obitools3/src/obidms.c

/********************************************************************
 * OBIDMS functions                                                 *
 ********************************************************************/

/**
 * @file obidms.c
 * @author Eric Coissac (eric.coissac@metabarcoding.org)
 * @date 23 May 2015
 * @brief OBIDMS functions.
 */


#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <stdbool.h>
#include <sys/stat.h>
#include <fcntl.h>
#include <sys/types.h>
#include <dirent.h>
#include <unistd.h>
#include <libgen.h>   /* <EC> : Added July 28th 2017 to include basename */

#include "obidms.h"
#include "obierrno.h"
#include "obidebug.h"
#include "obidmscolumn.h"
#include "obiview.h"
#include "obiblob_indexer.h"
#include "utils.h"
#include "obilittlebigman.h"


#define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)


// Initialize global list of opened DMS
OBIDMS_p global_opened_dms_list[MAX_NB_OPENED_DMS+1] = { 0 };


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


/**
 * Internal function building the OBIDMS directory name from an OBIDMS name.
 *
 * The function builds the directory name corresponding to an OBIDMS.
 * It also checks that the name is not too long.
 *
 * @warning The returned pointer has to be freed by the caller.
 *
 * @param dms_name The name of the OBIDMS.
 *
 * @returns A pointer to the directory name.
 * @retval NULL if an error occurred.
 *
 * @since May 2015
 * @author Eric Coissac (eric.coissac@metabarcoding.org)
 */
static char* build_directory_name(const char* dms_name);


/**
 * Internal function building the informations file name from an OBIDMS name.
 *
 * The function builds the file name for the informations file of an OBIDMS.
 *
 * @warning The returned pointer has to be freed by the caller.
 *
 * @param dms_name The name of the OBIDMS.
 *
 * @returns A pointer to the file name.
 * @retval NULL if an error occurred.
 *
 * @since November 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
static char* build_infos_file_name(const char* dms_name);


/**
 * Internal function creating the file containing basic informations on the OBIDMS.
 *
 * This file contains:
 * 		- The endianness of the platform
 *
 * @warning The returned pointer has to be freed by the caller.
 *
 * @param dms_file_descriptor The file descriptor for the OBIDMS directory.
 * @param dms_name The name of the OBIDMS.
 *
 * @retval 0 if the operation was successfully completed.
 * @retval -1 if an error occurred.
 *
 * @since November 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
int create_dms_infos_file(int dms_file_descriptor, const char* dms_name);


/**
 * Internal function adding a DMS in the global list of DMS opened by a program.
 *
 * @param dms A pointer on the DMS to add.
 *
 * @retval 0 if the operation was successfully completed.
 * @retval -1 if an error occurred.
 *
 * @since October 2017
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
static int list_dms(OBIDMS_p dms);


/**
 * Internal function removing a DMS from the global list of DMS opened by a program.
 *
 * @param dms A pointer on the DMS to remove.
 *
 * @since October 2017
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
static void unlist_dms(OBIDMS_p dms);


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

static char* build_directory_name(const char* dms_name)
{
	char* directory_name;

	// Build the database directory name
	directory_name = (char*) malloc((strlen(dms_name) + 8)*sizeof(char));
	if (sprintf(directory_name, "%s.obidms", dms_name) < 0)
	{
		obi_set_errno(OBIDMS_MEMORY_ERROR);
		obidebug(1, "\nProblem building an OBIDMS directory name");
		return NULL;
	}

	// Test if the database name is not too long
	if (strlen(directory_name) >= OBIDMS_MAX_NAME)
	{
		obi_set_errno(OBIDMS_LONG_NAME_ERROR);
		obidebug(1, "\nProblem building an OBIDMS directory name");
		free(directory_name);
		return NULL;
	}

	return directory_name;
}


static char* build_infos_file_name(const char* dms_name)
{
	char* file_name;

	// Build file name
	file_name = (char*) malloc((strlen(dms_name) + 7)*sizeof(char));
	if (sprintf(file_name, "%s_infos", dms_name) < 0)
	{
		obi_set_errno(OBIDMS_MEMORY_ERROR);
		obidebug(1, "\nProblem building an informations file name");
		return NULL;
	}

	return file_name;
}


int create_dms_infos_file(int dms_file_descriptor, const char* dms_name)
{
	char* 	file_name;
	int 	infos_file_descriptor;
	off_t 	file_size;
	bool	little_endian;

	file_size = sizeof(bool);

	// Create file name
	file_name = build_infos_file_name(dms_name);
	if (file_name == NULL)
		return -1;

    // Create file
	infos_file_descriptor = openat(dms_file_descriptor,
								   file_name,
								   O_RDWR | O_CREAT | O_EXCL, 0777);
	if (infos_file_descriptor < 0)
	{
		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
		obidebug(1, "\nError creating an informations file");
		free(file_name);
		return -1;
	}

	free(file_name);

	// Truncate the infos file to the right size
	if (ftruncate(infos_file_descriptor, file_size) < 0)
	{
		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
		obidebug(1, "\nError truncating an informations file");
		close(infos_file_descriptor);
		return -1;
	}

	// Write endianness
	little_endian = obi_is_little_endian();
	if (write(infos_file_descriptor, &little_endian, sizeof(bool)) < ((ssize_t) sizeof(bool)))
	{
		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
		obidebug(1, "\nError writing the endianness in an informations file");
		close(infos_file_descriptor);
		return -1;
	}

	// Close file
	if (close(infos_file_descriptor) < 0)
	{
		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
		obidebug(1, "\nError closing a DMS information file");
		return -1;
	}

	return 0;
}


static int list_dms(OBIDMS_p dms)
{
	int i = 0;
	while (global_opened_dms_list[i] != NULL)
		i++;
	if (i == (MAX_NB_OPENED_DMS-1))
	{
		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
		obidebug(1, "\nError opening a DMS: maximum number of DMS opened by a program reached");
		return -1;
	}
	global_opened_dms_list[i] = dms;
	return 0;
}


static void unlist_dms(OBIDMS_p dms)
{
	int i = 0;
	while (global_opened_dms_list[i] != dms)
		i++;
	while (global_opened_dms_list[i] != NULL)
	{
		global_opened_dms_list[i] = global_opened_dms_list[i+1];
		i++;
	}
}


/**********************************************************************
 *
 * 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_dms_exists(const char* dms_path)
{
    struct stat buffer;
	char*       directory_name;
    int 		check_dir;

	// Build and check the directory name
    directory_name = build_directory_name(dms_path);
	if (directory_name == NULL)
		return -1;

	check_dir = stat(directory_name, &buffer);

	free(directory_name);

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


OBIDMS_p obi_create_dms(const char* dms_path)
{
	char*  directory_name;
	DIR*   dms_dir;
	int    dms_file_descriptor;

	// Build and check the directory name
	directory_name = build_directory_name(dms_path);
	if (directory_name == NULL)
		return NULL;

	// Try to create the directory
	if (mkdir(directory_name, 00777) < 0)
	{
		if (errno == EEXIST)
		{
			obi_set_errno(OBIDMS_EXIST_ERROR);
			obidebug(1, "\nAn OBIDMS directory with the same name already exists in this directory.");
		}
		else
			obi_set_errno(OBIDMS_UNKNOWN_ERROR);
		obidebug(1, "\nProblem creating an OBIDMS directory");
		free(directory_name);
		return NULL;
	}

	// Get file descriptor of DMS directory to create other directories
	dms_dir = opendir(directory_name);
	if (dms_dir == NULL)
	{
		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
		obidebug(1, "\nProblem opening a newly created OBIDMS directory");
		free(directory_name);
		return NULL;
	}

	free(directory_name);

	dms_file_descriptor = dirfd(dms_dir);
	if (dms_file_descriptor < 0)
	{
		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
		obidebug(1, "\nProblem getting the file descriptor of a newly created OBIDMS directory");
		return NULL;
	}

	// Create the indexer directory
	if (mkdirat(dms_file_descriptor, INDEXER_DIR_NAME, 00777) < 0)
	{
		obi_set_errno(OBI_INDEXER_ERROR);
		obidebug(1, "\nProblem creating the indexer directory");
		return NULL;
	}

	// Create the view directory
	if (mkdirat(dms_file_descriptor, VIEW_DIR_NAME, 00777) < 0)
	{
		obi_set_errno(OBIVIEW_ERROR);
		obidebug(1, "\nProblem creating the view directory");
		return NULL;
	}

	// Create the taxonomy directory
	if (mkdirat(dms_file_descriptor, TAXONOMY_DIR_NAME, 00777) < 0)
	{
		obi_set_errno(OBIVIEW_ERROR);
		obidebug(1, "\nProblem creating the taxonomy directory");
		return NULL;
	}

/*
	// Isolate the dms name
	j = 0;
	for (i=0; i<strlen(dms_path); i++)
	{
		if (dms_path[i] == '/')
			j = i+1;
		i++;
	}
*/

	// Create the informations file
	if (create_dms_infos_file(dms_file_descriptor, basename((char*)dms_path)) < 0)
		return NULL;

	return obi_open_dms(dms_path);
}


OBIDMS_p obi_open_dms(const char* dms_path)
{
	OBIDMS_p	dms;
	char*	 	complete_dms_path;
	char* 		infos_file_name;
	int			infos_file_descriptor;
	bool		little_endian_dms;
	bool 		little_endian_platform;

	dms = NULL;

	// Allocate the data structure
	dms = (OBIDMS_p) malloc(sizeof(OBIDMS_t));
	if (dms == NULL)
	{
		obi_set_errno(OBIDMS_MEMORY_ERROR);
		obidebug(1, "\nError allocating the memory for the OBIDMS structure");
		return NULL;
	}

/*
	// Isolate and store the dms name
	j = 0;
	for (i=0; i<strlen(dms_path); i++)
	{
		if (dms_path[i] == '/')
			j = i+1;
		i++;
	}
*/
	strcpy(dms->dms_name, basename((char*)dms_path));

	// Build and check the directory name including the relative path
	complete_dms_path = build_directory_name(dms_path);
	if (complete_dms_path == NULL)
	{
		free(dms);
		return NULL;
	}

	// Get and store the absolute path to the DMS directory
	if (realpath(complete_dms_path, dms->directory_path) == NULL)
	{
		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
		obidebug(1, "\nError getting the absolute path to the DMS directory (DMS does not exist)");
		free(complete_dms_path);
		return NULL;
	}

	free(complete_dms_path);

	// Try to open the directory
	dms->directory = opendir(dms->directory_path);
	if (dms->directory == NULL)
	{
		switch (errno)
		{
			case ENOENT:
				obi_set_errno(OBIDMS_NOT_EXIST_ERROR);
				break;

			case EACCES:
				obi_set_errno(OBIDMS_ACCESS_ERROR);
				break;

			case ENOMEM:
				obi_set_errno(OBIDMS_MEMORY_ERROR);
				break;

			default:
				obi_set_errno(OBIDMS_UNKNOWN_ERROR);
		}
		obidebug(1, "\nCan't open OBIDMS directory");
		free(dms);
		return NULL;
	}

	// Get and store file descriptor of DMS directory to open the informations file
	dms->dir_fd = dirfd(dms->directory);
	if (dms->dir_fd < 0)
	{
		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
		obidebug(1, "\nError getting the file descriptor for a newly created OBIDMS directory");
		closedir(dms->directory);
		free(dms);
		return NULL;
	}

	// Open informations file to check endianness
	infos_file_name = build_infos_file_name(dms->dms_name);
	infos_file_descriptor = openat(dms->dir_fd, infos_file_name, O_RDONLY, 0777);
	if (infos_file_descriptor < 0)
	{
		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
		obidebug(1, "\nError opening an informations file");
		closedir(dms->directory);
		free(dms);
		return NULL;
	}

	free(infos_file_name);

	// Check endianness of the platform and DMS
	little_endian_platform = obi_is_little_endian();
	if (read(infos_file_descriptor, &little_endian_dms, sizeof(bool)) < ((ssize_t) sizeof(bool)))
	{
		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
		obidebug(1, "\nError reading the endianness in an informations file");
		close(infos_file_descriptor);
		closedir(dms->directory);
		free(dms);
		return NULL;
	}
	if (little_endian_platform != little_endian_dms)
	{
		obi_set_errno(OBIDMS_BAD_ENDIAN_ERROR);
		obidebug(1, "\nError: The DMS and the platform have different endianness");
		close(infos_file_descriptor);
		closedir(dms->directory);
		free(dms);
		return NULL;
	}

	if (close(infos_file_descriptor) < 0)
	{
		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
		obidebug(1, "\nError closing a DMS information file");
		return NULL;
	}

	dms->little_endian = little_endian_dms;

	// Open the indexer directory
	dms->indexer_directory = opendir_in_dms(dms, INDEXER_DIR_NAME);
	if (dms->indexer_directory == NULL)
	{
		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
		obidebug(1, "\nError opening the indexer directory");
		closedir(dms->directory);
		free(dms);
		return NULL;
	}

	// Store the indexer directory's file descriptor
	dms->indexer_dir_fd = dirfd(dms->indexer_directory);
	if (dms->indexer_dir_fd < 0)
	{
		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
		obidebug(1, "\nError getting the file descriptor of the indexer directory");
		closedir(dms->indexer_directory);
		closedir(dms->directory);
		free(dms);
		return NULL;
	}

	// Open the view directory
	dms->view_directory = opendir_in_dms(dms, VIEW_DIR_NAME);
	if (dms->view_directory == NULL)
	{
		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
		obidebug(1, "\nError opening the view directory");
		closedir(dms->indexer_directory);
		closedir(dms->directory);
		free(dms);
		return NULL;
	}

	// Store the view directory's file descriptor
	dms->view_dir_fd = dirfd(dms->view_directory);
	if (dms->view_dir_fd < 0)
	{
		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
		obidebug(1, "\nError getting the file descriptor of the view directory");
		closedir(dms->view_directory);
		closedir(dms->directory);
		free(dms);
		return NULL;
	}

	// Open the taxonomy directory
	dms->tax_directory = opendir_in_dms(dms, TAXONOMY_DIR_NAME);
	if (dms->tax_directory == NULL)
	{
		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
		obidebug(1, "\nError opening the taxonomy directory");
		closedir(dms->indexer_directory);
		closedir(dms->view_directory);
		closedir(dms->directory);
		free(dms);
		return NULL;
	}

	// Store the taxonomy directory's file descriptor
	dms->tax_dir_fd = dirfd(dms->tax_directory);
	if (dms->tax_dir_fd < 0)
	{
		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
		obidebug(1, "\nError getting the file descriptor of the taxonomy directory");
		closedir(dms->indexer_directory);
		closedir(dms->tax_directory);
		closedir(dms->view_directory);
		closedir(dms->directory);
		free(dms);
		return NULL;
	}

	// Clean unfinished views
	if (obi_clean_unfinished_views(dms) < 0)
	{
		obidebug(1, "\nError cleaning unfinished views when opening an OBIDMS");
		closedir(dms->indexer_directory);
		closedir(dms->tax_directory);
		closedir(dms->view_directory);
		closedir(dms->directory);
		free(dms);
		return NULL;
	}

	// Clean unfinished columns
	if (obi_clean_unfinished_columns(dms) < 0)
	{
		obidebug(1, "\nError cleaning unfinished columns when opening an OBIDMS");
		closedir(dms->indexer_directory);
		closedir(dms->tax_directory);
		closedir(dms->view_directory);
		closedir(dms->directory);
		free(dms);
		return NULL;
	}

	// Initialize the list of opened columns
	dms->opened_columns = (Opened_columns_list_p) malloc(sizeof(Opened_columns_list_t));
	(dms->opened_columns)->nb_opened_columns = 0;

	// Initialize the list of opened indexers
	dms->opened_indexers = (Opened_indexers_list_p) malloc(sizeof(Opened_indexers_list_t));
	(dms->opened_indexers)->nb_opened_indexers = 0;

	// Add in the global list of opened DMS
	list_dms(dms);

	return dms;
}


OBIDMS_p obi_test_open_dms(const char* dms_name)
{
	int exists;

	exists = obi_dms_exists(dms_name);

	switch (exists)
	{
		case 0:
			return NULL;
		case 1:
			return obi_open_dms(dms_name);
	};

	obidebug(1, "\nError checking if an OBIDMS directory exists");
	return NULL;
}


OBIDMS_p obi_dms(const char* dms_name)
{
	int exists;

	exists = obi_dms_exists(dms_name);

	switch (exists)
	{
		case 0:
			return obi_create_dms(dms_name);
		case 1:
			return obi_open_dms(dms_name);
	};

	obidebug(1, "\nError checking if an OBIDMS directory exists");
	return NULL;
}


int obi_close_dms(OBIDMS_p dms)
{
	if (dms != NULL)
	{
		// Close all columns
		while ((dms->opened_columns)->nb_opened_columns > 0)
			obi_close_column(*((dms->opened_columns)->columns));

		// Close dms, and view, indexer and taxonomy directories
		if (closedir(dms->indexer_directory) < 0)
		{
			obi_set_errno(OBI_INDEXER_ERROR);
			obidebug(1, "\nError closing an indexer directory");
			free(dms);
			return -1;
		}
		if (closedir(dms->view_directory) < 0)
		{
			obi_set_errno(OBIVIEW_ERROR);
			obidebug(1, "\nError closing a view directory");
			free(dms);
			return -1;
		}
		if (closedir(dms->tax_directory) < 0)
		{
			obi_set_errno(OBIVIEW_ERROR);
			obidebug(1, "\nError closing a taxonomy directory");
			free(dms);
			return -1;
		}
		if (closedir(dms->directory) < 0)
		{
			obi_set_errno(OBIDMS_MEMORY_ERROR);
			obidebug(1, "\nError closing an OBIDMS directory");
			free(dms);
			return -1;
		}

		// Remove DMS from global list of opened DMS
		unlist_dms(dms);

		free(dms);
	}

	return 0;
}


OBIDMS_column_p obi_dms_get_column_from_list(OBIDMS_p dms, const char* column_name, obiversion_t version)
{
	int i;

	for (i=0; i < ((dms->opened_columns)->nb_opened_columns); i++)
	{
		if (!strcmp(((*(((dms->opened_columns)->columns)+i))->header)->name, column_name)
				&& (((*(((dms->opened_columns)->columns)+i))->header)->version == version))
		{	// Found the column already opened, return it
			return *(((dms->opened_columns)->columns)+i);
		}
	}
	// Didn't find the column
	return NULL;
}


void obi_dms_list_column(OBIDMS_p dms, OBIDMS_column_p column)	// TODO add check if column already in list?
{
	*(((dms->opened_columns)->columns)+((dms->opened_columns)->nb_opened_columns)) = column;
	((dms->opened_columns)->nb_opened_columns)++;
}


int obi_dms_unlist_column(OBIDMS_p dms, OBIDMS_column_p column)
{
	int i;
	Opened_columns_list_p columns_list;

	columns_list = dms->opened_columns;

	for (i=0; i < columns_list->nb_opened_columns; i++)
	{
		if (!strcmp(((*((columns_list->columns)+i))->header)->name, (column->header)->name)
				&& (((*((columns_list->columns)+i))->header)->version == (column->header)->version))
		{	// Found the column. Rearrange list
			(columns_list->nb_opened_columns)--;
			(columns_list->columns)[i] = (columns_list->columns)[columns_list->nb_opened_columns];
			return 0;
		}
	}

	obidebug(1, "\nCould not find the column to delete from list of open columns");
	return -1;
}


Obi_indexer_p obi_dms_get_indexer_from_list(OBIDMS_p dms, const char* indexer_name)
{
	int i;
	Opened_indexers_list_p indexers_list;

	indexers_list = dms->opened_indexers;

	for (i=0; i < (indexers_list->nb_opened_indexers); i++)
	{
		if (!strcmp(obi_indexer_get_name((indexers_list->indexers)[i]), indexer_name))
		{	// Found the indexer already opened, return it
			return (indexers_list->indexers)[i];
		}
	}
	// Didn't find the indexer
	return NULL;
}


void obi_dms_list_indexer(OBIDMS_p dms, Obi_indexer_p indexer)  	// TODO add check if indexer already in list?
{
	*(((dms->opened_indexers)->indexers)+((dms->opened_indexers)->nb_opened_indexers)) = indexer;
	((dms->opened_indexers)->nb_opened_indexers)++;
}


int obi_dms_unlist_indexer(OBIDMS_p dms, Obi_indexer_p indexer)
{
	int i;
	Opened_indexers_list_p indexers_list;

	indexers_list = dms->opened_indexers;

	for (i=0; i < indexers_list->nb_opened_indexers; i++)
	{
		if (!strcmp(obi_indexer_get_name((indexers_list->indexers)[i]), indexer->name))
		{	// Found the indexer. Rearrange list
			(indexers_list->nb_opened_indexers)--;
			(indexers_list->indexers)[i] = (indexers_list->indexers)[indexers_list->nb_opened_indexers];
			return 0;
		}
	}

	obidebug(1, "\nCould not find the indexer to delete from list of open indexers");
	return -1;
}


char* obi_dms_get_dms_path(OBIDMS_p dms)
{
	char* full_path;

	full_path = (char*) malloc((MAX_PATH_LEN)*sizeof(char));
	if (full_path == NULL)
	{
		obi_set_errno(OBI_MALLOC_ERROR);
		obidebug(1, "\nError allocating memory for the char* path to a file or directory");
		return NULL;
	}

	strcpy(full_path, dms->directory_path);

	return full_path;
}


char* obi_dms_get_full_path(OBIDMS_p dms, const char* path_name)
{
	char* full_path;

	full_path = obi_dms_get_dms_path(dms);
	strcat(full_path, "/");
	strcat(full_path, path_name);

	return full_path;
}


DIR* opendir_in_dms(OBIDMS_p dms, const char* path_name)
{
	char* full_path;
	DIR* directory;

	full_path = obi_dms_get_full_path(dms, path_name);
	if (full_path == NULL)
		return NULL;

	directory = opendir(full_path);
	if (directory == NULL)
	{
		obi_set_errno(OBI_UTILS_ERROR);
		obidebug(1, "\nError opening a directory");
	}

	free(full_path);

	return directory;
}


// TODO move somewhere else maybe
// TODO discuss arguments
obiversion_t obi_import_column(const char* dms_path_1, const char* dms_path_2, const char* column_name, obiversion_t version_number)
{
	OBIDMS_p				dms_1;
	OBIDMS_p 				dms_2;
	OBIDMS_column_p 		column_1;
	OBIDMS_column_p 	   	column_2;
	OBIDMS_column_header_p 	header_1;
	OBIDMS_column_header_p 	header_2;
	int 					avl_exists;
	const char* 			avl_name;
	char* 					new_avl_name;
	obiversion_t 			new_version;
	int 					i;
	int 					avl_count;
	char*		 			avl_name_1;
	char* 					avl_name_2;
	char* 					avl_file_path_1;
	char* 					avl_file_path_2;
	char* 					avl_data_file_path_1;
	char* 					avl_data_file_path_2;
	char* 					complete_avl_name;
	Obi_indexer_p 			avl_group;

	dms_1 = obi_open_dms(dms_path_1);
	if (dms_1 == NULL)
	{
		obidebug(1, "\nError opening a DMS to import a column from it");
		return -1;
	}

	dms_2 = obi_dms(dms_path_2);
	if (dms_2 == NULL)
	{
		obidebug(1, "\nError opening or creating a DMS to import a column into it");
		return -1;
	}

	column_1 = obi_open_column(dms_1, column_name, version_number);
	if (column_1 == NULL)
	{
		obidebug(1, "\nError opening a column to import in another DMS");
		return -1;
	}

	header_1 = column_1->header;

	// Check if associated indexer exists BEFORE creating the new column as that will automatically create it if it doesn't already exist
	avl_name = header_1->indexer_name;
	avl_exists = obi_indexer_exists(dms_2, avl_name);
	if (avl_exists == -1)
	{
		obidebug(1, "\nError checking if an indexer exists while importing a column");
		return -1;
	}
	if (avl_exists)
		// Use automatic name
		new_avl_name = NULL;
	else
		// Name can stay the same
		new_avl_name = header_1->indexer_name;

	// Create new column
	column_2 = obi_create_column(dms_2, column_name, header_1->returned_data_type, header_1->line_count,
								 header_1->nb_elements_per_line, header_1->elements_names, true, header_1->tuples,
								 new_avl_name, (header_1->associated_column).column_name, (header_1->associated_column).version,
								 header_1->comments);

	if (column_2 == NULL)
	{
		obidebug(1, "\nError creating the new column while importing a column");
		return -1;
	}

	header_2 = column_2->header;

	// Get the new version to return
	new_version = header_2->version;

	// Copy lines_used informations
	header_2->lines_used = header_1->lines_used;

	// Copy data TODO check how much time and memory that costs, eventually use write() instead
	memcpy(column_2->data, column_1->data, header_1->data_size);

	// Copy the AVL files if there are some (overwriting the automatically created files)
	if ((header_1->returned_data_type == OBI_STR) || (header_1->returned_data_type == OBI_SEQ) || (header_1->returned_data_type == OBI_QUAL))
	{
		avl_name_1 = (char*) malloc((strlen(header_1->indexer_name) + 1)  * sizeof(char));
		if (avl_name_1 == NULL)
		{
			obi_set_errno(OBI_MALLOC_ERROR);
			obidebug(1, "\nError allocating memory for an AVL name when importing a column");
			return -1;
		}
		strcpy(avl_name_1, header_1->indexer_name);

		avl_name_2 = (char*) malloc((strlen(header_2->indexer_name) + 1)  * sizeof(char));
		if (avl_name_2 == NULL)
		{
			obi_set_errno(OBI_MALLOC_ERROR);
			obidebug(1, "\nError allocating memory for an AVL name when importing a column");
			return -1;
		}
		strcpy(avl_name_2, header_2->indexer_name);

		avl_count = (column_1->indexer->last_avl_idx) + 1;

		// Close column to manipulate AVL files safely (but not multithreading safe) (TODO not sure how important this is, can't find informations about conflicts when using write() on mmapped files)
		if (obi_close_column(column_1) < 0)
		{
			obidebug(1, "\nError closing an imported column");
			return -1;
		}
		if (obi_close_column(column_2) < 0)
		{
			obidebug(1, "\nError closing an imported column");
			return -1;
		}

		for (i=0; i < avl_count; i++)
		{
			avl_file_path_1 = obi_get_full_path_of_avl_file_name(dms_1, avl_name_1, i);
			if (avl_file_path_1 == NULL)
			{
				obidebug(1, "\nError getting an AVL file path while importing a column");
				return -1;
			}

			avl_data_file_path_1 = obi_get_full_path_of_avl_data_file_name(dms_1, avl_name_1, i);
			if (avl_data_file_path_1 == NULL)
			{
				obidebug(1, "\nError getting an AVL file path while importing a column");
				return -1;
			}
			avl_file_path_2 = obi_get_full_path_of_avl_file_name(dms_2, avl_name_2, i);
			if (avl_file_path_2 == NULL)
			{
				obidebug(1, "\nError getting an AVL file path while importing a column");
				return -1;
			}
			avl_data_file_path_2 = obi_get_full_path_of_avl_data_file_name(dms_2, avl_name_2, i);
			if (avl_data_file_path_2 == NULL)
			{
				obidebug(1, "\nError getting an AVL file path while importing a column");
				return -1;
			}

			// Copy AVL file
			if (copy_file(avl_file_path_1, avl_file_path_2) < 0)
			{
				obidebug(1, "\nError copying an AVL file while importing a column");
				return -1;
			}

			// Copy AVL data file
			if (copy_file(avl_data_file_path_1, avl_data_file_path_2) < 0)
			{
				obidebug(1, "\nError copying a data AVL file while importing a column");
				return -1;
			}

			free(avl_file_path_1);
			free(avl_file_path_2);
			free(avl_data_file_path_1);
			free(avl_data_file_path_2);
		}

		// Update AVL names in headers
		avl_group = obi_open_indexer(dms_2, avl_name_2);
		for (i=0; i < avl_count; i++)
		{
			complete_avl_name = obi_build_avl_name_with_idx(avl_name_2, i);
			strcpy((((avl_group->sub_avls)[i])->header)->avl_name, complete_avl_name);
			strcpy(((((avl_group->sub_avls)[i])->data)->header)->avl_name, complete_avl_name);
			free(complete_avl_name);
		}

		free(avl_name_1);
		free(avl_name_2);
	}
	else
	{
		if (obi_close_column(column_1) < 0)
		{
			obidebug(1, "\nError closing an imported column");
			return -1;
		}
		if (obi_close_column(column_2) < 0)
		{
			obidebug(1, "\nError closing an imported column");
			return -1;
		}
	}

	// Copy associated column (update version)
	//new_associated_col_version = import_column(dms_path_1, dms_path_2, header_1->associated_column_name, header_1->associated_column_version);
	// TODO no? because if iterating over all columns in a view etc.... iterate and change associated columns version refs afterwards?

	// Close the DMS
	obi_close_dms(dms_1);
	obi_close_dms(dms_2);

	return new_version;
}


// TODO move somewhere else maybe
// TODO discuss arguments
int obi_import_view(const char* dms_path_1, const char* dms_path_2, const char* view_name_1, const char* view_name_2)
{
	OBIDMS_p 		dms_1;
	OBIDMS_p	 	dms_2;
	Obiview_p 		view_1;
	Obiview_p 		view_2;
	obiversion_t 	new_version;
	int 			i;

	dms_1 = obi_open_dms(dms_path_1);
	if (dms_1 == NULL)
	{
		obidebug(1, "\nError opening a DMS to import a view from it");
		return -1;
	}

	dms_2 = obi_dms(dms_path_2);
	if (dms_2 == NULL)
	{
		obidebug(1, "\nError opening or creating a DMS to import a view into it");
		return -1;
	}

	// Open view to import
	view_1 = obi_open_view(dms_1, view_name_1);

	// Create new view
	if (strcmp((view_1->infos)->view_type, VIEW_TYPE_NUC_SEQS) == 0)
		view_2 = obi_new_view_nuc_seqs(dms_2, view_name_2, NULL, NULL, (view_1->infos)->comments, false);
	else	// Non-typed view
		view_2 = obi_new_view(dms_2, view_name_2, NULL, NULL, (view_1->infos)->comments);

	// Import line count
	view_2->infos->line_count = view_1->infos->line_count;

	// Import the line selection column if there is one
	if (! view_1->infos->all_lines)
	{
		view_2->infos->all_lines = false;
		new_version = obi_import_column(dms_path_1, dms_path_2, ((view_1->infos)->line_selection).column_name, ((view_1->infos)->line_selection).version);
		if (new_version == -1)
		{
			obidebug(1, "\nError importing a line selection column while importing a view");
			return -1;
		}
		strcpy(((view_2->infos)->line_selection).column_name, ((view_1->infos)->line_selection).column_name);
		((view_2->infos)->line_selection).version = new_version;
		view_2->line_selection = obi_open_column(dms_2, ((view_2->infos)->line_selection).column_name, ((view_2->infos)->line_selection).version);
		if (view_2->line_selection == NULL)
		{
			obidebug(1, "\nError opening a line selection column while importing a view");
			return -1;
		}
	}

	// Import each column and update with the new version number
	for (i=0; i < (view_1->infos->column_count); i++)
	{
		new_version = obi_import_column(dms_path_1, dms_path_2, ((((view_1->infos)->column_references)[i]).column_refs).column_name, ((((view_1->infos)->column_references)[i]).column_refs).version);
		if (new_version == -1)
		{
			obidebug(1, "\nError importing a column while importing a view");
			return -1;
		}

		if (obi_view_add_column(view_2,
							    ((((view_1->infos)->column_references)[i]).column_refs).column_name,
							    new_version,
							    (((view_1->infos)->column_references)[i]).alias,
							    0,
								0,
								0,
								NULL,
								false,
								NULL,
								NULL,
								-1,
								NULL,
								false) < 0)
			{
				obidebug(1, "\nError adding a column to a view while importing it");
				return -1;
			}
	}

	// Close the views
	if (obi_save_and_close_view(view_1) < 0)
	{
		obidebug(1, "\nError closing a view after importing from it");
		return -1;
	}
	if (obi_save_and_close_view(view_2) < 0)
	{
		obidebug(1, "\nError closing a view after importing it");
		return -1;
	}

	// Close the DMS
	obi_close_dms(dms_1);
	obi_close_dms(dms_2);

	return 0;
}


void obi_close_atexit()
{
	int i=0;

	while (global_opened_dms_list[i] != NULL)
	{
        obi_close_dms(global_opened_dms_list[i]);
		i++;
	}
}