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Doxygen documentation corrected and completed.

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This commit is contained in:
Celine Mercier
2015-09-30 12:03:46 +02:00
parent 45af8396b8
commit 4b7f2d268b
25 changed files with 670 additions and 689 deletions
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16
src/obidebug.h
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@ -1,8 +1,12 @@
/*
* obidebug.h
*
* Created on: June 25th 2015
* Author: Celine Mercier (celine.mercier@metabarcoding.org)
/****************************************************************************
* Header file for the debugging code *
****************************************************************************/
/**
* @file obidebug.h
* @author Celine Mercier (celine.mercier@metabarcoding.org)
* @date 25 June 2015
* @brief Header file for the debugging code.
*/
@ -12,7 +16,7 @@
#include <limits.h>
//#ifndef DEBUG_LEVEL
//#ifndef DEBUG_LEVEL // TODO
//#define DEBUG_LEVEL MAXINT
//#endif

38
src/obidms.c
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@ -1,10 +1,15 @@
/*
* obidms.c
*
* @date 23 May 2015
* @Author: coissac
/********************************************************************
* 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>
@ -18,7 +23,7 @@
#include "obidmscolumn.h"
#define DEBUG_LEVEL 0
#define DEBUG_LEVEL 0 // TODO has to be defined somewhere else (cython compil flag?)
/**************************************************************************
@ -29,27 +34,22 @@
/**
* Internal function building the directory name from an OBIDMS name.
* Internal function building the OBIDMS directory name from an OBIDMS name.
*
* The function builds the directory name corresponding to an OBIDMS.
* It checks also that the name is not too long.
* 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
* @param dms_name The name of the OBIDMS.
*
* @return a pointer to the directory name
* @retvalue <directory_name> if everything is ok
* @retvalue NULL if an error occurs
*
* ###Error values
* - OBIDMS_MEMORY_ERROR : something wrong occurred during memory allocation.
* - OBIDMS_LONG_NAME_ERROR : the database name exceeds the limit.
* @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);
static char* build_directory_name(const char* dms_name);
/************************************************************************
@ -58,9 +58,9 @@ static char *build_directory_name(const char *dms_name);
*
************************************************************************/
static char *build_directory_name(const char *dms_name)
static char* build_directory_name(const char* dms_name)
{
char *directory_name;
char* directory_name;
// Build the database directory name
if (asprintf(&directory_name, "%s.obidms", dms_name) < 0)

100
src/obidms.h
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@ -1,13 +1,19 @@
/*
* obidms.h
*
* Created on: 23 mai 2015
* Author: coissac
/********************************************************************
* OBIDMS header file *
********************************************************************/
/**
* @file obidmscolumn.h
* @author Eric Coissac (eric.coissac@metabarcoding.org)
* @date 23 May 2015
* @brief Header file for the OBIDMS functions and structures.
*/
#ifndef OBIDMS_H_
#define OBIDMS_H_
#include <stdlib.h>
#include <sys/stat.h>
#include <errno.h>
@ -17,38 +23,37 @@
#include "obierrno.h"
#define OBIDMS_MAX_NAME (2048) /**< The maximum length of an OBIDMS name
*/
/** @brief A structure describing an OBIDMS instance
/**
* @brief A structure describing an OBIDMS instance
*
* A pointer to this structure is returned on creation
* and opening of an OBITools Data Management System (DMS)
*/
typedef struct OBIDMS {
char directory_name[OBIDMS_MAX_NAME+1]; /**< The name of the directory
* containing the DMS
* containing the DMS.
*/
DIR* directory; /**< A directory entry usable to
* refer and scan the database directory
* refer and scan the database directory.
*/
} OBIDMS_t, *OBIDMS_p;
/*@
* @brief Checks if an OBIDMS exists
/**
* @brief Checks if an OBIDMS exists.
*
* @param dms_name a pointer to a C string containing the name of the database.
* The actual directory name used to store the DMS will be
* `<dms_name>.obidms`.
* @param dms_name A pointer to a C string containing the name of the database.
*
* @return an integer value indicating the status of the database
* @retvalue 1 the database exist
* @retvalue 0 the database does not exist
* @retvalue -1 an error occurred
* @returns An integer value indicating the status of the database
* @retval 1 if the database exists.
* @retval 0 if the database does not exist.
* @retval -1 if an error occurred.
*
* @see obi_close_dms()
* @since May 2015
* @author Eric Coissac (eric.coissac@metabarcoding.org)
*/
@ -62,79 +67,62 @@ int obi_dms_exists(const char* dms_name);
* if a directory with this name does not already exist
* before creating the new database.
*
* @param dms_name a pointer to a C string containing the name of the database.
* The actual directory name used to store the DMS will be
* `<name>.obidms`
* @param dms_name A pointer to a C string containing the name of the database.
* The actual directory name used to store the DMS will be
* `<dms_name>.obidms`.
*
* @return a pointer to an OBIDMS structure describing the newly created DMS
* @retval NULL on error and the `obi_errno` variable is set.
*
* ###Error values
* - OBIDMS_EXIST_ERROR : a database with the same name already exists.
* - OBIDMS_LONG_NAME_ERROR : the database name exceeds the limit.
* - OBIDMS_MEMORY_ERROR : something wrong occurred during memory allocation.
* @returns A pointer to an OBIDMS structure describing the newly created DMS.
* @retval NULL if an error occurred.
*
* @see obi_close_dms()
* @since May 2015
* @author Eric Coissac (eric.coissac@metabarcoding.org)
*/
OBIDMS_p obi_create_dms(const char *dms_name);
OBIDMS_p obi_create_dms(const char* dms_name);
/**
* @brief Opens an existing OBITools Data Management instance (OBIDMS).
*
* @param dms_name a pointer to a C string containing the name of the database.
* The actual directory name used to store the DMS will be
* `<name>.obidms`
* @param dms_name A pointer to a C string containing the name of the database.
*
* @return a pointer to an OBIDMS structure describing the newly created DMS
* @retval NULL on error and the `obi_errno`variable is set.
*
* ###Error values
* - OBIDMS_LONG_NAME_ERROR : the database name exceeds the limit.
* - OBIDMS_MEMORY_ERROR : something wrong occurred during memory allocation.
* @returns A pointer to an OBIDMS structure describing the opened DMS.
* @retval NULL if an error occurred.
*
* @see obi_close_dms()
* @since May 2015
* @author Eric Coissac (eric.coissac@metabarcoding.org)
*/
OBIDMS_p obi_open_dms(const char *dms_name);
OBIDMS_p obi_open_dms(const char* dms_name);
/**
* @brief Creates a new OBIDMS instance.
* @brief Creates or opens a new OBIDMS instance.
*
* If the database already exists, this function opens it, otherwise it
* creates a new database.
*
* @param dms_name a pointer to a C string containing the name of the database.
* The actual directory name used to store the DMS is
* `<name>.obidms`
* @param dms_name A pointer to a C string containing the name of the database.
*
* @return a pointer to an OBIDMS structure describing the newly created DMS
* @retval NULL on error and the `obi_errno`variable is set.
*
* ###Error values
* - OBIDMS_LONG_NAME_ERROR : the database name exceeds the limit.
* - OBIDMS_MEMORY_ERROR : something wrong occurred during memory allocation.
* @returns A pointer to an OBIDMS structure describing the OBIDMS.
* @retval NULL if an error occurred.
*
* @see obi_close_dms()
* @since May 2015
* @author Eric Coissac (eric.coissac@metabarcoding.org)
*/
OBIDMS_p obi_dms(const char *dms_name);
OBIDMS_p obi_dms(const char* dms_name);
/**
* @brief Closes an opened OBITools Data Management instance (OBIDMS).
*
* @param dms a pointer as returned by obi_create_dms() or obi_open_dms()
* @param dms A pointer as returned by obi_create_dms() or obi_open_dms().
*
* @return an integer value indicating the success of the operation. Even on
* error, the `OBIDMS` structure is freed
* @retvalue 0 on success
* @retvalue -1 on failure and the `obi_errno` variable is set.
* @returns An integer value indicating the success of the operation. Even on
* error, the `OBIDMS` structure is freed.
* @retval 0 on success.
* @retval -1 if an error occurred?-.
*
* @see obi_create_dms()
* @see obi_open_dms()

122
src/obidmscolumn.c
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@ -1,12 +1,12 @@
/****************************************************************************
* OBIDMS_column functions *
* OBIDMS columns functions *
****************************************************************************/
/**
* @file obidmscolumn.c
* @author Celine Mercier
* @author Celine Mercier (celine.mercier@metabarcoding.org)
* @date 22 May 2015
* @brief Functions for the shared elements of all the OBIColumn structures.
* @brief Functions shared by all the OBIDMS columns.
*/
@ -19,7 +19,7 @@
#include <fcntl.h>
#include <stdbool.h>
#include <math.h>
#include <sys/mman.h> /* mmap() is defined in this header */
#include <sys/mman.h>
#include "obidmscolumn.h"
#include "obidmscolumndir.h"
@ -30,7 +30,7 @@
#include "obilittlebigman.h"
#define DEBUG_LEVEL 0
#define DEBUG_LEVEL 0 // TODO has to be defined somewhere else (cython compil flag?)
/**************************************************************************
@ -47,18 +47,16 @@
*
* @warning The returned pointer has to be freed by the caller.
*
* @param column_name the name of the OBIDMS column.
* @param column_name The name of the OBIDMS column file.
* @param version_number The version number of the OBIDMS column file.
*
* @return a pointer to the column file name
* @retvalue NULL if an error occurs
*
* ###Error values
* - OBIDMS_MEMORY_ERROR : something wrong occurred during memory allocation.
* @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);
static char* build_column_file_name(const char* column_name, obiversion_t version_number);
/**
@ -69,32 +67,28 @@ static char *build_column_file_name(const char *column_name, obiversion_t versio
*
* @warning The returned pointer has to be freed by the caller.
*
* @param column_name the name of the OBIDMS column.
* @param column_name The name of the OBIDMS column.
*
* @return a pointer to the version file name
* @retvalue NULL if an error occurs
*
* ###Error values
* - OBIDMS_MEMORY_ERROR : something wrong occurs during memory allocation.
* @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);
static char* build_version_file_name(const char* column_name);
/**
* @brief Internal function returning a new column version number
* in the `dms` database
* in the OBIDMS database.
*
* @param dms a pointer as returned by obi_create_dms() or obi_open_dms()
* @param column_name the name of the column
* @param block is the call is blocking or not
* - `true` the call is blocking
* - `false` the call is not blocking
* @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.
*
* @return the bigger version number used for this column
* @retvalue -1 if the column does not exist
* @returns The next version number for this column.
* @retval -1 if an error occurred.
*
* @since May 2015
* @author Eric Coissac (eric.coissac@metabarcoding.org)
@ -104,50 +98,50 @@ static obiversion_t obi_get_new_version_number(OBIDMS_column_directory_p column_
/**
* @brief Internal function creating a new column version file
* in the `dms` database
* in the OBIDMS database.
*
* The new file is initialized with the minimum version number `0`.
*
* @param dms a pointer as returned by obi_create_dms() or obi_open_dms()
* @param column_name the name of the column
* @param column_directory A pointer as returned by obi_create_column_directory() or obi_open_column_directory().
*
* @return the next usable version number for this column : `0`
* @retvalue -1 if the column does not exist
* @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 int create_version_file(OBIDMS_column_directory_p column_directory);
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.
* 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
* @param column A pointer as returned by obi_create_column().
* @param elements_names The names of the elements with ';' as separator.
*
* @return 0 if the operation was successfully completed
* @retvalue -1 if an error occurred
* @retval 0 if the operation was successfully completed.
* @retval -1 if an error occurred.
*
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_column_set_elements_names(OBIDMS_column_p column, const char* elements_names);
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 fill in a memory page.
* @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
* @param data_type The data OBIType.
* @param nb_elements_per_line The number of elements per line.
*
* @return the line count for one memory page
* @returns The line count for one memory page.
*
* @since September 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
size_t get_line_count_per_page(OBIType_t data_type, size_t nb_elements_per_line);
static size_t get_line_count_per_page(OBIType_t data_type, size_t nb_elements_per_line);
/************************************************************************
@ -232,10 +226,10 @@ static obiversion_t obi_get_new_version_number(OBIDMS_column_directory_p column_
else
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError opening a version file");
free(version_file_name);
return -1;
}
obidebug(1, "\nError opening a version file");
free(version_file_name);
}
// Test if the version file size is ok
@ -346,7 +340,7 @@ static obiversion_t obi_get_new_version_number(OBIDMS_column_directory_p column_
}
static int create_version_file(OBIDMS_column_directory_p column_directory)
static obiversion_t create_version_file(OBIDMS_column_directory_p column_directory)
{
off_t loc_size;
obiversion_t version_number;
@ -652,7 +646,6 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
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");
@ -723,6 +716,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
if (column_file_descriptor < 0)
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError opening a column file");
free(column_file_name);
return NULL;
}
@ -800,11 +794,11 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
header->creation_date = time(NULL);
header->version = version_number;
header->cloned_from = -1;
header->comments[0] = 0x0;
header->comments[0] = 0x0; // TODO
obi_column_set_elements_names(new_column, elements_names);
strncpy(header->name, column_name, OBIDMS_MAX_COLNAME);
strncpy(header->name, column_name, OBIDMS_COLUMN_MAX_NAME);
// Fill the data with NA values
obi_ini_to_NA_values(new_column, 0, nb_lines);
@ -816,7 +810,9 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
}
OBIDMS_column_p obi_open_column(OBIDMS_p dms, const char* column_name, obiversion_t version_number)
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;
@ -941,7 +937,10 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms, const char* column_name, obiversio
}
OBIDMS_column_p obi_clone_column(OBIDMS_p dms, const char* column_name, obiversion_t version_number, bool clone_data)
OBIDMS_column_p obi_clone_column(OBIDMS_p dms,
const char* column_name,
obiversion_t version_number,
bool clone_data)
{
OBIDMS_column_p column_to_clone;
OBIDMS_column_p new_column;
@ -1032,7 +1031,7 @@ int obi_close_column(OBIDMS_column_p column)
}
int obi_truncate_column_to_lines_used(OBIDMS_column_p column)
int obi_truncate_column_to_lines_used(OBIDMS_column_p column) // TODO is it necessary to unmap/remap?
{
size_t file_size;
size_t data_size;
@ -1193,7 +1192,8 @@ int obi_enlarge_column(OBIDMS_column_p column)
return -1;
}
// Remap the data: try enlarging mapped region (this actually never works on my mac without the MAP_FIXED flag which overwrites everything)
// Remap the data: try enlarging mapped region (TODO this actually never works on my mac without the MAP_FIXED flag which overwrites everything)
// TODO : makes separate function even if it's only used here?
//obidebug(2, "\ntry enlarging mapped region: old size = %ld, new size = %ld, size = %ld", old_data_size, new_data_size, new_data_size - old_data_size);
new_data = mmap(column->data,
new_data_size - old_data_size,
@ -1267,7 +1267,9 @@ int obi_truncate_and_close_column(OBIDMS_column_p column)
}
void obi_ini_to_NA_values(OBIDMS_column_p column, size_t start, size_t nb_lines)
void obi_ini_to_NA_values(OBIDMS_column_p column,
size_t start,
size_t nb_lines)
{
size_t i, end, nb_elements;
@ -1311,7 +1313,7 @@ void obi_ini_to_NA_values(OBIDMS_column_p column, size_t start, size_t nb_lines)
}
void obi_column_make_unwritable(OBIDMS_column_p column)
void obi_column_make_unwritable(OBIDMS_column_p column) // TODO this might be irrelevant
{
column->writable = false;
}
@ -1410,7 +1412,7 @@ OBIType_t obi_column_get_data_type_from_name(OBIDMS_p dms, const char* column_na
return -1;
}
// Check endianness?
// TODO Check endianness?
data_type = header->data_type;
@ -1496,7 +1498,7 @@ size_t obi_column_get_line_count_from_name(OBIDMS_p dms, const char* column_name
return -1;
}
// Check endianness?
// TODO Check endianness?
line_count = header->line_count;
@ -1524,7 +1526,7 @@ size_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const char
if (elements_names == NULL)
{
obidebug(1, "\nError strdup-ing the elements names");
return -1;
return SIZE_MAX; //TODO
}
element_index = 0;
@ -1550,7 +1552,7 @@ size_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const char
obidebug(1, "\nCan't find an element name");
free(elements_names);
return -1;
return SIZE_MAX; //TODO
}

252
src/obidmscolumn.h
View File

@ -1,14 +1,15 @@
/****************************************************************************
* OBIDMS_column header file *
* OBIDMS columns header file *
****************************************************************************/
/**
* @file obidmscolumn.h
* @author Celine Mercier
* @author Celine Mercier (celine.mercier@metabarcoding.org)
* @date 12 May 2015
* @brief Header file for the shared elements of all the OBIDMS column structures.
* @brief Header file for the functions and structures shared by all the OBIDMS columns.
*/
#ifndef OBIDMSCOLUMN_H_
#define OBIDMSCOLUMN_H_
@ -25,64 +26,76 @@
#include "obilittlebigman.h"
#include "obidmscolumndir.h"
#define ELEMENTS_NAMES_MAX (2048)
#define GROWTH_FACTOR (2)
#define MAXIMUM_LINE_COUNT (1000000)
#define ELEMENTS_NAMES_MAX (2048) /**< The maximum length of the list of elements names.
*/
#define GROWTH_FACTOR (2) /**< The growth factor when a column is enlarged.
*/
#define MAXIMUM_LINE_COUNT (1000000) /**< The maximum line count for the data of a column. //TODO
*/
typedef int32_t obiversion_t; /**< Used to store the column version number
*/
/**
* @brief OBIColumnHeader structure.
*/
/**
* @brief OBIDMS column header structure.
*/
typedef struct OBIDMS_column_header {
bool little_endian; /**< endianness of the column:
* - `true` on little endian platforms
* - `false` on big endian platforms
*
* @see obi_is_little_endian()
*/
int header_size; /**< size of the header in bytes */
size_t line_count; /**< number of lines of data */
size_t lines_used; /**< number of lines of data used */
size_t nb_elements_per_line; /**< number of elements per line (default : 1) */
char elements_names[ELEMENTS_NAMES_MAX+1]; /**< names of the line elements (default : "["column_name"]") */
OBIType_t data_type; /**< type of the data */
time_t creation_date; /**< date of creation of the file */
obiversion_t version; /**< version of the OBIColumn */
obiversion_t cloned_from; /**< version of the OBIColumn from which the column was cloned from (-1 if it does not come from cloning).*/
char name[OBIDMS_MAX_COLNAME+1]; /**< The column name as a NULL
* terminated string.
*/
char comments[1]; /**< comments stored as a classical
zero end C string.
The size of the comment is only limited
by the header size
*/
bool little_endian; /**< Endianness of the column:
* - `true` on little endian platforms
* - `false` on big endian platforms
* @see obi_is_little_endian()
*/
int header_size; /**< Size of the header in bytes.
*/
size_t line_count; /**< Number of lines of data allocated.
*/
size_t lines_used; /**< Number of lines of data used.
*/
size_t nb_elements_per_line; /**< Number of elements per line (default: 1).
*/
char elements_names[ELEMENTS_NAMES_MAX+1]; /**< Names of the line elements with ';' as separator
* (should be the column name if one element per line).
*/
OBIType_t data_type; /**< Type of the data.
*/
time_t creation_date; /**< Date of creation of the file.
*/
obiversion_t version; /**< Version of the column.
*/
obiversion_t cloned_from; /**< Version of the column from which this column
* was cloned from (-1 if it was not created by cloning
* another column).
*/
char name[OBIDMS_COLUMN_MAX_NAME+1]; /**< The column name as a NULL terminated string.
*/
char comments[1]; /**< Comments stored as a classical zero end C string.
* The size of the comment is only limited by the header size.
*/
} OBIDMS_column_header_t, *OBIDMS_column_header_p;
/**
* @brief Structure describing a Column of the OBITools DMS
* @brief OBIDMS column structure.
*
* A data structure of this type is returned by the functions
* creating, opening or cloning an OBIDMS_column.
* creating, opening or cloning an OBIDMS column.
*/
typedef struct OBIDMS_column {
OBIDMS_p dms; /**< A pointer to a DMS instance */
OBIDMS_column_directory_p column_directory; /**< A pointer to an OBIDMS column directory instance */
OBIDMS_column_header_p header; /**< A pointer to the header of the column */
void* data; /**< A `void` pointer to the beginning of the
* data.
OBIDMS_p dms; /**< A pointer to the OBIDMS structure to which the column belongs.
*/
OBIDMS_column_directory_p column_directory; /**< A pointer to the OBIDMS column directory structure to which the column belongs.
*/
OBIDMS_column_header_p header; /**< A pointer to the header of the column.
*/
void* data; /**< A `void` pointer to the beginning of the data.
*
* @warning never use this member directly
* outside of the code of the
* low level functions
* of the OBITools DMS
* @warning Never use this member directly outside of the code of the
* low level functions of the OBIDMS.
*/
bool writable; /**< Indicates if the column is writable or not.
bool writable; /**< Indicates if the column is writable or not. TODO delete?
* - `true` the column is writable
* - `false` the column is read-only
*
@ -93,23 +106,30 @@ typedef struct OBIDMS_column {
/**
* @brief Returns the latest version of a column in a column directory
* @brief Returns the latest version number of a column in a column directory using the column directory structure.
*
* @param column_directory
* @param column_directory A pointer as returned by obi_create_column_directory() or obi_open_column_directory().
*
* @return the latest version number kept in the version file
* @return -1 if an error occurred
* @returns The latest version number kept in the version file.
* @retval -1 if an error occurred.
*
* @since May 2015
* @author Eric Coissac (eric.coissac@metabarcoding.org)
*/
obiversion_t obi_get_latest_version_number(OBIDMS_column_directory_p column_directory);
/**
* @brief Returns the latest version of a column in a column directory
* @brief Returns the latest version of a column in a column directory using the column name.
*
* @param column_name
* @param dms A pointer on an OBIDMS.
* @param column_name The column name.
*
* @return the latest version number kept in the version file
* @return -1 if an error occurred
* @returns The latest version number kept in the version file.
* @retval -1 if an error occurred.
*
* @since May 2015
* @author Eric Coissac (eric.coissac@metabarcoding.org)
*/
obiversion_t obi_column_get_latest_version_from_name(OBIDMS_p dms, const char* column_name);
@ -118,9 +138,9 @@ obiversion_t obi_column_get_latest_version_from_name(OBIDMS_p dms, const char* c
* @brief Returns the header size in bytes of a column on this platform.
*
* The header size is defined as a multiple of the memory page size.
* Up to now the header size is defined as one time the page size.
* As of now the header size is defined as one time the page size.
*
* @return a `size_t` value corresponding to the header size in bytes
* @returns a `size_t` value corresponding to the header size in bytes.
*
* @since May 2015
* @author Eric Coissac (eric.coissac@metabarcoding.org)
@ -131,30 +151,40 @@ size_t obi_get_platform_header_size();
/**
* @brief Creates a column.
*
* @param dms a pointer on an OBIDMS
* @param column_name the name of the new column
* @param type the OBIType code used to create the column
* @param nb_lines the number of lines to be stored
* The minimum data size allocated is one memory page, and the data is initialized to the NA value of the OBIType.
*
* @warning If there is one element per line, elements_names should be equal to column_name. // TODO change this condition?
*
* @param dms A pointer on an OBIDMS.
* @param column_name The name of the new column.
* @param data_type The OBIType code of the data.
* @param nb_lines The number of lines to be stored.
* @param nb_elements_per_line The number of elements per line.
* @param elements_names The names of the elements with ';' as separator.
*
* @returns A pointer on the newly created column structure.
* @retval NULL if an error occurred.
*
* @since May 2015
* @author Eric Coissac (eric.coissac@metabarcoding.org)
*/
OBIDMS_column_p obi_create_column(OBIDMS_p dms,
const char* column_name,
OBIType_t type,
OBIType_t data_type,
size_t nb_lines,
size_t nb_elements_per_line,
const char* elements_names);
const char* elements_names);
/**
* @brief Opens a column in read-only mode.
*
* @param dms a pointer on an OBIDMS
* @param column_name the name of the column
* @param version_number the version of the column that should be opened (if -1, the latest version number is retrieved)
* @param dms A pointer on an OBIDMS.
* @param column_name The name of the column.
* @param version_number The version of the column that should be opened (if -1, the latest version is retrieved).
*
* @return a pointer to the opened column
* @returns A pointer on the opened column structure.
* @retval NULL if an error occurred.
*
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
@ -165,12 +195,13 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms, const char* column_name, obiversio
/**
* @brief Clones a column, and returns a pointer to the writable new column.
*
* @param dms a pointer on an OBIDMS
* @param column_name the name of the column to clone
* @param version_number the version of the column that should be cloned (if -1, the latest version number is retrieved)
* @param clone_data whether the data should be copied or not
* @param dms A pointer on an OBIDMS.
* @param column_name The name of the column to clone.
* @param version_number The version of the column that should be cloned (if -1, the latest version is retrieved).
* @param clone_data Whether the data should be copied or not.
*
* @return a pointer to the created column
* @returns A pointer to the created column.
* @retval NULL if an error occurred.
*
* @since August 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
@ -181,10 +212,10 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p dms, const char* column_name, obiversi
/**
* @brief Closes a column.
*
* @param column a pointer on an OBIDMS column
* @param column A pointer on an OBIDMS column.
*
* @return 0 if the operation was successfully completed
* @return -1 if an error occurred
* @retval 0 if the operation was successfully completed.
* @retval -1 if an error occurred.
*
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
@ -193,12 +224,13 @@ int obi_close_column(OBIDMS_column_p column);
/**
* @brief Truncates a column file to the number of lines used.
* @brief Truncates a column file to the number of lines used rounded to the nearest
* greater multiple of the page size.
*
* @param column a pointer on an OBIDMS column
* @param column A pointer on an OBIDMS column.
*
* @return 0 if the operation was successfully completed
* @return -1 if an error occurred
* @retval 0 if the operation was successfully completed.
* @retval -1 if an error occurred.
*
* @since August 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
@ -209,10 +241,10 @@ int obi_truncate_column_to_lines_used(OBIDMS_column_p column);
/**
* @brief Enlarges a column file.
*
* @param column a pointer on an OBIDMS column
* @param column A pointer on an OBIDMS column.
*
* @return 0 if the operation was successfully completed
* @return -1 if an error occurred
* @retval 0 if the operation was successfully completed.
* @retval -1 if an error occurred.
*
* @since August 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
@ -221,12 +253,13 @@ int obi_enlarge_column(OBIDMS_column_p column);
/**
* @brief Truncates a column file to the number of lines used and closes it.
* @brief Truncates a column file to the number of lines used rounded to the nearest
* greater multiple of the page size and closes it.
*
* @param column a pointer on an OBIDMS column
* @param column A pointer on an OBIDMS column.
*
* @return 0 if the operation was successfully completed
* @return -1 if an error occurred
* @retval 0 if the operation was successfully completed.
* @retval -1 if an error occurred.
*
* @since August 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
@ -235,11 +268,11 @@ int obi_truncate_and_close_column(OBIDMS_column_p column);
/*
* @brief Sets the data in a column to the NA value of the data type.
* @brief Sets the data in a column to the NA value of the data OBIType.
*
* @param column a pointer on an OBIDMS column
* @param start the first line number of the block that should be set
* @param nb_lines the number of lines that should be set
* @param column A pointer on an OBIDMS column.
* @param start The first line number of the block that should be set.
* @param nb_lines The number of lines that should be set.
*
* @since August 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
@ -248,9 +281,9 @@ void obi_ini_to_NA_values(OBIDMS_column_p column, size_t start, size_t nb_lines)
/**
* @brief Sets the 'writable' header attribute of an OBIDMS column to False.
* @brief Sets the 'writable' header attribute of an OBIDMS column to False. // TODO delete?
*
* @param column a pointer on an OBIDMS column
* @param column A pointer on an OBIDMS column
*
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
@ -261,9 +294,9 @@ void obi_column_make_unwritable(OBIDMS_column_p column);
/**
* @brief Recovers the line count of an OBIDMS column.
*
* @param column a pointer on an OBIDMS column
* @param column A pointer on an OBIDMS column.
*
* @return the line count of the column
* @returns The line count of the column.
*
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
@ -274,9 +307,9 @@ size_t obi_column_get_line_count(OBIDMS_column_p column);
/**
* @brief Recovers the number of lines used in an OBIDMS column.
*
* @param column a pointer on an OBIDMS column
* @param column A pointer on an OBIDMS column.
*
* @return the number of lines used in the column
* @returns The number of lines used in the column.
*
* @since August 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
@ -287,9 +320,9 @@ size_t obi_column_get_nb_lines_used(OBIDMS_column_p column);
/**
* @brief Recovers the data type of an OBIDMS column.
*
* @param column a pointer on an OBIDMS column
* @param column A pointer on an OBIDMS column.
*
* @return the data type of the column
* @returns The data type of the column.
*
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
@ -300,10 +333,10 @@ OBIType_t obi_column_get_data_type(OBIDMS_column_p column);
/**
* @brief Recovers the data type of an OBIDMS column from the column name.
*
* @param dms a pointer on an OBIDMS
* @param column_name the name of an OBIDMS column
* @param dms A pointer on an OBIDMS.
* @param column_name The name of an OBIDMS column.
*
* @return the data type of the column
* @returns The data type of the column.
*
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
@ -314,10 +347,10 @@ OBIType_t obi_column_get_data_type_from_name(OBIDMS_p dms, const char* column_na
/**
* @brief Recovers the line count of an OBIDMS column from the column name.
*
* @param dms a pointer on an OBIDMS
* @param column_name the name of an OBIDMS column
* @param dms A pointer on an OBIDMS.
* @param column_name The name of an OBIDMS column.
*
* @return the line count of the column
* @returns The line count of the column.
*
* @since September 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
@ -328,9 +361,9 @@ size_t obi_column_get_line_count_from_name(OBIDMS_p dms, const char* column_name
/**
* @brief Recovers the elements names of an OBIDMS column.
*
* @param column a pointer on an OBIDMS column
* @param column A pointer on an OBIDMS column.
*
* @return the elements names
* @returns The elements names.
*
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
@ -339,12 +372,13 @@ const char* obi_column_get_elements_names(OBIDMS_column_p column);
/**
* @brief Recovers the index of an element in an OBIDMS column from its name.
* @brief Recovers the index of an element in an OBIDMS column from the element's name.
*
* @param column a pointer on an OBIDMS column
* @param element_name the name of the element
* @param column A pointer on an OBIDMS column.
* @param element_name The name of the element.
*
* @return the index of the element in a line of the column
* @returns The index of the element in a line of the column.
* @retval SIZE_MAX if an error occurred.
*
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
@ -355,9 +389,9 @@ size_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const char
/**
* @brief Recovers the number of elements per line in an OBIDMS column.
*
* @param column a pointer on an OBIDMS column
* @param column A pointer on an OBIDMS column.
*
* @return the number of elements per line
* @returns The number of elements per line
*
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)

12
src/obidmscolumn_bool.c
View File

@ -1,5 +1,5 @@
/****************************************************************************
* OBIDMS_column_bool functions *
* OBIDMS_column_bool functions *
****************************************************************************/
/**
@ -19,7 +19,7 @@
#include "obidebug.h"
#define DEBUG_LEVEL 0
#define DEBUG_LEVEL 0 // TODO has to be defined somewhere else (cython compil flag?)
/**********************************************************************
@ -69,7 +69,7 @@ obibool_t obi_column_get_obibool_with_elt_idx(OBIDMS_column_p column, size_t lin
}
int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obibool_t value)
int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name, obibool_t value)
{
size_t element_idx;
@ -87,7 +87,7 @@ int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column, size_t line_nb,
else
{
element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == -1)
if (element_idx == SIZE_MAX) //TODO
return -1;
}
@ -97,7 +97,7 @@ int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column, size_t line_nb,
}
obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name)
obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name)
{
size_t element_idx;
@ -115,7 +115,7 @@ obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column, size_t li
else
{
element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == -1)
if (element_idx == SIZE_MAX) //TODO
return OBIBool_NA;
}

78
src/obidmscolumn_bool.h
View File

@ -10,6 +10,10 @@
*/
#ifndef OBIDMSCOLUMN_BOOL_H_
#define OBIDMSCOLUMN_BOOL_H_
#include <stdlib.h>
#include <stdio.h>
@ -20,19 +24,16 @@
/**
* @brief Sets a value in an OBIDMS column containing data with the type OBI_BOOL, using the index of the element in the line.
*
* @param column a pointer as returned by obi_create_column()
* @warning Pointers returned by obi_open_column() don't allow writing.
*
* @param line_nb the number of the line where the value should be set
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
* @param line_nb The number of the line where the value should be set.
* @param element_idx The index of the element that should be set in the line.
* @param value The value that should be set.
*
* @param element_idx the index of the element that should be set in the line
*
* @param value the value that should be set
*
* @return an integer value indicating the success of the operation.
*
* @retvalue 0 on success
* @retvalue -1 on failure and the `obi_errno` variable is set.
* @returns An integer value indicating the success of the operation.
* @retvalue 0 on success.
* @retvalue -1 if an error occurred.
*
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
@ -43,13 +44,12 @@ int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column, size_t line_nb,
/**
* @brief Recovers a value in an OBIDMS column containing data with the type OBI_BOOL.
*
* @param column a pointer as returned by obi_create_column()
* @param column A pointer as returned by obi_create_column().
* @param line_nb The number of the line where the value should be recovered.
* @param element_idx The index of the element that should be recovered in the line.
*
* @param line_nb the number of the line where the value should be recovered
*
* @param element_idx the index of the element that should be recovered in the line
*
* @return the recovered value
* @returns The recovered value.
* @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
*
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
@ -58,44 +58,44 @@ obibool_t obi_column_get_obibool_with_elt_idx(OBIDMS_column_p column, size_t lin
/**
* @brief Sets a value in an OBIDMS column containing data with the type OBI_BOOL, using the name of the element in the line.
* @brief Sets a value in an OBIDMS column containing data with the type OBI_BOOL,
* using the name of the element in the line.
*
* @param column a pointer as returned by obi_create_column()
* @warning Pointers returned by obi_open_column() don't allow writing.
*
* @param line_nb the number of the line where the value should be set
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
* @param line_nb The number of the line where the value should be set.
* @param element_name The name of the element that should be set in the line.
* If empty, it is checked that there is only one element per line.
* @param value The value that should be set.
*
* @param element_name the name of the element that should be set in the line
* If empty, it is checked that there is only one element per line
*
* @param value the value that should be set
*
* @return an integer value indicating the success of the operation.
*
* @retvalue 0 on success
* @retvalue -1 on failure and the `obi_errno` variable is set.
* @returns An integer value indicating the success of the operation.
* @retval 0 on success.
* @retvalue -1 if an error occurred.
*
* @since August 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obibool_t value);
int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name, obibool_t value);
/**
* @brief Recovers a value in an OBIDMS column containing data with the type OBI_BOOL, using the name of the element in the line.
* @brief Recovers a value in an OBIDMS column containing data with the type OBI_BOOL,
* using the name of the element in the line.
*
* @param column a pointer as returned by obi_create_column()
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
* @param line_nb The number of the line where the value should be recovered.
* @param element_name The name of the element that should be recovered in the line.
* If empty, it is checked that there is only one element per line.
*
* @param line_nb the number of the line where the value should be recovered
*
* @param element_name the name of the element that should be recovered in the line
* If empty, it is checked that there is only one element per line
*
* @return the recovered value
* @retvalue -1 on failure and the `obi_errno` variable is set. TODO an other value must be chosen
* @returns The recovered value.
* @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
*
* @since August 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);
obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name);
#endif /* OBIDMSCOLUMN_BOOL_H_ */

10
src/obidmscolumn_char.c
View File

@ -19,7 +19,7 @@
#include "obidebug.h"
#define DEBUG_LEVEL 0
#define DEBUG_LEVEL 0 // TODO has to be defined somewhere else (cython compil flag?)
/**********************************************************************
@ -70,7 +70,7 @@ obichar_t obi_column_get_obichar_with_elt_idx(OBIDMS_column_p column, size_t lin
}
int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obichar_t value)
int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name, obichar_t value)
{
size_t element_idx;
@ -88,7 +88,7 @@ int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column, size_t line_nb,
else
{
element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == -1)
if (element_idx == SIZE_MAX) //TODO
return -1;
}
@ -98,7 +98,7 @@ int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column, size_t line_nb,
}
obichar_t obi_column_get_obichar_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name)
obichar_t obi_column_get_obichar_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name)
{
size_t element_idx;
@ -116,7 +116,7 @@ obichar_t obi_column_get_obichar_with_elt_name(OBIDMS_column_p column, size_t li
else
{
element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == -1)
if (element_idx == SIZE_MAX) //TODO
return OBIChar_NA;
}

82
src/obidmscolumn_char.h
View File

@ -10,6 +10,10 @@
*/
#ifndef OBIDMSCOLUMN_CHAR_H_
#define OBIDMSCOLUMN_CHAR_H_
#include <stdlib.h>
#include <stdio.h>
@ -20,82 +24,78 @@
/**
* @brief Sets a value in an OBIDMS column containing data with the type OBI_CHAR, using the index of the element in the line.
*
* @param column a pointer as returned by obi_create_column()
* @warning Pointers returned by obi_open_column() don't allow writing.
*
* @param line_nb the number of the line where the value should be set
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
* @param line_nb The number of the line where the value should be set.
* @param element_idx The index of the element that should be set in the line.
* @param value The value that should be set.
*
* @param element_idx the index of the element that should be set in the line
*
* @param value the value that should be set
*
* @return an integer value indicating the success of the operation.
*
* @retvalue 0 on success
* @retvalue -1 on failure and the `obi_errno` variable is set.
* @returns An integer value indicating the success of the operation.
* @retvalue 0 on success.
* @retvalue -1 if an error occurred.
*
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_column_set_obichar_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obichar_t* value);
int obi_column_set_obichar_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obichar_t value);
/**
* @brief Recovers a value in an OBIDMS column containing data with the type OBI_CHAR.
*
* @param column a pointer as returned by obi_create_column()
* @param column A pointer as returned by obi_create_column().
* @param line_nb The number of the line where the value should be recovered.
* @param element_idx The index of the element that should be recovered in the line.
*
* @param line_nb the number of the line where the value should be recovered
*
* @param element_idx the index of the element that should be recovered in the line
*
* @return the recovered value
* @returns The recovered value.
* @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
*
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
obichar_t* obi_column_get_obichar_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx);
obichar_t obi_column_get_obichar_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx);
/**
* @brief Sets a value in an OBIDMS column containing data with the type OBI_CHAR, using the name of the element in the line.
* @brief Sets a value in an OBIDMS column containing data with the type OBI_CHAR,
* using the name of the element in the line.
*
* @param column a pointer as returned by obi_create_column()
* @warning Pointers returned by obi_open_column() don't allow writing.
*
* @param line_nb the number of the line where the value should be set
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
* @param line_nb The number of the line where the value should be set.
* @param element_name The name of the element that should be set in the line.
* If empty, it is checked that there is only one element per line.
* @param value The value that should be set.
*
* @param element_name the name of the element that should be set in the line
* If empty, it is checked that there is only one element per line
*
* @param value the value that should be set
*
* @return an integer value indicating the success of the operation.
*
* @retvalue 0 on success
* @retvalue -1 on failure and the `obi_errno` variable is set.
* @returns An integer value indicating the success of the operation.
* @retval 0 on success.
* @retvalue -1 if an error occurred.
*
* @since August 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obichar_t value);
int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name, obichar_t value);
/**
* @brief Recovers a value in an OBIDMS column containing data with the type OBI_CHAR, using the name of the element in the line.
* @brief Recovers a value in an OBIDMS column containing data with the type OBI_CHAR,
* using the name of the element in the line.
*
* @param column a pointer as returned by obi_create_column()
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
* @param line_nb The number of the line where the value should be recovered.
* @param element_name The name of the element that should be recovered in the line.
* If empty, it is checked that there is only one element per line.
*
* @param line_nb the number of the line where the value should be recovered
*
* @param element_name the name of the element that should be recovered in the line
* If empty, it is checked that there is only one element per line
*
* @return the recovered value
* @retvalue NULL on failure and the `obi_errno` variable is set. TODO an other value should be chosen maybe
* @returns The recovered value.
* @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
*
* @since August 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
obichar_t obi_column_get_obichar_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);
obichar_t obi_column_get_obichar_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name);
#endif /* OBIDMSCOLUMN_CHAR_H_ */

10
src/obidmscolumn_float.c
View File

@ -19,7 +19,7 @@
#include "obidebug.h"
#define DEBUG_LEVEL 0
#define DEBUG_LEVEL 0 // TODO has to be defined somewhere else (cython compil flag?)
/**********************************************************************
@ -69,7 +69,7 @@ obifloat_t obi_column_get_obifloat_with_elt_idx(OBIDMS_column_p column, size_t l
}
int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obifloat_t value)
int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name, obifloat_t value)
{
size_t element_idx;
@ -87,7 +87,7 @@ int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, size_t line_nb
else
{
element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == -1)
if (element_idx == SIZE_MAX) //TODO
return -1;
}
@ -97,7 +97,7 @@ int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, size_t line_nb
}
obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name)
obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name)
{
size_t element_idx;
@ -115,7 +115,7 @@ obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column, size_t
else
{
element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == -1)
if (element_idx == SIZE_MAX) //TODO
return OBIFloat_NA;
}

78
src/obidmscolumn_float.h
View File

@ -10,6 +10,10 @@
*/
#ifndef OBIDMSCOLUMN_FLOAT_H_
#define OBIDMSCOLUMN_FLOAT_H_
#include <stdlib.h>
#include <stdio.h>
@ -20,19 +24,16 @@
/**
* @brief Sets a value in an OBIDMS column containing data with the type OBI_FLOAT, using the index of the element in the line.
*
* @param column a pointer as returned by obi_create_column()
* @warning Pointers returned by obi_open_column() don't allow writing.
*
* @param line_nb the number of the line where the value should be set
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
* @param line_nb The number of the line where the value should be set.
* @param element_idx The index of the element that should be set in the line.
* @param value The value that should be set.
*
* @param element_idx the index of the element that should be set in the line
*
* @param value the value that should be set
*
* @return an integer value indicating the success of the operation.
*
* @retvalue 0 on success
* @retvalue -1 on failure and the `obi_errno` variable is set.
* @returns An integer value indicating the success of the operation.
* @retvalue 0 on success.
* @retvalue -1 if an error occurred.
*
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
@ -43,13 +44,12 @@ int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column, size_t line_nb,
/**
* @brief Recovers a value in an OBIDMS column containing data with the type OBI_FLOAT.
*
* @param column a pointer as returned by obi_create_column()
* @param column A pointer as returned by obi_create_column().
* @param line_nb The number of the line where the value should be recovered.
* @param element_idx The index of the element that should be recovered in the line.
*
* @param line_nb the number of the line where the value should be recovered
*
* @param element_idx the index of the element that should be recovered in the line
*
* @return the recovered value
* @returns The recovered value.
* @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
*
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
@ -58,44 +58,44 @@ obifloat_t obi_column_get_obifloat_with_elt_idx(OBIDMS_column_p column, size_t l
/**
* @brief Sets a value in an OBIDMS column containing data with the type OBI_FLOAT, using the name of the element in the line.
* @brief Sets a value in an OBIDMS column containing data with the type OBI_FLOAT,
* using the name of the element in the line.
*
* @param column a pointer as returned by obi_create_column()
* @warning Pointers returned by obi_open_column() don't allow writing.
*
* @param line_nb the number of the line where the value should be set
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
* @param line_nb The number of the line where the value should be set.
* @param element_name The name of the element that should be set in the line.
* If empty, it is checked that there is only one element per line.
* @param value The value that should be set.
*
* @param element_name the name of the element that should be set in the line
* If empty, it is checked that there is only one element per line
*
* @param value the value that should be set
*
* @return an integer value indicating the success of the operation.
*
* @retvalue 0 on success
* @retvalue -1 on failure and the `obi_errno` variable is set.
* @returns An integer value indicating the success of the operation.
* @retval 0 on success.
* @retvalue -1 if an error occurred.
*
* @since August 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obifloat_t value);
int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name, obifloat_t value);
/**
* @brief Recovers a value in an OBIDMS column containing data with the type OBI_FLOAT, using the name of the element in the line.
* @brief Recovers a value in an OBIDMS column containing data with the type OBI_FLOAT,
* using the name of the element in the line.
*
* @param column a pointer as returned by obi_create_column()
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
* @param line_nb The number of the line where the value should be recovered.
* @param element_name The name of the element that should be recovered in the line.
* If empty, it is checked that there is only one element per line.
*
* @param line_nb the number of the line where the value should be recovered
*
* @param element_name the name of the element that should be recovered in the line
* If empty, it is checked that there is only one element per line
*
* @return the recovered value
* @retvalue -1 on failure and the `obi_errno` variable is set. TODO an other value must be chosen
* @returns The recovered value.
* @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
*
* @since August 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);
obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name);
#endif /* OBIDMSCOLUMN_FLOAT_H_ */

10
src/obidmscolumn_idx.c
View File

@ -19,7 +19,7 @@
#include "obidebug.h"
#define DEBUG_LEVEL 0
#define DEBUG_LEVEL 0 // TODO has to be defined somewhere else (cython compil flag?)
/**********************************************************************
@ -69,7 +69,7 @@ obiidx_t obi_column_get_obiidx_with_elt_idx(OBIDMS_column_p column, size_t line_
}
int obi_column_set_obiidx_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obiidx_t value)
int obi_column_set_obiidx_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name, obiidx_t value)
{
size_t element_idx;
@ -87,7 +87,7 @@ int obi_column_set_obiidx_with_elt_name(OBIDMS_column_p column, size_t line_nb,
else
{
element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == -1)
if (element_idx == SIZE_MAX) //TODO
return -1;
}
@ -97,7 +97,7 @@ int obi_column_set_obiidx_with_elt_name(OBIDMS_column_p column, size_t line_nb,
}
obiidx_t obi_column_get_obiidx_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name)
obiidx_t obi_column_get_obiidx_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name)
{
size_t element_idx;
@ -115,7 +115,7 @@ obiidx_t obi_column_get_obiidx_with_elt_name(OBIDMS_column_p column, size_t line
else
{
element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == -1)
if (element_idx == SIZE_MAX) //TODO
return OBIIdx_NA;
}

78
src/obidmscolumn_idx.h
View File

@ -10,6 +10,10 @@
*/
#ifndef OBIDMSCOLUMN_IDX_H_
#define OBIDMSCOLUMN_IDX_H_
#include <stdlib.h>
#include <stdio.h>
@ -20,19 +24,16 @@
/**
* @brief Sets a value in an OBIDMS column containing data with the type OBI_IDX, using the index of the element in the line.
*
* @param column a pointer as returned by obi_create_column()
* @warning Pointers returned by obi_open_column() don't allow writing.
*
* @param line_nb the number of the line where the value should be set
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
* @param line_nb The number of the line where the value should be set.
* @param element_idx The index of the element that should be set in the line.
* @param value The value that should be set.
*
* @param element_idx the index of the element that should be set in the line
*
* @param value the value that should be set
*
* @return an integer value indicating the success of the operation.
*
* @retvalue 0 on success
* @retvalue -1 on failure and the `obi_errno` variable is set.
* @returns An integer value indicating the success of the operation.
* @retvalue 0 on success.
* @retvalue -1 if an error occurred.
*
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
@ -43,13 +44,12 @@ int obi_column_set_obiidx_with_elt_idx(OBIDMS_column_p column, size_t line_nb, s
/**
* @brief Recovers a value in an OBIDMS column containing data with the type OBI_IDX.
*
* @param column a pointer as returned by obi_create_column()
* @param column A pointer as returned by obi_create_column().
* @param line_nb The number of the line where the value should be recovered.
* @param element_idx The index of the element that should be recovered in the line.
*
* @param line_nb the number of the line where the value should be recovered
*
* @param element_idx the index of the element that should be recovered in the line
*
* @return the recovered value
* @returns The recovered value.
* @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
*
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
@ -58,44 +58,44 @@ obiidx_t obi_column_get_obiidx_with_elt_idx(OBIDMS_column_p column, size_t line_
/**
* @brief Sets a value in an OBIDMS column containing data with the type OBI_IDX, using the name of the element in the line.
* @brief Sets a value in an OBIDMS column containing data with the type OBI_IDX,
* using the name of the element in the line.
*
* @param column a pointer as returned by obi_create_column()
* @warning Pointers returned by obi_open_column() don't allow writing.
*
* @param line_nb the number of the line where the value should be set
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
* @param line_nb The number of the line where the value should be set.
* @param element_name The name of the element that should be set in the line.
* If empty, it is checked that there is only one element per line.
* @param value The value that should be set.
*
* @param element_name the name of the element that should be set in the line
* If empty, it is checked that there is only one element per line
*
* @param value the value that should be set
*
* @return an integer value indicating the success of the operation.
*
* @retvalue 0 on success
* @retvalue -1 on failure and the `obi_errno` variable is set.
* @returns An integer value indicating the success of the operation.
* @retval 0 on success.
* @retvalue -1 if an error occurred.
*
* @since August 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_column_set_obiidx_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obiidx_t value);
int obi_column_set_obiidx_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name, obiidx_t value);
/**
* @brief Recovers a value in an OBIDMS column containing data with the type OBI_IDX, using the name of the element in the line.
* @brief Recovers a value in an OBIDMS column containing data with the type OBI_IDX,
* using the name of the element in the line.
*
* @param column a pointer as returned by obi_create_column()
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
* @param line_nb The number of the line where the value should be recovered.
* @param element_name The name of the element that should be recovered in the line.
* If empty, it is checked that there is only one element per line.
*
* @param line_nb the number of the line where the value should be recovered
*
* @param element_name the name of the element that should be recovered in the line
* If empty, it is checked that there is only one element per line
*
* @return the recovered value
* @retvalue -1 on failure and the `obi_errno` variable is set. TODO an other value must be chosen
* @returns The recovered value.
* @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
*
* @since August 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
obiidx_t obi_column_get_obiidx_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);
obiidx_t obi_column_get_obiidx_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name);
#endif /* OBIDMSCOLUMN_IDX_H_ */

10
src/obidmscolumn_int.c
View File

@ -19,7 +19,7 @@
#include "obidebug.h"
#define DEBUG_LEVEL 0
#define DEBUG_LEVEL 0 // TODO has to be defined somewhere else (cython compil flag?)
/**********************************************************************
@ -69,7 +69,7 @@ obiint_t obi_column_get_obiint_with_elt_idx(OBIDMS_column_p column, size_t line_
}
int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obiint_t value)
int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name, obiint_t value)
{
size_t element_idx;
@ -87,7 +87,7 @@ int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column, size_t line_nb,
else
{
element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == -1)
if (element_idx == SIZE_MAX) //TODO
return -1;
}
@ -97,7 +97,7 @@ int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column, size_t line_nb,
}
obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name)
obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name)
{
size_t element_idx;
@ -115,7 +115,7 @@ obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column, size_t line
else
{
element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == -1)
if (element_idx == SIZE_MAX) //TODO
return OBIInt_NA;
}

80
src/obidmscolumn_int.h
View File

@ -5,11 +5,15 @@
/**
* @file obidsmcolumn_int.h
* @author Celine Mercier
* @date July 21st 2015
* @date August 10th 2015
* @brief Header file for the functions handling OBIColumns containing data with the OBIType OBI_INT.
*/
#ifndef OBIDMSCOLUMN_INT_H_
#define OBIDMSCOLUMN_INT_H_
#include <stdlib.h>
#include <stdio.h>
@ -20,19 +24,16 @@
/**
* @brief Sets a value in an OBIDMS column containing data with the type OBI_INT, using the index of the element in the line.
*
* @param column a pointer as returned by obi_create_column()
* @warning Pointers returned by obi_open_column() don't allow writing.
*
* @param line_nb the number of the line where the value should be set
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
* @param line_nb The number of the line where the value should be set.
* @param element_idx The index of the element that should be set in the line.
* @param value The value that should be set.
*
* @param element_idx the index of the element that should be set in the line
*
* @param value the value that should be set
*
* @return an integer value indicating the success of the operation.
*
* @retvalue 0 on success
* @retvalue -1 on failure and the `obi_errno` variable is set.
* @returns An integer value indicating the success of the operation.
* @retvalue 0 on success.
* @retvalue -1 if an error occurred.
*
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
@ -43,13 +44,12 @@ int obi_column_set_obiint_with_elt_idx(OBIDMS_column_p column, size_t line_nb, s
/**
* @brief Recovers a value in an OBIDMS column containing data with the type OBI_INT.
*
* @param column a pointer as returned by obi_create_column()
* @param column A pointer as returned by obi_create_column().
* @param line_nb The number of the line where the value should be recovered.
* @param element_idx The index of the element that should be recovered in the line.
*
* @param line_nb the number of the line where the value should be recovered
*
* @param element_idx the index of the element that should be recovered in the line
*
* @return the recovered value
* @returns The recovered value.
* @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
*
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
@ -58,44 +58,44 @@ obiint_t obi_column_get_obiint_with_elt_idx(OBIDMS_column_p column, size_t line_
/**
* @brief Sets a value in an OBIDMS column containing data with the type OBI_INT, using the name of the element in the line.
* @brief Sets a value in an OBIDMS column containing data with the type OBI_INT,
* using the name of the element in the line.
*
* @param column a pointer as returned by obi_create_column()
* @warning Pointers returned by obi_open_column() don't allow writing.
*
* @param line_nb the number of the line where the value should be set
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
* @param line_nb The number of the line where the value should be set.
* @param element_name The name of the element that should be set in the line.
* If empty, it is checked that there is only one element per line.
* @param value The value that should be set.
*
* @param element_name the name of the element that should be set in the line
* If empty, it is checked that there is only one element per line
*
* @param value the value that should be set
*
* @return an integer value indicating the success of the operation.
*
* @retvalue 0 on success
* @retvalue -1 on failure and the `obi_errno` variable is set.
* @returns An integer value indicating the success of the operation.
* @retval 0 on success.
* @retvalue -1 if an error occurred.
*
* @since August 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obiint_t value);
int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name, obiint_t value);
/**
* @brief Recovers a value in an OBIDMS column containing data with the type OBI_INT, using the name of the element in the line.
* @brief Recovers a value in an OBIDMS column containing data with the type OBI_INT,
* using the name of the element in the line.
*
* @param column a pointer as returned by obi_create_column()
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
* @param line_nb The number of the line where the value should be recovered.
* @param element_name The name of the element that should be recovered in the line.
* If empty, it is checked that there is only one element per line.
*
* @param line_nb the number of the line where the value should be recovered
*
* @param element_name the name of the element that should be recovered in the line
* If empty, it is checked that there is only one element per line
*
* @return the recovered value
* @retvalue -1 on failure and the `obi_errno` variable is set. TODO an other value must be chosen
* @returns The recovered value.
* @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
*
* @since August 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);
obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name);
#endif /* OBIDMSCOLUMN_INT_H_ */

19
src/obidmscolumndir.c
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@ -4,7 +4,7 @@
/**
* @file obidmscolumndir.c
* @author Celine Mercier
* @author Celine Mercier (celine.mercier@metabarcoding.org)
* @date 18 June 2015
* @brief Functions for OBIDMS column directories.
*/
@ -25,7 +25,7 @@
#include "obidebug.h"
#define DEBUG_LEVEL 0
#define DEBUG_LEVEL 0 // TODO has to be defined somewhere else (cython compil flag?)
/**************************************************************************
@ -43,15 +43,10 @@
*
* @warning The returned pointer has to be freed by the caller.
*
* @param column_name the name of the OBIDMS column
* @param column_name The name of the OBIDMS column.
*
* @return a pointer to the OBIDMS column directory name
* @retvalue <column_directory_name> if everything is ok
* @retvalue NULL if an error occurs
*
* ###Error values
* - OBIDMS_MEMORY_ERROR : something wrong occurred during memory allocation.
* - OBIDMS_LONG_NAME_ERROR : the database name exceeds the limit.
* @returns A pointer to the OBIDMS column directory name.
* @retval NULL if an error occurred.
*
* @since June 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
@ -78,10 +73,10 @@ static char* build_column_directory_name(const char* column_name)
}
// Test if the database name is not too long
if (strlen(column_directory_name) >= OBIDMS_COLUMN_DIR_MAX_NAME)
if (strlen(column_directory_name) >= OBIDMS_COLUMN_MAX_NAME)
{
obi_set_errno(OBICOLDIR_LONG_NAME_ERROR);
obidebug(1, "\nError building a column directory name");
obidebug(1, "\nError due to column name too long");
free(column_directory_name);
return NULL;
}

95
src/obidmscolumndir.h
View File

@ -6,57 +6,56 @@
* @file obidmscolumndir.h
* @author Celine Mercier
* @date 18 June 2015
* @brief Header file for OBIDMS column directories.
* @brief Header file for the OBIDMS column directories structures and functions.
*/
#ifndef OBIDMSCOLUMNGROUP_H_
#define OBIDMSCOLUMNGROUP_H_
#include <stdlib.h>
#include <stdio.h>
#include <dirent.h>
#include "obidms.h"
#define OBIDMS_MAX_COLNAME (128) /**< The maximum length of an OBIDMS column name
*/
#define OBIDMS_COLUMN_DIR_MAX_NAME (2048) /**< The maximum length of an OBIDMS column directory name
*/
#define OBIDMS_COLUMN_MAX_NAME (2048) /**< The maximum length of an OBIDMS column name.
*/
/** @brief A structure describing an OBIDMS column directory instance
/**
* @brief A structure describing an OBIDMS column directory instance.
*
* A pointer to this structure is returned on creation
* and opening of an OBIDMS column directory.
*/
typedef struct OBIDMS_column_directory {
OBIDMS_p dms; /**< A pointer to a DMS instance.
OBIDMS_p dms; /**< A pointer to a DMS instance.
*/
char column_name[OBIDMS_MAX_COLNAME+1]; /**< The name of the column
* contained in the directory.
char column_name[OBIDMS_COLUMN_MAX_NAME+1]; /**< The name of the column
* contained in the directory.
*/
char directory_name[OBIDMS_COLUMN_DIR_MAX_NAME+1]; /**< The name of the directory
* containing the column.
char directory_name[OBIDMS_COLUMN_MAX_NAME+1]; /**< The name of the directory
* containing the column.
*/
DIR* directory; /**< A directory entry usable to
* refer and scan the database directory.
DIR* directory; /**< A directory entry usable to
* refer and scan the database directory.
*/
} OBIDMS_column_directory_t, *OBIDMS_column_directory_p;
/*@
* @brief Checks if an OBIDMS column directory exists
/**
* @brief Checks if an OBIDMS column directory exists.
*
* @param dms a pointer to an OBIDMS as returned by obi_create_dms() or obi_open_dms()
* @param column_name a pointer to a C string containing the name of the column.
* The actual directory name used to store the column is
* `<column_name>.obicol`.
* @param dms A pointer to an OBIDMS as returned by obi_create_dms() or obi_open_dms().
* @param column_name A pointer to a C string containing the name of the column.
*
* @return an integer value indicating the status of the column directory
* @retvalue 1 the directory exist
* @retvalue 0 the directory does not exist
* @retvalue -1 an error occurred
* @returns An integer value indicating the status of the column directory.
* @retval 1 if the directory exists.
* @retval 0 if the directory does not exist.
* @retval -1 if an error occurred.
*
* @see obi_close_column_directory()
* @since June 2015
@ -72,17 +71,14 @@ int obi_column_directory_exists(OBIDMS_p dms, const char* column_name);
* if a directory with this name does not already exist
* before creating the new column directory.
*
* @param dms a pointer to an OBIDMS as returned by obi_create_dms() or obi_open_dms()
* @param column_name a pointer to a C string containing the name of the column.
* @param dms A pointer to an OBIDMS as returned by obi_create_dms() or obi_open_dms().
* @param column_name A pointer to a C string containing the name of the column.
* The actual directory name used to store the column will be
* `<column_name>.obicol`.
*
* @return a pointer to an OBIDMS column directory structure describing the newly created
* directory
* @retval NULL on error and the `obi_errno` variable is set.
*
* ###Error values
* - OBIDMS_COL_DIR_EXIST_ERROR : xxxxx a database with the same name already exists.
* @returns A pointer to an OBIDMS column directory structure describing the newly created
* directory.
* @retval NULL if an error occurred.
*
* @see obi_close_column_directory()
* @since June 2015
@ -94,16 +90,13 @@ OBIDMS_column_directory_p obi_create_column_directory(OBIDMS_p dms, const char*
/**
* @brief Opens an existing OBIDMS column directory instance.
*
* @param dms a pointer to an OBIDMS as returned by obi_create_dms() or obi_open_dms()
* @param column_name a pointer to a C string containing the name of the column.
* @param dms A pointer to an OBIDMS as returned by obi_create_dms() or obi_open_dms().
* @param column_name A pointer to a C string containing the name of the column.
* The actual directory name used to store the column is
* `<column_name>.obicol`.
*
* @return a pointer to the OBIDMS column directory structure describing the directory
* @retval NULL on error and the `obi_errno`variable is set.
*
* ###Error values
* - OBIDMS_COL_DIR_ERROR : xxxxx a database with the same name already exists.
* @returns A pointer to the OBIDMS column directory structure describing the directory.
* @retval NULL if an error occurred.
*
* @see obi_close_column_directory()
* @since June 2015
@ -118,17 +111,13 @@ OBIDMS_column_directory_p obi_open_column_directory(OBIDMS_p dms, const char* co
* If the directory already exists, this function opens it, otherwise it
* creates a new column directory.
*
* @param dms a pointer to an OBIDMS as returned by obi_create_dms() or obi_open_dms()
* @param column_name a pointer to a C string containing the name of the column.
* @param dms A pointer to an OBIDMS as returned by obi_create_dms() or obi_open_dms().
* @param column_name A pointer to a C string containing the name of the column.
* The actual directory name used to store the column is
* `<column_name>.obicol`.
*
* @return a pointer to the OBIDMS column directory structure describing the directory
* @retval NULL on error and the `obi_errno`variable is set.
*
* ###Error values
* - OBIDMS_LONG_NAME_ERROR : the database name exceeds the limit.
* - OBIDMS_MEMORY_ERROR : something wrong occurred during memory allocation.
* @returns A pointer to the OBIDMS column directory structure describing the directory.
* @retval NULL if an error occurred.
*
* @since June 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
@ -139,13 +128,13 @@ OBIDMS_column_directory_p obi_column_directory(OBIDMS_p dms, const char* column_
/**
* @brief Closes an opened OBIDMS column directory instance.
*
* @param column_directory a pointer to an OBIDMS column directory as returned by
* obi_create_column_directory() or obi_open_column_directory()
* @param column_directory A pointer to an OBIDMS column directory as returned by
* obi_create_column_directory() or obi_open_column_directory().
*
* @return an integer value indicating the success of the operation. Even on
* error, the `OBIDMS_column_directory` structure is freed
* @retvalue 0 on success
* @retvalue -1 on failure and the `obi_errno` variable is set.
* @returns An integer value indicating the success of the operation. Even on
* error, the `OBIDMS_column_directory` structure is freed.
* @retval 0 on success.
* @retval -1 if an error occurred.
*
* @see obi_create_column_directory()
* @see obi_open_column_directory()

14
src/obierrno.c
View File

@ -1,8 +1,12 @@
/*
* obierrno.c
*
* Created on: 23 mai 2015
* Author: coissac
/****************************************************************************
* Code for obi errnos *
****************************************************************************/
/**
* @file obierrno.c
* @author Eric Coissac (eric.coissac@metabarcoding.org)
* @date 23 May 2015
* @brief Code for obi errnos.
*/

26
src/obierrno.h
View File

@ -1,20 +1,26 @@
/*
* obierrno.h
*
* Created on: 23 mai 2015
* Author: coissac
/****************************************************************************
* Header file for obi errnos *
****************************************************************************/
/**
* @file obierrno.h
* @author Eric Coissac (eric.coissac@metabarcoding.org)
* @date 23 May 2015
* @brief Header file for obi errnos.
*/
#ifndef OBIERRNO_H_
#define OBIERRNO_H_
/**
* @brief The declaration of the external variable `obi_errno`.
*
* `obi_errno` is an equivalent of `errno` for the system level error,
* but for errors generated by the C layer of the OBITools framework.
* but for errors generated by the C layer of the OBITools3 framework.
*
* @todo We have to look into defining this variable as thread specific.
* @TODO We have to look into defining this variable as thread specific.
*/
extern int obi_errno;
@ -24,8 +30,8 @@ extern int obi_errno;
* the specified `err` code
*
* This function is defined as a macro to reduce the risk
* of increasing the problem generating the error by calling
* a new function.
* of increasing the problem by generating another error by calling
* another function.
*
* @param err The error code as an integer value.
*
@ -41,6 +47,8 @@ extern int obi_errno;
* Error codes set in errno following an error related
* to the manipulation of an OBIDMS.
*
* @TODO
*
* @{
*/
#define OBIDMS_EXIST_ERROR (1) /**< Trying to create an OBIDMS with a name

14
src/obilittlebigman.c
View File

@ -1,8 +1,12 @@
/*
* littlebigman.c
*
* Created on: 23 mai 2015
* Author: coissac
/****************************************************************************
* Code for endianness checking *
****************************************************************************/
/**
* @file obilittlebigman.c
* @author Eric Coissac (eric.coissac@metabarcoding.org)
* @date 23 May 2015
* @brief Code endianness checking.
*/
#include "obilittlebigman.h"

19
src/obilittlebigman.h
View File

@ -1,15 +1,22 @@
/*
* littlebigman.h
*
* Created on: 23 mai 2015
* Author: coissac
/****************************************************************************
* Header file for endianness checking *
****************************************************************************/
/**
* @file obilittlebigman.h
* @author Eric Coissac (eric.coissac@metabarcoding.org)
* @date 23 May 2015
* @brief Header file for endianness checking.
*/
#ifndef OBILITTLEBIGMAN_H_
#define OBILITTLEBIGMAN_H_
#include <stdbool.h>
/**
* Test if the architecture of the processor is little endian.
*
@ -41,7 +48,7 @@
* In this architecture, the last address is
* used to store the byte of lighter weight (LITTLE ENDian)
*
* @return a `bool` value:
* @returns a `bool` value:
* - `true` if the architecture is little endian
* - `false` if the architecture is big endian
*

16
src/obitypes.c
View File

@ -1,8 +1,12 @@
/*
* obitypes.c
*
* Created on: 23 mai 2015
* Author: coissac
/****************************************************************************
* OBITypes functions *
****************************************************************************/
/**
* @file obitypes.h
* @author Eric Coissac (eric.coissac@metabarcoding.org)
* @date 23 May 2015
* @brief Functions for the handling of OBITypes.
*/
@ -13,7 +17,7 @@
#include "obierrno.h"
#define DEBUG_LEVEL 0
#define DEBUG_LEVEL 0 // TODO has to be defined somewhere else (cython compil flag?)
size_t obi_sizeof(OBIType_t type)

60
src/obitypes.h
View File

@ -1,10 +1,15 @@
/****************************************************************************
* Header file for OBITypes *
****************************************************************************/
/**
* @file obitypes.h
* @author Celine Mercier
* @author Celine Mercier (celine.mercier@metabarcoding.org)
* @date 18 May 2015
* @brief Header file for the OBITypes.
* @brief Header file for the handling of OBITypes.
*/
#ifndef OBITYPES_H_
#define OBITYPES_H_
@ -13,10 +18,11 @@
#include <stdint.h>
#define OBIInt_NA (INT32_MIN)
#define OBIIdx_NA (SIZE_MAX)
#define OBIFloat_NA (float_NA())
#define OBIChar_NA (0) // TODO not sure about this one as it can be impossible to distinguish from uninitialized values
#define OBIInt_NA (INT32_MIN) /**< NA value for the type OBI_INT */
#define OBIIdx_NA (SIZE_MAX) /**< NA value for the type OBI_IDX */
#define OBIFloat_NA (float_NA()) /**< NA value for the type OBI_FLOAT */
#define OBIChar_NA (0) /**< NA value for the type OBI_CHAR */
// TODO not sure about this one as it can be impossible to distinguish from uninitialized values
/**
@ -48,6 +54,9 @@ typedef char obichar_t;
typedef size_t obiidx_t;
/**
* @brief Union used to compute the NA value of the OBI_FLOAT OBIType.
*/
typedef union
{
double value;
@ -55,7 +64,11 @@ typedef union
} ieee_double;
static double float_NA(void) // as defined in R
/**
* @brief Returns the NA value of the OBI_FLOAT OBIType.
* This value corresponds to the float NA value as defined in R.
*/
static double float_NA(void)
{
volatile ieee_double x;
x.word[0] = 0x7ff00000;
@ -65,12 +78,12 @@ static double float_NA(void) // as defined in R
/**
* @brief returns the memory size in bytes of an OBIType
* @brief Returns the memory size in bytes of an OBIType.
*
* @param type the OBIType code used as query
* @param type The OBIType code used as query.
*
* @return the size in bytes of the type
* @retval 0 on error (unknown type)
* @returns The size in bytes of the type.
* @retval 0 if an error occurred (unknown type).
*
* @since May 2015
* @author Eric Coissac (eric.coissac@metabarcoding.org)
@ -79,31 +92,32 @@ size_t obi_sizeof(OBIType_t type);
/**
* @brief returns the size requested to store an array of OBIType
* @brief Returns the size required to store an array of elements with an OBIType.
*
* The returned size is large enough to store an array of size nbelement
* but rounded at a multiple of the memory page size.
* The returned size is large enough to store an array large enough
* to store all the elements but rounded at a multiple of the memory page size. // TODO this might be redundant but still a good thing
*
* @param type the OBIType code used as query
* @param nbelement the number of elements to be stored
* @param data_type The OBIType of the elements.
* @param nb_lines The number of lines to be stored.
* @param nb_elements_per_line The number of elements per line.
*
* @return the size in bytes of the array
* @retval 0 on error (unknown type)
* @returns The size in bytes of the array.
* @retval 0 if an error occurred (unknown type).
*
* @since May 2015
* @author Eric Coissac (eric.coissac@metabarcoding.org)
*/
size_t obi_array_sizeof(OBIType_t type, size_t nbelements, size_t nb_elements_per_line);
size_t obi_array_sizeof(OBIType_t data_type, size_t nb_lines, size_t nb_elements_per_line);
/**
* @brief returns the name in the form of a character string of an OBIType
* @brief Returns the name in the form of a character string of an OBIType.
*
*
* @param data_type the OBIType code used as query
* @param data_type The OBIType code used as query.
*
* @return the name of the OBIType
* @retval NULL on error (unknown type or error allocating the memory for the character string)
* @returns The name of the OBIType.
* @retval NULL if an error occurred (unknown type or error allocating the memory for the character string).
*
* @since August 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)

49
src/private_at_functions.c
View File

@ -3,8 +3,8 @@
****************************************************************************/
/**
* @file private_at_functions.h
* @author Celine Mercier
* @file private_at_functions.c
* @author Celine Mercier (celine.mercier@metabarcoding.org)
* @date 15 June 2015
* @brief Private replacement functions for *at functions.
*/
@ -23,14 +23,7 @@
#include "obierrno.h"
#define DEBUG_LEVEL 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
*
**********************************************************************/
#define DEBUG_LEVEL 0 // TODO has to be defined somewhere else (cython compil flag?)
char* get_full_path(int directory_file_descriptor, const char* path_name)
@ -77,39 +70,3 @@ DIR* private_opendirat(int directory_file_descriptor, const char* path_name)
}
//int private_openat(int directory_file_descriptor, const char* path_name, int flags)
//{
// char* full_path;
// int file_descriptor;
//
// full_path = get_full_path(directory_file_descriptor, path_name);
// if (full_path == NULL)
// return -1;
//
// file_descriptor = open(full_path, flags);
//
// free(full_path);
//
// return file_descriptor;
//}
//
//
//int private_mkdirat(int directory_file_descriptor, const char* path_name, mode_t mode)
//{
// char* full_path;
//
// full_path = get_full_path(directory_file_descriptor, path_name);
// if (full_path == NULL)
// return -1;
//
// if (mkdir(full_path, mode) < 0)
// {
// free(full_path);
// return -1;
// }
//
// free(full_path);
//
// return 0;
//}

71
src/private_at_functions.h
View File

@ -1,10 +1,15 @@
/****************************************************************************
* Header file for private *at functions *
****************************************************************************/
/**
* @file private_openat.h
* @author Celine Mercier
* @file private_at_functions.h
* @author Celine Mercier (celine.mercier@metabarcoding.org)
* @date 15 June 2015
* @brief Header file for the replacement *at function.
* @brief Header file for the private replacement functions for *at functions.
*/
#ifndef PRIVATE_OPENAT_H_
#define PRIVATE_OPENAT_H_
@ -12,27 +17,22 @@
#include <sys/stat.h>
#define MAX_PATH_LEN 4096
#define MAX_PATH_LEN 4096 /**< Maximum length for the character string defining a
file or directory path */
/**
* Internal function getting the full path of a file or a directory from its
* path relative to a directory file descriptor.
*
* @brief Internal function getting the full path of a file or a directory from its
* path relative to a directory file descriptor.
*
* @warning The returned pointer has to be freed by the caller.
*
* @param directory_file_descriptor the file descriptor for the directory to which
* path_name is relative
* @param path_name the path name for the file or directory, relative to directory_file_descriptor
* @param directory_file_descriptor The file descriptor for the directory to which
* path_name is relative.
* @param path_name The path name for the file or directory, relative to directory_file_descriptor.
*
* @return a pointer to the full path
* @retvalue <full_path> if everything is ok
* @retvalue NULL if an error occurs
*
* ###Error values
* - OBIDMS_MEMORY_ERROR : something wrong occurred during memory allocation.
* - OBIDMS_LONG_NAME_ERROR : the database name exceeds the limit.
* @returns A pointer to the full path.
* @retval NULL if an error occurs.
*
* @since June 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
@ -43,10 +43,11 @@ char* get_full_path(int directory_file_descriptor, const char* path_name);
/**
* @brief Replacement function for opendirat() : open a directory relative to a directory file descriptor.
*
* @param directory_file_descriptor the file descriptor for the directory in which the directory should be opened
* @param path_name the path name for the directory to be opened, relative to directory_file_descriptor
* @param directory_file_descriptor The file descriptor for the directory in which the directory should be opened.
* @param path_name The path name for the directory to be opened, relative to directory_file_descriptor.
*
* @return the file descriptor of the opened directory
* @returns The file descriptor of the opened directory.
* @retval NULL if an error occurred.
*
* @since June 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
@ -54,34 +55,4 @@ char* get_full_path(int directory_file_descriptor, const char* path_name);
DIR* private_opendirat(int directory_file_descriptor, const char* path_name);
///**
// * @brief Replacement function for openat() : open a file relative to a directory file descriptor.
// *
// * @param directory_file_descriptor the file descriptor for the directory in which the file should be opened
// * @param path_name the path name for the file, relative to directory_file_descriptor
// * @param flags the access modes
// *
// * @return the file descriptor of the opened file
// *
// * @since June 2015
// * @author Celine Mercier (celine.mercier@metabarcoding.org)
// */
//int private_openat(int directory_file_descriptor, const char* path_name, int flags);
//
//
///**
// * @brief Replacement function for mkdirat() : create a directory relative to a directory file descriptor.
// *
// * @param directory_file_descriptor the file descriptor for the directory in which the directory should be created
// * @param path_name the path name for the new directory, relative to directory_file_descriptor
// * @param mode the access mode
// *
// * @return the file descriptor of the created directory
// *
// * @since June 2015
// * @author Celine Mercier (celine.mercier@metabarcoding.org)
// */
//int private_mkdirat(int directory_file_descriptor, const char* path_name, mode_t mode);
#endif /* PRIVATEOPENAT_H_ */