Fixed major bug when cloning an AVL group (last AVL of new group was not

correctly enlarged before copying the data) + minor improvements

src/obiavl.c

@@ -790,7 +790,7 @@ int truncate_avl_to_size_used(OBIDMS_avl_p avl)	// TODO is it necessary to unmap
 
 	// Set new data size and new max node count
 	(avl->header)->avl_size     = new_data_size;
-	(avl->header)->nb_items_max = floor(new_data_size / sizeof(AVL_node_t));
+	(avl->header)->nb_items_max	= (index_t) floor(((double) (avl->header)->avl_size) / ((double) sizeof(AVL_node_t)));
 
 	return 0;
 }
@@ -905,12 +905,12 @@ int grow_avl(OBIDMS_avl_p avl)		// TODO Lock when needed
 		return -1;
 	}
 
-	// Set new maximum number of items
-	(avl->header)->nb_items_max = floor(((double) new_data_size) / ((double) sizeof(AVL_node_t)));
-
 	// Set the new avl size
 	(avl->header)->avl_size = new_data_size;
 
+	// Set new maximum number of items
+	(avl->header)->nb_items_max	 = (index_t) floor(((double) (avl->header)->avl_size) / ((double) sizeof(AVL_node_t)));
+
 	return 0;
 }
 
@@ -1012,7 +1012,7 @@ int unmap_an_avl(OBIDMS_avl_p avl)
 		obidebug(1, "\nError unmapping the data of an AVL tree");
 		return -1;
 	}
-	if (munmap(avl->tree, (((avl->header)->nb_items_max) * sizeof(AVL_node_t))) < 0)
+	if (munmap(avl->tree, (avl->header)->avl_size) < 0)
 	{
 		obi_set_errno(OBI_AVL_ERROR);
 		obidebug(1, "\nError unmapping the tree of an AVL tree");
@@ -1038,7 +1038,7 @@ int remap_an_avl(OBIDMS_avl_p avl)
 	}
 
 	avl->tree = mmap(NULL,
-					 ((avl->header)->nb_items_max) * sizeof(AVL_node_t),
+					 (avl->header)->avl_size,
 					 PROT_READ,
 					 MAP_SHARED,
 					 avl->avl_fd,
@@ -1686,7 +1686,7 @@ OBIDMS_avl_p obi_create_avl(OBIDMS_p dms, const char* avl_name, int avl_idx)
 	(avl->header)->header_size 	 = header_size;
 	(avl->header)->avl_size 	 = data_size;
 	(avl->header)->nb_items	 	 = 0;
-	(avl->header)->nb_items_max	 = (index_t) floor(((double) get_initial_avl_size()) / ((double) sizeof(AVL_node_t)));
+	(avl->header)->nb_items_max	 = (index_t) floor(((double) (avl->header)->avl_size) / ((double) sizeof(AVL_node_t)));
 	(avl->header)->root_idx      = -1;
 	(avl->header)->creation_date = time(NULL);
 	strcpy((avl->header)->avl_name, complete_avl_name);
@@ -1916,7 +1916,7 @@ OBIDMS_avl_p obi_open_avl(OBIDMS_p dms, const char* avl_name, int avl_idx)
 	}
 
 	avl->tree = mmap(NULL,
-					 (((avl->header)->nb_items_max) * sizeof(AVL_node_t)),
+					 (avl->header)->avl_size,
 			         PROT_READ,
 			         MAP_SHARED,
 			         avl_file_descriptor,
@@ -2069,8 +2069,20 @@ OBIDMS_avl_group_p obi_open_avl_group(OBIDMS_p dms, const char* avl_name)
 }
 
 
-void obi_clone_avl(OBIDMS_avl_p avl, OBIDMS_avl_p new_avl)
+int obi_clone_avl(OBIDMS_avl_p avl, OBIDMS_avl_p new_avl)
 {
+	// Grow the new AVL as needed before copying
+	while (((new_avl->header)->nb_items_max) < ((avl->header)->nb_items))
+	{
+		if (grow_avl(new_avl) < 0)
+			return -1;
+	}
+	while ((((new_avl->data)->header)->data_size_max) < (((avl->data)->header)->data_size_used))
+	{
+		if (grow_avl_data(new_avl->data) < 0)
+			return -1;
+	}
+
 	// Clone AVL tree
 	memcpy(new_avl->tree, avl->tree, (avl->header)->avl_size);
 	(new_avl->header)->avl_size     = (avl->header)->avl_size;
@@ -2083,6 +2095,9 @@ void obi_clone_avl(OBIDMS_avl_p avl, OBIDMS_avl_p new_avl)
 	((new_avl->data)->header)->data_size_used = ((avl->data)->header)->data_size_used;
 	((new_avl->data)->header)->data_size_max  = ((avl->data)->header)->data_size_max;
 	((new_avl->data)->header)->nb_items       = ((avl->data)->header)->nb_items;
+
+	//avl_print(new_avl);
+	return 0;
 }
 
 
@@ -2093,27 +2108,42 @@ OBIDMS_avl_group_p obi_clone_avl_group(OBIDMS_avl_group_p avl_group, const char*
 
 	// Create the new AVL group
 	new_avl_group = obi_create_avl_group(avl_group->dms, new_avl_name);
+	if (new_avl_group == NULL)
+		return NULL;
 
 	// Create hard links to all the full AVLs that won't be modified: all but the last one
 	for (i=0; i<(avl_group->last_avl_idx); i++)
 	{
 		if (add_existing_avl_in_group(new_avl_group, avl_group, i) < 0)
+		{
+			obidebug(1, "\nError adding an existing AVL tree in a new group of AVL trees");
 			return NULL;
+		}
 	}
 
 	// Create the last AVL to copy data in it
 	if (add_new_avl_in_group(new_avl_group) < 0)
 	{
+		obidebug(1, "\nError creating a new AVL tree in a new group of AVL trees");
 		obi_close_avl_group(new_avl_group);
 		return NULL;
 	}
 
-	// Copy the data from the last AVL to a new one that can be modified
+	// Copy the data from the last AVL to the new one that can be modified
-	obi_clone_avl((avl_group->sub_avls)[avl_group->last_avl_idx], (new_avl_group->sub_avls)[new_avl_group->last_avl_idx]);
+	if ((((avl_group->sub_avls)[avl_group->last_avl_idx])->header)->nb_items > 0)
+	{
+		if (obi_clone_avl((avl_group->sub_avls)[avl_group->last_avl_idx], (new_avl_group->sub_avls)[new_avl_group->last_avl_idx]) < 0)
+		{
+			obidebug(1, "\nError copying an AVL tree in a new group of AVL trees");
+			obi_close_avl_group(new_avl_group);
+			return NULL;
+		}
+	}
 
 	// Close old AVL group
 	if (obi_close_avl_group(avl_group) < 0)
 	{
+		obidebug(1, "\nError closing a group of AVL trees after cloning it to make a new group");
 		obi_close_avl_group(new_avl_group);
 		return NULL;
 	}

src/obiavl.h

@@ -298,10 +298,13 @@ OBIDMS_avl_group_p obi_open_avl_group(OBIDMS_p dms, const char* avl_name);
  * @param avl A pointer on the AVL to clone.
  * @param new_avl A pointer on the new AVL to fill.
  *
+ * @retval 0 if the operation was successfully completed.
+ * @retval -1 if an error occurred.
+ *
  * @since May 2016
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-void obi_clone_avl(OBIDMS_avl_p avl, OBIDMS_avl_p new_avl);
+int obi_clone_avl(OBIDMS_avl_p avl, OBIDMS_avl_p new_avl);
 
 
 /**