obiavl.c 59 KB
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/****************************************************************************
 * OBIDMS AVL tree functions	                                            *
 ****************************************************************************/

/**
 * @file obiavl.c
 * @author Celine Mercier
 * @date December 3rd 2015
 * @brief Functions handling AVL trees for storing and retrieving bit arrays.
 */


#include <stdlib.h>
#include <stdio.h>
#include <stdint.h>
#include <string.h>
#include <time.h>
#include <sys/mman.h>
#include <fcntl.h>
#include <math.h>

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#include "bloom.h"
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#include "crc64.h"
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#include "obiavl.h"
#include "obierrno.h"
#include "obitypes.h"
#include "obidebug.h"
#include "encode.h"
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#include "utils.h"
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#define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)


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/**************************************************************************
 *
 * D E C L A R A T I O N   O F   T H E   P R I V A T E   F U N C T I O N S
 *
 **************************************************************************/

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/**
 * @brief Internal function building the complete AVL name for an AVL with an associated index (for AVL groups).
 *
 * @warning The returned pointer has to be freed by the caller.
 *
 * @param avl_name The base name of the AVL tree.
 * @param avl_idx The index associated with that AVL.
 *
 * @returns A pointer to the complete name of the AVL.
 * @retval NULL if an error occurred.
 *
 * @since April 2016
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
static char* build_avl_name_with_idx(const char* avl_name, int avl_idx);


/**
 * @brief Internal function building the full path of an AVL directory containing an AVL or an AVL group.
 *
 * @warning The returned pointer has to be freed by the caller.
 *
 * @param dms A pointer to the OBIDMS to which the AVL tree belongs.
 * @param avl_name The name of the AVL tree or the base name of the AVL tree group.
 *
 * @returns A pointer to the full path of the AVL directory.
 * @retval NULL if an error occurred.
 *
 * @since April 2016
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
char* get_full_path_of_avl_dir(OBIDMS_p dms, const char* avl_name);


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/**
 * @brief Internal function building the file name for an AVL tree file.
 *
 * @warning The returned pointer has to be freed by the caller.
 *
 * @param avl_name The name of the AVL tree.
 *
 * @returns A pointer to the name of the file where the AVL tree is stored.
 * @retval NULL if an error occurred.
 *
 * @since December 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
static char* build_avl_file_name(const char* avl_name);


/**
 * @brief Internal function building the file name for an AVL tree file.
 *
 * @warning The returned pointer has to be freed by the caller.
 *
 * @param avl_name The name of the AVL tree.
 *
 * @returns A pointer to the name of the file where the data referred to by the AVL tree is stored.
 * @retval NULL if an error occurred.
 *
 * @since December 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
static char* build_avl_data_file_name(const char* avl_name);


/**
 * @brief Internal function returning the size of an AVL tree header on this platform.
 *
 * @returns The size of an AVL tree header in bytes.
 *
 * @since December 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
size_t get_avl_header_size();


/**
 * @brief Internal function returning the initial size of an AVL tree on this platform.
 *
 * @returns The initial size of an AVL tree in bytes.
 *
 * @since December 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
size_t get_initial_avl_size();


/**
 * @brief Internal function returning the size, on this platform, of the header of the data
 *        referred to by an AVL tree.
 *
 * @returns The size of an AVL data header in bytes.
 *
 * @since December 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
size_t get_avl_data_header_size();


/**
 * @brief Internal function returning the initial size, on this platform, of the data
 *        referred to by an AVL tree.
 *
 * @returns The initial size of an AVL data array in bytes.
 *
 * @since December 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
size_t get_initial_avl_data_size();


/**
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 * @brief Internal function truncating an AVL tree file to the minimum size that is a multiple of the page size.
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 *
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 * @param avl A pointer to the AVL tree structure.
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 *
 * @retval 0 if the operation was successfully completed.
 * @retval -1 if an error occurred.
 *
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 * @since April 2016
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 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
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int truncate_avl_to_size_used(OBIDMS_avl_p avl);


/**
 * @brief Internal function truncating an AVL tree data file to the minimum size that is a multiple of the page size.
 *
 * @param avl A pointer to the the data structure referred to by an AVL tree.
 *
 * @retval 0 if the operation was successfully completed.
 * @retval -1 if an error occurred.
 *
 * @since April 2016
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
int truncate_avl_data_to_size_used(OBIDMS_avl_data_p avl_data);
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/**
 * @brief Internal function enlarging an AVL tree.
 *
 * @param avl A pointer to the AVL tree structure.
 *
 * @retval 0 if the operation was successfully completed.
 * @retval -1 if an error occurred.
 *
 * @since December 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
int grow_avl(OBIDMS_avl_p avl);


/**
 * @brief Internal function enlarging the data array referred to by an AVL tree.
 *
 * @param avl A pointer to the AVL tree structure.
 *
 * @retval 0 if the operation was successfully completed.
 * @retval -1 if an error occurred.
 *
 * @since December 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
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int grow_avl_data(OBIDMS_avl_data_p avl_data);
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/**
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 * @brief Internal function closing an AVL data structure where the data referred to by an AVL tree is stored.
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 *
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 * @param avl_data A pointer to the data structure referred to by an AVL tree.
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 *
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 * @retval 0 if the operation was successfully completed.
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 * @retval -1 if an error occurred.
 *
 * @since December 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
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int close_avl_data(OBIDMS_avl_data_p avl_data);


/**
 * @brief Internal function unmapping the tree and data parts of an AVL tree structure.
 *
 * @param avl A pointer to the AVL tree structure.
 *
 * @retval 0 if the operation was successfully completed.
 * @retval -1 if an error occurred.
 *
 * @since April 2016
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
int unmap_an_avl(OBIDMS_avl_p avl);


/**
 * @brief Internal function (re)mapping the tree and data parts of an AVL tree structure.
 *
 * @param avl A pointer to the AVL tree structure.
 *
 * @retval 0 if the operation was successfully completed.
 * @retval -1 if an error occurred.
 *
 * @since April 2016
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
int remap_an_avl(OBIDMS_avl_p avl);


/**
 * @brief Internal function (re)mapping the tree and data parts of an AVL tree structure.
 *
 * @param avl A pointer to the AVL tree group structure.
 *
 * @retval 0 if the operation was successfully completed.
 * @retval -1 if an error occurred.
 *
 * @since April 2016
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
int add_new_avl_in_group(OBIDMS_avl_group_p avl_group);


/**
 * @brief Internal function testing if a value might already be stored in an AVL tree.
 *
 * The function checks a bloom filter. No false negatives, possible false positives.
 *
 * @param avl A pointer to the AVL tree structure.
 * @param value A pointer to the byte array structure.
 *
 * @retval 0 if the value is definitely not already stored in the AVL tree.
 * @retval 1 if the value might already be stored in the AVL tree.
 *
 * @since April 2016
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
int maybe_in_avl(OBIDMS_avl_p avl, Obi_byte_array_p value);
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/**
 * @brief Internal function comparing two byte arrays.
 *
 * The encoding is compared first, then the length of the
 * values, then the values themselves.
 *
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 * @param value_1 A pointer to the first byte array structure.
 * @param value_2 A pointer to the second byte array structure.
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 *
 * @returns A value < 0 if value_1 < value_2,
 * 			a value > 0 if value_1 > value_2,
 * 			and 0 if value_1 == value_2.
 *
 * @since October 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
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int byte_array_compare(Obi_byte_array_p value_1, Obi_byte_array_p value_2);
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/**
 * @brief Internal function calculating the size in bytes of a byte array.
 *
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 * @param value A pointer to the byte array structure.
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 *
 * @returns The size of the byte array in bytes.
 *
 * @since October 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
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int32_t byte_array_sizeof(Obi_byte_array_p value);


/**
 * @brief Internal function storing a value (byte array) in the data array referred to by an AVL tree.
 *
 * @param avl A pointer to the AVL tree structure.
 * @param value A pointer to the value (byte array structure).
 *
 * @returns The index of the stored value.
 * @retval -1 if an error occurred.
 *
 * @since December 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
index_t avl_add_value_in_data_array(OBIDMS_avl_p avl, Obi_byte_array_p value);
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/**
 * @brief Internal function initializing a node in an AVL tree.
 *
 * @param avl A pointer to the AVL tree structure.
 * @param node_idx The index of the node to initialize in the mmapped AVL tree.
 *
 * @returns The node structure initialized.
 *
 * @since December 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
AVL_node_p avl_create_node(OBIDMS_avl_p avl, index_t node_idx);


/**
 * @brief Internal function updating the balance factors in an AVL tree
 *        after adding a node, only in the subtree that will have to be balanced.
 *        That subtree is found using the avl->path_idx array and the directions taken
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 *        down the tree to add the new node are stored in the avl->path_dir array.
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 *
 * @param avl A pointer to the AVL tree structure.
 *
 * @since December 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
void avl_update_balance_factors(OBIDMS_avl_p avl);


/**
 * @brief Internal function rotating a node with a "left left rotation".
 *
 * @param avl A pointer to the AVL tree structure.
 * @param node A pointer to the node that has to be rotated.
 * @param node_idx The index of the node that has to be rotated.
 *
 * @returns The new root of the subtree.
 *
 * @since December 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
index_t avl_rotate_leftleft(OBIDMS_avl_p avl, AVL_node_p node, index_t node_idx);

/**
 * @brief Internal function rotating a node with a "left right rotation".
 *
 * @param avl A pointer to the AVL tree structure.
 * @param node A pointer to the node that has to be rotated.
 * @param node_idx The index of the node that has to be rotated.
 *
 * @returns The new root of the subtree.
 *
 * @since December 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
index_t avl_rotate_leftright(OBIDMS_avl_p avl, AVL_node_p node, index_t node_idx);


/**
 * @brief Internal function rotating a node with a "right left rotation".
 *
 * @param avl A pointer to the AVL tree structure.
 * @param node A pointer to the node that has to be rotated.
 * @param node_idx The index of the node that has to be rotated.
 *
 * @returns The new root of the subtree.
 *
 * @since December 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
index_t avl_rotate_rightleft(OBIDMS_avl_p avl, AVL_node_p node, index_t node_idx);


/**
 * @brief Internal function rotating a node with a "right right rotation".
 *
 * @param avl A pointer to the AVL tree structure.
 * @param node A pointer to the node that has to be rotated.
 * @param node_idx The index of the node that has to be rotated.
 *
 * @returns The new root of the subtree.
 *
 * @since December 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
index_t avl_rotate_rightright(OBIDMS_avl_p avl, AVL_node_p node, index_t node_idx);


/**
 * @brief Internal function balancing one node.
 *
 * @param avl A pointer to the AVL tree structure.
 * @param node A pointer to the node that has to be balanced.
 * @param node_idx The index of the node that has to be balanced.
 *
 * @returns The new root of the subtree.
 *
 * @since December 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
index_t avl_balance_node(OBIDMS_avl_p avl, AVL_node_p node, index_t node_idx);


/**
 * @brief Internal function balancing the nodes of an AVL tree after adding a node,
 *        only in the subtree that eventually has to be balanced.
 *        That subtree is found using the avl->path_idx array.
 *
 * @param avl A pointer to the AVL tree structure.
 *
 * @since December 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
void avl_balance(OBIDMS_avl_p avl);


/**
 * @brief Internal function printing a depth first traverse of a node.
 *
 * @param avl A pointer to the AVL tree structure.
 * @param node A pointer to the node.
 * @param node_idx The index of the node.
 * @param depth The depth of the node.
 *
 * @since December 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
void avl_print_node(OBIDMS_avl_p avl, AVL_node_p node, index_t node_idx, int depth);


/**
 * @brief Internal function printing a depth first traverse of an AVL tree.
 *
 * @param avl A pointer to the AVL tree structure.
 *
 * @since December 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
void avl_print(OBIDMS_avl_p avl);


/************************************************************************
 *
 * D E F I N I T I O N   O F   T H E   P R I V A T E   F U N C T I O N S
 *
 ************************************************************************/

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static char* build_avl_name_with_idx(const char* avl_name, int avl_idx)
{
	char* avl_name_with_idx;
	int   avl_idx_length;

	if (avl_idx < 0)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError building an AVL tree name with index: index < 0");
		return NULL;
	}

	avl_idx_length = avl_idx == 0 ? 1 : (int)(log10(avl_idx)+1);
	avl_name_with_idx = malloc((strlen(avl_name) + avl_idx_length + 2)*sizeof(char));
	if (avl_name_with_idx == NULL)
	{
		obi_set_errno(OBI_MALLOC_ERROR);
		obidebug(1, "\nError allocating memory for an AVL name");
		return NULL;
	}
	if (sprintf(avl_name_with_idx, "%s_%u", avl_name, avl_idx) < 0)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError building an AVL tree name with index");
		return NULL;
	}

	return avl_name_with_idx;
}


char* get_full_path_of_avl_dir(OBIDMS_p dms, const char* avl_name)
{
	char* avl_dir_name;

	avl_dir_name = get_full_path(dms, AVL_TREES_DIR_NAME);
	if (avl_dir_name == NULL)
	{
		obidebug(1, "\nError getting path for the DMS AVL directory");
		return NULL;
	}
	strcat(avl_dir_name, "/");
	strcat(avl_dir_name, avl_name);

	return avl_dir_name;
}


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static char* build_avl_file_name(const char* avl_name)
{
	char* file_name;

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	// Test if the AVL name is not too long
	if (strlen(avl_name) >= AVL_MAX_NAME)
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	{
		obi_set_errno(OBI_AVL_ERROR);
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		obidebug(1, "\nError due to AVL tree name too long");
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		return NULL;
	}

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	// Build the file name
	file_name = (char*) malloc((strlen(avl_name) + 5)*sizeof(char));
	if (file_name == NULL)
	{
		obi_set_errno(OBI_MALLOC_ERROR);
		obidebug(1, "\nError allocating memory for an AVL file name");
		return NULL;
	}
	if (sprintf(file_name,"%s.oda", avl_name) < 0)
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	{
		obi_set_errno(OBI_AVL_ERROR);
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		obidebug(1, "\nError building an AVL tree file name");
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		free(file_name);
		return NULL;
	}

	return file_name;
}


static char* build_avl_data_file_name(const char* avl_name)
{
	char* file_name;

	// Build the file name
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	file_name = (char*) malloc((strlen(avl_name) + 5)*sizeof(char));
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	if (file_name == NULL)
	{
		obi_set_errno(OBI_MALLOC_ERROR);
		obidebug(1, "\nError allocating memory for an AVL data file name");
		return NULL;
	}
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	if (sprintf(file_name,"%s.odd", avl_name) < 0)
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	{
		obi_set_errno(OBI_AVL_ERROR);
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		obidebug(1, "\nError building an AVL tree data file name");
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		return NULL;
	}

	return file_name;
}


size_t get_avl_header_size()
{
	size_t header_size;
	size_t rounded_header_size;
	double multiple;

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	header_size = sizeof(OBIDMS_avl_header_t) + bloom_filter_size(MAX_NODE_COUNT_PER_AVL, BLOOM_FILTER_ERROR_RATE);
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	multiple = 	ceil((double) header_size / (double) getpagesize());

	rounded_header_size = multiple * getpagesize();

	return rounded_header_size;
}


size_t get_initial_avl_size()
{
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	size_t s;
	size_t m;

	m = 1;
	s = getpagesize() * m;

	return s;
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}


size_t get_avl_data_header_size()
{
	size_t header_size;
	size_t rounded_header_size;
	double multiple;

	header_size = sizeof(OBIDMS_avl_data_header_t);

	multiple = 	ceil((double) header_size / (double) getpagesize());

	rounded_header_size = multiple * getpagesize();

	return rounded_header_size;
}


size_t get_initial_avl_data_size()
{
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	size_t s;
	size_t m;

	m = 1;
	s = getpagesize() * m;

	return s;
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}


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int truncate_avl_to_size_used(OBIDMS_avl_p avl)	// TODO is it necessary to unmap/remap?
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{
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	size_t  			file_size;
	size_t  			new_data_size;
	double  			multiple;
	int 				file_descriptor;

	// Compute the new size: used size rounded to the nearest greater multiple of page size greater than 0
	multiple = ceil((double) (ONE_IF_ZERO((avl->header)->nb_items * sizeof(AVL_node_t))) / (double) getpagesize());
	new_data_size = ((int) multiple) * getpagesize();

	// Check that it is actually greater than the current size of the file, otherwise no need to truncate
	if ((avl->header)->avl_size == new_data_size)
		return 0;

	// Get the file descriptor
	file_descriptor = avl->avl_fd;

	// Unmap the tree before truncating the file
	if (munmap(avl->tree, (avl->header)->avl_size) < 0)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError munmapping the tree of an AVL before truncating");
		return -1;
	}

	// Truncate the file
	file_size = (avl->header)->header_size + new_data_size;
	if (ftruncate(file_descriptor, file_size) < 0)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError truncating an AVL file");
		return -1;
	}
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	// Remap the data
	avl->tree = mmap(NULL,
			         new_data_size,
					 PROT_READ | PROT_WRITE,
					 MAP_SHARED,
					 file_descriptor,
					 (avl->header)->header_size
					);

	if (avl->tree == MAP_FAILED)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError re-mmapping the tree of an AVL after truncating");
		return -1;
	}

	// 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));

	return 0;
}


int truncate_avl_data_to_size_used(OBIDMS_avl_data_p avl_data)	// TODO is it necessary to unmap/remap?
{
	size_t  			file_size;
	index_t  			new_data_size;
	double  			multiple;
	int 				file_descriptor;

	// Compute the new size: used size rounded to the nearest greater multiple of page size greater than 0
	multiple = ceil((double) (ONE_IF_ZERO((avl_data->header)->data_size_used)) / (double) getpagesize());
	new_data_size = ((int) multiple) * getpagesize();

	// Check that it is actually greater than the current size of the file, otherwise no need to truncate
	if ((avl_data->header)->data_size_max == new_data_size)
		return 0;

	// Get the file descriptor
	file_descriptor = avl_data->data_fd;

	// Unmap the data before truncating the file
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	if (munmap(avl_data->data, (avl_data->header)->data_size_max) < 0)
	{
		obi_set_errno(OBI_AVL_ERROR);
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		obidebug(1, "\nError munmapping the data of an AVL before truncating");
		return -1;
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	}

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	// Truncate the file
	file_size = (avl_data->header)->header_size + new_data_size;
	if (ftruncate(file_descriptor, file_size) < 0)
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	{
		obi_set_errno(OBI_AVL_ERROR);
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		obidebug(1, "\nError truncating an AVL data file");
		return -1;
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	}

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	// Remap the data
	avl_data->data = mmap(NULL,
					      new_data_size,
						  PROT_READ | PROT_WRITE,
						  MAP_SHARED,
						  file_descriptor,
						  (avl_data->header)->header_size
					     );
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	if (avl_data->data == MAP_FAILED)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError re-mmapping the data of an AVL after truncating");
		return -1;
	}

	// Set new data size
	(avl_data->header)->data_size_max = new_data_size;

	return 0;
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}


int grow_avl(OBIDMS_avl_p avl)		// TODO Lock when needed
{
	size_t	file_size;
	size_t 	old_data_size;
	size_t 	new_data_size;
	size_t 	header_size;
	int 	avl_file_descriptor;

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	avl_file_descriptor = avl->avl_fd;
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	// Calculate the new file size
	old_data_size = (avl->header)->avl_size;
	new_data_size = old_data_size * AVL_GROWTH_FACTOR;
	header_size = (avl->header)->header_size;
	file_size = header_size + new_data_size;

	// Enlarge the file
	if (ftruncate(avl_file_descriptor, file_size) < 0)
	{
		obi_set_errno(OBI_AVL_ERROR);
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		obidebug(1, "\nError enlarging an AVL tree file");
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		close(avl_file_descriptor);
		return -1;
	}

	// Unmap and re-map the data

	if (munmap(avl->tree, old_data_size) < 0)
	{
		obi_set_errno(OBI_AVL_ERROR);
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		obidebug(1, "\nError munmapping the tree of an AVL tree file before enlarging");
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		close(avl_file_descriptor);
		return -1;
	}

	avl->tree = mmap(NULL,
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					 new_data_size,
					 PROT_READ | PROT_WRITE,
					 MAP_SHARED,
					 avl_file_descriptor,
					 header_size
					);
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	if (avl->tree == MAP_FAILED)
	{
		obi_set_errno(OBI_AVL_ERROR);
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		obidebug(1, "\nError re-mmapping the tree of an AVL tree file after enlarging the file");
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		close(avl_file_descriptor);
		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;

	return 0;
}


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int grow_avl_data(OBIDMS_avl_data_p avl_data)		// TODO Lock when needed
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{
	size_t 	file_size;
	index_t old_data_size;
	index_t new_data_size;
	size_t 	header_size;
	int 	avl_data_file_descriptor;

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	avl_data_file_descriptor = avl_data->data_fd;
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	// Calculate the new file size
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	old_data_size = (avl_data->header)->data_size_max;
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	new_data_size = old_data_size * AVL_GROWTH_FACTOR;
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	header_size = (avl_data->header)->header_size;
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	file_size = header_size + new_data_size;

	// Enlarge the file
	if (ftruncate(avl_data_file_descriptor, file_size) < 0)
	{
		obi_set_errno(OBI_AVL_ERROR);
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		obidebug(1, "\nError enlarging an AVL tree data file");
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		close(avl_data_file_descriptor);
		return -1;
	}

	// Unmap and re-map the data

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	if (munmap(avl_data->data, old_data_size) < 0)
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	{
		obi_set_errno(OBI_AVL_ERROR);
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		obidebug(1, "\nError munmapping the data of an AVL tree data file before enlarging");
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		close(avl_data_file_descriptor);
		return -1;
	}

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	avl_data->data = mmap(NULL,
						  new_data_size,
						  PROT_READ | PROT_WRITE,
						  MAP_SHARED,
						  avl_data_file_descriptor,
						  header_size
						 );
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	if (avl_data->data == MAP_FAILED)
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	{
		obi_set_errno(OBI_AVL_ERROR);
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		obidebug(1, "\nError re-mmapping the data of an AVL tree data file after enlarging the file");
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		close(avl_data_file_descriptor);
		return -1;
	}

	// Set new data size
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	(avl_data->header)->data_size_max = new_data_size;
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	// Initialize new data to 0
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	memset((avl_data->data)+old_data_size, 0, new_data_size - old_data_size);
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	return 0;
}


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int close_avl_data(OBIDMS_avl_data_p avl_data)
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{
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	int ret_val = 0;
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	ret_val = truncate_avl_data_to_size_used(avl_data);
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	if (munmap(avl_data->data, (avl_data->header)->data_size_max) < 0)
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	{
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		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError munmapping the data of an AVL tree data file");
		ret_val = -1;
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	}

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	if (munmap(avl_data->header, (avl_data->header)->header_size) < 0)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError munmapping the header of an AVL tree data file");
		ret_val = -1;
	}
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	close(avl_data->data_fd);
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	free(avl_data);
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	return ret_val;
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}


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int unmap_an_avl(OBIDMS_avl_p avl)
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{
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	if (munmap((avl->data)->data, ((avl->data)->header)->data_size_max) < 0)
	{
		obi_set_errno(OBI_AVL_ERROR);
		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)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError unmapping the tree of an AVL tree");
		return -1;
	}
	return 0;
}
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int remap_an_avl(OBIDMS_avl_p avl)
{
	(avl->data)->data = mmap(NULL,
							 ((avl->data)->header)->data_size_max,
							 PROT_READ,
							 MAP_SHARED,
							 (avl->data)->data_fd,
							 ((avl->data)->header)->header_size);
	if ((avl->data)->data == NULL)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError mapping the data of an AVL tree");
		return -1;
	}
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	avl->tree = mmap(NULL,
					 ((avl->header)->nb_items_max) * sizeof(AVL_node_t),
					 PROT_READ,
					 MAP_SHARED,
					 avl->avl_fd,
					 (avl->header)->header_size);
	if (avl->tree == NULL)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError mapping the tree of an AVL tree");
		return -1;
	}

	return 0;
}
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int add_new_avl_in_group(OBIDMS_avl_group_p avl_group)
{
	// Check that maximum number of AVLs in a group was not reached
	if (avl_group->current_avl_idx == (MAX_NB_OF_AVLS_IN_GROUP-1))
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	{
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		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError: Trying to add new AVL in AVL group but maximum number of AVLs in a group reached");
		return -1;
	}

	// Unmap the previous AVL
	if (unmap_an_avl((avl_group->sub_avls)[avl_group->current_avl_idx]) < 0)
		return -1;

	// Increment current AVL index
	(avl_group->current_avl_idx)++;
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	// Create the new AVL
	(avl_group->sub_avls)[avl_group->current_avl_idx] = obi_create_avl(avl_group->dms, avl_group->avl_name, avl_group->current_avl_idx);
	if ((avl_group->sub_avls)[avl_group->current_avl_idx] == NULL)
	{
		obidebug(1, "\nError creating a new AVL tree in a group");
		return -1;
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	}

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	return 0;
}


int maybe_in_avl(OBIDMS_avl_p avl, Obi_byte_array_p value)
{
	return (bloom_check(&((avl->header)->bloom_filter), value, byte_array_sizeof(value)));
}


int byte_array_compare(Obi_byte_array_p value_1, Obi_byte_array_p value_2)
{
	int 	comp;
	int32_t b;

	if (value_1->element_size != value_2->element_size)
		return (value_1->element_size - value_2->element_size);

	if (value_1->length_encoded_value != value_2->length_encoded_value)
		return (value_1->length_encoded_value - value_2->length_encoded_value);

	if (value_1->element_size != ELEMENT_SIZE_STR) // because if so, length_decoded_value == length_encoded_value
	{
		if (value_1->length_decoded_value != value_2->length_decoded_value)
			return (value_1->length_decoded_value - value_2->length_decoded_value);
	}

	b = 0;
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	comp = 0;
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	while (!comp && (b < value_1->length_encoded_value))
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	{
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		//fprintf(stderr, "\ncomparing %c and %c", *((value_1->value)+b), *((value_2->value)+b));
		comp = *((value_1->value)+b) - *((value_2->value)+b);
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		b++;
	}
	return comp;
}


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int32_t byte_array_sizeof(Obi_byte_array_p value)
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{
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	return (sizeof(Obi_byte_array_t) + (value->length_encoded_value));
}


index_t avl_add_value_in_data_array(OBIDMS_avl_p avl, Obi_byte_array_p value)
{
	index_t value_idx;
	int32_t value_size;

	value_idx = ((avl->data)->header)->data_size_used;

	// Grow the data if needed
	value_size = byte_array_sizeof(value);
	while (((avl->data)->header)->data_size_max < (value_idx + value_size))
	{
		if (grow_avl_data(avl->data) < 0)
			return -1;
	}

	// Store the value itself at the end of the data
	memcpy((((avl->data)->data)+value_idx), value, value_size);

	// Update the data size
	((avl->data)->header)->data_size_used = value_idx + value_size;

	// Update the number of items
	(((avl->data)->header)->nb_items)++;

	return value_idx;
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}


AVL_node_p avl_create_node(OBIDMS_avl_p avl, index_t node_idx)
{
	AVL_node_p node;

	node = (avl->tree)+node_idx;

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	node->left_child     = -1;
	node->right_child    = -1;
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	node->balance_factor = 0;
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	node->value          = -1;
	node->crc64          = 0; 	// TODO no NA value
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	return node;
}


// Update the balance factors of the nodes from the node that will need balancing
void avl_update_balance_factors(OBIDMS_avl_p avl)
{
	uint8_t n;
	AVL_node_p node;

	// Update balance factors from the node where balancing might be needed
	node=(avl->tree)+((avl->path_idx)[1]);

	for (n=1; (avl->path_dir)[n] != -1; n++)
	{
		if ((avl->path_dir)[n]) // Went right
		{
			(node->balance_factor)--;
			node=RIGHT_CHILD(node);
		}
		else 	// Went left
		{
			(node->balance_factor)++;
			node=LEFT_CHILD(node);
		}
	}
}


// Left Left Rotate
index_t avl_rotate_leftleft(OBIDMS_avl_p avl, AVL_node_p node, index_t node_idx)
{
	AVL_node_p left_child = LEFT_CHILD(node);
	index_t left_child_idx = node->left_child;

	node->left_child = left_child->right_child;
	left_child->right_child = node_idx;

	node->balance_factor = 0;
	left_child->balance_factor = 0;

	return left_child_idx;
}


// Left Right Rotate
index_t avl_rotate_leftright(OBIDMS_avl_p avl, AVL_node_p node, index_t node_idx)
{
	AVL_node_p left_child = LEFT_CHILD(node);
	index_t left_child_idx = node->left_child;
	AVL_node_p rc_of_lc = RIGHT_CHILD(left_child);
	index_t rc_of_lc_idx = left_child->right_child;

	node->left_child = rc_of_lc->right_child;
	left_child->right_child = rc_of_lc->left_child;
	rc_of_lc->left_child = left_child_idx;
	rc_of_lc->right_child = node_idx;

	if (rc_of_lc->balance_factor == -1)
	{
		left_child->balance_factor = 1;
		node->balance_factor = 0;
	}
	else if (rc_of_lc->balance_factor == 0)
	{
		left_child->balance_factor = 0;
		node->balance_factor = 0;
	}
	else	// if (rc_of_lc->balance_factor == 1)
	{
		left_child->balance_factor = 0;
		node->balance_factor = -1;
	}

	rc_of_lc->balance_factor = 0;

	return rc_of_lc_idx;
}


// Right Left Rotate
index_t avl_rotate_rightleft(OBIDMS_avl_p avl, AVL_node_p node, index_t node_idx)
{
	AVL_node_p right_child = RIGHT_CHILD(node);
	index_t right_child_idx = node->right_child;;
	AVL_node_p lc_of_rc = LEFT_CHILD(right_child);
	index_t lc_of_rc_idx = right_child->left_child;

	node->right_child = lc_of_rc->left_child;
	right_child->left_child = lc_of_rc->right_child;
	lc_of_rc->right_child = right_child_idx;
	lc_of_rc->left_child = node_idx;

	if (lc_of_rc->balance_factor == 1)
	{
		right_child->balance_factor = 1;
		node->balance_factor = 0;
	}
	else if (lc_of_rc->balance_factor == 0)
	{
		right_child->balance_factor = 0;
		node->balance_factor = 0;
	}
	else	// if (lc_of_rc->balance_factor == -1)
	{
		right_child->balance_factor = 0;
		node->balance_factor = 1;
	}

	lc_of_rc->balance_factor = 0;

	return lc_of_rc_idx;
}


// Right Right Rotate
index_t avl_rotate_rightright(OBIDMS_avl_p avl, AVL_node_p node, index_t node_idx)
{
	AVL_node_p right_child = RIGHT_CHILD(node);
	index_t right_child_idx = node->right_child;

	node->right_child = right_child->left_child;
	right_child->left_child = node_idx;

	node->balance_factor = 0;
	right_child->balance_factor = 0;

	return right_child_idx;
}


// Balance a given node
index_t avl_balance_node(OBIDMS_avl_p avl, AVL_node_p node, index_t node_idx)
{
	index_t new_root = 0;

	if (node->balance_factor == 2)
	{ // Left Heavy
		if ((LEFT_CHILD(node))->balance_factor == -1)
			new_root = avl_rotate_leftright(avl, node, node_idx);
		else
			new_root = avl_rotate_leftleft(avl, node, node_idx);
	}
	else if (node->balance_factor == -2)
	{ // Right Heavy
		if ((RIGHT_CHILD(node))->balance_factor == 1)
			new_root = avl_rotate_rightleft(avl, node, node_idx);
		else
			new_root = avl_rotate_rightright(avl, node, node_idx);
	}
	else
	// Node is balanced
		new_root = node_idx;

	return new_root;
}


// Balance a given tree
void avl_balance(OBIDMS_avl_p avl)
{
	index_t new_root;
	index_t node_index;
	AVL_node_p node_to_balance;
	AVL_node_p parent_of_node_to_balance;

	node_index = (avl->path_idx)[1];
	node_to_balance = (avl->tree)+node_index;
	parent_of_node_to_balance = (avl->tree)+((avl->path_idx)[0]);

	// Balance the 2nd node stored in the path (the first is only kept to connect the new root
	// of the subtree if needed).
	new_root = avl_balance_node(avl, node_to_balance, node_index);

	if (new_root != node_index)
	// If the root of the subtree has changed
	{
		// If the subtree's root is the tree's root, store the new root
		if (node_index == (avl->header)->root_idx)
			(avl->header)->root_idx = new_root;
		// Else, connect the new subtree's root to the parent of the subtree
		else if ((avl->path_dir)[0])	   // Subtree is the right child of its parent
			parent_of_node_to_balance->right_child = new_root;
		else	   // Subtree is the left child of its parent
			parent_of_node_to_balance->left_child = new_root;
	}
}


// Print a depth first traverse of a node
void avl_print_node(OBIDMS_avl_p avl, AVL_node_p node, index_t node_idx, int depth)
{
	int i = 0;

	if (node->left_child != -1)
		avl_print_node(avl, LEFT_CHILD(node), node->left_child, depth+2);

	for (i = 0; i < depth; i++)
		putchar(' ');

	fprintf(stderr, "Node idx: %lld, Value idx: %lld, Left child: %lld, Right child: %lld, "
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			"Balance factor: %d, CRC: %llu\n", node_idx, node->value, node->left_child, node->right_child, node->balance_factor, node->crc64);
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	if (node->right_child != -1)
		avl_print_node(avl, RIGHT_CHILD(node), node->right_child, depth+2);
}


// Print a depth first traverse of a tree
void avl_print(OBIDMS_avl_p avl)
{
	fprintf(stderr, "\nRoot index: %lld\n", (avl->header)->root_idx);
	avl_print_node(avl, (avl->tree)+((avl->header)->root_idx), (avl->header)->root_idx, 0);
}


/**********************************************************************
 *
 * D E F I N I T I O N   O F   T H E   P U B L I C   F U N C T I O N S
 *
 **********************************************************************/

int obi_avl_exists(OBIDMS_p dms, const char* avl_name)
{
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	struct stat buffer;
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	char* 	    avl_dir_path;
	char*		avl_dir_relative_path;
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	int			relative_path_size;
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	int 	    check_dir;
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	// Build the AVL tree file path
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	relative_path_size = strlen(avl_name) + strlen(AVL_TREES_DIR_NAME) + 2;
	avl_dir_relative_path = (char*) malloc(relative_path_size*sizeof(char));
	if (avl_dir_relative_path == NULL)
	{
		obi_set_errno(OBI_MALLOC_ERROR);
		obidebug(1, "\nError allocating memory for the path to the AVL directory");
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		return -1;
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	}
	strcpy(avl_dir_relative_path, AVL_TREES_DIR_NAME);
	strcat(avl_dir_relative_path, "/");
	strcat(avl_dir_relative_path, avl_name);
	avl_dir_path = get_full_path(dms, avl_dir_relative_path);
	if (avl_dir_path == NULL)
	{
		obidebug(1, "\nError getting the directory path for an AVL tree");
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		return -1;
	}

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	check_dir = stat(avl_dir_path, &buffer);
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	free(avl_dir_path);
	free(avl_dir_relative_path);
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	if (check_dir == 0)
		return 1;
	else
		return 0;
}


1324
OBIDMS_avl_p obi_create_avl(OBIDMS_p dms, const char* avl_name, int avl_idx)
1325
{
1326 1327
	char* 				complete_avl_name;
	char*				avl_dir_name;
1328 1329 1330 1331 1332 1333 1334
	char* 				avl_file_name;
	char* 				avl_data_file_name;
	size_t				header_size;
	size_t				data_size;
	size_t				file_size;
	int					avl_file_descriptor;
	int					avl_data_file_descriptor;
1335
	int					avl_dir_fd;
1336 1337
	OBIDMS_avl_data_p   avl_data;
	OBIDMS_avl_p		avl;
1338 1339 1340 1341 1342 1343 1344 1345 1346 1347 1348 1349 1350 1351 1352 1353 1354 1355 1356 1357 1358 1359 1360 1361 1362 1363 1364 1365 1366 1367 1368 1369 1370 1371 1372 1373 1374 1375 1376 1377 1378 1379 1380 1381 1382 1383 1384 1385 1386 1387 1388 1389 1390 1391 1392 1393 1394 1395 1396 1397 1398
 	DIR*				directory;
    struct stat 		buffer;
    int 				check_dir;

	// Get complete name of AVL if index
	if (avl_idx >= 0)
	{
		complete_avl_name = build_avl_name_with_idx(avl_name, avl_idx);
		if (complete_avl_name == NULL)
			return NULL;
	}
	else
	{
		complete_avl_name = (char*) malloc((strlen(avl_name)+1)*sizeof(char));
		if (complete_avl_name == NULL)
		{
    		obi_set_errno(OBI_MALLOC_ERROR);
    		obidebug(1, "\nError allocating memory for an AVL name");
			return NULL;
		}
		strcpy(complete_avl_name, avl_name);
	}

	// Create that AVL's directory if needed
	avl_dir_name = get_full_path_of_avl_dir(dms, avl_name);
	if (avl_dir_name == NULL)
		return NULL;
	// Check if the AVL's directory already exists
	check_dir = stat(avl_dir_name, &buffer);
	// Create that AVL's directory if it doesn't already exist
   	if (check_dir < 0)
   	{
		if (mkdirat(dms->avl_dir_fd, avl_dir_name, 00777) < 0)
		{
			obi_set_errno(OBI_AVL_ERROR);
			obidebug(1, "\nError creating an AVL directory");
			if (avl_idx >= 0)
				free(complete_avl_name);
			free(avl_dir_name);
			return NULL;
		}
   	}
    // Open the AVL directory
    directory = opendir(avl_dir_name);
	if (directory == NULL)
	{
		obidebug(1, "\nError opening an AVL directory");
		if (avl_idx >= 0)
			free(complete_avl_name);
		free(avl_dir_name);
		return NULL;
	}
	free(avl_dir_name);
    avl_dir_fd = dirfd(directory);
	if (avl_dir_fd < 0)
	{
		obidebug(1, "\nError getting an AVL directory file descriptor");
		if (avl_idx >= 0)
			free(complete_avl_name);
		return NULL;
	}
1399 1400 1401 1402

	// Create the data file

		// Build file name
1403
	avl_data_file_name = build_avl_data_file_name(complete_avl_name);
1404
	if (avl_data_file_name == NULL)
1405 1406 1407
	{
		if (avl_idx >= 0)
			free(complete_avl_name);
1408
		return NULL;
1409
	}
1410 1411

		// Create file
1412
	avl_data_file_descriptor = openat(avl_dir_fd, avl_data_file_name, O_RDWR | O_CREAT | O_EXCL, 0777);
1413 1414 1415
	if (avl_data_file_descriptor < 0)
	{
		obi_set_errno(OBI_AVL_ERROR);
1416
		obidebug(1, "\nError creating an AVL tree data file");
1417 1418
		if (avl_idx >= 0)
			free(complete_avl_name);
1419 1420 1421 1422 1423 1424 1425 1426 1427 1428
		free(avl_data_file_name);
		return NULL;
	}
	free(avl_data_file_name);

		// Calculate the size needed
	header_size = get_avl_data_header_size();
	data_size   = get_initial_avl_data_size();
	file_size   = header_size + data_size;

1429
		// Truncate the AVL tree data file to the right size
1430 1431 1432
	if (ftruncate(avl_data_file_descriptor, file_size) < 0)
	{
		obi_set_errno(OBI_AVL_ERROR);
1433
		obidebug(1, "\nError truncating an AVL tree data file to the right size");
1434 1435
		if (avl_idx >= 0)
			free(complete_avl_name);
1436 1437 1438 1439
		close(avl_data_file_descriptor);
		return NULL;
	}

1440
		// Allocate the memory for the AVL tree data structure
1441 1442 1443
	avl_data = (OBIDMS_avl_data_p) malloc(sizeof(OBIDMS_avl_data_t));
	if (avl_data == NULL)
	{
1444
		obi_set_errno(OBI_MALLOC_ERROR);
1445
		obidebug(1, "\nError allocating the memory for the AVL tree data structure");
1446 1447
		if (avl_idx >= 0)
			free(complete_avl_name);
1448 1449 1450 1451
		close(avl_data_file_descriptor);
		return NULL;
	}

1452
		// Fill the AVL tree data structure
1453 1454 1455 1456 1457 1458 1459 1460 1461 1462
	avl_data->header = mmap(NULL,
			                header_size,
			                PROT_READ | PROT_WRITE,
			                MAP_SHARED,
			                avl_data_file_descriptor,
			                0
			               );
	if (avl_data->header == MAP_FAILED)
	{
		obi_set_errno(OBI_AVL_ERROR);
1463
		obidebug(1, "\nError mmapping the header of an AVL tree data file");
1464 1465
		if (avl_idx >= 0)
			free(complete_avl_name);
1466 1467 1468 1469 1470 1471 1472 1473 1474 1475 1476 1477 1478 1479 1480
		close(avl_data_file_descriptor);
		free(avl_data);
		return NULL;
	}

	avl_data->data   = mmap(NULL,
			                data_size,
			                PROT_READ | PROT_WRITE,
			                MAP_SHARED,
			                avl_data_file_descriptor,
			                header_size
			               );
	if (avl_data->data == MAP_FAILED)
	{
		obi_set_errno(OBI_AVL_ERROR);
1481
		obidebug(1, "\nError mmapping the data of an AVL tree data file");
1482 1483
		if (avl_idx >= 0)
			free(complete_avl_name);
1484 1485 1486 1487 1488 1489 1490 1491 1492 1493 1494
		munmap(avl_data->header, header_size);
		close(avl_data_file_descriptor);
		free(avl_data);
		return NULL;
	}

	(avl_data->header)->header_size 	 = header_size;
	(avl_data->header)->data_size_max	 = data_size;
	(avl_data->header)->data_size_used   = 0;
	(avl_data->header)->nb_items	 	 = 0;
	(avl_data->header)->creation_date    = time(NULL);
1495 1496 1497
	strcpy((avl_data->header)->avl_name, complete_avl_name);

	avl_data->data_fd = avl_data_file_descriptor;
1498 1499 1500 1501 1502

	// Initialize all bits to 0
	memset(avl_data->data, 0, (avl_data->header)->data_size_max);


1503
	// Create the AVL tree file
1504 1505

		// Build file name
1506
	avl_file_name = build_avl_file_name(complete_avl_name);
1507 1508 1509 1510 1511 1512 1513 1514 1515 1516 1517 1518
	if (avl_file_name == NULL)
	{
		close_avl_data(avl_data);
		return NULL;
	}

		// Calculate the size needed
	header_size = get_avl_header_size();
	data_size = get_initial_avl_size();
	file_size = header_size + data_size;

		// Create file
1519
	avl_file_descriptor = openat(avl_dir_fd, avl_file_name, O_RDWR | O_CREAT | O_EXCL, 0777);
1520 1521 1522
	if (avl_file_descriptor < 0)
	{
		obi_set_errno(OBI_AVL_ERROR);
1523
		obidebug(1, "\nError creating an AVL tree file");
1524 1525
		if (avl_idx >= 0)
			free(complete_avl_name);
1526 1527 1528 1529 1530 1531
		close_avl_data(avl_data);
		free(avl_file_name);
		return NULL;
	}
	free(avl_file_name);

1532
		// Truncate the AVL tree file to the right size
1533 1534 1535
	if (ftruncate(avl_file_descriptor, file_size) < 0)
	{
		obi_set_errno(OBI_AVL_ERROR);
1536
		obidebug(1, "\nError truncating an AVL tree file to the right size");
1537 1538
		if (avl_idx >= 0)
			free(complete_avl_name);
1539 1540 1541 1542 1543
		close_avl_data(avl_data);
		close(avl_file_descriptor);
		return NULL;
	}

1544
		// Allocate the memory for the AVL tree structure
1545 1546 1547
	avl = (OBIDMS_avl_p) malloc(sizeof(OBIDMS_avl_t));
	if (avl == NULL)
	{
1548
		obi_set_errno(OBI_MALLOC_ERROR);
1549
		obidebug(1, "\nError allocating the memory for the AVL tree structure");
1550 1551
		if (avl_idx >= 0)
			free(complete_avl_name);
1552 1553 1554 1555 1556
		close_avl_data(avl_data);
		close(avl_file_descriptor);
		return NULL;
	}

1557
		// Fill the AVL tree structure
1558 1559 1560 1561 1562 1563 1564 1565 1566 1567
	avl->header = mmap(NULL,
			           header_size,
			           PROT_READ | PROT_WRITE,
			           MAP_SHARED,
			           avl_file_descriptor,
			           0
			          );
	if (avl->header == MAP_FAILED)
	{
		obi_set_errno(OBI_AVL_ERROR);
1568
		obidebug(1, "\nError mmapping the header of an AVL tree file");
1569 1570
		if (avl_idx >= 0)
			free(complete_avl_name);
1571 1572 1573 1574 1575 1576 1577 1578 1579 1580 1581 1582 1583 1584 1585 1586
		close_avl_data(avl_data);
		close(avl_file_descriptor);
		free(avl);
		return NULL;
	}

	avl->tree  = mmap(NULL,
			          data_size,
			          PROT_READ | PROT_WRITE,
			          MAP_SHARED,
			          avl_file_descriptor,
			          header_size
			         );
	if (avl->tree == MAP_FAILED)
	{
		obi_set_errno(OBI_AVL_ERROR);
1587
		obidebug(1, "\nError mmapping the data of an AVL tree file");