obitools3/src/obidmscolumn.c

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

/**
 * @file obidmscolumn.c
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 * @date 22 May 2015
 * @brief Functions shared by all the OBIDMS columns.
 */


#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <sys/types.h>
#include <dirent.h>
#include <unistd.h>
#include <time.h>
#include <fcntl.h>
#include <stdbool.h>
#include <math.h>
#include <sys/mman.h>

#include "obidmscolumn.h"
#include "obidmscolumn_idx.h"
#include "obidmscolumndir.h"
#include "obidms.h"
#include "obitypes.h"
#include "obierrno.h"
#include "obidebug.h"
#include "obilittlebigman.h"
#include "obiblob_indexer.h"
#include "utils.h"


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


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


/**
 * @brief Internal function building the file name for a column.
 *
 * The function builds the file name corresponding to a column of an OBIDMS.
 *
 * @warning The returned pointer has to be freed by the caller.
 *
 * @param column_name The name of the OBIDMS column file.
 * @param version_number The version number of the OBIDMS column file.
 *
 * @returns A pointer to the column file name.
 * @retval NULL if an error occurred.
 *
 * @since May 2015
 * @author Eric Coissac (eric.coissac@metabarcoding.org)
 */
static char* build_column_file_name(const char* column_name, obiversion_t version_number);


/**
 * @brief Internal function building the file name for a column version file.
 *
 * The column version file indicates the latest version number for a column.
 * This function returns the name of the file storing this information.
 *
 * @warning The returned pointer has to be freed by the caller.
 *
 * @param column_name The name of the OBIDMS column.
 *
 * @returns A pointer to the version file name.
 * @retval NULL if an error occurred.
 *
 * @since May 2015
 * @author Eric Coissac (eric.coissac@metabarcoding.org)
 */
static char* build_version_file_name(const char* column_name);


/**
 * @brief Internal function returning a new column version number
 *        in the OBIDMS database.
 *
 * @param column_directory A pointer as returned by obi_create_column_directory() or obi_open_column_directory().
 * @param block Whether the call is blocking or not:
 *              	- `true` the call is blocking
 *                  - `false` the call is not blocking.
 *
 * @returns The next version number for this column.
 * @retval -1 if an error occurred.
 *
 * @since May 2015
 * @author Eric Coissac (eric.coissac@metabarcoding.org)
 */
static obiversion_t obi_get_new_version_number(OBIDMS_column_directory_p column_directory, bool block);


/**
 * @brief Internal function creating a new column version file
 *        in the OBIDMS database.
 *
 * The new file is initialized with the minimum version number `0`.
 *
 * @param column_directory A pointer as returned by obi_create_column_directory() or obi_open_column_directory().
 *
 * @returns The next usable version number for this column : `0`.
 * @retval -1 if an error occurred.
 *
 * @since May 2015
 * @author Eric Coissac (eric.coissac@metabarcoding.org)
 */
static obiversion_t create_version_file(OBIDMS_column_directory_p column_directory);


/**
 * @brief Internal function setting the elements names of the lines of a
 *        column in the header of the OBIDMS column structure.
 *
 * @param column A pointer as returned by obi_create_column().
 * @param elements_names The names of the elements with ';' as separator.
 *
 * @retval 0 if the operation was successfully completed.
 * @retval -1 if an error occurred.
 *
 * @since July 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
static int obi_column_set_elements_names(OBIDMS_column_p column, const char* elements_names);


/**
 * @brief Internal function computing how many lines of an OBIDMS column
 *        fit in a memory page.
 *
 * @param data_type The data OBIType.
 * @param nb_elements_per_line The number of elements per line.
 *
 * @returns The line count for one memory page.
 *
 * @since September 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
static index_t get_line_count_per_page(OBIType_t data_type, index_t nb_elements_per_line);


/************************************************************************
 *
 * 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_column_file_name(const char* column_name, obiversion_t version_number)
{
	char* file_name;
	int version_number_length;

	// Build the file name
	version_number_length = (version_number == 0 ? 1 : (int)(log10(version_number)+1));
	file_name =	(char*) malloc((strlen(column_name) + version_number_length + 6)*sizeof(char));
	if (file_name == NULL)
	{
		obi_set_errno(OBI_MALLOC_ERROR);
		obidebug(1, "\nError allocating the memory for a column file name");
		return NULL;
	}

	if (sprintf(file_name,"%s@%d.odc", column_name, version_number) < 0)
	{
		obi_set_errno(OBICOL_MEMORY_ERROR);
		obidebug(1, "\nError building a column file name");
		return NULL;
	}

	return file_name;
}


static char* build_version_file_name(const char* column_name)
{
	char* file_name;

	// Build the file name
	file_name =	(char*) malloc((strlen(column_name) + 5)*sizeof(char));
	if (file_name == NULL)
	{
		obi_set_errno(OBI_MALLOC_ERROR);
		obidebug(1, "\nError allocating the memory for a version file name");
		return NULL;
	}

	if (sprintf(file_name,"%s.odv", column_name) < 0)
	{
		obi_set_errno(OBICOL_MEMORY_ERROR);
		obidebug(1, "\nError building a version file name");
		return NULL;
	}

	return file_name;
}


static obiversion_t obi_get_new_version_number(OBIDMS_column_directory_p column_directory, bool block)
{
	off_t 			loc_size;
	obiversion_t 	new_version_number;
	char* 			version_file_name;
	int    			version_file_descriptor;
	int 			lock_mode;

	new_version_number = 0;
	loc_size = sizeof(obiversion_t);

	// Select the correct lockf operation according to the blocking mode
	if (block)
		lock_mode=F_LOCK;
	else
		lock_mode=F_TLOCK;

	// Build the version file name
	version_file_name = build_version_file_name(column_directory->column_name);
	if (version_file_name == NULL)
		return -1;

	// Open the version file
	version_file_descriptor = openat(column_directory->dir_fd, version_file_name, O_RDWR);
	if (version_file_descriptor < 0)
	{
		if (errno == ENOENT)
			return create_version_file(column_directory);
		else
		{
			obi_set_errno(OBICOL_UNKNOWN_ERROR);
			obidebug(1, "\nError opening a version file");
			free(version_file_name);
			return -1;
		}
	}

	free(version_file_name);

	// Test if the version file size is ok
	if (lseek(version_file_descriptor, 0, SEEK_END) < loc_size)
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError testing if a version file size is ok");
		close(version_file_descriptor);
		return -1;
	}

	// Reset offset to 0
	if (lseek(version_file_descriptor, 0, SEEK_SET) != 0)
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError positioning offset in version file");
		close(version_file_descriptor);
		return -1;
	}

	// Lock the file
	if (lockf(version_file_descriptor, lock_mode, loc_size) < 0)
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError locking a version file");
		close(version_file_descriptor);
		return -1;
	}

    // Read the current version number
    if (read(version_file_descriptor, &new_version_number, sizeof(obiversion_t)) < ((ssize_t) sizeof(obiversion_t)))
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError reading a version file");
		close(version_file_descriptor);
		return -1;
	}

    new_version_number++;

    // Reset offset to 0 to write the new version number
	if (lseek(version_file_descriptor, 0, SEEK_SET) != 0)
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError positioning offset in version file");
		close(version_file_descriptor);
		return -1;
	}

    // Write the new version number
	if (write(version_file_descriptor, &new_version_number, sizeof(obiversion_t)) < ((ssize_t) sizeof(obiversion_t)))
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError writing a new version number in a version file");
		close(version_file_descriptor);
		return -1;
	}

	// Reset offset to 0 (TODO: why?)
	if (lseek(version_file_descriptor, 0, SEEK_SET) != 0)
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError positioning offset in version file");
		close(version_file_descriptor);
		return -1;
	}

	// Unlock the file
	if (lockf(version_file_descriptor, F_ULOCK, loc_size) < 0)
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError unlocking a version file");
		close(version_file_descriptor);
		return -1;
	}

	if (close(version_file_descriptor) < 0)
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError closing a version file");
		return -1;
	}

	return new_version_number;
}


static obiversion_t create_version_file(OBIDMS_column_directory_p column_directory)
{
	off_t 			loc_size;
	obiversion_t 	version_number;
	char* 			version_file_name;
	int    			version_file_descriptor;

	loc_size = sizeof(obiversion_t);
	version_number = 0;

	version_file_name = build_version_file_name(column_directory->column_name);
	if (version_file_name == NULL)
		return -1;

	// Get the file descriptor associated to the version file
	version_file_descriptor = openat(column_directory->dir_fd, version_file_name, O_RDWR | O_CREAT | O_EXCL, 0777);
	if (version_file_descriptor < 0)
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError opening a version file");
		free(version_file_name);
		return -1;
	}

	free(version_file_name);

	// Lock the file
	if (lockf(version_file_descriptor, F_LOCK, loc_size) < 0)
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError locking a version file");
		close(version_file_descriptor);
		return -1;
	}

	// Truncate the version file to the right size
	if (ftruncate(version_file_descriptor, loc_size) < 0)
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError truncating a version file");
		close(version_file_descriptor);
		return -1;
	}

	// Position offset to 0 to prepare for writing		// TODO Unnecessary?
	if (lseek(version_file_descriptor, 0, SEEK_SET) != 0)
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError changing offset of a version file");
		close(version_file_descriptor);
		return -1;
	}

	// Write version number
	if (write(version_file_descriptor, &version_number, sizeof(obiversion_t)) < ((ssize_t) sizeof(obiversion_t)))
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError writing version number in a version file");
		close(version_file_descriptor);
		return -1;
	}

	// Prepare for unlocking
	if (lseek(version_file_descriptor, 0, SEEK_SET) != 0)		// TODO Unnecessary?
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError preparing a version file for unlocking");
		close(version_file_descriptor);
		return -1;
	}

	// Unlock the file
	if (lockf(version_file_descriptor, F_ULOCK, loc_size) < 0)
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError unlocking a version file");
		close(version_file_descriptor);
		return -1;
	}

	if (close(version_file_descriptor) < 0)
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError closing a version file");
		return -1;
	}

	return version_number;
}


int obi_column_set_elements_names(OBIDMS_column_p column, const char* elements_names)
{
	strcpy((column->header)->elements_names, elements_names);
	return 0;
}

index_t get_line_count_per_page(OBIType_t data_type, index_t nb_elements_per_line)
{
	return getpagesize() / (obi_sizeof(data_type) * nb_elements_per_line);
}


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

obiversion_t obi_get_latest_version_number(OBIDMS_column_directory_p column_directory)
{
	off_t 			loc_size;
	obiversion_t 	latest_version_number;
	char * 			version_file_name;
	int    			version_file_descriptor;

	loc_size = sizeof(obiversion_t);
	latest_version_number = 0;

	version_file_name = build_version_file_name(column_directory->column_name);
	if (version_file_name==NULL)
		return -1;

	// Get the file descriptor associated to the version file
	version_file_descriptor = openat(column_directory->dir_fd, version_file_name, O_RDONLY);
	if (version_file_descriptor < 0)
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError opening a version file");
		free(version_file_name);
		return -1;
	}

	free(version_file_name);

	// Check that the version file size is ok
	if (lseek(version_file_descriptor, 0, SEEK_END) < loc_size)
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError testing if a version file size is ok");
		close(version_file_descriptor);
		return -1;
	}

	// Set the offset to 0 in the version file
	if (lseek(version_file_descriptor, 0, SEEK_SET) != 0)
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError setting the offset of a version file to 0");
		close(version_file_descriptor);
		return -1;
	}

    // Read the latest version number
    if (read(version_file_descriptor, &latest_version_number, sizeof(obiversion_t)) < ((ssize_t) sizeof(obiversion_t)))
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError reading the latest version number in a version file");
		close(version_file_descriptor);
		return -1;
	}

	if (close(version_file_descriptor) < 0)
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError closing a version file");
		return -1;
	}

	return latest_version_number;
}


obiversion_t obi_column_get_latest_version_from_name(OBIDMS_p dms, const char* column_name)
{
	OBIDMS_column_directory_p	column_directory;
	obiversion_t	   			latest_version;

	// Get the column directory structure associated to the column
	column_directory = obi_open_column_directory(dms, column_name);
	if (column_directory == NULL)
	{
		obidebug(1, "\nProblem opening a column directory structure");
		return -1;
	}

	// Get the latest version number
	latest_version = obi_get_latest_version_number(column_directory);
	if (latest_version < 0)
	{
		obidebug(1, "\nProblem getting the latest version number in a column directory");
		return -1;
	}

	return latest_version;
}


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

	header_size = sizeof(OBIDMS_column_header_t);

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

	rounded_header_size = multiple * getpagesize();

	return rounded_header_size;
}


OBIDMS_column_p obi_create_column(OBIDMS_p     dms,
		                          const char*  column_name,
								  OBIType_t    data_type,
								  index_t      nb_lines,
								  index_t      nb_elements_per_line,
								  const char*  elements_names,
								  const char*  indexer_name,
								  const char*  associated_column_name,
								  obiversion_t associated_column_version,
								  const char*  comments
								 )
{
	OBIDMS_column_p 			new_column;
	OBIDMS_column_directory_p	column_directory;
	OBIDMS_column_header_p 		header;
	size_t 						file_size;
	obiversion_t 				version_number;
	char* 						column_file_name;
	int 						column_file_descriptor;
	size_t 						header_size;
	size_t 						data_size;
	index_t						minimum_line_count;
	OBIType_t  					returned_data_type;
	OBIType_t  					stored_data_type;
	char*			    		final_indexer_name;

	new_column = NULL;

	// Check that the informations given are not NULL/invalid/greater than the allowed sizes
	if (dms == NULL)
	{
		obidebug(1, "\nCan't create column because of invalid DMS");
		return NULL;
	}
	if (column_name == NULL)
	{
		obidebug(1, "\nCan't create column because of empty column name");
		return NULL;
	}
	if ((data_type < 1) || (data_type > 8))		// TODO check in more robust way
	{
		obidebug(1, "\nCan't create column because of invalid data type");
		return NULL;
	}

	// Get the column directory structure associated to the column
	column_directory = obi_column_directory(dms, column_name);
	if (column_directory == NULL)
	{
		obi_set_errno(OBICOLDIR_UNKNOWN_ERROR);
		obidebug(1, "\nError opening a column directory structure");
		return NULL;
	}

	// Get the latest version number
	version_number = obi_get_new_version_number(column_directory, true);
	if (version_number < 0)
	{
		return NULL;
	}

	// Build the indexer name if needed
	if ((data_type == OBI_STR) || (data_type == OBI_SEQ) || (data_type == OBI_QUAL))
	{
		if (strcmp(indexer_name, "") == 0)
		{
			final_indexer_name = obi_build_indexer_name(column_name, version_number);
			if (final_indexer_name == NULL)
				return NULL;
		}
		else
		{
			final_indexer_name = (char*) malloc((strlen(indexer_name)+1)*sizeof(char));
			strcpy(final_indexer_name, indexer_name);
		}
	}

	returned_data_type = data_type;
	if ((data_type == OBI_STR) || (data_type == OBI_SEQ) || (data_type == OBI_QUAL))
	// stored data is indices referring to data stored elsewhere
		stored_data_type = OBI_IDX;
	else
		stored_data_type = returned_data_type;

	// The initial line count should be between the minimum (corresponding to the page size) and the maximum allowed
	minimum_line_count = get_line_count_per_page(stored_data_type, nb_elements_per_line);
	if (nb_lines > MAXIMUM_LINE_COUNT)
	{
		obidebug(1, "\nCan't create column because of line count greater than the maximum allowed (%d)", MAXIMUM_LINE_COUNT);
		return NULL;
	}
	else if (nb_lines < minimum_line_count)
		nb_lines = minimum_line_count;

	// The number of elements names should be equal to the number of elements per line
	if ((elements_names == NULL) && (nb_elements_per_line > 1))
	{
		obidebug(1, "\nCan't create column because no elements names were given for a number of elements per line greater than 1");
		return NULL;
	}
	else if ((elements_names != NULL) && (nb_elements_per_line > 1))
	{
		char* token;
		index_t n = 0;
		token = strdup(elements_names);
		token = strtok(token, ";");
		while (token != NULL)
		{
			token = strtok(NULL, ";");
			n++;
		}
		if (n != nb_elements_per_line)
		{
			obidebug(1, "\nCan't create column because the number of elements names given is not equal to the number of elements per line");
			return NULL;
		}
	}
	else if ((nb_elements_per_line == 1) && (strcmp(elements_names, column_name) != 0))
	{
		obidebug(1, "\nCan't create column because the element name does not match the column name");
		return NULL;
	}

	// Calculate the size needed
	header_size = obi_get_platform_header_size();
	data_size = obi_array_sizeof(stored_data_type, nb_lines, nb_elements_per_line);
	file_size = header_size + data_size;

	// Get the column file name
	column_file_name = build_column_file_name(column_name, version_number);
	if (column_file_name == NULL)
	{
		return NULL;
	}

	// Open the column file
	column_file_descriptor = openat(column_directory->dir_fd, column_file_name, O_RDWR | O_CREAT | O_EXCL, 0777);
	if (column_file_descriptor < 0)
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError opening a column file %s", column_file_name);
		free(column_file_name);
		return NULL;
	}

	free(column_file_name);

	// Truncate the column file to the right size
	if (ftruncate(column_file_descriptor, file_size) < 0)
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError truncating a column file to the right size");
		close(column_file_descriptor);
		return NULL;
	}

	// Allocate the memory for the column structure
	new_column = (OBIDMS_column_p) malloc(sizeof(OBIDMS_column_t));
	if (new_column == NULL)
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError allocating the memory for the column structure");
		close(column_file_descriptor);
		return NULL;
	}

	// Fill the column structure
	new_column->dms    			 = dms;
	new_column->column_directory = column_directory;
	new_column->header 			 = mmap(NULL,
			                  	  	    header_size,
			                  	  	    PROT_READ | PROT_WRITE,
			                  	  	    MAP_SHARED,
			                  	  	    column_file_descriptor,
			                  	  	    0
			                 	 	   );

	if (new_column->header == MAP_FAILED)
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError mmapping the header of a column");
		close(column_file_descriptor);
		free(new_column);
		return NULL;
	}

	new_column->data   			 = mmap(NULL,
			                 	 	 	data_size,
			                 	 	 	PROT_READ | PROT_WRITE,
			                 	 	 	MAP_SHARED,
			                 	 	 	column_file_descriptor,
			                 	 	 	header_size
			                			);

	if (new_column->data == MAP_FAILED)
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError mmapping the data of a column");
		munmap(new_column->header, header_size);
		close(column_file_descriptor);
		free(new_column);
		return NULL;
	}

	new_column->writable = true;

	header 				  		 		  = new_column->header;
	header->header_size   		   		  = header_size;
	header->data_size			 		  = data_size;
	header->line_count   	 	 		  = nb_lines;
	header->lines_used    		          = 0;
	header->nb_elements_per_line          = nb_elements_per_line;
	header->stored_data_type     		  = stored_data_type;
	header->returned_data_type   		  = returned_data_type;
	header->creation_date 		 		  = time(NULL);
	header->version       		          = version_number;
	header->cloned_from    		          = -1;

	obi_column_set_elements_names(new_column, elements_names);

	strncpy(header->name, column_name, OBIDMS_COLUMN_MAX_NAME);

	if (comments != NULL)
		strncpy(header->comments, comments, COMMENTS_MAX_LENGTH);

	// Store the associated column reference if needed // TODO discuss cases
	if (data_type == OBI_QUAL)
	{
		if (associated_column_name == NULL)
		{
			obidebug(1, "\nError: The name of the associated column when creating a new column is NULL");
			munmap(new_column->header, header_size);
			close(column_file_descriptor);
			free(new_column);
			return NULL;
		}
		strcpy((header->associated_column).column_name, associated_column_name);

		if (associated_column_version == -1)
		{
			obidebug(1, "\nError: The version of the associated column when creating a new column is not defined");
			munmap(new_column->header, header_size);
			close(column_file_descriptor);
			free(new_column);
			return NULL;
		}
		(header->associated_column).version = associated_column_version;
	}

	// If the data type is OBI_STR, OBI_SEQ or OBI_QUAL, the associated obi_indexer is opened or created
	if ((returned_data_type == OBI_STR) || (returned_data_type == OBI_SEQ) || (returned_data_type == OBI_QUAL))
	{
		new_column->indexer = obi_indexer(dms, final_indexer_name);
		if (new_column->indexer == NULL)
		{
			obidebug(1, "\nError opening or creating the indexer associated with a column");
			munmap(new_column->header, header_size);
			close(column_file_descriptor);
			free(new_column);
			return NULL;
		}
		strncpy(header->indexer_name, final_indexer_name, INDEXER_MAX_NAME);
	}

	// Fill the data with NA values
	obi_ini_to_NA_values(new_column, 0, nb_lines);

	if (close(column_file_descriptor) < 0)
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError closing a column file");
		return NULL;
	}

	// Add in the list of opened columns
	obi_dms_list_column(dms, new_column);

	// Set counter to 1 // TODO Discuss counters
	new_column->counter = 1;

	return new_column;
}


OBIDMS_column_p obi_open_column(OBIDMS_p     dms,
								const char*  column_name,
								obiversion_t version_number)
{
	OBIDMS_column_p 		    column;
	OBIDMS_column_directory_p	column_directory;
	char* 						column_file_name;
	int 						column_file_descriptor;
	size_t 						header_size;

	column = NULL;

	// Get the column directory structure associated to the column
	column_directory = obi_open_column_directory(dms, column_name);
	if (column_directory == NULL)
	{
		obidebug(1, "\nError opening a column directory structure");
		return NULL;
	}

	// Get the latest version number if it has the value -1 (not given by user)
	if (version_number == -1)
	{
		version_number = obi_get_latest_version_number(column_directory);
		if (version_number < 0)
		{
			obidebug(1, "\nError getting the latest version number in a column directory");
			return NULL;
		}
	}

	// Check if the column is already in the list of opened columns
	column = obi_dms_get_column_from_list(dms, column_name, version_number);
	// If it's found, increment its counter and return it
	if (column != NULL)
	{
		(column->counter)++;
		if (obi_close_column_directory(column_directory) < 0)
		{
			obi_set_errno(OBICOL_UNKNOWN_ERROR);
			obidebug(1, "\nError closing a column directory");
			return NULL;
		}
		return column;
	}

	// Get the column file name
	column_file_name = build_column_file_name(column_name, version_number);
	if (column_file_name == NULL)
	{
		return NULL;
	}

	// Open the column file, ALWAYS READ-ONLY
	column_file_descriptor = openat(column_directory->dir_fd, column_file_name, O_RDONLY);
	if (column_file_descriptor < 0)
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError opening column file");
		free(column_file_name);
		return NULL;
	}

	free(column_file_name);

	// Allocate the memory for the column structure
	column = (OBIDMS_column_p) malloc(sizeof(OBIDMS_column_t));
	if (column == NULL)
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError allocating the memory for a column structure");
		close(column_file_descriptor);
		return NULL;
	}

	// Read the header size
	if (read(column_file_descriptor, &header_size, sizeof(size_t)) < ((ssize_t) sizeof(size_t)))
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError reading the header size to open a column");
		close(column_file_descriptor);
		free(column);
		return NULL;
	}

	// Fill the column structure
	column->dms    			 = dms;
	column->column_directory = column_directory;
	column->header 			 = mmap(NULL,
			                  	  	header_size,
			                  	  	PROT_READ,
			                  	  	MAP_SHARED,
			                  	  	column_file_descriptor,
			                  	  	0
			                 	   );

	if (column->header == MAP_FAILED)
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError mmapping the header of a column");
		close(column_file_descriptor);
		free(column);
		return NULL;
	}

	// Map the data
	column->data   			 = mmap(NULL,
			                 	 	(column->header)->data_size,
			                 	 	PROT_READ,
									MAP_SHARED,
			                 	 	column_file_descriptor,
			                 	 	header_size
			                	   );

	if (column->data == MAP_FAILED)
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError mmapping the data of a column");
		munmap(column->header, header_size);
		close(column_file_descriptor);
		free(column);
		return NULL;
	}

	column->writable = false;

	// If the data type is OBI_STR, OBI_SEQ or OBI_QUAL, the associated indexer is opened
	if (((column->header)->returned_data_type == OBI_STR) || ((column->header)->returned_data_type == OBI_SEQ) || ((column->header)->returned_data_type == OBI_QUAL))
	{
		column->indexer = obi_open_indexer(dms, (column->header)->indexer_name);
		if (column->indexer == NULL)
		{
			obidebug(1, "\nError opening the indexer associated with a column");
			munmap(column->header, header_size);
			close(column_file_descriptor);
			free(column);
			return NULL;
		}
	}

	if (close(column_file_descriptor) < 0)
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError closing a column file");
		return NULL;
	}

	// Add in the list of opened columns
	obi_dms_list_column(dms, column);

	// Set counter to 1
	column->counter = 1;

	return column;
}


OBIDMS_column_p obi_clone_column(OBIDMS_p         dms,
								 OBIDMS_column_p  line_selection,
								 const char*      column_name,
								 obiversion_t     version_number,
								 bool 		      clone_data)
{
	OBIDMS_column_p   column_to_clone;
	OBIDMS_column_p   new_column;
	index_t 		  nb_lines = 0;
	index_t			  nb_elements_per_line;
	OBIType_t		  data_type;
	size_t 			  line_size;
	index_t			  i, index;

	column_to_clone = obi_open_column(dms, column_name, version_number);
	if (column_to_clone == NULL)
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError opening the column to clone");
		return NULL;
	}

	data_type = (column_to_clone->header)->returned_data_type;

	nb_elements_per_line = (column_to_clone->header)->nb_elements_per_line;

	if (clone_data && (line_selection == NULL))
		nb_lines = (column_to_clone->header)->line_count;
	else if (clone_data && (line_selection != NULL))
		nb_lines = (line_selection->header)->line_count;

	new_column = obi_create_column(dms,
								   column_name,
								   data_type,
								   nb_lines,
								   nb_elements_per_line,
								   (column_to_clone->header)->elements_names,
								   (column_to_clone->header)->indexer_name,
								   ((column_to_clone->header)->associated_column).column_name,
								   ((column_to_clone->header)->associated_column).version,
								   (column_to_clone->header)->comments
								  );

	if (new_column == NULL)
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError creating the new column when cloning a column");
		// The new file is deleted TODO check if it exists before
		//const char* column_file_name = build_column_file_name(column_name, version_number);
		//if (remove(column_file_name) < 0)
		//	obidebug(1, "\nError deleting a bad cloned file");
		return NULL;
	}

	(new_column->header)->cloned_from = (column_to_clone->header)->version;

	if (clone_data && (line_selection == NULL))
	{
		if ((new_column->header)->data_size != (column_to_clone->header)->data_size)
		{
			obi_set_errno(OBICOL_UNKNOWN_ERROR);
			obidebug(1, "\nError cloning a column: the sizes of the data source and destination are not equal: source %zu bytes, destination %zu bytes.",
					(column_to_clone->header)->data_size, (new_column->header)->data_size);
			return NULL;
		}
		// Copy all the data to the new column
		memcpy(new_column->data, column_to_clone->data, (column_to_clone->header)->data_size);
		(new_column->header)->lines_used = (column_to_clone->header)->lines_used;
	}
	else if (clone_data && (line_selection != NULL))
	{
		line_size = obi_sizeof((new_column->header)->stored_data_type) * (new_column->header)->nb_elements_per_line;
		// Copy each line at the right index to the new column
		for (i=0; i<nb_lines; i++)
		{
			// Get the index in the line selection column
			index = obi_column_get_index(line_selection, i);
			// Copy the line at the index in the column to clone to the new column
			memcpy((new_column->data)+(i*line_size), (column_to_clone->data)+(index*line_size), line_size);
		}
		(new_column->header)->lines_used = (line_selection->header)->lines_used;
	}

	// Close column_to_clone
	if (obi_close_column(column_to_clone) < 0)
	{
		obidebug(1, "\nError closing a column that has been cloned");
		// TODO return NULL or not?
	}

	return new_column;
}


int obi_close_column(OBIDMS_column_p column)
{
	int     ret_val = 0;

	// Truncate the column to the number of lines used if it's not read-only
	if (column->writable)
		ret_val = obi_truncate_column(column);

	(column->counter)--;

	if (column->counter == 0)
	{
		// Delete from the list of opened columns
		if (obi_dms_unlist_column(column->dms, column) < 0)
			ret_val = -1;

		// If the data type is OBI_STR, OBI_SEQ or OBI_QUAL, the associated indexer is closed
		if (((column->header)->returned_data_type == OBI_STR) || ((column->header)->returned_data_type == OBI_SEQ) || ((column->header)->returned_data_type == OBI_QUAL))
			if (obi_close_indexer(column->indexer) < 0)
				ret_val = -1;

		// Munmap data
		if (munmap(column->data, (column->header)->data_size) < 0)
		{
			obi_set_errno(OBICOL_UNKNOWN_ERROR);
			obidebug(1, "\nError munmapping column data");
			ret_val = -1;
		}

		// Munmap header
		if (munmap(column->header, (column->header)->header_size) < 0)
		{
			obi_set_errno(OBICOL_UNKNOWN_ERROR);
			obidebug(1, "\nError munmapping a column header");
			ret_val = -1;
		}

		// Close column directory
		if (obi_close_column_directory(column->column_directory) < 0)
			ret_val = -1;

		free(column);
	}

	return ret_val;
}


int obi_truncate_column(OBIDMS_column_p column)	// TODO is it necessary to unmap/remap?
{
	size_t  file_size;
	size_t  data_size;
	index_t new_line_count;
	double  multiple;
	int 	column_file_descriptor;
	char* 	column_file_name;

	// Compute the new line count = the number of lines used rounded to the nearest greater multiple of page size greater than 0
	multiple = ceil((double) (ONE_IF_ZERO((column->header)->lines_used) * (column->header)->nb_elements_per_line * obi_sizeof((column->header)->stored_data_type)) / (double) getpagesize());
	new_line_count = floor((((int) multiple) * getpagesize()) / ((column->header)->nb_elements_per_line * obi_sizeof((column->header)->stored_data_type)));

	data_size = obi_array_sizeof((column->header)->stored_data_type, new_line_count, (column->header)->nb_elements_per_line);

	// Check that it is actually greater than the current data size, otherwise no need to truncate
	if ((column->header)->data_size == data_size)
		return 0;
	else if ((column->header)->data_size < data_size)
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError truncating a column: The current data size seems smaller than needed.");
		return -1;
	}

	// Get the column file name
	column_file_name = build_column_file_name((column->header)->name, (column->header)->version);
	if (column_file_name == NULL)
		return -1;

	// Open the column file
	column_file_descriptor = openat((column->column_directory)->dir_fd, column_file_name, O_RDWR);
	if (column_file_descriptor < 0)
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError getting the file descriptor of a column file");
		free(column_file_name);
		return -1;
	}

	free(column_file_name);

	// Unmap the data before truncating the file
	if (munmap(column->data, (column->header)->data_size) < 0)
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError munmapping the data of a column before truncating");
		close(column_file_descriptor);
		return -1;
	}

	// Truncate the column file
	file_size = (column->header)->header_size + data_size;
	if (ftruncate(column_file_descriptor, file_size) < 0)
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError truncating a column file at the number of lines used");
		close(column_file_descriptor);
		return -1;
	}

	// Remap the data
	column->data = mmap(NULL,
						data_size,
						PROT_READ | PROT_WRITE,
						MAP_SHARED,
						column_file_descriptor,
						(column->header)->header_size
					   );

	if (column->data == MAP_FAILED)
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError re-mmapping the data of a column after truncating");
		close(column_file_descriptor);
		return -1;
	}

	// Set new line_count and new data size
	(column->header)->line_count = new_line_count;
	(column->header)->data_size = data_size;

	if (close(column_file_descriptor) < 0)
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError closing a column file");
		return -1;
	}

	return 0;
}


int obi_enlarge_column(OBIDMS_column_p column)
{
	size_t  file_size;
	size_t  old_data_size;
	size_t  new_data_size;
	size_t  header_size;
	index_t old_line_count;
	index_t new_line_count;
	int 	column_file_descriptor;
	char* 	column_file_name;

	// Check if the column is read-only
	if (!(column->writable))
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError trying to enlarge a read-only column");
    	return -1;
	}

	// Get the column file name
	column_file_name = build_column_file_name((column->header)->name, (column->header)->version);
	if (column_file_name == NULL)
	{
		return -1;
	}

	// Open the column file
	column_file_descriptor = openat((column->column_directory)->dir_fd, column_file_name, O_RDWR);
	if (column_file_descriptor < 0)
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError getting the file descriptor of a column file");
		free(column_file_name);
		return -1;
	}

	free(column_file_name);

	// Calculate the new file size
	old_line_count = (column->header)->line_count;
	new_line_count = old_line_count * COLUMN_GROWTH_FACTOR;

	if (new_line_count > MAXIMUM_LINE_COUNT)
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError enlarging a column file: new line count greater than the maximum allowed");
		close(column_file_descriptor);
		return -1;
	}
	old_data_size = (column->header)->data_size;
	new_data_size = obi_array_sizeof((column->header)->stored_data_type, new_line_count, (column->header)->nb_elements_per_line);
	header_size = (column->header)->header_size;
	file_size = header_size + new_data_size;

	// Enlarge the file // TODO isn't it possible that this makes the file "move"?
	if (ftruncate(column_file_descriptor, file_size) < 0)
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError enlarging a column file");
		close(column_file_descriptor);
		return -1;
	}

	// Unmap and remap the data
	if (munmap(column->data, old_data_size) < 0)
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError munmapping the data of a column before enlarging");
		close(column_file_descriptor);
		return -1;
	}

	column->data  = mmap(NULL,
						 new_data_size,
						 PROT_READ | PROT_WRITE,
						 MAP_SHARED,
						 column_file_descriptor,
						 header_size
						);
	if (column->data == MAP_FAILED)
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError re-mmapping the data of a column after enlarging the file");
		close(column_file_descriptor);
		return -1;
	}

	// Set new line count and new data size
	(column->header)->line_count = new_line_count;
	(column->header)->data_size = new_data_size;

	// Initialize new data lines to NA
	obi_ini_to_NA_values(column, old_line_count, new_line_count - old_line_count);

	if (close(column_file_descriptor) < 0)
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError closing a column file");
		return -1;
	}

	return 0;
}


void obi_ini_to_NA_values(OBIDMS_column_p column,
						  index_t first_line_nb,
						  index_t nb_lines)
{
	index_t i, start, end, nb_elements;

	nb_elements = nb_lines*((column->header)->nb_elements_per_line);
	start = first_line_nb*((column->header)->nb_elements_per_line);
	end = start + nb_elements;

	switch ((column->header)->stored_data_type) {
	case OBI_VOID:  // TODO;
					break;

	case OBI_INT:   for (i=start;i<end;i++)
					{
						*(((obiint_t*) (column->data)) + i) = OBIInt_NA;
					}
					break;

	case OBI_FLOAT: for (i=start;i<end;i++)
					{
						*(((obifloat_t*) (column->data)) + i) = OBIFloat_NA;
					}
					break;

	case OBI_BOOL:  for (i=start;i<end;i++)
					{
						*(((obibool_t*) (column->data)) + i) = OBIBool_NA;
					}
					break;

	case OBI_CHAR:  for (i=start;i<end;i++)
					{
						*(((obichar_t*) (column->data)) + i) = OBIChar_NA;
					}
					break;

	case OBI_IDX:   for (i=start;i<end;i++)
					{
						*(((index_t*) (column->data)) + i) = OBIIdx_NA;
					}
					break;

	case OBI_QUAL:  for (i=start;i<end;i++)		// case not used since OBI_QUAL is only a returned_data_type
					{
						*(((index_t*) (column->data)) + i) = OBIIdx_NA;
					}
					break;

	case OBI_STR:   for (i=start;i<end;i++)		// case not used since OBI_QUAL is only a returned_data_type
					{
						*(((index_t*) (column->data)) + i) = OBIIdx_NA;
					}
					break;

	case OBI_SEQ:   for (i=start;i<end;i++)		// case not used since OBI_QUAL is only a returned_data_type
					{
						*(((index_t*) (column->data)) + i) = OBIIdx_NA;
					}
					break;
	}
}


OBIDMS_column_header_p obi_column_get_header_from_name(OBIDMS_p dms, const char* column_name, obiversion_t version_number)
{
	OBIDMS_column_header_p 		header;
	OBIDMS_column_directory_p	column_directory;
	char* 						column_file_name;
	int 						column_file_descriptor;
	size_t 						header_size;

	// Get the column directory structure associated to the column
	column_directory = obi_open_column_directory(dms, column_name);
	if (column_directory == NULL)
	{
		obidebug(1, "\nError opening a column directory structure");
		return NULL;
	}

	// Get the latest version number if not provided
	if (version_number < 0)
	{
		version_number = obi_get_latest_version_number(column_directory);
		if (version_number < 0)
		{
			obidebug(1, "\nError getting the latest version number in a column directory");
			return NULL;
		}
	}

	// Get the column file name
	column_file_name = build_column_file_name(column_name, version_number);
	if (column_file_name == NULL)
	{
		return NULL;
	}

	// Open the column file (READ-ONLY)
	column_file_descriptor = openat(column_directory->dir_fd, column_file_name, O_RDONLY);
	if (column_file_descriptor < 0)
	{
		obidebug(1, "\nError opening a column file");
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		free(column_file_name);
		return NULL;
	}

	free(column_file_name);

	// Read the header size
	if (read(column_file_descriptor, &header_size, sizeof(size_t)) < ((ssize_t) sizeof(size_t)))
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError reading the header size to read a header");
		close(column_file_descriptor);
		return NULL;
	}

	// Fill the header structure
	header = mmap(NULL,
			 	  header_size,
				  PROT_READ,
				  MAP_SHARED,
				  column_file_descriptor,
				  0
			 	 );

	if (header == MAP_FAILED)
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError mmapping the header of a column");
		close(column_file_descriptor);
		return NULL;
	}

	if (close(column_file_descriptor) < 0)
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError closing a column file");
		return NULL;
	}

	return header;
}


int obi_close_header(OBIDMS_column_header_p header)
{
	if (munmap(header, header->header_size) < 0)
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError munmapping a column header");
		return -1;
	}
	return 0;
}


// TODO to be rewritten in an optimized and safe way if possible
index_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const char* element_name)
{
	char*   elements_names;
	char*   name;
	index_t element_index;

	elements_names = strdup((column->header)->elements_names);
	if (elements_names == NULL)
	{
		obidebug(1, "\nError strdup-ing the elements names");
		return OBIIdx_NA;
	}

	element_index = 0;

	name = strtok(elements_names, ";");	// TODO not thread safe, see strtok_r maybe
	if (strcmp(element_name, name) == 0)
	{
		free(elements_names);
		return element_index;
	}
	element_index++;

	while (name != NULL)
	{
		name = strtok(NULL, ";");			// TODO not thread safe, see strtok_r maybe
		if (strcmp(element_name, name) == 0)
		{
			free(elements_names);
			return element_index;
		}
		element_index++;
	}

	obidebug(1, "\nCan't find an element name");
	free(elements_names);
	return OBIIdx_NA;
}


int obi_column_prepare_to_set_value(OBIDMS_column_p column, index_t line_nb)
{
	// Check if the column is read-only
	if (!(column->writable))
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError trying to set a value in a read-only column");
    	return -1;
	}

	// Check that the line number is not greater than the maximum allowed
	if (line_nb >= MAXIMUM_LINE_COUNT)
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError trying to set a value at a line number greater than the maximum allowed");
    	return -1;
	}

	// Check if the file needs to be enlarged
	while ((line_nb+1) > (column->header)->line_count)
	{
		// Enlarge the file
		if (obi_enlarge_column(column) < 0)
	    	return -1;
	}

	// Update lines used
	if ((line_nb+1) > (column->header)->lines_used)
		(column->header)->lines_used = line_nb+1;

	return 0;
}


int obi_column_prepare_to_get_value(OBIDMS_column_p column, index_t line_nb)	// TODO problem with some columns in a view being empty or shorter and triggering an error because they've been truncated when the view was closed. Fixed with obiview.c in update_lines() for now
{
	if ((line_nb+1) > ((column->header)->line_count))
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError trying to get a value that is beyond the current number of lines of the column");
		return -1;
	}
	return 0;
}