obiavl.c 62.9 KB
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/****************************************************************************
 * OBIDMS AVL tree functions	                                            *
 ****************************************************************************/

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


#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"
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#include "obiblob.h"
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#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 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);


/**
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 * @brief Internal function returning the size of an AVL tree header on this platform,
 *        including the size of the bloom filter associated with the AVL tree.
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 *
 * @returns The size of an AVL tree header in bytes.
 *
 * @since December 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
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size_t get_avl_header_size(void);
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/**
 * @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)
 */
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size_t get_initial_avl_size(void);
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/**
 * @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)
 */
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size_t get_avl_data_header_size(void);
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/**
 * @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)
 */
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size_t get_initial_avl_data_size(void);
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/**
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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);


/**
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 * @brief Internal function creating and adding a new AVL in an AVL group.
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 *
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 * @warning The previous AVL in the list of the group is unmapped,
 * 			if it's not the 1st AVL being added.
 *
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 * @param avl_group A pointer on the AVL tree group structure.
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 *
 * @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);


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/**
 * @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);


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/**
 * @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.
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 * @param value A pointer to the blob structure.
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 *
 * @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)
 */
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int maybe_in_avl(OBIDMS_avl_p avl, Obi_blob_p value);
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/**
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 * @brief Internal function storing a value (blob) in the data array referred to by an AVL tree.
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 *
 * @param avl A pointer to the AVL tree structure.
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 * @param value A pointer to the value (blob structure).
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 *
 * @returns The index of the stored value.
 * @retval -1 if an error occurred.
 *
 * @since December 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
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index_t avl_add_value_in_data_array(OBIDMS_avl_p avl, Obi_blob_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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char* get_full_path_of_avl_dir(OBIDMS_p dms, const char* avl_name)
{
	char* avl_dir_name;

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	avl_dir_name = obi_dms_get_full_path(dms, INDEXER_DIR_NAME);
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	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());
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	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;
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	(avl->header)->nb_items_max	= (index_t) floor(((double) (avl->header)->avl_size) / ((double) sizeof(AVL_node_t)));
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	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;
705 706 707 708 709 710 711 712 713 714 715

	// 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);
716
		obidebug(1, "\nError enlarging an AVL tree file");
717 718 719 720 721 722 723 724
		return -1;
	}

	// Unmap and re-map the data

	if (munmap(avl->tree, old_data_size) < 0)
	{
		obi_set_errno(OBI_AVL_ERROR);
725
		obidebug(1, "\nError munmapping the tree of an AVL tree file before enlarging");
726 727 728 729
		return -1;
	}

	avl->tree = mmap(NULL,
730 731 732 733 734 735
					 new_data_size,
					 PROT_READ | PROT_WRITE,
					 MAP_SHARED,
					 avl_file_descriptor,
					 header_size
					);
736 737 738 739

	if (avl->tree == MAP_FAILED)
	{
		obi_set_errno(OBI_AVL_ERROR);
740
		obidebug(1, "\nError re-mmapping the tree of an AVL tree file after enlarging the file");
741 742 743 744 745 746
		return -1;
	}

	// Set the new avl size
	(avl->header)->avl_size = new_data_size;

747 748 749
	// Set new maximum number of items
	(avl->header)->nb_items_max	 = (index_t) floor(((double) (avl->header)->avl_size) / ((double) sizeof(AVL_node_t)));

750 751 752 753
	return 0;
}


754
int grow_avl_data(OBIDMS_avl_data_p avl_data)		// TODO Lock when needed
755 756 757 758 759 760 761
{
	size_t 	file_size;
	index_t old_data_size;
	index_t new_data_size;
	size_t 	header_size;
	int 	avl_data_file_descriptor;

762
	avl_data_file_descriptor = avl_data->data_fd;
763 764

	// Calculate the new file size
765
	old_data_size = (avl_data->header)->data_size_max;
766
	new_data_size = old_data_size * AVL_GROWTH_FACTOR;
767
	header_size = (avl_data->header)->header_size;
768 769 770 771 772 773
	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);
774
		obidebug(1, "\nError enlarging an AVL tree data file");
775 776 777 778 779
		return -1;
	}

	// Unmap and re-map the data

780
	if (munmap(avl_data->data, old_data_size) < 0)
781 782
	{
		obi_set_errno(OBI_AVL_ERROR);
783
		obidebug(1, "\nError munmapping the data of an AVL tree data file before enlarging");
784 785 786
		return -1;
	}

787 788 789 790 791 792 793
	avl_data->data = mmap(NULL,
						  new_data_size,
						  PROT_READ | PROT_WRITE,
						  MAP_SHARED,
						  avl_data_file_descriptor,
						  header_size
						 );
794

795
	if (avl_data->data == MAP_FAILED)
796 797
	{
		obi_set_errno(OBI_AVL_ERROR);
798
		obidebug(1, "\nError re-mmapping the data of an AVL tree data file after enlarging the file");
799 800 801 802
		return -1;
	}

	// Set new data size
803
	(avl_data->header)->data_size_max = new_data_size;
804

805
	// Initialize new data to 0
806
	memset((avl_data->data)+old_data_size, 0, new_data_size - old_data_size);
807 808 809 810 811

	return 0;
}


812
int close_avl_data(OBIDMS_avl_data_p avl_data)
813
{
814
	int ret_val = 0;
815

816
	ret_val = truncate_avl_data_to_size_used(avl_data);
817

818
	if (munmap(avl_data->data, (avl_data->header)->data_size_max) < 0)
819
	{
820 821 822
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError munmapping the data of an AVL tree data file");
		ret_val = -1;
823 824
	}

825 826 827 828 829 830
	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;
	}
831

832 833 834 835 836 837
	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;
	}
838

839
	free(avl_data);
840

841
	return ret_val;
842 843 844
}


845
int unmap_an_avl(OBIDMS_avl_p avl)
846
{
847 848 849 850 851 852
	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;
	}
853
	if (munmap(avl->tree, (avl->header)->avl_size) < 0)
854 855 856 857 858 859 860
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError unmapping the tree of an AVL tree");
		return -1;
	}
	return 0;
}
861 862


863 864 865 866 867 868 869 870 871 872 873 874 875 876
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;
	}
877

878
	avl->tree = mmap(NULL,
879
					 (avl->header)->avl_size,
880 881 882 883 884 885 886 887 888 889 890 891 892
					 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;
}
893 894


895 896 897
int add_new_avl_in_group(OBIDMS_avl_group_p avl_group)
{
	// Check that maximum number of AVLs in a group was not reached
898
	if (avl_group->last_avl_idx == (MAX_NB_OF_AVLS_IN_GROUP - 1))
899
	{
900 901 902 903 904
		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;
	}

905 906 907 908
	// Unmap the previous AVL if it's not the 1st
	if (avl_group->last_avl_idx > 0)
		if (unmap_an_avl((avl_group->sub_avls)[avl_group->last_avl_idx]) < 0)
			return -1;
909 910

	// Increment current AVL index
911
	(avl_group->last_avl_idx)++;
912

913
	// Create the new AVL
914 915
	(avl_group->sub_avls)[avl_group->last_avl_idx] = obi_create_avl(avl_group->dms, avl_group->name, avl_group->last_avl_idx);
	if ((avl_group->sub_avls)[avl_group->last_avl_idx] == NULL)
916 917 918
	{
		obidebug(1, "\nError creating a new AVL tree in a group");
		return -1;
919 920
	}

921 922 923 924
	return 0;
}


925 926
int add_existing_avl_in_group(OBIDMS_avl_group_p avl_group_dest, OBIDMS_avl_group_p avl_group_source, int avl_idx)
{
927
	if (link(obi_get_full_path_of_avl_file_name(avl_group_source->dms, avl_group_source->name, avl_idx), obi_get_full_path_of_avl_file_name(avl_group_dest->dms, avl_group_dest->name, avl_idx)) < 0)
928 929 930 931 932
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError creating a hard link to an existing AVL tree file");
		return -1;
	}
933
	if (link(obi_get_full_path_of_avl_data_file_name(avl_group_source->dms, avl_group_source->name, avl_idx), obi_get_full_path_of_avl_data_file_name(avl_group_dest->dms, avl_group_dest->name, avl_idx)) < 0)
934 935 936 937 938 939 940 941 942
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError creating a hard link to an existing AVL data file");
		return -1;
	}

	// Increment current AVL index
	(avl_group_dest->last_avl_idx)++;

943
	// Open AVL for that group 		TODO ideally not needed because AVL open twice, but needed for now
944 945 946 947 948 949 950 951 952 953
	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)
	{
		obidebug(1, "\nError opening an AVL to add in an AVL group");
		return -1;
	}

	return 0;
}

954

955
int maybe_in_avl(OBIDMS_avl_p avl, Obi_blob_p value)
956
{
957
	return (bloom_check(&((avl->header)->bloom_filter), value, obi_blob_sizeof(value)));
958 959 960
}


961
index_t avl_add_value_in_data_array(OBIDMS_avl_p avl, Obi_blob_p value)
962 963
{
	index_t value_idx;
964
	int value_size;
965 966 967 968

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

	// Grow the data if needed
969
	value_size = obi_blob_sizeof(value);
970 971 972 973 974 975 976 977 978 979 980 981 982 983 984 985
	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;
986 987 988 989 990 991 992 993 994
}


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

	node = (avl->tree)+node_idx;

995 996
	node->left_child     = -1;
	node->right_child    = -1;
997
	node->balance_factor = 0;
998 999
	node->value          = -1;
	node->crc64          = 0; 	// TODO no NA value
1000 1001 1002 1003 1004 1005 1006 1007

	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)
{
1008
	uint8_t    n;
1009 1010 1011 1012 1013 1014 1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030 1031 1032 1033 1034 1035 1036 1037 1038 1039 1040 1041 1042 1043 1044 1045 1046 1047 1048 1049 1050 1051 1052 1053 1054 1055 1056 1057 1058 1059 1060 1061 1062 1063 1064 1065 1066 1067 1068 1069 1070 1071 1072 1073 1074 1075 1076 1077 1078 1079 1080 1081 1082 1083 1084 1085 1086 1087 1088 1089 1090 1091 1092 1093 1094 1095 1096 1097 1098 1099 1100 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 1116 1117 1118 1119 1120 1121 1122 1123 1124 1125 1126 1127 1128 1129 1130 1131 1132 1133 1134 1135 1136 1137 1138 1139 1140 1141 1142 1143 1144 1145 1146 1147 1148 1149 1150 1151 1152 1153 1154 1155 1156 1157 1158 1159 1160 1161
	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)
{
1162 1163
	index_t    new_root;
	index_t    node_index;
1164 1165 1166 1167 1168 1169 1170 1171 1172 1173 1174 1175 1176 1177 1178 1179 1180 1181 1182 1183 1184 1185 1186 1187 1188 1189 1190 1191 1192 1193 1194 1195 1196 1197 1198 1199 1200 1201
	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, "
1202 1203
			"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))));
1204 1205 1206 1207 1208 1209 1210 1211 1212 1213 1214 1215 1216 1217 1218 1219 1220 1221 1222 1223

	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
 *
 **********************************************************************/

1224 1225 1226 1227 1228 1229 1230 1231 1232 1233 1234 1235 1236 1237 1238 1239 1240 1241 1242 1243 1244 1245 1246 1247 1248 1249 1250 1251 1252 1253 1254 1255 1256 1257 1258 1259 1260 1261 1262 1263 1264 1265 1266 1267 1268 1269 1270 1271 1272 1273 1274 1275 1276 1277 1278 1279 1280 1281 1282 1283 1284 1285 1286 1287 1288 1289 1290 1291 1292 1293 1294 1295 1296 1297 1298 1299 1300 1301 1302 1303 1304 1305 1306 1307 1308 1309 1310 1311 1312 1313 1314 1315 1316 1317 1318 1319 1320 1321 1322 1323 1324 1325 1326 1327 1328 1329 1330 1331 1332 1333 1334 1335 1336 1337 1338 1339 1340 1341 1342 1343 1344 1345 1346 1347 1348 1349 1350 1351

char* obi_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* obi_get_full_path_of_avl_file_name(OBIDMS_p dms, const char* avl_name, int avl_idx)
{
	char* complete_avl_name;
	char* full_path;
	char* avl_file_name;

	if (avl_idx >= 0)
	{
		complete_avl_name = obi_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);
	}

	avl_file_name = build_avl_file_name(complete_avl_name);
	if (avl_file_name == NULL)
	{
		free(complete_avl_name);
		return NULL;
	}

	full_path = get_full_path_of_avl_dir(dms, avl_name);
	if (full_path == NULL)
	{
		free(complete_avl_name);
		free(avl_file_name);
		return NULL;
	}

	strcat(full_path, "/");
	strcat(full_path, avl_file_name);

	free(complete_avl_name);

	return full_path;
}


char* obi_get_full_path_of_avl_data_file_name(OBIDMS_p dms, const char* avl_name, int avl_idx)
{
	char* complete_avl_name;
	char* full_path;
	char* avl_data_file_name;

	if (avl_idx >= 0)
	{
		complete_avl_name = obi_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);
	}

	avl_data_file_name = build_avl_data_file_name(complete_avl_name);
	if (avl_data_file_name == NULL)
	{
		free(complete_avl_name);
		return NULL;
	}

	full_path = get_full_path_of_avl_dir(dms, avl_name);
	if (full_path == NULL)
	{
		free(complete_avl_name);
		free(avl_data_file_name);
		return NULL;
	}

	strcat(full_path, "/");
	strcat(full_path, avl_data_file_name);

	free(complete_avl_name);

	return full_path;
}


1352 1353
int obi_avl_exists(OBIDMS_p dms, const char* avl_name)
{
1354
	struct stat buffer;
1355
	char* 	    avl_dir_path;
1356
	int 	    check_dir;
1357

Celine Mercier committed
1358
	// Build the AVL tree file path
1359
	avl_dir_path = get_full_path_of_avl_dir(dms, avl_name);
1360
	if (avl_dir_path == NULL)
1361 1362
		return -1;

1363
	check_dir = stat(avl_dir_path, &buffer);
1364

1365
	free(avl_dir_path);
1366 1367 1368 1369 1370 1371 1372 1373

	if (check_dir == 0)
		return 1;
	else
		return 0;
}


1374
OBIDMS_avl_p obi_create_avl(OBIDMS_p dms, const char* avl_name, int avl_idx)
1375
{
1376 1377
	char* 				complete_avl_name;
	char*				avl_dir_name;
1378 1379 1380 1381 1382 1383 1384
	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;
1385
	int					avl_dir_fd;
1386 1387
	OBIDMS_avl_data_p   avl_data;
	OBIDMS_avl_p		avl;
1388 1389 1390 1391 1392 1393 1394
 	DIR*				directory;
    struct stat 		buffer;
    int 				check_dir;

	// Get complete name of AVL if index
	if (avl_idx >= 0)
	{
1395
		complete_avl_name = obi_build_avl_name_with_idx(avl_name, avl_idx);
1396 1397 1398 1399 1400 1401 1402 1403 1404 1405 1406 1407 1408 1409 1410 1411 1412 1413 1414 1415 1416 1417 1418 1419
		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)
   	{
Celine Mercier committed
1420
		if (mkdirat(dms->indexer_dir_fd, avl_dir_name, 00777) < 0)
1421 1422 1423 1424 1425 1426 1427 1428 1429 1430 1431 1432 1433 1434 1435 1436 1437 1438 1439 1440 1441 1442 1443 1444 1445 1446 1447 1448
		{
			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;
	}
1449 1450 1451 1452

	// Create the data file

		// Build file name
1453
	avl_data_file_name = build_avl_data_file_name(complete_avl_name);
1454
	if (avl_data_file_name == NULL)
1455 1456 1457
	{
		if (avl_idx >= 0)
			free(complete_avl_name);
1458
		return NULL;
1459
	}
1460 1461

		// Create file
1462
	avl_data_file_descriptor = openat(avl_dir_fd, avl_data_file_name, O_RDWR | O_CREAT | O_EXCL, 0777);
1463 1464 1465
	if (avl_data_file_descriptor < 0)
	{
		obi_set_errno(OBI_AVL_ERROR);
1466
		obidebug(1, "\nError creating an AVL tree data file");
1467 1468
		if (avl_idx >= 0)
			free(complete_avl_name);
1469 1470 1471 1472 1473 1474 1475 1476 1477 1478
		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;

1479
		// Truncate the AVL tree data file to the right size
1480 1481 1482
	if (ftruncate(avl_data_file_descriptor, file_size) < 0)
	{
		obi_set_errno(OBI_AVL_ERROR);
1483
		obidebug(1, "\nError truncating an AVL tree data file to the right size");
1484 1485
		if (avl_idx >= 0)
			free(complete_avl_name);
1486 1487 1488 1489
		close(avl_data_file_descriptor);
		return NULL;
	}

1490
		// Allocate the memory for the AVL tree data structure
1491 1492 1493
	avl_data = (OBIDMS_avl_data_p) malloc(sizeof(OBIDMS_avl_data_t));
	if (avl_data == NULL)
	{
1494
		obi_set_errno(OBI_MALLOC_ERROR);
1495
		obidebug(1, "\nError allocating the memory for the AVL tree data structure");
1496 1497
		if (avl_idx >= 0)
			free(complete_avl_name);
1498 1499 1500 1501
		close(avl_data_file_descriptor);
		return NULL;
	}

1502
		// Fill the AVL tree data structure
1503 1504 1505 1506 1507 1508 1509 1510 1511 1512
	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);
1513
		obidebug(1, "\nError mmapping the header of an AVL tree data file");
1514 1515
		if (avl_idx >= 0)
			free(complete_avl_name);
1516 1517 1518 1519 1520 1521 1522 1523 1524 1525 1526 1527 1528 1529 1530
		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);
1531
		obidebug(1, "\nError mmapping the data of an AVL tree data file");
1532 1533
		if (avl_idx >= 0)
			free(complete_avl_name);
1534 1535 1536 1537 1538 1539 1540 1541 1542 1543 1544
		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);
1545 1546 1547
	strcpy((avl_data->header)->avl_name, complete_avl_name);

	avl_data->data_fd = avl_data_file_descriptor;
1548 1549 1550 1551 1552

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


1553
	// Create the AVL tree file
1554 1555

		// Build file name
1556
	avl_file_name = build_avl_file_name(complete_avl_name);
1557 1558 1559 1560 1561 1562 1563 1564 1565 1566 1567 1568
	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
1569
	avl_file_descriptor = openat(avl_dir_fd, avl_file_name, O_RDWR | O_CREAT | O_EXCL, 0777);
1570 1571 1572
	if (avl_file_descriptor < 0)
	{
		obi_set_errno(OBI_AVL_ERROR);
1573
		obidebug(1, "\nError creating an AVL tree file");
1574 1575
		if (avl_idx >= 0)
			free(complete_avl_name);
1576 1577 1578 1579 1580 1581
		close_avl_data(avl_data);
		free(avl_file_name);
		return NULL;
	}
	free(avl_file_name);

1582
		// Truncate the AVL tree file to the right size
1583 1584 1585
	if (ftruncate(avl_file_descriptor, file_size) < 0)
	{
		obi_set_errno(OBI_AVL_ERROR);
1586
		obidebug(1, "\nError truncating an AVL tree file to the right size");
1587 1588
		if (avl_idx >= 0)
			free(complete_avl_name);
1589 1590 1591 1592 1593
		close_avl_data(avl_data);
		close(avl_file_descriptor);
		return NULL;
	}

1594
		// Allocate the memory for the AVL tree structure
1595 1596 1597
	avl = (OBIDMS_avl_p) malloc(sizeof(OBIDMS_avl_t));
	if (avl == NULL)
	{
1598
		obi_set_errno(OBI_MALLOC_ERROR);
1599
		obidebug(1, "\nError allocating the memory for the AVL tree structure");
1600 1601
		if (avl_idx >= 0)
			free(complete_avl_name);
1602 1603 1604 1605 1606
		close_avl_data(avl_data);
		close(avl_file_descriptor);
		return NULL;
	}

1607
		// Fill the AVL tree structure
1608 1609 1610 1611 1612 1613 1614 1615 1616 1617
	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);
1618
		obidebug(1, "\nError mmapping the header of an AVL tree file");
1619 1620
		if (avl_idx >= 0)
			free(complete_avl_name);
1621 1622 1623 1624 1625 1626 1627 1628 1629 1630 1631 1632 1633 1634 1635 1636
		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);
1637
		obidebug(1, "\nError mmapping the data of an AVL tree file");
1638 1639
		if (avl_idx >= 0)
			free(complete_avl_name);
1640 1641 1642 1643 1644 1645 1646
		close_avl_data(avl_data);
		munmap(avl->header, header_size);
		close(avl_file_descriptor);
		free(avl);
		return NULL;
	}

1647 1648 1649
	avl->dms       = dms;
	avl->data      = avl_data;
	avl->avl_fd    = avl_file_descriptor;
1650 1651 1652 1653

	(avl->header)->header_size 	 = header_size;
	(avl->header)->avl_size 	 = data_size;
	(avl->header)->nb_items	 	 = 0;
1654
	(avl->header)->nb_items_max	 = (index_t) floor(((double) (avl->header)->avl_size) / ((double) sizeof(AVL_node_t)));
1655
	(avl->header)->root_idx      = -1;
1656
	(avl->header)->creation_date = time(NULL);
1657
	strcpy((avl->header)->avl_name, complete_avl_name);
1658 1659

	// Bloom filter
1660
	bloom_init(&((avl->header)->bloom_filter), MAX_NODE_COUNT_PER_AVL);
1661

1662
	free(complete_avl_name);
1663

1664 1665 1666 1667 1668 1669 1670
	if (closedir(directory) < 0)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError closing an AVL directory");
		return NULL;
	}

1671 1672 1673 1674
	return avl;
}


1675
OBIDMS_avl_p obi_open_avl(OBIDMS_p dms, const char* avl_name, int avl_idx)
1676 1677
{
	char* 	 			avl_file_name;
1678 1679
	char*				complete_avl_name;
	char*				avl_dir_name;
1680
	char* 				avl_data_file_name;
1681
	DIR*				directory;
1682 1683 1684 1685 1686 1687
	size_t				header_size;
	int					avl_file_descriptor;
	int					avl_data_file_descriptor;
	int					avl_dir_file_descriptor;
	OBIDMS_avl_data_p   avl_data;
	OBIDMS_avl_p		avl;
1688 1689 1690 1691

	// Get complete name of AVL if index
	if (avl_idx >= 0)
	{
1692
		complete_avl_name = obi_build_avl_name_with_idx(avl_name, avl_idx);
1693 1694 1695 1696 1697 1698 1699 1700 1701 1702 1703 1704 1705 1706
		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);
	}
1707

1708 1709 1710 1711 1712 1713 1714 1715 1716 1717 1718 1719 1720 1721 1722 1723 1724 1725 1726 1727 1728 1729 1730 1731 1732 1733 1734 1735
    // Open the AVL directory
	avl_dir_name = get_full_path_of_avl_dir(dms, avl_name);
	if (avl_dir_name == NULL)
	{
		if (avl_idx >= 0)
			free(complete_avl_name);
		return NULL;
	}
    directory = opendir(avl_dir_name);
	if (directory == NULL)
	{
		obi_set_errno(OBI_AVL_ERROR);
		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_file_descriptor = dirfd(directory);
	if (avl_dir_file_descriptor < 0)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError getting the file descriptor of an AVL directory");
		if (avl_idx >= 0)
			free(complete_avl_name);
		return NULL;
	}
1736

1737 1738

	// Open the data file
1739 1740

		// Build file name
1741
	avl_data_file_name = build_avl_data_file_name(complete_avl_name);
1742 1743 1744 1745
	if (avl_data_file_name == NULL)
		return NULL;

		// Open file
1746
	avl_data_file_descriptor = openat(avl_dir_file_descriptor, avl_data_file_name, O_RDWR, 0777);
1747 1748 1749
	if (avl_data_file_descriptor < 0)
	{
		obi_set_errno(OBI_AVL_ERROR);
1750
		obidebug(1, "\nError opening an AVL tree data file");
1751 1752
		if (avl_idx >= 0)
			free(complete_avl_name);
1753 1754 1755 1756 1757
		free(avl_data_file_name);
		return NULL;
	}
	free(avl_data_file_name);

1758
		// Allocate the memory for the AVL tree data structure
1759 1760 1761
	avl_data = (OBIDMS_avl_data_p) malloc(sizeof(OBIDMS_avl_data_t));
	if (avl_data == NULL)
	{
1762
		obi_set_errno(OBI_MALLOC_ERROR);
1763
		obidebug(1, "\nError allocating the memory for the AVL tree data structure");
1764 1765
		if (avl_idx >= 0)
			free(complete_avl_name);
1766 1767 1768 1769 1770 1771 1772 1773
		close(avl_data_file_descriptor);
		return NULL;
	}

	// Read the header size
	if (read(avl_data_file_descriptor, &header_size, sizeof(size_t)) < ((ssize_t) sizeof(size_t)))
	{
		obi_set_errno(OBI_AVL_ERROR);
1774
		obidebug(1, "\nError reading the header size to open an AVL tree data file");
1775 1776
		if (avl_idx >= 0)
			free(complete_avl_name);
1777 1778 1779 1780 1781 1782 1783
		close(avl_data_file_descriptor);
		return NULL;
	}

		// Fill the avl data structure
	avl_data->header = mmap(NULL,
			                header_size,
1784
							PROT_READ | PROT_WRITE,
1785 1786 1787 1788 1789 1790 1791
			                MAP_SHARED,
			                avl_data_file_descriptor,
			                0
			               );
	if (avl_data->header == MAP_FAILED)
	{
		obi_set_errno(OBI_AVL_ERROR);
1792
		obidebug(1, "\nError mmapping the header of an AVL tree data file");
1793 1794
		if (avl_idx >= 0)
			free(complete_avl_name);
1795 1796 1797 1798 1799 1800 1801
		close(avl_data_file_descriptor);
		free(avl_data);
		return NULL;
	}

	avl_data->data   = mmap(NULL,
			                (avl_data->header)->data_size_max,
1802
			                PROT_READ,
1803 1804 1805 1806 1807 1808 1809
			                MAP_SHARED,
			                avl_data_file_descriptor,
			                header_size
			               );
	if (avl_data->data == MAP_FAILED)
	{
		obi_set_errno(OBI_AVL_ERROR);
1810
		obidebug(1, "\nError mmapping the data of an AVL tree data file");
1811 1812
		if (avl_idx >= 0)
			free(complete_avl_name);
1813 1814 1815 1816 1817 1818
		munmap(avl_data->header, header_size);
		close(avl_data_file_descriptor);
		free(avl_data);
		return NULL;
	}

1819
	avl_data->data_fd = avl_data_file_descriptor;
1820 1821


1822
	// Open the AVL tree file
1823 1824

		// Build file name
1825
	avl_file_name = build_avl_file_name(complete_avl_name);
1826 1827 1828 1829 1830 1831 1832
	if (avl_file_name == NULL)
	{
		close_avl_data(avl_data);
		return NULL;
	}

		// Open file
1833
	avl_file_descriptor = openat(avl_dir_file_descriptor, avl_file_name, O_RDWR, 0777);
1834 1835 1836
	if (avl_file_descriptor < 0)
	{
		obi_set_errno(OBI_AVL_ERROR);
1837
		obidebug(1, "\nError opening an AVL tree file");
1838 1839
		if (avl_idx >= 0)
			free(complete_avl_name);
1840 1841 1842 1843 1844 1845
		close_avl_data(avl_data);
		free(avl_file_name);
		return NULL;
	}
	free(avl_file_name);

1846
		// Allocate the memory for the AVL tree structure
1847 1848 1849
	avl = (OBIDMS_avl_p) malloc(sizeof(OBIDMS_avl_t));
	if (avl == NULL)
	{
1850
		obi_set_errno(OBI_MALLOC_ERROR);
1851
		obidebug(1, "\nError allocating the memory for the AVL tree structure");
1852 1853
		if (avl_idx >= 0)
			free(complete_avl_name);
1854 1855 1856 1857 1858 1859 1860 1861 1862
		close_avl_data(avl_data);
		close(avl_file_descriptor);
		return NULL;
	}

		// Read the header size
	if (read(avl_file_descriptor, &header_size, sizeof(size_t)) < ((ssize_t) sizeof(size_t)))
	{
		obi_set_errno(OBI_AVL_ERROR);
1863
		obidebug(1, "\nError reading the header size to open an AVL tree");
1864 1865
		if (avl_idx >= 0)
			free(complete_avl_name);
1866 1867 1868 1869 1870 1871 1872
		close(avl_file_descriptor);
		return NULL;
	}

		// Fill the avl structure
	avl->header = mmap(NULL,
			           header_size,
1873
					   PROT_READ | PROT_WRITE,
1874 1875 1876 1877 1878 1879 1880
			           MAP_SHARED,
			           avl_file_descriptor,
			           0
			          );
	if (avl->header == MAP_FAILED)
	{
		obi_set_errno(OBI_AVL_ERROR);
1881
		obidebug(1, "\nError mmapping the header of an AVL tree file");