obitools3/src/obiview.c

/********************************************************************
 * Obiview functions                                                 *
 ********************************************************************/

/**
 * @file obiview.c
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 * @date 16 December 2015
 * @brief Obiview functions.
 */


#include <stdlib.h>
#include <stdio.h>
#include <stdbool.h>
#include <fcntl.h>
#include <sys/mman.h>

#include "obiview.h"
#include "obidms.h"
#include "obidmscolumn.h"
#include "obidmscolumn_idx.h"
#include "obidmscolumn_bool.h"
#include "obidmscolumn_char.h"
#include "obidmscolumn_float.h"
#include "obidmscolumn_int.h"
#include "obidmscolumn_seq.h"
#include "obidmscolumn_str.h"
#include "obierrno.h"
#include "obidebug.h"
#include "obilittlebigman.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
 *
 **************************************************************************/


/**
 * Internal function building the file name where obiviews are stored.
 *
 * @warning The returned pointer has to be freed by the caller.
 *
 * @returns A pointer to the file name.
 * @retval NULL if an error occurred.
 *
 * @param dms_name The name of the OBIDMS.
 *
 * @since December 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
static char* build_obiview_file_name();


/**	TODO public?
 * 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_obiview_file(int dms_file_descriptor);


/**
 * @brief Internal function to update the line count in the context of a view.
 *
 * All columns of the view are enlarged to contain at least the new line count.
 *
 * @warning The view must be writable.
 *
 * @param view A pointer on the view.
 * @param line_count The new line count.
 *
 * @returns A value indicating the success of the operation.
 * @retval 0 if the operation was successfully completed.
 * @retval -1 if an error occurred.
 *
 * @since February 2016
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
int update_lines(Obiview_p view, index_t line_count);


/**
 * @brief Internal function to clone a column in the context of a view.
 *
 * Clones with the right line selection and replaces the cloned columns with the new ones in the view.
 * If there is a line selection, all columns have to be cloned, otherwise only the column of interest is cloned.
 *
 * @param view A pointer on the view.
 * @param column_name The name of the column in the view that should be cloned.
 *
 * @returns A pointer on the new column.
 * @retval NULL if an error occurred.
 *
 * @since February 2016
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
OBIDMS_column_p clone_column_in_view(Obiview_p view, const char* column_name);


/**
 * Internal function preparing to set a value in a column, in the context of a view.
 *
 * The function checks that the view is not read-only, clones the column or all columns if needed,
 * and updates the line count if needed.
 *
 * @param view The view.
 * @param column_pp A pointer on the pointer on the column, to allow replacing the column if it is cloned.
 * @param line_nb_p A pointer on the index of the line that will be modified, to allow replacing it if needed.
 *
 * @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 prepare_to_set_value_in_column(Obiview_p view, OBIDMS_column_p* column_pp, index_t* line_nb_p);


/**
 * Internal function preparing to get a value from a column, in the context of a view.
 *
 * The function checks that the line index is not beyond the current line count of the view,
 * and modifies it if there is a line selection associated with the view.
 *
 * @param view The view.
 * @param line_nb_p A pointer on the index of the line, to allow replacing it if needed.
 *
 * @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 prepare_to_get_value_from_column(Obiview_p view, index_t* line_nb_p);


/************************************************************************
 *
 * 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_obiview_file_name()
{
	char* file_name;

	// Build file name
	file_name = (char*) malloc((strlen(OBIVIEW_FILE_NAME) + 1)*sizeof(char));
	if (file_name == NULL)
	{
		obi_set_errno(OBI_MALLOC_ERROR);
		obidebug(1, "\nError allocating memory for a view file name");
		return NULL;
	}
	if (sprintf(file_name, OBIVIEW_FILE_NAME) < 0)
	{
		obi_set_errno(OBIVIEW_ERROR);
		obidebug(1, "\nProblem building an obiview file name");
		return NULL;
	}

	return file_name;
}


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

	header_size = sizeof(Obiviews_header_t);

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

	rounded_header_size = multiple * getpagesize();

	return rounded_header_size;
}


size_t get_platform_views_size(int nb_of_views)
{
	size_t obiview_size;
	size_t rounded_obiview_size;
	double multiple;

	obiview_size = sizeof(Obiview_infos_t);

	multiple = 	ceil((double) (obiview_size*nb_of_views) / (double) getpagesize());

	rounded_obiview_size = multiple * getpagesize();

	return rounded_obiview_size;
}


int create_obiview_file(int dms_file_descriptor)
{
	char* 				file_name;
	int 				obiview_file_descriptor;
	size_t  			header_size;
	size_t  			file_size;
	Obiviews_header_p 	header;

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

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

	free(file_name);

	// Truncate file to the right size
	header_size = get_platform_header_size();
	file_size = header_size;

	if (ftruncate(obiview_file_descriptor, file_size) < 0)
	{
		obi_set_errno(OBIVIEW_ERROR);
		obidebug(1, "\nError truncating an obiview file to the right size");
		close(obiview_file_descriptor);
		return -1;
	}

	// Map the header
	header = mmap(NULL,
  	  	   	      header_size,
				  PROT_READ | PROT_WRITE,
				  MAP_SHARED,
				  obiview_file_descriptor,
				  0
 	 	   	   	 );
	if (header == MAP_FAILED)
	{
		obi_set_errno(OBIVIEW_ERROR);
		obidebug(1, "\nError mmapping an obiview file header");
		close(obiview_file_descriptor);
		return -1;
	}

	// Initialize the header
	header->header_size = header_size;
	header->views_size = 0;
	header->view_count = 0;

	// Unmap the header
	if (munmap(header, header_size) < 0)
	{
		obi_set_errno(OBIVIEW_ERROR);
		obidebug(1, "\nError munmapping an obiview file header");
		close(obiview_file_descriptor);
		return -1;
	}

	close(obiview_file_descriptor);

	return 0;
}


int update_lines(Obiview_p view, index_t line_count)
{
	int i;

	for (i=0; i<(view->column_count); i++)
	{
		while (line_count > (((view->columns)[i])->header)->line_count)
		{
			// Enlarge the column
			if (obi_enlarge_column((view->columns)[i]) < 0)
		    	return -1;
		}
	}

	view->line_count = line_count;

	return 0;
}


OBIDMS_column_p clone_column_in_view(Obiview_p view, const char* column_name)
{
	int i;
	OBIDMS_column_p current_line_selection = NULL;
	OBIDMS_column_p column;
	OBIDMS_column_p column_buffer;

	// Check that the view is not read-only
	if (view->read_only)
	{
		obi_set_errno(OBIVIEW_ERROR);
		obidebug(1, "\nError trying to delete a column in a read-only view");
		return NULL;
	}

	if (view->new_line_selection != NULL)	// TODO Probably shouldn't happen, trigger error?
		current_line_selection = view->new_line_selection;
	else
		current_line_selection = view->line_selection;

	for (i=0; i<(view->column_count); i++)
	{
		if ((current_line_selection != NULL) || (!(strcmp((((view->columns)[i])->header)->name, column_name))))
		{ // Clone with the right line selection and replace (for all columns if there is a line selection)

			// Save pointer to close column after cloning
			column_buffer = (view->columns)[i];

			// Clone and replace the column in the view
			(view->columns)[i] = obi_clone_column(view->dms, current_line_selection, (((view->columns)[i])->header)->name, (((view->columns)[i])->header)->version, 1);
			if ((view->columns)[i] == NULL)
			{
				obi_set_errno(OBIVIEW_ERROR);
				obidebug(1, "\nError cloning a column to replace in a view");
				return NULL;
			}

			// Close old cloned column
			obi_close_column(column_buffer);

			if (!(strcmp((((view->columns)[i])->header)->name, column_name)))
				// Found the column to return
				column = (view->columns)[i];
		}
	}

	// Close old line selections
	if (view->line_selection != NULL)
	{
		obi_close_column(view->line_selection);
		view->line_selection = NULL;
	}
	if (view->new_line_selection != NULL)
	{
		obi_close_column(view->new_line_selection);
		view->new_line_selection = NULL;
	}

	return column;
}


int prepare_to_set_value_in_column(Obiview_p view, OBIDMS_column_p* column_pp, index_t* line_nb_p)
{
	// Check that the view is not read-only
	if (view->read_only)
	{
		obi_set_errno(OBIVIEW_ERROR);
		obidebug(1, "\nError trying to set a value in a column in a read-only view");
		return -1;
	}

	// If there is a line selection associated with the view or if the column
	// is read-only, all columns or this column respectively must be cloned
	if ((view->line_selection != NULL) || (!((*column_pp)->writable)))
	{
		// Get the right line number
		if (view->line_selection != NULL)
			(*line_nb_p) = *(((index_t*) ((view->line_selection)->data)) + (*line_nb_p));

		(*column_pp) = clone_column_in_view(view, ((*column_pp)->header)->name);
		if ((*column_pp) == NULL)
		{
			obidebug(1, "\nError trying to clone a column to modify it");
			return -1;
		}
	}

	if (((*line_nb_p)+1) > view->line_count)
	{
		if (update_lines(view, ((*line_nb_p)+1)) < 0)
			return -1;
	}

	return 0;
}


int prepare_to_get_value_from_column(Obiview_p view, index_t* line_nb_p)
{
	if (((*line_nb_p)+1) > (view->line_count))
	{
		obi_set_errno(OBICOL_UNKNOWN_ERROR);
		obidebug(1, "\nError trying to get a value that is beyond the current line count of the view");
		return -1;
	}

	if (view->line_selection)
		(*line_nb_p) = *(((index_t*) ((view->line_selection)->data)) + (*line_nb_p));

	return 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
 *
 **********************************************************************/

Obiview_p obi_new_view(OBIDMS_p dms, const char* view_name, Obiview_p view_to_clone, index_t* line_selection, const char* comments)
{
	Obiview_p view;
	int i;
	index_t line_nb;
	Obiviews_infos_all_p views_infos;

	// Check uniqueness of name TODO but problem if view not written yet has the same name. Save lists of open views in DMS ?
	views_infos = obi_read_views(dms);
	if (views_infos != NULL)
	{
		for (i=0; i<((views_infos->header)->view_count); i++)
		{
			if (strcmp(((views_infos->view_infos)+i)->name, view_name) == 0)		// TODO discuss what to do
			{
				obi_set_errno(OBIVIEW_ERROR);
				obidebug(1, "\nView name already exists for a previous view");
				obi_unmap_read_views(views_infos);
				return NULL;
			}
		}
	obi_unmap_read_views(views_infos);
	}

	view = (Obiview_p) malloc(sizeof(Obiview_t));
	if (view == NULL)
	{
		obi_set_errno(OBIVIEW_ERROR);
		obidebug(1, "\nError allocating memory for a view");
		return NULL;
	}

	// Clone view to clone if there is one
	if (view_to_clone != NULL)
	{
		if (!(view_to_clone->read_only))
		{
			obi_set_errno(OBIVIEW_ERROR);
			obidebug(1, "\nA view can not be cloned if it is not read-only");
			free(view);
			return NULL;
		}

		view->dms = dms;
		view->column_count = view_to_clone->column_count;

		// If the view to clone has an associated line selection and there is no new line selection, open the associated line selection
		if ((view_to_clone->line_selection != NULL) && (line_selection == NULL))
		{
			view->line_selection = obi_open_column(dms, ((view_to_clone->line_selection)->header)->name, ((view_to_clone->line_selection)->header)->version);
			if (view->line_selection == NULL)
				return NULL;
			view->line_count = view_to_clone->line_count;
		}
		// If there is a new line selection, build it by combining it with the one from the view to clone if there is one
		else if (line_selection != NULL)
		{
			view->line_selection = obi_create_column(view->dms, LINES_COLUMN_NAME, OBI_IDX, 0, 1, LINES_COLUMN_NAME, NULL, NULL);
			if ((view->line_selection) == NULL)
			{
				obidebug(1, "\nError creating a column corresponding to a line selection");
				return NULL;
			}
			view->line_count = 0;
			i = 0;
			for (i=0; line_selection[i] != -1; i++)
			{
				line_nb = line_selection[i];

				if (line_nb > view_to_clone->line_count)
				{
					obi_set_errno(OBIVIEW_ERROR);
					obidebug(1, "\nError trying to select a line for a new view that is beyond the line count of the view to clone");
					obi_close_column(view->line_selection);
					free(view);
					return NULL;
				}

				if (view_to_clone->line_selection != NULL)
					line_nb = obi_column_get_index(view_to_clone->line_selection, line_nb);

				if (obi_column_set_index(view->line_selection, ((view->line_selection)->header)->lines_used, line_nb) < 0)
				{
					obi_close_column(view->line_selection);
					free(view);
					return NULL;
				}

				// Update view line count
				(view->line_count)++;
			}
		}
		else	// If there is no line selection associated with the view to clone or the new view
		{
			view->line_selection = NULL;
			view->line_count = view_to_clone->line_count;
		}

		for (i=0; i<(view_to_clone->column_count); i++)
		{
			(view->columns)[i] = obi_open_column(dms, (((view_to_clone->columns)[i])->header)->name, (((view_to_clone->columns)[i])->header)->version);
			if ((view->columns)[i] == NULL)
			{
				obi_close_column(view->line_selection);
				free(view);
				return NULL;
			}
		}

		strcpy(view->view_type, view_to_clone->view_type);
		strcpy(view->created_from, view_to_clone->name);
		view->new_line_selection = NULL;
	}
	// Else, fill empty view structure
	else
	{
		view->dms                = dms;
		view->column_count       = 0;
		view->line_count         = 0;
		view->line_selection     = NULL;
		view->new_line_selection = NULL;
		(view->created_from)[0]  = '\0';
		(view->view_type)[0]     = '\0';
		//view->columns          = NULL;  // TODO
	}

	strcpy(view->name, view_name);
	strcpy(view->comments, comments);
	view->read_only = 0;

	return view;
}


Obiview_p obi_new_view_cloned_from_name(OBIDMS_p dms, const char* view_name, const char* view_to_clone_name, index_t* line_selection, const char* comments)
{
	Obiview_p view;
	Obiview_p view_to_clone;

	view_to_clone = obi_open_view(dms, view_to_clone_name);
	if (view_to_clone == NULL)
		return NULL;
	view = obi_new_view(dms, view_name, view_to_clone, line_selection, comments);

	obi_close_view(view_to_clone);

	return view;
}


Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p view_to_clone, index_t* line_selection, const char* comments)
{
	Obiview_p view;

	if (view_to_clone != NULL)
	{ // Check that the view to clone is already a NUC_SEQS view (TODO discuss possibility of transforming type of a view)
		if (strcmp(view_to_clone->view_type, VIEW_TYPE_NUC_SEQS))
		{
			obi_set_errno(OBIVIEW_ERROR);
			obidebug(1, "Trying to clone a non-NUC SEQS view to create a NUC SEQS view");
			return NULL;
		}
	}

	view = obi_new_view(dms, view_name, view_to_clone, line_selection, comments);
	if (view== NULL)
		return NULL;

	strcpy(view->view_type, VIEW_TYPE_NUC_SEQS);

	if (view_to_clone == NULL)
	{
		// Adding sequence column
		if (obi_view_add_column(view, NUC_SEQUENCE_COLUMN, -1, OBI_SEQ, 0, 1, NUC_SEQUENCE_COLUMN, NUC_SEQUENCE_INDEXER, "Nucleotide sequences", true) < 0)
		{
			obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
			return NULL;
		}
		// Adding id column
		if (obi_view_add_column(view, ID_COLUMN, -1, OBI_STR, 0, 1, ID_COLUMN, ID_INDEXER, "Ids", true) < 0)
		{
			obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
			return NULL;
		}
		// Adding definition column
		if (obi_view_add_column(view, DEFINITION_COLUMN, -1, OBI_STR, 0, 1, DEFINITION_COLUMN, DEFINITION_INDEXER, "Definitions", true) < 0)
		{
			obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
			return NULL;
		}
	}

	return view;
}


Obiview_p obi_new_view_nuc_seqs_cloned_from_name(OBIDMS_p dms, const char* view_name, const char* view_to_clone_name, index_t* line_selection, const char* comments)
{
	Obiview_p view;
	Obiview_p view_to_clone;

	view_to_clone = obi_open_view(dms, view_to_clone_name);
	if (view_to_clone == NULL)
		return NULL;
	view = obi_new_view_nuc_seqs(dms, view_name, view_to_clone, line_selection, comments);

	obi_close_view(view_to_clone);

	return view;
}


Obiview_p obi_open_view(OBIDMS_p dms, const char* view_name)
{
	Obiview_p			view;
	bool      			first_view;
	char*       		view_file_name;
	int 				obiview_file_descriptor;
	size_t  			header_size;
	Obiviews_header_p 	header;
	Obiview_infos_p 	views;
	Obiview_infos_p     view_infos;
	OBIDMS_column_p     column;
	int					i;
	int 				view_number;

	// Check if 1st view : view file doesn't exist
	first_view = 0;

	view_file_name = build_obiview_file_name();
	if (view_file_name == NULL)
		return NULL;

	// Open view file, read header size and map header and views
	obiview_file_descriptor = openat(dms->dir_fd, view_file_name, O_RDWR, 0777);
	if (obiview_file_descriptor < 0)
	{
		obi_set_errno(OBIVIEW_ERROR);
		obidebug(1, "\nError opening an obiview file");
		free(view_file_name);
		return NULL;
	}

	free(view_file_name);

	// Read the header size
	if (read(obiview_file_descriptor, &header_size, sizeof(size_t)) < ((ssize_t) sizeof(size_t)))
	{
		obi_set_errno(OBIVIEW_ERROR);
		obidebug(1, "\nError reading the header size of an obiview file (trying to open a view when there are none?)");
		close(obiview_file_descriptor);
		return NULL;
	}

	// Map the header
	header = mmap(NULL,
				  header_size,
				  PROT_READ | PROT_WRITE,
				  MAP_SHARED,
				  obiview_file_descriptor,
				  0
 	 	   	   	 );
	if (header == MAP_FAILED)
	{
		obi_set_errno(OBIVIEW_ERROR);
		obidebug(1, "\nError mmapping an obiview file header");
		close(obiview_file_descriptor);
		return NULL;
	}

	// Map the views
	views = mmap(NULL,
				 header->views_size,
				 PROT_READ | PROT_WRITE,
				 MAP_SHARED,
				 obiview_file_descriptor,
				 header_size
 	 	   	   	);
	if (views == MAP_FAILED)
	{
		obi_set_errno(OBIVIEW_ERROR);
		obidebug(1, "\nError mmapping the views from an obiview file");
		munmap(header, header_size);
		close(obiview_file_descriptor);
		return NULL;
	}

	// Find and open the view that should be read with the line selection associated
	view_number = -1;
	if (view_name == NULL)	// If view name is NULL, open the latest view TODO discuss
		view_number = (header->view_count) - 1;
	else
	{
		for (i=0; i<(header->view_count); i++)
		{
			if (!strcmp((views+i)->name, view_name))
			{	// Found the view to open
				view_number = i;
			}
		}
	}

	if (view_number == -1)
	{
		obi_set_errno(OBIVIEW_ERROR);
		obidebug(1, "\nError: the view '%s' to open was not found", view_name);
		munmap(views, header->views_size);
		munmap(header, header_size);
		close(obiview_file_descriptor);
		return NULL;
	}

	view_infos = views + view_number;

	view = (Obiview_p) malloc(sizeof(Obiview_t));
	if (view == NULL)
	{
		obi_set_errno(OBIVIEW_ERROR);
		obidebug(1, "\nError allocating memory for a view");
		munmap(views, header->views_size);
		munmap(header, header_size);
		close(obiview_file_descriptor);
		return NULL;
	}

	if (view_infos->all_lines)
		view->line_selection = NULL;
	else
	{
		view->line_selection = obi_open_column(dms, (view_infos->line_selection).column_name, (view_infos->line_selection).version);
		if (view->line_selection == NULL)
		{
			munmap(views, header->views_size);
			munmap(header, header_size);
			close(obiview_file_descriptor);
			return NULL;
		}
	}

	view->dms = dms;
	view->new_line_selection = NULL;
	view->read_only = 1;
	view->column_count = 0;
	view->line_count = view_infos->line_count;
	strcpy(view->created_from, view_infos->created_from);
	strcpy(view->name, view_infos->name);
	strcpy(view->view_type, view_infos->view_type);
	strcpy(view->comments, view_infos->comments);

	// Open the columns to read
	for (i=0; i<(view_infos->column_count); i++)
	{
		column = obi_open_column(dms, ((view_infos->column_references)+i)->column_name, ((view_infos->column_references)+i)->version);
		if (column == NULL)
		{
			obidebug(1, "\nError opening a column for a view: column %d: %s, version %d", i, ((view_infos->column_references)+i)->column_name, ((view_infos->column_references)+i)->version);
			munmap(views, header->views_size);
			munmap(header, header_size);
			close(obiview_file_descriptor);
			return NULL;
		}
		// Store column in the view
		(view->columns)[view->column_count] = column;
		view->column_count++;
	}

	// Munmap and close things
	munmap(views, header->views_size);
	munmap(header, header_size);
	close(obiview_file_descriptor);

	return view;
}


int obi_view_add_column(Obiview_p view,
						const char* column_name,
						obiversion_t version_number,
						OBIType_t data_type,
						index_t nb_lines,
						index_t nb_elements_per_line,
						const char* elements_names,
						const char* indexer_name,
						const char* comments,
						bool create)	// all infos for creation or open
{
	OBIDMS_column_p column;

	// Check that the view is not read-only
	if (view->read_only)
	{
		obi_set_errno(OBIVIEW_ERROR);
		obidebug(1, "\nError trying to add a column in a read-only view");
		return -1;
	}

	if (view->line_count > nb_lines)
		nb_lines = view->line_count;
	else if (nb_lines > view->line_count)
		obi_view_update_lines(view, nb_lines);

	// Open or create the column
	if (create)
	{	// Create column
		column = obi_create_column(view->dms, column_name, data_type, nb_lines, nb_elements_per_line, elements_names, indexer_name, comments);
	}
	else
	{ // Open column
		column = obi_open_column(view->dms, column_name, version_number);
	}

	if (column == NULL)
	{
		obidebug(1, "\nError creating or opening a column to add to a view");
		return -1;
	}

	// Store column in the view
	(view->columns)[view->column_count] = column;
	view->column_count++;
	if (view->column_count == 1)	// first column in the view
		view->line_count = (column->header)->lines_used;

	return 0;
}


int obi_view_delete_column(Obiview_p view, const char* column_name)
{
	int  i;
	bool found;

	// TODO check that not deleting an obligatory column?

	// Check that the view is not read-only
	if (view->read_only)
	{
		obi_set_errno(OBIVIEW_ERROR);
		obidebug(1, "\nError trying to delete a column in a read-only view");
		return -1;
	}

	found = 0;

	for (i=0; i<(view->column_count); i++)
	{
		if (!strcmp((((view->columns)[i])->header)->name, column_name))
		{
			obi_close_column((view->columns)[i]);
			found = 1;
		}
		if (found)
		{
			if (i != ((view->column_count) - 1))	// not the last one
				(view->columns)[i] = (view->columns)[i+1];
			else  	// Last column
				(view->columns)[i] = NULL;
		}
	}

	if (!found)
		return -1;

	(view->column_count)--;

	return 0;
}


OBIDMS_column_p obi_view_get_column(Obiview_p view, const char* column_name)
{
	int i;

	for (i=0; i<(view->column_count); i++)
	{
		if (!(strcmp((((view->columns)[i])->header)->name, column_name)))
			return (view->columns)[i];
	}
	return NULL;
}


OBIDMS_column_p* obi_view_get_pointer_on_column_in_view(Obiview_p view, const char* column_name)
{
	int i;

	for (i=0; i<(view->column_count); i++)
	{
		if (!(strcmp((((view->columns)[i])->header)->name, column_name)))
			return ((view->columns)+i);
	}
	return NULL;
}


int obi_select_line(Obiview_p view, index_t line_nb)
{
	// Check that the view is not read-only
	if (view->read_only)
	{
		obi_set_errno(OBIVIEW_ERROR);
		obidebug(1, "\nError trying to select a line in a read-only view");
		return -1;
	}

	// If the column for line selection doesn't already exists, create it and store its informations
	if ((view->new_line_selection) == NULL)
	{
		view->new_line_selection = obi_create_column(view->dms, LINES_COLUMN_NAME, OBI_IDX, 0, 1, LINES_COLUMN_NAME, NULL, NULL);
		if ((view->new_line_selection) == NULL)
		{
			obidebug(1, "\nError creating a column corresponding to a line selection");
			return -1;
		}
	}

	// If we are already working on a line selection, get the pointed line number
	if (view->line_selection)
		line_nb = obi_column_get_index(view->line_selection, line_nb);

	if (obi_column_set_index(view->new_line_selection, ((view->new_line_selection)->header)->lines_used, line_nb) < 0)
		return -1;

	return 0;
}


int obi_select_lines(Obiview_p view, index_t* line_nbs)
{
	int i;
	index_t line_nb;

	// Check that the view is not read-only
	if (view->read_only)
	{
		obi_set_errno(OBIVIEW_ERROR);
		obidebug(1, "\nError trying to select a line in a read-only view");
		return -1;
	}

	// If column for line selection doesn't already exists, create it and store its informations
	if ((view->new_line_selection) == NULL)
	{
		view->new_line_selection = obi_create_column(view->dms, LINES_COLUMN_NAME, OBI_IDX, 0, 1, LINES_COLUMN_NAME, NULL, NULL);
		if ((view->new_line_selection) == NULL)
		{
			obidebug(1, "\nError creating a column corresponding to a line selection");
			return -1;
		}
	}

	for (i=0; line_nbs[i] != -1; i++)
	{
		line_nb = line_nbs[i];

		// If we are already working on a line selection, get the pointed line number
		if (view->line_selection)
			line_nb = obi_column_get_index(view->line_selection, line_nb);

		if (obi_column_set_index(view->new_line_selection, ((view->new_line_selection)->header)->lines_used, line_nb) < 0)
			return -1;
	}

	return 0;
}


int obi_save_view(Obiview_p view)
{
	int i;
    struct stat 		buffer;
	char*       		view_file_name;
	char*  				full_path;
    int         		check_file;
	int 				obiview_file_descriptor;
	size_t  			header_size;
	size_t				views_size;
	size_t  			file_size;
	Obiviews_header_p 	header;
	Obiview_infos_p 	views;
	Obiview_infos_p     view_infos;
	OBIDMS_column_p     current_line_selection;

	// Check that the view is not read-only
	if (view->read_only)
	{
		obi_set_errno(OBIVIEW_ERROR);
		obidebug(1, "\nError trying to save a read-only view");
		return -1;
	}

	view_file_name = build_obiview_file_name();
	if (view_file_name == NULL)
		return -1;

	// Get the full path for the column directory
	full_path = obi_dms_get_full_path(view->dms, view_file_name);
	if (full_path == NULL)
	{
		obi_set_errno(OBIVIEW_ERROR);
		obidebug(1, "\nError getting the full path of an obiview file");
		free(view_file_name);
		return -1;
	}

	check_file = stat(full_path, &buffer);
    if (check_file < 0)
    { // 1st view: create view file
    	if (create_obiview_file((view->dms)->dir_fd) < 0)
    		return -1;
    }

	// Open view file, read header size and map header and views
	obiview_file_descriptor = openat((view->dms)->dir_fd, view_file_name, O_RDWR, 0777);
	if (obiview_file_descriptor < 0)
	{
		obi_set_errno(OBIVIEW_ERROR);
		obidebug(1, "\nError opening an obiview file");
		free(view_file_name);
		return -1;
	}

	free(view_file_name);

	// Read the header size
	if (read(obiview_file_descriptor, &header_size, sizeof(size_t)) < ((ssize_t) sizeof(size_t)))
	{
		obi_set_errno(OBIVIEW_ERROR);
		obidebug(1, "\nError reading the header size of an obiview file");
		close(obiview_file_descriptor);
		return -1;
	}

	// Map the header
	header = mmap(NULL,
				  header_size,
				  PROT_READ | PROT_WRITE,
				  MAP_SHARED,
				  obiview_file_descriptor,
				  0
 	 	   	   	 );
	if (header == MAP_FAILED)
	{
		obi_set_errno(OBIVIEW_ERROR);
		obidebug(1, "\nError mmapping an obiview file header");
		close(obiview_file_descriptor);
		return -1;
	}

	// Truncate file to the right size to add a new view // TODO lock for multithreading
	views_size = get_platform_views_size((header->view_count)+1);
	file_size = header_size + views_size;

	if (ftruncate(obiview_file_descriptor, file_size) < 0)
	{
		obi_set_errno(OBIVIEW_ERROR);
		obidebug(1, "\nError truncating an obiview file to the right size");
		munmap(header, header_size);
		close(obiview_file_descriptor);
		return -1;
	}

	header->views_size = views_size;

	// Map the views
	views = mmap(NULL,
				 header->views_size,
				 PROT_READ | PROT_WRITE,
				 MAP_SHARED,
				 obiview_file_descriptor,
				 header_size
 	 	   	   	);
	if (views == MAP_FAILED)
	{
		obi_set_errno(OBIVIEW_ERROR);
		obidebug(1, "\nError mmapping the views from an obiview file");
		munmap(header, header_size);
		close(obiview_file_descriptor);
		return -1;
	}

    // Write view infos
	view_infos = views + (header->view_count);
	view_infos->view_number = (header->view_count);
	view_infos->column_count = view->column_count;
	view_infos->creation_date = time(NULL);
	strcpy(view_infos->created_from, view->created_from);
	strcpy(view_infos->name, view->name);
	strcpy(view_infos->view_type, view->view_type);
	strcpy(view_infos->comments, view->comments);

	// Store reference for the line selection associated with that view
	if (view->new_line_selection != NULL)
	{
		view_infos->line_count = ((view->new_line_selection)->header)->lines_used;
		current_line_selection = view->new_line_selection;
	}
	else
	{
		view_infos->line_count = view->line_count;
		current_line_selection = view->line_selection;
	}
	if (current_line_selection != NULL)
	{
		view_infos->all_lines = 0;
		strcpy((view_infos->line_selection).column_name, (current_line_selection->header)->name);
		(view_infos->line_selection).version = (current_line_selection->header)->version;
	}
	else
	{
		view_infos->all_lines = 1;
		((view_infos->line_selection).column_name)[0] = '\0';
		(view_infos->line_selection).version = -1;
	}
	for (i=0; i<view->column_count; i++)
	{
		strcpy(((view_infos->column_references)+i)->column_name, (((view->columns)[i])->header)->name);
		((view_infos->column_references)+i)->version = (((view->columns)[i])->header)->version;
	}

	// Increment view count
	(header->view_count)++;

	// Unmap and close file
	munmap(views, header->views_size);
	munmap(header, header_size);
	close(obiview_file_descriptor);

	return 0;
}


int obi_close_view(Obiview_p view)
{
	int i;

	for (i=0; i < (view->column_count); i++)
	{
		obi_close_column((view->columns)[i]);
	}

	free(view);

	return 0;
}


int obi_save_and_close_view(Obiview_p view)
{
	if (!(view->read_only))
	{
		if (obi_save_view(view) < 0)
			return -1;
	}
	if (obi_close_view(view) < 0)
		return -1;
	return 0;
}


Obiviews_infos_all_p obi_read_view_infos(OBIDMS_p dms)
{
	char*       		 view_file_name;
	int 				 obiview_file_descriptor;
	size_t  			 header_size;
	Obiviews_header_p 	 header;
	Obiview_infos_p 	 view_infos;
	Obiviews_infos_all_p views;

	view_file_name = build_obiview_file_name();
	if (view_file_name == NULL)
		return NULL;

	// Open view file, read header size and map header and views
	obiview_file_descriptor = openat(dms->dir_fd, view_file_name, O_RDWR, 0777);
	if (obiview_file_descriptor < 0)
	{	// No views yet
		free(view_file_name);
		return NULL;
	}

	free(view_file_name);

	// Read the header size
	if (read(obiview_file_descriptor, &header_size, sizeof(size_t)) < ((ssize_t) sizeof(size_t)))
	{
		obi_set_errno(OBIVIEW_ERROR);
		obidebug(1, "\nError reading the header size of an obiview file (trying to open a view when there are none?)");
		close(obiview_file_descriptor);
		return NULL;
	}

	// Map the header
	header = mmap(NULL,
				  header_size,
				  PROT_READ | PROT_WRITE,
				  MAP_SHARED,
				  obiview_file_descriptor,
				  0
 	 	   	   	 );
	if (header == MAP_FAILED)
	{
		obi_set_errno(OBIVIEW_ERROR);
		obidebug(1, "\nError mmapping an obiview file header");
		close(obiview_file_descriptor);
		return NULL;
	}

	// Map the views
	view_infos = mmap(NULL,
				 header->views_size,
				 PROT_READ | PROT_WRITE,
				 MAP_SHARED,
				 obiview_file_descriptor,
				 header_size
 	 	   	   	);
	if (view_infos == MAP_FAILED)
	{
		obi_set_errno(OBIVIEW_ERROR);
		obidebug(1, "\nError mmapping the views from an obiview file");
		munmap(header, header_size);
		close(obiview_file_descriptor);
		return NULL;
	}

	views = (Obiviews_infos_all_p) malloc(sizeof(Obiviews_infos_all_t));
	if (views == NULL)
	{
		obi_set_errno(OBIVIEW_ERROR);
		obidebug(1, "\nError mmapping the views from an obiview file");
		munmap(view_infos, header->views_size);
		munmap(header, header_size);
		close(obiview_file_descriptor);
		return NULL;
	}

	views->header = header;
	views->view_infos = view_infos;

	close(obiview_file_descriptor);

	return views;
}


int obi_close_view_infos(Obiviews_infos_all_p views)
{
	if (munmap(views->view_infos, (views->header)->views_size) < 0)
	{
		obi_set_errno(OBIVIEW_ERROR);
		obidebug(1, "\nError unmapping the views of an obiview file");
		free(views);
		return -1;
	}
	if (munmap(views->header, (views->header)->header_size) < 0)
	{
		obi_set_errno(OBIVIEW_ERROR);
		obidebug(1, "\nError unmapping the header of an obiview file");
		free(views);
		return -1;

	}
	free(views);
	return 0;
}


/*********** FOR BOOL COLUMNS ***********/

int obi_column_set_obibool_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, obibool_t value)
{
	if (prepare_to_set_value_in_column(view, &column, &line_nb) < 0)
		return -1;
	return obi_column_set_obibool_with_elt_idx(column, line_nb, element_idx, value);
}


obibool_t obi_column_get_obibool_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx)
{
	if (prepare_to_get_value_from_column(view, &line_nb) < 0)
		return OBIBool_NA;
	return obi_column_get_obibool_with_elt_idx(column, line_nb, element_idx);
}


int obi_column_set_obibool_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, obibool_t value)
{
	index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
	if (element_idx == OBIIdx_NA)
		return -1;
	return obi_column_set_obibool_with_elt_idx_in_view(view, column, line_nb, element_idx, value);
}


obibool_t obi_column_get_obibool_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name)
{
	index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
	if (element_idx == OBIIdx_NA)
		return OBIBool_NA;
	return obi_column_get_obibool_with_elt_idx_in_view(view, column, line_nb, element_idx);
}

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


/*********** FOR CHAR COLUMNS ***********/

int obi_column_set_obichar_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, obichar_t value)
{
	if (prepare_to_set_value_in_column(view, &column, &line_nb) < 0)
		return -1;
	return obi_column_set_obichar_with_elt_idx(column, line_nb, element_idx, value);
}


obichar_t obi_column_get_obichar_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx)
{
	if (prepare_to_get_value_from_column(view, &line_nb) < 0)
		return OBIChar_NA;
	return obi_column_get_obichar_with_elt_idx(column, line_nb, element_idx);
}


int obi_column_set_obichar_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, obichar_t value)
{
	index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
	if (element_idx == OBIIdx_NA)
		return -1;
	return obi_column_set_obichar_with_elt_idx_in_view(view, column, line_nb, element_idx, value);
}


obichar_t obi_column_get_obichar_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name)
{
	index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
	if (element_idx == OBIIdx_NA)
		return OBIChar_NA;
	return obi_column_get_obichar_with_elt_idx_in_view(view, column, line_nb, element_idx);
}

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


/*********** FOR FLOAT COLUMNS ***********/

int obi_column_set_obifloat_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, obifloat_t value)
{
	if (prepare_to_set_value_in_column(view, &column, &line_nb) < 0)
		return -1;
	return obi_column_set_obifloat_with_elt_idx(column, line_nb, element_idx, value);
}


obifloat_t obi_column_get_obifloat_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx)
{
	if (prepare_to_get_value_from_column(view, &line_nb) < 0)
		return OBIFloat_NA;
	return obi_column_get_obifloat_with_elt_idx(column, line_nb, element_idx);
}


int obi_column_set_obifloat_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, obifloat_t value)
{
	index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
	if (element_idx == OBIIdx_NA)
		return -1;
	return obi_column_set_obifloat_with_elt_idx_in_view(view, column, line_nb, element_idx, value);
}


obifloat_t obi_column_get_obifloat_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name)
{
	index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
	if (element_idx == OBIIdx_NA)
		return OBIFloat_NA;
	return obi_column_get_obifloat_with_elt_idx_in_view(view, column, line_nb, element_idx);
}

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


/*********** FOR INT COLUMNS ***********/

int obi_column_set_obiint_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, obiint_t value)
{
	if (prepare_to_set_value_in_column(view, &column, &line_nb) < 0)
		return -1;
	return obi_column_set_obiint_with_elt_idx(column, line_nb, element_idx, value);
}


obiint_t obi_column_get_obiint_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx)
{
	if (prepare_to_get_value_from_column(view, &line_nb) < 0)
		return OBIInt_NA;
	return obi_column_get_obiint_with_elt_idx(column, line_nb, element_idx);
}


int obi_column_set_obiint_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, obiint_t value)
{
	index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
	if (element_idx == OBIIdx_NA)
		return -1;
	return obi_column_set_obiint_with_elt_idx_in_view(view, column, line_nb, element_idx, value);
}


obiint_t obi_column_get_obiint_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name)
{
	index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
	if (element_idx == OBIIdx_NA)
		return OBIInt_NA;
	return obi_column_get_obiint_with_elt_idx_in_view(view, column, line_nb, element_idx);
}

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


/*********** FOR SEQ COLUMNS ***********/

int obi_column_set_obiseq_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, const char* value)
{
	if (prepare_to_set_value_in_column(view, &column, &line_nb) < 0)
		return -1;
	return obi_column_set_obiseq_with_elt_idx(column, line_nb, element_idx, value);
}


char* obi_column_get_obiseq_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx)
{
	if (prepare_to_get_value_from_column(view, &line_nb) < 0)
		return OBISeq_NA;
	return obi_column_get_obiseq_with_elt_idx(column, line_nb, element_idx);
}


int obi_column_set_obiseq_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, const char* value)
{
	index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
	if (element_idx == OBIIdx_NA)
		return -1;
	return obi_column_set_obiseq_with_elt_idx_in_view(view, column, line_nb, element_idx, value);
}


char* obi_column_get_obiseq_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name)
{
	index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
	if (element_idx == OBIIdx_NA)
		return OBISeq_NA;
	return obi_column_get_obiseq_with_elt_idx_in_view(view, column, line_nb, element_idx);
}

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


/*********** FOR STR COLUMNS ***********/

int obi_column_set_obistr_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, const char* value)
{
	if (prepare_to_set_value_in_column(view, &column, &line_nb) < 0)
		return -1;
	return obi_column_set_obistr_with_elt_idx(column, line_nb, element_idx, value);
}


const char* obi_column_get_obistr_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx)
{
	if (prepare_to_get_value_from_column(view, &line_nb) < 0)
		return OBIStr_NA;
	return obi_column_get_obistr_with_elt_idx(column, line_nb, element_idx);
}


int obi_column_set_obistr_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, const char* value)
{
	index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
	if (element_idx == OBIIdx_NA)
		return -1;
	return obi_column_set_obistr_with_elt_idx_in_view(view, column, line_nb, element_idx, value);
}


const char* obi_column_get_obistr_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name)
{
	index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
	if (element_idx == OBIIdx_NA)
		return OBIStr_NA;
	return obi_column_get_obistr_with_elt_idx_in_view(view, column, line_nb, element_idx);
}

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