if (H5I_UID == H5I_get_type(uid)) {
         if(NULL == (uid_info = (H5I_t *)H5I_object(uid)))
             HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid user identifier")
@@ -1168,6 +1166,7 @@ H5Iremove_verify(hid_t uid, H5I_type_t id_type)
     else {
         id = uid;
     }
+#endif
 
     if(H5I_IS_LIB_TYPE(id_type))
         HGOTO_ERROR(H5E_ATOM, H5E_BADGROUP, NULL, "cannot call public function on library type")
@@ -1305,7 +1304,6 @@ int
 H5Idec_ref(hid_t uid)
 {
     H5I_t *uid_info;                    /* user id structure */
-    hid_t id;
     int ret_value;                      /* Return value */
 
     FUNC_ENTER_API(FAIL)
@@ -1318,20 +1316,18 @@ H5Idec_ref(hid_t uid)
     if (H5I_UID == H5I_get_type(uid)) {
         if(NULL == (uid_info = (H5I_t *)H5I_object(uid)))
             HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid user identifier")
-        id = uid_info->obj_id;
+
+        if((ret_value = H5I_dec_app_ref(uid_info->obj_id)) < 0)
+            HGOTO_ERROR(H5E_ATOM, H5E_CANTDEC, FAIL, "can't decrement ID ref count")
+
+        if((ret_value = H5I_dec_app_ref(uid)) < 0)
+            HGOTO_ERROR(H5E_ATOM, H5E_CANTDEC, FAIL, "can't decrement ID ref count")
     }
     else {
-        id = uid;
+        /* Do actual decrement operation */
+        if((ret_value = H5I_dec_app_ref(uid)) < 0)
+            HGOTO_ERROR(H5E_ATOM, H5E_CANTDEC, FAIL, "can't decrement ID ref count")
     }
-
-    /* Check arguments */
-    if(id < 0)
-	HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL, "invalid ID")
-
-    /* Do actual decrement operation */
-    if((ret_value = H5I_dec_app_ref(id)) < 0)
-        HGOTO_ERROR(H5E_ATOM, H5E_CANTDEC, FAIL, "can't decrement ID ref count")
-
 done:
     FUNC_LEAVE_API(ret_value)
 } /* end H5Idec_ref() */
@@ -1523,11 +1519,10 @@ int
 H5Iinc_ref(hid_t uid)
 {
     H5I_t *uid_info;                    /* user id structure */
-    hid_t id;
     int ret_value;                      /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE1("Is", "i", id);
+    H5TRACE1("Is", "i", uid);
 
     /* Check arguments */
     if(uid < 0)
@@ -1536,19 +1531,20 @@ H5Iinc_ref(hid_t uid)
     if (H5I_UID == H5I_get_type(uid)) {
         if(NULL == (uid_info = (H5I_t *)H5I_object(uid)))
             HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid user identifier")
-        id = uid_info->obj_id;
+
+        if((ret_value = H5I_inc_ref(uid_info->obj_id, TRUE)) < 0)
+            HGOTO_ERROR(H5E_ATOM, H5E_CANTINC, FAIL, "can't increment ID ref count")
+
+        if((ret_value = H5I_inc_ref(uid, TRUE)) < 0)
+            HGOTO_ERROR(H5E_ATOM, H5E_CANTINC, FAIL, "can't increment ID ref count")
     }
     else {
-        id = uid;
+        /* Do actual increment operation */
+        if((ret_value = H5I_inc_ref(uid, TRUE)) < 0)
+            HGOTO_ERROR(H5E_ATOM, H5E_CANTINC, FAIL, "can't increment ID ref count")
     }
 
-    /* Check arguments */
-    if(id < 0)
-	HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL, "invalid ID")
 
-    /* Do actual increment operation */
-    if((ret_value = H5I_inc_ref(id, TRUE)) < 0)
-        HGOTO_ERROR(H5E_ATOM, H5E_CANTINC, FAIL, "can't increment ID ref count")
 
 done:
     FUNC_LEAVE_API(ret_value)
@@ -1627,19 +1623,18 @@ done:
  *-------------------------------------------------------------------------
  */
 int
-H5Iget_ref(hid_t uid)
+H5Iget_ref(hid_t id)
 {
-    H5I_t *uid_info;                    /* user id structure */
-    hid_t id;
     int ret_value;                      /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE1("Is", "i", uid);
+    H5TRACE1("Is", "i", id);
 
     /* Check arguments */
-    if(uid < 0)
+    if(id < 0)
 	HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL, "invalid ID")
 
+#if 0
     if (H5I_UID == H5I_get_type(uid)) {
         if(NULL == (uid_info = (H5I_t *)H5I_object(uid)))
             HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid user identifier")
@@ -1652,7 +1647,7 @@ H5Iget_ref(hid_t uid)
     /* Check arguments */
     if(id < 0)
 	HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL, "invalid ID")
-
+#endif
     /* Do actual retrieve operation */
     if((ret_value = H5I_get_ref(id, TRUE)) < 0)
         HGOTO_ERROR(H5E_ATOM, H5E_CANTGET, FAIL, "can't get ID ref count")
@@ -1979,18 +1974,15 @@ done:
  *-------------------------------------------------------------------------
  */
 htri_t
-H5Iis_valid(hid_t uid)
+H5Iis_valid(hid_t id)
 {
     H5I_id_info_t   *id_ptr;            /* ptr to the ID */
-    H5I_t *uid_info;                    /* user id structure */
-    hid_t id;
     htri_t          ret_value = TRUE;   /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE1("t", "i", uid);
+    H5TRACE1("t", "i", id);
 
-    id = uid;
-    /*
+#if 0
     if (H5I_UID == H5I_get_type(uid)) {
         if(NULL == (uid_info = (H5I_t *)H5I_object(uid)))
             HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid user identifier")
@@ -1999,10 +1991,7 @@ H5Iis_valid(hid_t uid)
     else {
         id = uid;
     }
-
-    if(id < 0)
-	HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL, "invalid ID")
-    */
+#endif
 
     /* Find the ID */
     if (NULL == (id_ptr = H5I_find_id(id)))
@@ -2091,8 +2080,8 @@ H5I_search(H5I_type_t type, H5I_search_func_t func, void *key, hbool_t app_ref)
     H5I_id_type_t	*type_ptr;	/*ptr to the type	*/
     void		*ret_value = NULL;	/*return value		*/
 
-    FUNC_ENTER_NOAPI(NULL)
-
+    FUNC_ENTER_NOAPI(NULL
+)
     /* Check arguments */
     if(type <= H5I_BADID || type >= H5I_next_type)
 	HGOTO_ERROR(H5E_ARGS, H5E_BADRANGE, NULL, "invalid type number")
@@ -2274,15 +2263,12 @@ H5Iget_file_id(hid_t uid)
     else {
         id = uid;
     }
-
+    
     if((ret_value = H5I_get_file_id(id, TRUE)) < 0)
         HGOTO_ERROR(H5E_ATOM, H5E_CANTGET, FAIL, "can't retrieve file ID")
 
-    if (H5I_replace_with_uids (&ret_value, 1) <= 0)
+    if (H5I_replace_with_uids (&ret_value, 1) < 0)
         HGOTO_ERROR(H5E_ATOM, H5E_CANTGET, FAIL, "can't retrieve file ID")
-    /* Increment reference count on atom. */
-    if(H5I_inc_ref(ret_value, TRUE) < 0)
-        HGOTO_ERROR(H5E_ATOM, H5E_CANTSET, FAIL, "incrementing file ID failed")
 
 done:
     FUNC_LEAVE_API(ret_value)
@@ -2318,6 +2304,10 @@ H5I_get_file_id(hid_t obj_id, hbool_t app_ref)
         if(H5I_inc_ref(obj_id, app_ref) < 0)
             HGOTO_ERROR(H5E_ATOM, H5E_CANTSET, FAIL, "incrementing file ID failed")
 
+        /* Increment reference count on upper level ID. */
+        if(H5I_inc_ref_uid(obj_id, app_ref) < 0)
+            HGOTO_ERROR(H5E_ATOM, H5E_CANTSET, FAIL, "incrementing user ID failed")
+
         /* Set return value */
         ret_value = obj_id;
     } /* end if */
@@ -2339,8 +2329,6 @@ done:
     FUNC_LEAVE_NOAPI(ret_value)
 } /* end H5I_get_file_id() */
 
-
-
 
 /*-------------------------------------------------------------------------
  * Function:	H5I_replace_with_uids
@@ -2356,7 +2344,7 @@ done:
  *-------------------------------------------------------------------------
  */
 int
-H5I_replace_with_uids(hid_t *oid_list, ssize_t num_ids)
+H5I_replace_with_uids(hid_t *old_list, ssize_t num_ids)
 {
     ssize_t j;
     int  ret_value = 0;      /* Return value */
@@ -2364,11 +2352,13 @@ H5I_replace_with_uids(hid_t *oid_list, ssize_t num_ids)
     FUNC_ENTER_NOAPI(FAIL)
 
     for (j=0 ; j<num_ids ; j++) {
-        H5I_id_type_t	*type_ptr;	/*ptr to the type	*/
+        H5I_id_type_t   *type_ptr;      /*ptr to the type       */
         hbool_t replaced = FALSE;
 
-        if (H5I_FILE != H5I_get_type(oid_list[j])) 
+        if (H5I_FILE != H5I_get_type(old_list[j])) {
+            ret_value ++;
             continue;
+        }
 
         type_ptr = H5I_id_type_list_g[H5I_UID];
 
@@ -2377,9 +2367,9 @@ H5I_replace_with_uids(hid_t *oid_list, ssize_t num_ids)
 
         /* Only iterate through hash table if there are IDs in group */
         if(type_ptr->ids > 0) {
-            H5I_id_info_t	*id_ptr;	/*ptr to the new ID	*/
+            H5I_id_info_t       *id_ptr;        /*ptr to the new ID     */
             H5I_t *uid_info;                    /* user id structure */
-            unsigned i;			/*counter		*/
+            unsigned i;                 /*counter               */
 
             /* Start at the beginning of the array */
             for(i = 0; i < type_ptr->hash_size; i++) {
@@ -2387,8 +2377,8 @@ H5I_replace_with_uids(hid_t *oid_list, ssize_t num_ids)
                 while(id_ptr) {
                     if(NULL == (uid_info = (H5I_t *)H5I_object(id_ptr->id)))
                         HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid user identifier")
-                    if (uid_info->obj_id == oid_list[j]) {
-                        oid_list[j] = id_ptr->id;
+                    if (uid_info->obj_id == old_list[j]) {
+                        old_list[j] = id_ptr->id;
                         ret_value ++;
                         replaced = TRUE;
                         break;
@@ -2398,7 +2388,7 @@ H5I_replace_with_uids(hid_t *oid_list, ssize_t num_ids)
                 if (replaced)
                     break;
             } /* end for */
-        } /* end if */        
+        } /* end if */
     }
 done:
     FUNC_LEAVE_NOAPI(ret_value)
@@ -2406,6 +2396,60 @@ done:
 
 
 /*-------------------------------------------------------------------------
+ * Function:	H5I_inc_ref_uid
+ *
+ * Purpose:     change the ids used by the HDF5 libraries to the UIDs that
+ *              are provided to the user
+ *
+ * Return:	How many IDs were replaced.
+ *
+ * Programmer:	Mohamad Chaarawi
+ *              Feb 2012
+ *
+ *-------------------------------------------------------------------------
+ */
+int
+H5I_inc_ref_uid(hid_t fid, hbool_t app_ref)
+{
+    H5I_id_type_t   *type_ptr;      /*ptr to the type       */
+    int  ret_value = 0;      /* Return value */
+
+    FUNC_ENTER_NOAPI(FAIL)
+
+    type_ptr = H5I_id_type_list_g[H5I_UID];
+
+    if(type_ptr == NULL || type_ptr->count <= 0)
+        HGOTO_ERROR(H5E_ATOM, H5E_BADGROUP, FAIL, "invalid type")
+
+    /* Only iterate through hash table if there are IDs in group */
+    if(type_ptr->ids > 0) {
+        H5I_id_info_t       *id_ptr;        /*ptr to the new ID     */
+        H5I_t *uid_info;                    /* user id structure */
+        unsigned i;                 /*counter               */
+
+        /* Start at the beginning of the array */
+        for(i = 0; i < type_ptr->hash_size; i++) {
+            id_ptr = type_ptr->id_list[i];
+            while(id_ptr) {
+                if(NULL == (uid_info = (H5I_t *)H5I_object(id_ptr->id)))
+                    HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid user identifier")
+                if (uid_info->obj_id == fid) {
+                    /* Increment reference count on atom. */
+                    if((ret_value = H5I_inc_ref(id_ptr->id, app_ref)) < 0)
+                        HGOTO_ERROR(H5E_ATOM, H5E_CANTSET, FAIL, "incrementing file ID failed")
+                    HGOTO_DONE(ret_value)
+                }
+                id_ptr = id_ptr->next;
+            } /* end while */
+        } /* end for */
+    } /* end if */
+
+done:
+    FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5I_inc_ref_uid() */
+
+
+/*-------------------------------------------------------------------------
  * Function:	H5I_debug
  *
  * Purpose:	Dump the contents of a type to stderr for debugging.
diff --git a/src/H5Iprivate.h b/src/H5Iprivate.h
index 6ffc3c9..bc2f354 100644
--- a/src/H5Iprivate.h
+++ b/src/H5Iprivate.h
@@ -81,5 +81,6 @@ H5_DLL int H5I_inc_type_ref(H5I_type_t type);
 H5_DLL herr_t H5I_dec_type_ref(H5I_type_t type);
 H5_DLL int H5I_get_type_ref(H5I_type_t type);
 H5_DLL herr_t H5I_replace_with_uids(hid_t *oid_list, ssize_t num_ids);
+H5_DLL int H5I_inc_ref_uid(hid_t fid, hbool_t app_ref);
 #endif /* _H5Iprivate_H */
 
diff --git a/src/H5VL.c b/src/H5VL.c
index 03eba8a..981fe68 100644
--- a/src/H5VL.c
+++ b/src/H5VL.c
@@ -692,7 +692,7 @@ H5VL_flush(hid_t uid, H5F_scope_t scope)
 
     /* Check/fix arguments. */
     if(H5I_UID != H5I_get_type(uid))
-	HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a user ID")
+        HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a user ID")
 
     /* get the ID struct */
     if(NULL == (uid_info = (H5I_t *)H5I_object(uid)))
diff --git a/src/H5VLnative.c b/src/H5VLnative.c
index 08f62d3..e3b998a 100644
--- a/src/H5VLnative.c
+++ b/src/H5VLnative.c
@@ -46,12 +46,8 @@ static hid_t H5VL_NATIVE_g = 0;
 
 
 /* Prototypes */
-static hid_t  H5VL_native_open(const char *name, unsigned flags, hid_t fcpl_id, 
-                               hid_t fapl_id, hid_t dxpl_id);
-static herr_t H5VL_native_close(hid_t fid);
-static hid_t  H5VL_native_create(const char *name, unsigned flags, hid_t fcpl_id, hid_t fapl_id);
-static herr_t H5VL_native_flush(hid_t fid, H5F_scope_t scope);
-static herr_t H5VL_native_get(hid_t file_id, H5VL_file_get_t get_type, void *data, int argc, void **argv);
+static herr_t H5VL_native_get(hid_t file_id, H5VL_file_get_t get_type, 
+                              void *data, int argc, void **argv);
 static herr_t H5VL_native_term(void);
 
 static const H5VL_class_t H5VL_native_g = {
@@ -226,7 +222,7 @@ done:
  *
  *-------------------------------------------------------------------------
  */
-static hid_t
+hid_t
 H5VL_native_open(const char *name, unsigned flags, hid_t fcpl_id, 
                  hid_t fapl_id, hid_t dxpl_id)
 {
@@ -273,7 +269,7 @@ done:
  *
  *-------------------------------------------------------------------------
  */
-static hid_t
+hid_t
 H5VL_native_create(const char *name, unsigned flags, hid_t fcpl_id, hid_t fapl_id)
 {
     H5F_t *new_file;           /* file struct */
@@ -281,6 +277,15 @@ H5VL_native_create(const char *name, unsigned flags, hid_t fcpl_id, hid_t fapl_i
 
     FUNC_ENTER_NOAPI_NOINIT
 
+    /*
+     * Adjust bit flags by turning on the creation bit and making sure that
+     * the EXCL or TRUNC bit is set.  All newly-created files are opened for
+     * reading and writing.
+     */
+    if (0==(flags & (H5F_ACC_EXCL|H5F_ACC_TRUNC)))
+	flags |= H5F_ACC_EXCL;	 /*default*/
+    flags |= H5F_ACC_RDWR | H5F_ACC_CREAT;
+
     /* Create the file */ 
     if(NULL == (new_file = H5F_open(name, flags, fcpl_id, fapl_id, H5AC_dxpl_id)))
         HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, FAIL, "unable to create file")
@@ -313,7 +318,7 @@ done:
  *
  *-------------------------------------------------------------------------
  */
-static herr_t
+herr_t
 H5VL_native_close(hid_t file_id)
 {
     int nref;
@@ -367,7 +372,7 @@ done:
  *
  *-------------------------------------------------------------------------
  */
-static herr_t
+herr_t
 H5VL_native_flush(hid_t object_id, H5F_scope_t scope)
 {
     H5F_t	*f = NULL;              /* File to flush */
@@ -461,7 +466,7 @@ H5VL_native_flush(hid_t object_id, H5F_scope_t scope)
             /* Call the flush routine for mounted file hierarchies */
             if(H5F_flush_mounts(f, H5AC_dxpl_id) < 0)
                 HGOTO_ERROR(H5E_FILE, H5E_CANTFLUSH, FAIL, "unable to flush mounted file hierarchy")
-            } /* end if */
+        } /* end if */
         else {
             /* Call the flush routine, for this file */
             if(H5F_flush(f, H5AC_dxpl_id, FALSE) < 0)
@@ -633,16 +638,6 @@ H5VL_native_get(hid_t obj_id, H5VL_file_get_t get_type, void *data, int argc, vo
             ret = (ssize_t)len;
             break;
         }
-    /* H5Fget_ */
-    case H5F_GET_OBJ_COUNT:
-        {
-            break;
-        }
-    /* H5Fget_create_plist */
-    case H5F_GET_OBJ_IDS:
-        {
-            break;
-        }
     /* H5Fget_vfd_handle */
     case H5F_GET_VFD_HANDLE:
         {
diff --git a/src/H5VLnative.h b/src/H5VLnative.h
index 36177ed..ab4dd20 100644
--- a/src/H5VLnative.h
+++ b/src/H5VLnative.h
@@ -30,6 +30,11 @@ extern "C" {
 
 H5_DLL hid_t H5VL_native_init(void);
 H5_DLL herr_t H5Pset_fapl_native(hid_t fapl_id);
+H5_DLL hid_t  H5VL_native_open(const char *name, unsigned flags, hid_t fcpl_id, 
+                               hid_t fapl_id, hid_t dxpl_id);
+H5_DLL herr_t H5VL_native_close(hid_t fid);
+H5_DLL hid_t  H5VL_native_create(const char *name, unsigned flags, hid_t fcpl_id, hid_t fapl_id);
+H5_DLL herr_t H5VL_native_flush(hid_t fid, H5F_scope_t scope);
 
 #ifdef __cplusplus
 }