Fixed major bug when cloning an AVL where the bloom filter was not

copied properly (because the sutructure copy via assignation does not
work for structures with a variable size)

src/obiavl.c

@@ -294,7 +294,7 @@ int remap_an_avl(OBIDMS_avl_p avl);
  * @warning The previous AVL in the list of the group is unmapped,
  * 			if it's not the 1st AVL being added.
  *
- * @param avl A pointer on the AVL tree group structure.
+ * @param avl_group A pointer on the AVL tree group structure.
  *
  * @retval 0 if the operation was successfully completed.
  * @retval -1 if an error occurred.
@@ -305,6 +305,24 @@ int remap_an_avl(OBIDMS_avl_p avl);
 int add_new_avl_in_group(OBIDMS_avl_group_p avl_group);
 
 
+/**
+ * @brief Internal function adding an existing AVL in an AVL group.
+ *
+ * The AVL is hard-linked in the AVL group directory, and opened for that group.
+ *
+ * @param avl_group_dest A pointer on the destination AVL group to which the AVL should be added.
+ * @param avl_group_source A pointer on the source AVL group where the AVL already exists.
+ * @param avl_idx Index of the AVL in the source AVL group.
+ *
+ * @retval 0 if the operation was successfully completed.
+ * @retval -1 if an error occurred.
+ *
+ * @since June 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int add_existing_avl_in_group(OBIDMS_avl_group_p avl_group_dest, OBIDMS_avl_group_p avl_group_source, int avl_idx);
+
+
 /**
  * @brief Internal function testing if a value might already be stored in an AVL tree.
  *
@@ -875,7 +893,6 @@ int grow_avl(OBIDMS_avl_p avl)		// TODO Lock when needed
 	{
 		obi_set_errno(OBI_AVL_ERROR);
 		obidebug(1, "\nError enlarging an AVL tree file");
-		close(avl_file_descriptor);
 		return -1;
 	}
 
@@ -885,7 +902,6 @@ int grow_avl(OBIDMS_avl_p avl)		// TODO Lock when needed
 	{
 		obi_set_errno(OBI_AVL_ERROR);
 		obidebug(1, "\nError munmapping the tree of an AVL tree file before enlarging");
-		close(avl_file_descriptor);
 		return -1;
 	}
 
@@ -901,7 +917,6 @@ int grow_avl(OBIDMS_avl_p avl)		// TODO Lock when needed
 	{
 		obi_set_errno(OBI_AVL_ERROR);
 		obidebug(1, "\nError re-mmapping the tree of an AVL tree file after enlarging the file");
-		close(avl_file_descriptor);
 		return -1;
 	}
 
@@ -936,7 +951,6 @@ int grow_avl_data(OBIDMS_avl_data_p avl_data)		// TODO Lock when needed
 	{
 		obi_set_errno(OBI_AVL_ERROR);
 		obidebug(1, "\nError enlarging an AVL tree data file");
-		close(avl_data_file_descriptor);
 		return -1;
 	}
 
@@ -946,7 +960,6 @@ int grow_avl_data(OBIDMS_avl_data_p avl_data)		// TODO Lock when needed
 	{
 		obi_set_errno(OBI_AVL_ERROR);
 		obidebug(1, "\nError munmapping the data of an AVL tree data file before enlarging");
-		close(avl_data_file_descriptor);
 		return -1;
 	}
 
@@ -962,7 +975,6 @@ int grow_avl_data(OBIDMS_avl_data_p avl_data)		// TODO Lock when needed
 	{
 		obi_set_errno(OBI_AVL_ERROR);
 		obidebug(1, "\nError re-mmapping the data of an AVL tree data file after enlarging the file");
-		close(avl_data_file_descriptor);
 		return -1;
 	}
 
@@ -996,7 +1008,12 @@ int close_avl_data(OBIDMS_avl_data_p avl_data)
 		ret_val = -1;
 	}
 
-	close(avl_data->data_fd);
+	if (close(avl_data->data_fd) < 0)
+	{
+		obi_set_errno(OBI_AVL_ERROR);
+		obidebug(1, "\nError closing an AVL tree data file");
+		ret_val = -1;
+	}
 
 	free(avl_data);
 
@@ -1084,7 +1101,6 @@ int add_new_avl_in_group(OBIDMS_avl_group_p avl_group)
 }
 
 
-// TODO doc
 int add_existing_avl_in_group(OBIDMS_avl_group_p avl_group_dest, OBIDMS_avl_group_p avl_group_source, int avl_idx)
 {
 	if (link(get_full_path_of_avl_file_name(avl_group_source->dms, avl_group_source->name, avl_idx), get_full_path_of_avl_file_name(avl_group_dest->dms, avl_group_dest->name, avl_idx)) < 0)
@@ -1103,7 +1119,7 @@ int add_existing_avl_in_group(OBIDMS_avl_group_p avl_group_dest, OBIDMS_avl_grou
 	// Increment current AVL index
 	(avl_group_dest->last_avl_idx)++;
 
-	// Open AVL for that group 		TODO ideally not needed, but needed for now
+	// Open AVL for that group 		TODO ideally not needed because AVL open twice, but needed for now
 	avl_group_dest->sub_avls[avl_group_dest->last_avl_idx] = obi_open_avl(avl_group_source->dms, avl_group_source->name, avl_idx);
 	if ((avl_group_dest->sub_avls)[avl_group_dest->last_avl_idx] == NULL)
 	{
@@ -1114,6 +1130,7 @@ int add_existing_avl_in_group(OBIDMS_avl_group_p avl_group_dest, OBIDMS_avl_grou
 	return 0;
 }
 
+
 int maybe_in_avl(OBIDMS_avl_p avl, Obi_blob_p value)
 {
 	return (bloom_check(&((avl->header)->bloom_filter), value, obi_blob_sizeof(value)));
@@ -1361,7 +1378,8 @@ void avl_print_node(OBIDMS_avl_p avl, AVL_node_p node, index_t node_idx, int dep
 		putchar(' ');
 
 	fprintf(stderr, "Node idx: %lld, Value idx: %lld, Left child: %lld, Right child: %lld, "
-			"Balance factor: %d, CRC: %llu\n", node_idx, node->value, node->left_child, node->right_child, node->balance_factor, node->crc64);
+			"Balance factor: %d, CRC: %llu\nValue:", node_idx, node->value, node->left_child, node->right_child, node->balance_factor, node->crc64);
+	print_bits(((avl->data)->data)+(node->value), obi_blob_sizeof((Obi_blob_p)(((avl->data)->data)+(node->value))));
 
 	if (node->right_child != -1)
 		avl_print_node(avl, RIGHT_CHILD(node), node->right_child, depth+2);
@@ -1679,8 +1697,6 @@ OBIDMS_avl_p obi_create_avl(OBIDMS_p dms, const char* avl_name, int avl_idx)
 
 	avl->dms       = dms;
 	avl->data      = avl_data;
-	avl->directory = dms->indexer_directory;
-	avl->dir_fd    = avl_dir_fd;
 	avl->avl_fd    = avl_file_descriptor;
 
 	(avl->header)->header_size 	 = header_size;
@@ -1696,6 +1712,13 @@ OBIDMS_avl_p obi_create_avl(OBIDMS_p dms, const char* avl_name, int avl_idx)
 
 	free(complete_avl_name);
 
+	if (closedir(directory) < 0)
+	{
+		obi_set_errno(OBI_AVL_ERROR);
+		obidebug(1, "\nError closing an AVL directory");
+		return NULL;
+	}
+
 	return avl;
 }
 
@@ -1937,12 +1960,17 @@ OBIDMS_avl_p obi_open_avl(OBIDMS_p dms, const char* avl_name, int avl_idx)
 
 	avl->dms       = dms;
 	avl->data      = avl_data;
-	avl->directory = dms->indexer_directory;
-	avl->dir_fd    = avl_dir_file_descriptor;
 	avl->avl_fd    = avl_file_descriptor;
 
 	free(complete_avl_name);
 
+	if (closedir(directory) < 0)
+	{
+		obi_set_errno(OBI_AVL_ERROR);
+		obidebug(1, "\nError closing an AVL directory");
+		return NULL;
+	}
+
 	return avl;
 }
 
@@ -1996,6 +2024,9 @@ OBIDMS_avl_group_p obi_create_avl_group(OBIDMS_p dms, const char* avl_name)
 		return NULL;
 	}
 
+	// Store pointer on directory
+	avl_group->directory = opendir(avl_dir_name);
+
 	// Add in the list of open indexers
 	obi_dms_list_indexer(dms, avl_group);
 
@@ -2005,6 +2036,8 @@ OBIDMS_avl_group_p obi_create_avl_group(OBIDMS_p dms, const char* avl_name)
 	// Set as writable
 	avl_group->writable = true;
 
+	free(avl_dir_name);
+
 	return avl_group;
 }
 
@@ -2051,11 +2084,16 @@ OBIDMS_avl_group_p obi_open_avl_group(OBIDMS_p dms, const char* avl_name)
 		if ((avl_group->sub_avls)[i] == NULL)
 			return NULL;
 	}
-	avl_group->last_avl_idx = avl_count-1;			// TODO latest. discuss
+
+	// Store the index of the last AVL (the one to be modified)
+	avl_group->last_avl_idx = avl_count-1;
 	strcpy(avl_group->name, avl_name);
 
 	avl_group->dms = dms;
 
+	// Store pointer on directory
+	avl_group->directory = opendir(avl_dir_name);
+
 	// Add in the list of open indexers
 	obi_dms_list_indexer(dms, avl_group);
 
@@ -2065,6 +2103,8 @@ OBIDMS_avl_group_p obi_open_avl_group(OBIDMS_p dms, const char* avl_name)
 	// Set as read-only
 	avl_group->writable = false;
 
+	free(avl_dir_name);
+
 	return avl_group;
 }
 
@@ -2085,10 +2125,10 @@ int obi_clone_avl(OBIDMS_avl_p avl, OBIDMS_avl_p new_avl)
 
 	// Clone AVL tree
 	memcpy(new_avl->tree, avl->tree, (avl->header)->avl_size);
+	memcpy(&((new_avl->header)->bloom_filter), &((avl->header)->bloom_filter), bloom_filter_size(MAX_NODE_COUNT_PER_AVL, BLOOM_FILTER_ERROR_RATE));
 	(new_avl->header)->avl_size     = (avl->header)->avl_size;
 	(new_avl->header)->nb_items     = (avl->header)->nb_items;
 	(new_avl->header)->root_idx     = (avl->header)->root_idx;
-	(new_avl->header)->bloom_filter = (avl->header)->bloom_filter;
 
 	// Clone AVL data
 	memcpy((new_avl->data)->data, (avl->data)->data, ((avl->data)->header)->data_size_used);
@@ -2174,7 +2214,12 @@ int obi_close_avl(OBIDMS_avl_p avl)
 		ret_val = -1;
 	}
 
-	close(avl->avl_fd);
+	if (close(avl->avl_fd) < 0)
+	{
+		obi_set_errno(OBI_AVL_ERROR);
+		obidebug(1, "\nError closing an AVL tree file");
+		ret_val = -1;
+	}
 
 	free(avl);
 
@@ -2209,6 +2254,13 @@ int obi_close_avl_group(OBIDMS_avl_group_p avl_group)
 				ret_val = -1;
 		}
 
+		if (closedir(avl_group->directory) < 0)
+		{
+			obi_set_errno(OBI_AVL_ERROR);
+			obidebug(1, "\nError closing an AVL group directory");
+			ret_val = -1;
+		}
+
 		free(avl_group);
 	}
 
@@ -2474,8 +2526,8 @@ index_t obi_avl_group_add(OBIDMS_avl_group_p avl_group, Obi_blob_p value)
 	}
 
 	// Add in the current AVL
-	bloom_add(&((((avl_group->sub_avls)[avl_group->last_avl_idx])->header)->bloom_filter), value, obi_blob_sizeof(value));
 	index_in_avl = (int32_t) obi_avl_add((avl_group->sub_avls)[avl_group->last_avl_idx], value);
+	bloom_add(&((((avl_group->sub_avls)[avl_group->last_avl_idx])->header)->bloom_filter), value, obi_blob_sizeof(value));
 
 	// Build the index containing the AVL index
 	index_with_avl = avl_group->last_avl_idx;

src/obiavl.h

@@ -143,12 +143,6 @@ typedef struct OBIDMS_avl {
 	OBIDMS_avl_data_p			data;						/**< A pointer to the structure containing the data
 													 	 	 *   that the AVL tree references.
 													 	 	 */
-	DIR*						directory;					/**< A directory entry usable to
-										 	 	 	 	 	 *    refer and scan the AVL tree directory.
-										 	 	 	 	 	 */
-	int							dir_fd;						/**< The file descriptor of the directory entry
-													 	 	 *    usable to refer and scan the AVL tree directory.
-													 	 	 */
 	int							avl_fd;						/**< The file descriptor of the file containing the AVL tree.
 													 	 	 */
 } OBIDMS_avl_t, *OBIDMS_avl_p;
@@ -168,6 +162,8 @@ typedef struct OBIDMS_avl_group {
 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
 	bool			writable;								/**< Indicates whether the AVL group is read-only or not.
 															 */
+	DIR*			directory;								/**< A directory entry usable to refer and scan the AVL group directory.
+										 	 	 	 	 	 */
 	size_t			counter;								/**< Indicates by how many threads/programs (TODO) the AVL group is used.
 													 	 	 */
 } OBIDMS_avl_group_t, *OBIDMS_avl_group_p;