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Major update: obiarrays with columns containing indices referring to

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character strings.
This commit is contained in:
Celine Mercier
2015-11-06 17:55:15 +01:00
parent 456551ffeb
commit 9b066f4327
35 changed files with 632 additions and 532 deletions
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313
src/obiarray.c
View File

@ -13,6 +13,7 @@
#include <stdlib.h>
#include <stdio.h>
#include <stdint.h>
#include <string.h>
#include <time.h>
#include <sys/mman.h>
#include <fcntl.h>
@ -20,7 +21,9 @@
#include "obiarray.h"
#include "obierrno.h"
#include "obitypes.h"
#include "obidebug.h"
#include "private_at_functions.h"
#define DEBUG_LEVEL 0 // TODO has to be defined somewhere else (cython compil flag?)
@ -37,7 +40,7 @@
*
* @warning The returned pointer has to be freed by the caller.
*
* @param name The name of the array.
* @param array_name The name of the array.
*
* @returns A pointer to the array file name.
* @retval NULL if an error occurred.
@ -53,7 +56,7 @@ static char* build_array_file_name(const char* array_name);
*
* @warning The returned pointer has to be freed by the caller.
*
* @param name The name of the array.
* @param array_name The name of the array.
*
* @returns A pointer to the array data file name.
* @retval NULL if an error occurred.
@ -65,62 +68,121 @@ static char* build_array_data_file_name(const char* array_name);
/**
* PRIVATE
*/
static char* build_array_file_path(OBIDMS_p dms, const char* array_name);
/**
* PRIVATE
* @brief Internal function returning the size of an array header on this platform.
*
* @returns The size of an array header in bytes.
*
* @since October 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
size_t get_array_header_size();
/**
* PRIVATE
* @brief Internal function returning the initial size of an array on this platform.
*
* @returns The initial size of an array in bytes.
*
* @since October 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
size_t get_initial_array_size();
/**
* PRIVATE
* @brief Internal function returning the size of a data array header on this platform.
*
* @returns The size of a data array header in bytes.
*
* @since October 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
size_t get_array_data_header_size();
/**
* PRIVATE
* @brief Internal function returning the initial size of a data array on this platform.
*
* @returns The initial size of a data array in bytes.
*
* @since October 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
size_t get_initial_array_data_size();
/**
* PRIVATE
* @brief Internal function closing a data array structure.
*
* @param array_data A pointer to the data array.
*
* @retval 0 if the operation was successfully completed.
* @retval -1 if an error occurred.
*
* @since October 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int close_array_data(OBIDMS_array_data_p array_data);
/**
* PRIVATE
* @brief Internal function enlarging an array.
*
* @param array A pointer to the array structure.
*
* @retval 0 if the operation was successfully completed.
* @retval -1 if an error occurred.
*
* @since October 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int grow_array(OBIDMS_array_p array);
/**
* PRIVATE
* @brief Internal function enlarging a data array.
*
* @param array A pointer to the array structure.
*
* @retval 0 if the operation was successfully completed.
* @retval -1 if an error occurred.
*
* @since October 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int grow_array_data(OBIDMS_array_p array);
/**
* PRIVATE
* @brief Internal function comparing two byte arrays.
*
* The encoding is compared first, then the length of the
* values, then the values themselves.
*
* @param value_1 A pointer to the first byte array.
* @param value_2 A pointer to the second byte array.
*
* @returns A value < 0 if value_1 < value_2,
* a value > 0 if value_1 > value_2,
* and 0 if value_1 == value_2.
*
* @since October 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int array_compare(byte_t* value_1, byte_t* value_2);
/**
* PRIVATE
* @brief Internal function calculating the size in bytes of a byte array.
*
* @param value A pointer to the byte array.
*
* @returns The size of the byte array in bytes.
*
* @since October 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int32_t array_sizeof(byte_t* value); // TODO not sure about type
size_t array_sizeof(byte_t* value); // TODO not sure about type
/************************************************************************
@ -170,33 +232,6 @@ static char* build_array_data_file_name(const char* array_name)
}
static char* build_array_file_path(OBIDMS_p dms, const char* array_name) // TODO store DIR in dms structure
{
char* array_file_path;
char* array_file_name;
// Build the array file name
array_file_name = build_array_file_name(array_name);
if (array_file_name == NULL)
return NULL;
// TODO use get_full_path(int directory_file_descriptor, const char* path_name)
array_file_path = (char*) malloc((strlen(dms->directory_name) + strlen("/arrays/") + strlen(array_file_name) + 1) * sizeof(char));
if (array_file_path == NULL)
{
obi_set_errno(OBI_ARRAY_ERROR);
obidebug(1, "\nError building an array file path");
return NULL;
}
strcpy(array_file_path, dms->directory_name);
strcat(array_file_path, "/arrays/");
strcat(array_file_path, array_file_name);
return array_file_path;
}
size_t get_array_header_size()
{
return getpagesize() * 1;
@ -272,7 +307,7 @@ int grow_array(OBIDMS_array_p array) // TODO Lock when needed
return -1;
}
// Open the array data file
// Open the array file
array_file_descriptor = openat(array_dir_file_descriptor, array_file_name, O_RDWR);
if (array_file_descriptor < 0)
{
@ -285,7 +320,7 @@ int grow_array(OBIDMS_array_p array) // TODO Lock when needed
free(array_file_name);
// Calculate the new file size
old_data_size = ((array->header)->nb_items_max) * sizeof(index_t);
old_data_size = (array->header)->array_size;
new_data_size = old_data_size * ARRAY_GROWTH_FACTOR;
header_size = (array->header)->header_size;
file_size = header_size + new_data_size;
@ -331,8 +366,11 @@ int grow_array(OBIDMS_array_p array) // TODO Lock when needed
// Set new maximum number of items
(array->header)->nb_items_max = ceil(((double) new_data_size) / ((double) sizeof(index_t)));
// Set the new array size
(array->header)->array_size = new_data_size;
// Initialize new data to 0
memset((array->first)+old_data_size, 0, new_data_size - old_data_size);
memset(((uint8_t*)(array->first))+old_data_size, 0, (new_data_size-old_data_size));
close(array_file_descriptor);
@ -343,8 +381,8 @@ int grow_array(OBIDMS_array_p array) // TODO Lock when needed
int grow_array_data(OBIDMS_array_p array) // TODO Lock when needed
{
size_t file_size;
size_t old_data_size;
size_t new_data_size;
index_t old_data_size;
index_t new_data_size;
size_t header_size;
int array_dir_file_descriptor;
int array_data_file_descriptor;
@ -444,7 +482,7 @@ int array_compare(byte_t* value_1, byte_t* value_2)
int32_t len_2;
int32_t b;
obidebug(1, "\nCOMPARING 1=%d,%.*s; 2=%d,%.*s", (int32_t) *(value_1+1), (int32_t) *(value_1+1), value_1+5, (int32_t) *(value_2+1), (int32_t) *(value_2+1), value_2+5);
//obidebug(1, "\nCOMPARING 1=%d,%.*s; 2=%d,%.*s", *((int32_t*)(value_1+1)), *((int32_t*)(value_1+1)), value_1+BYTE_ARRAY_HEADER_SIZE, *((int32_t*)(value_2+1)), *((int32_t*)(value_2+1)), value_2+BYTE_ARRAY_HEADER_SIZE);
size_1 = (uint8_t) *(value_1);
size_2 = (uint8_t) *(value_2);
@ -452,31 +490,26 @@ int array_compare(byte_t* value_1, byte_t* value_2)
if (size_1 != size_2)
return (size_1 - size_2);
len_1 = (int32_t) *(value_1+1);
len_2 = (int32_t) *(value_2+1);
obidebug(1, "\ncomp length = %d - %d = %d", len_1, len_2, (len_1 - len_2));
len_1 = *((int32_t*)(value_1+1));
len_2 = *((int32_t*)(value_2+1));
if (len_1 != len_2)
return (len_1 - len_2);
b = 0;
b = BYTE_ARRAY_HEADER_SIZE;
comp = 0;
while (!comp && (b < len_1))
while (!comp && (b < len_1+BYTE_ARRAY_HEADER_SIZE))
{
comp = *(value_1+b) - *(value_2+b);
b++;
}
obidebug(1, "\ncomp = %d", comp);
return comp;
}
int32_t array_sizeof(byte_t* value)
size_t array_sizeof(byte_t* value)
{
return (6 + (int32_t) *(value+1));
return (BYTE_ARRAY_HEADER_SIZE + *((int32_t*)(value+1)) + 1);
}
@ -490,14 +523,39 @@ int obi_array_exists(OBIDMS_p dms, const char* array_name)
{
struct stat buffer;
char* array_file_path;
char* array_file_name;
int check_dir;
int array_dir_file_descriptor;
// Get the file descriptor of the array directory
array_dir_file_descriptor = dirfd(dms->array_directory);
if (array_dir_file_descriptor < 0)
{
obi_set_errno(OBI_ARRAY_ERROR);
obidebug(1, "\nError getting the file descriptor for an array directory");
return -1;
}
// Build file name
array_file_name = build_array_file_name(array_name);
if (array_file_name == NULL)
{
close(array_dir_file_descriptor);
return -1;
}
// Build the array file path
array_file_path = build_array_file_path(dms, array_name);
array_file_path = get_full_path(array_dir_file_descriptor, array_file_name);
if (array_file_path == NULL)
{
obidebug(1, "\nError getting the file path for an array file");
return -1;
}
check_dir = stat(array_file_path, &buffer);
free(array_file_path);
free(array_file_name);
if (check_dir == 0)
return 1;
@ -549,8 +607,6 @@ OBIDMS_array_p obi_create_array(OBIDMS_p dms, const char* array_name)
return NULL;
}
obidebug(1, "\nboom");
// Build file name
array_data_file_name = build_array_data_file_name(array_name);
if (array_data_file_name == NULL)
@ -559,8 +615,6 @@ OBIDMS_array_p obi_create_array(OBIDMS_p dms, const char* array_name)
return NULL;
}
obidebug(1, "\nboom");
// Create file
array_data_file_descriptor = openat(array_dir_file_descriptor, array_data_file_name, O_RDWR | O_CREAT | O_EXCL, 0777);
if (array_data_file_descriptor < 0)
@ -719,7 +773,7 @@ OBIDMS_array_p obi_create_array(OBIDMS_p dms, const char* array_name)
return NULL;
}
array->first = mmap(NULL,
array->first = mmap(NULL,
data_size,
PROT_READ | PROT_WRITE,
MAP_SHARED,
@ -742,6 +796,7 @@ OBIDMS_array_p obi_create_array(OBIDMS_p dms, const char* array_name)
array->directory = dms->array_directory;
(array->header)->header_size = header_size;
(array->header)->array_size = data_size;
(array->header)->nb_items = 0;
(array->header)->nb_items_max = (index_t) ceil(((double) get_initial_array_size()) / ((double) sizeof(index_t)));
(array->header)->creation_date = time(NULL);
@ -751,7 +806,6 @@ OBIDMS_array_p obi_create_array(OBIDMS_p dms, const char* array_name)
memset(array->first, 0, data_size);
close(array_file_descriptor);
//close(array_dir_file_descriptor); TODO
return array;
}
@ -929,7 +983,6 @@ OBIDMS_array_p obi_open_array(OBIDMS_p dms, const char* array_name)
array->directory = dms->array_directory;
close(array_file_descriptor);
//close(array_dir_file_descriptor); TODO
return array;
}
@ -961,29 +1014,17 @@ int obi_close_array(OBIDMS_array_p array)
}
//int obi_delete_array(const char* array_name)
//{
//
//}
index_t obi_array_add(OBIDMS_array_p array, byte_t* value)
{
index_t idx;
index_t nb_items;
index_t nb_items_max;
index_t* a;
byte_t* data;
int64_t data_size_used;
int64_t* data_size_max_p;
int32_t value_size;
obidebug(1, "\n");
index_t idx;
index_t nb_items;
index_t nb_items_max;
index_t data_size_used;
index_t* data_size_max_p;
size_t value_size;
nb_items = (array->header)->nb_items;
nb_items_max = (array->header)->nb_items_max;
a = array->first;
data = (array->data)->data;
data_size_used = ((array->data)->header)->data_size_used;
data_size_max_p = &(((array->data)->header)->data_size_max);
@ -999,8 +1040,6 @@ index_t obi_array_add(OBIDMS_array_p array, byte_t* value)
else // First item
idx = 0;
obidebug(1, "\n");
// Grow the array if needed
if (nb_items == nb_items_max)
{
@ -1008,37 +1047,22 @@ index_t obi_array_add(OBIDMS_array_p array, byte_t* value)
return -1;
}
obidebug(1, "\n");
// Grow the data if needed
value_size = array_sizeof(value);
while (*data_size_max_p < (data_size_used + value_size))
while (*data_size_max_p < (data_size_used + value_size)) // TODO problem with types
{
if (grow_array_data(array) < 0)
return -1;
}
obidebug(1, "\nidx = %d", idx);
// Store the index of the value in the array
// Add the index of the value in the array
memmove((a+idx+1), (a+idx), ((nb_items - idx) * sizeof(index_t)));
a[idx] = data_size_used;
int i;
for (i=0; i<nb_items; i++)
fprintf(stderr, "\narray[%d] = %d\n", i, a[i]);
//fprintf(stderr, "\nBEFORE COPY DATA+5=%.5s, DATA+14=%.5s\n", data+5, data+14);
//fprintf(stderr, "\nBEFORE COPY DATA+8=%s\n", data+8);
fprintf(stderr, "\ndata size used = %lld, value size = %d", data_size_used, value_size);
if (nb_items > 0)
memmove(((array->first)+idx+1), ((array->first)+idx), ((nb_items - idx) * sizeof(index_t)));
(array->first)[idx] = data_size_used;
// Store the value itself at the end of the data
memcpy((data+data_size_used), value, value_size);
//fprintf(stderr, "\nAFTER COPY DATA+8=%s\n", data+8);
//fprintf(stderr, "\nAFTER COPY DATA+5=%.4s, DATA+14=%.5s\n", data+5, data+14);
memcpy((((array->data)->data)+data_size_used), value, value_size);
// Update the data size
((array->data)->header)->data_size_used = data_size_used + value_size;
@ -1047,18 +1071,18 @@ index_t obi_array_add(OBIDMS_array_p array, byte_t* value)
((array->header)->nb_items)++;
(((array->data)->header)->nb_items)++;
//obidebug(1, "\nSHOULD ++ : %d", (array->header)->nb_items);
for (i=0; i<(array->header)->nb_items; i++)
fprintf(stderr, "\narray[%d] = %d\n", i, a[i]);
fprintf(stderr, "\nreturning %lld\n", data_size_used);
// PRINT ARRAY
// fprintf(stderr, "\nARRAY:");
// int i;
// for (i=0; i<=nb_items; i++)
// fprintf(stderr, "\narray[%d] = %d -> %s", i, a[i], data+a[i]+BYTE_ARRAY_HEADER_SIZE);
// Return the data index of the value
return data_size_used;
}
byte_t* obi_array_get(OBIDMS_array_p array, index_t idx) // TODO copy?
byte_t* obi_array_get(OBIDMS_array_p array, index_t idx)
{
return (((array->data)->data)+idx);
}
@ -1080,48 +1104,37 @@ index_t obi_array_search(OBIDMS_array_p array, byte_t* value)
data = (array->data)->data;
a = array->first;
obidebug(1, "\nnb items = %d", nb_items);
if (nb_items == 0)
return 0;
return -1;
idx_max = nb_items;
idx_max = nb_items-1;
idx_min = 0;
obidebug(1, "\n");
while (idx_min < idx_max)
while (idx_min <= idx_max)
{
idx_mid = nb_items/2;
obidebug(1, "\ncomparing with idx = %d, data idx %d", idx_mid, a[idx_mid]);
//fprintf(stderr, "\ndata+14=%.5s\n", data+14);
idx_mid = (idx_min+idx_max)/2;
to_compare = obi_array_get(array, a[idx_mid]);
//fprintf(stderr, "\nto_compare=%.5s\n", to_compare+5);
comp = array_compare(to_compare, value);
obidebug(1, "\nCOMP = %d", comp);
if (!comp)
{
// Found
return a[idx_mid];
}
else if (comp < 0)
{
idx = idx_mid + 1;
// Search in upper half
idx = idx_mid + 1;
idx_min = idx_mid + 1;
}
else
idx = idx_mid;
{
// Search in lower half
idx = idx_mid;
idx_max = idx_mid - 1;
}
}
obidebug(1, "\nNOT FOUND, idx=%d", idx);
// Not found: return where the value should be
// Not found: return where the value should be in the array
return -(idx+1);
}
@ -1134,7 +1147,7 @@ byte_t* obi_str_to_obibytes(char* value)
size = 8;
length = strlen(value);
value_b = (byte_t*) malloc(length + 6);
value_b = (byte_t*) malloc(length + BYTE_ARRAY_HEADER_SIZE + 1);
if (value_b == NULL)
{
obi_set_errno(OBI_ARRAY_ERROR);
@ -1143,11 +1156,10 @@ byte_t* obi_str_to_obibytes(char* value)
}
*(value_b) = size;
*(value_b+1) = length;
strcpy(value_b+5, value);
*((int32_t*)(value_b+1)) = length;
// TODO 5 as macro
strcpy(value_b+BYTE_ARRAY_HEADER_SIZE, value);
return value_b;
}
@ -1157,17 +1169,8 @@ const char* obi_obibytes_to_str(byte_t* value_b)
{
const char* value;
value = value_b+5;
obidebug(1, "\nvalue = %s", value);
// TODO 5 as macro
value = value_b+BYTE_ARRAY_HEADER_SIZE;
return value;
}

152
src/obiarray.h
View File

@ -3,15 +3,15 @@
****************************************************************************/
/**
* @file array.h
* @file obiarray.h
* @author Celine Mercier
* @date October 19th 2015
* @brief Header file for handling arrays for storing and retrieving data arrays (i.e. character strings).
* @brief Header file for handling arrays for storing and retrieving byte arrays (i.e. coding for character strings).
*/
#ifndef ARRAY_H_
#define ARRAY_H_
#ifndef OBIARRAY_H_
#define OBIARRAY_H_
#include <stdlib.h>
@ -29,9 +29,10 @@
*/
#define ARRAY_GROWTH_FACTOR (2) /**< The growth factor when an array is enlarged.
*/
#define BYTE_ARRAY_HEADER_SIZE (5) /**< The size of the header of a byte array.
*/
typedef int32_t index_t; /**< Type of the array indices.
*/
typedef char byte_t; /**< Defining byte type since data is stored in bits
* and char (stored on one byte) is the smallest addressable unit.
*/
@ -43,9 +44,9 @@ typedef char byte_t; /**< Defining byte type since data is stored in bits
typedef struct OBIDMS_array_data_header {
int header_size; /**< Size of the header in bytes.
*/
int64_t data_size_used; /**< Size of the data used in bytes. // TODO not sure about type
index_t data_size_used; /**< Size of the data used in bytes.
*/
int64_t data_size_max; /**< Max size of the data in bytes. // TODO not sure about type
index_t data_size_max; /**< Max size of the data in bytes.
*/
index_t nb_items; /**< Number of items.
*/
@ -73,6 +74,8 @@ typedef struct OBIDMS_array_data {
typedef struct OBIDMS_array_header {
int header_size; /**< Size of the header in bytes.
*/
size_t array_size; /**< Size of the array in bytes.
*/
index_t nb_items; /**< Number of items in the array.
*/
index_t nb_items_max; /**< Maximum number of items in the array before it has to be enlarged.
@ -102,76 +105,181 @@ typedef struct OBIDMS_array {
/**
* @brief Checks if an obiarray already exists or not.
*
* @param dms The OBIDMS to which the obiarray belongs.
* @param array_name The name of the obiarray.
*
* @returns A value indicating whether the obiarray exists or not.
* @retval 1 if the obiarray exists.
* @retval 0 if the obiarray does not exist.
* @retval -1 if an error occurred.
*
* @since October 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_array_exists(OBIDMS_p dms, const char* array_name);
/**
* @brief Opens an obiarray and creates it if it does not already exist.
*
* Note: An obiarray is made of two files (referred to by two structures).
* One file contains the indices referring to the data, and the other
* file contains the data itself. The obiarray as a whole is referred
* to via the OBIDMS_array structure.
*
* @param dms The OBIDMS to which the obiarray belongs.
* @param array_name The name of the obiarray.
*
* @returns A pointer to the obiarray structure.
* @retval NULL if an error occurred.
*
* @since October 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
OBIDMS_array_p obi_array(OBIDMS_p dms, const char* array_name);
/**
* @brief Creates an obiarray. Fails if it already exists.
*
* Note: An obiarray is made of two files (referred to by two structures).
* One file contains the indices referring to the data, and the other
* file contains the data itself. The obiarray as a whole is referred
* to via the OBIDMS_array structure.
*
* @param dms The OBIDMS to which the obiarray belongs.
* @param array_name The name of the obiarray.
*
* @returns A pointer to the newly created obiarray structure.
* @retval NULL if an error occurred.
*
* @since October 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
OBIDMS_array_p obi_create_array(OBIDMS_p dms, const char* array_name);
/**
* @brief Opens an obiarray. Fails if it does not already exist.
*
* Note: An obiarray is made of two files (referred to by two structures).
* One file contains the indices referring to the data, and the other
* file contains the data itself. The obiarray as a whole is referred
* to via the OBIDMS_array structure.
*
* @param dms The OBIDMS to which the obiarray belongs.
* @param array_name The name of the obiarray.
*
* @returns A pointer to the obiarray structure.
* @retval NULL if an error occurred.
*
* @since October 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
OBIDMS_array_p obi_open_array(OBIDMS_p dms, const char* array_name);
/**
* @brief Closes an obiarray.
*
* Note: An obiarray is made of two files (referred to by two structures).
* One file contains the indices referring to the data, and the other
* file contains the data itself. The obiarray as a whole is referred
* to via the OBIDMS_array structure.
*
* @param array A pointer to the obiarray structure to close and free.
*
* @retval 0 if the operation was successfully completed.
* @retval -1 if an error occurred.
*
* @since October 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_close_array(OBIDMS_array_p array);
/**
* @brief Adds a value (byte array) in an obiarray, checking first if it is already in it.
*
*/
//int obi_delete_array(OBIDMS_p dms, const char* array_name);
/**
* The header is already in the byte array
* @warning The byte array to add must already be encoded and contain its header.
*
* @param array A pointer to the obiarray.
* @param value The byte array to add in the obiarray.
*
* @returns The index of the value, whether it was added or already in the obiarray.
* @retval -1 if an error occurred.
*
* @since October 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
index_t obi_array_add(OBIDMS_array_p array, byte_t* value);
/**
* Returns the entire array including the header
* @brief Recovers a value (byte array) in an obiarray.
*
* @warning The byte array recovered is encoded and contains its header.
*
* @param array A pointer to the obiarray.
* @param index The index of the value in the data array.
*
* @returns A pointer to the byte array recovered.
*
* @since October 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
byte_t* obi_array_get(OBIDMS_array_p array, index_t index);
/**
* @brief Searches a value (byte array) in an obiarray performing a binary search.
*
* @warning The byte array to search must already be encoded and contain its header.
*
* @param array A pointer to the obiarray.
* @param value The byte array to add in the obiarray.
*
* @returns If the value is found, its data index is returned.
* If the value is not found, the array index indicating where the value's data index
* should be in the array is returned in the form (- (index + 1)), as data indices in an
* obiarray are sorted according to the ascending order of the values (byte arrays) themselves.
*
* @since October 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
index_t obi_array_search(OBIDMS_array_p array, byte_t* value);
/**
* @brief Converts a character string to a byte array with a header.
*
* @warning The byte array must be freed by the caller.
*
* @param value The character string to convert.
*
* @returns A pointer to the byte array created.
* @retval NULL if an error occurred.
*
* @since October 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
byte_t* obi_str_to_obibytes(char* value);
/**
* @brief Converts a byte array to a character string.
*
* @param value_b The byte array to convert.
*
* @returns A pointer to the character string contained in the byte array.
*
* @since October 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
const char* obi_obibytes_to_str(byte_t* value_b);
/**
* TODO LATER
*/
// OBIDMS_array_p obi_column_arrayify(FILE, encoding);
#endif /* ARRAY_H_ */
#endif /* OBIARRAY_H_ */

4
src/obidms.c
View File

@ -163,8 +163,6 @@ OBIDMS_p obi_create_dms(const char* dms_name)
return NULL;
}
// TODO close file descriptor?
free(directory_name);
return obi_open_dms(dms_name);
@ -247,8 +245,6 @@ OBIDMS_p obi_open_dms(const char* dms_name)
free(directory_name);
// TODO test if close file descriptor
return dms;
}

2
src/obidms.h
View File

@ -72,6 +72,8 @@ int obi_dms_exists(const char* dms_name);
* if a directory with this name does not already exist
* before creating the new database.
*
* A directory to store obiarrays is also created.
*
* @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`.

44
src/obidmscolumn.c
View File

@ -143,7 +143,7 @@ static int obi_column_set_elements_names(OBIDMS_column_p column, const char* ele
* @since September 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
static size_t get_line_count_per_page(OBIType_t data_type, size_t nb_elements_per_line);
static index_t get_line_count_per_page(OBIType_t data_type, index_t nb_elements_per_line);
/************************************************************************
@ -463,7 +463,7 @@ int obi_column_set_elements_names(OBIDMS_column_p column, const char* elements_n
return 0;
}
size_t get_line_count_per_page(OBIType_t data_type, size_t nb_elements_per_line)
index_t get_line_count_per_page(OBIType_t data_type, index_t nb_elements_per_line)
{
return getpagesize() / (obi_sizeof(data_type) * nb_elements_per_line);
}
@ -595,15 +595,15 @@ obiversion_t obi_column_get_latest_version_from_name(OBIDMS_p dms, const char* c
size_t obi_get_platform_header_size()
{
return getpagesize() * 1;
return getpagesize() * 2;
}
OBIDMS_column_p obi_create_column(OBIDMS_p dms,
const char* column_name,
OBIType_t data_type,
size_t nb_lines,
size_t nb_elements_per_line,
index_t nb_lines,
index_t nb_elements_per_line,
const char* elements_names,
const char* array_name)
{
@ -618,7 +618,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
int column_dir_file_descriptor;
size_t header_size;
size_t data_size;
size_t minimum_line_count;
index_t minimum_line_count;
new_column = NULL;
@ -664,7 +664,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
else if ((elements_names != NULL) && (nb_elements_per_line > 1))
{
char* token;
size_t n = 0;
index_t n = 0;
token = strdup(elements_names);
token = strtok(token, ";");
while (token != NULL)
@ -989,8 +989,8 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p dms,
{
OBIDMS_column_p column_to_clone;
OBIDMS_column_p new_column;
size_t nb_lines;
size_t nb_elements_per_line;
index_t nb_lines;
index_t nb_elements_per_line;
size_t data_size;
OBIType_t data_type;
@ -1083,7 +1083,7 @@ int obi_truncate_column_to_lines_used(OBIDMS_column_p column) // TODO is it nece
{
size_t file_size;
size_t data_size;
size_t new_line_count;
index_t new_line_count;
double multiple;
int column_dir_file_descriptor;
int column_file_descriptor;
@ -1180,8 +1180,8 @@ int obi_enlarge_column(OBIDMS_column_p column)
size_t old_data_size;
size_t new_data_size;
size_t header_size;
size_t old_line_count;
size_t new_line_count;
index_t old_line_count;
index_t new_line_count;
int column_dir_file_descriptor;
int column_file_descriptor;
char* column_file_name;
@ -1316,10 +1316,10 @@ int obi_truncate_and_close_column(OBIDMS_column_p column)
void obi_ini_to_NA_values(OBIDMS_column_p column,
size_t first_line_nb,
size_t nb_lines)
index_t first_line_nb,
index_t nb_lines)
{
size_t i, start, end, nb_elements;
index_t i, start, end, nb_elements;
nb_elements = nb_lines*((column->header)->nb_elements_per_line);
start = first_line_nb*((column->header)->nb_elements_per_line);
@ -1355,14 +1355,14 @@ void obi_ini_to_NA_values(OBIDMS_column_p column,
case OBI_IDX: for (i=start;i<end;i++)
{
*(((obiidx_t*) (column->data)) + i) = OBIIdx_NA;
*(((index_t*) (column->data)) + i) = OBIIdx_NA;
}
break;
}
}
OBIDMS_column_header_p obi_column_get_header_from_name(OBIDMS_p dms, const char* column_name) // ADD VERSION ARGUMENT
OBIDMS_column_header_p obi_column_get_header_from_name(OBIDMS_p dms, const char* column_name) // TODO ADD VERSION ARGUMENT
{
OBIDMS_column_header_p header;
OBIDMS_column_directory_p column_directory;
@ -1391,7 +1391,7 @@ OBIDMS_column_header_p obi_column_get_header_from_name(OBIDMS_p dms, const char*
}
// Calculate the header size
header_size = obi_get_platform_header_size();
header_size = obi_get_platform_header_size(); // TODO read in header itself
// Get the latest version number
version_number = obi_get_latest_version_number(column_directory);
@ -1458,17 +1458,17 @@ int obi_unmap_header(OBIDMS_column_header_p header)
// TODO to be rewritten in an optimized and safe way
size_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const char* element_name)
index_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const char* element_name)
{
char* elements_names;
char* name;
size_t element_index;
index_t element_index;
elements_names = strdup((column->header)->elements_names);
if (elements_names == NULL)
{
obidebug(1, "\nError strdup-ing the elements names");
return SIZE_MAX; //TODO
return OBIIdx_NA;
}
element_index = 0;
@ -1494,7 +1494,7 @@ 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 SIZE_MAX; //TODO
return OBIIdx_NA;
}

20
src/obidmscolumn.h
View File

@ -53,13 +53,13 @@ typedef struct OBIDMS_column_header {
* - `false` on big endian platforms
* @see obi_is_little_endian()
*/
int header_size; /**< Size of the header in bytes.
size_t header_size; /**< Size of the header in bytes.
*/
size_t line_count; /**< Number of lines of data allocated.
index_t line_count; /**< Number of lines of data allocated.
*/
size_t lines_used; /**< Number of lines of data used.
index_t lines_used; /**< Number of lines of data used.
*/
size_t nb_elements_per_line; /**< Number of elements per line (default: 1).
index_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).
@ -149,7 +149,7 @@ obiversion_t obi_column_get_latest_version_from_name(OBIDMS_p dms, const char* c
* The header size is defined as a multiple of the memory page size.
* As of now the header size is defined as one time the page size.
*
* @returns a `size_t` value corresponding to the header size in bytes.
* @returns The header size in bytes.
*
* @since May 2015
* @author Eric Coissac (eric.coissac@metabarcoding.org)
@ -161,6 +161,7 @@ size_t obi_get_platform_header_size();
* @brief Creates a column.
*
* The minimum data size allocated is one memory page, and the data is initialized to the NA value of the OBIType.
* If there is an array associated with the column, it is opened or created if it does not already exist.
*
* @warning If there is one element per line, elements_names should be equal to column_name. // TODO change this condition?
*
@ -170,6 +171,7 @@ size_t obi_get_platform_header_size();
* @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.
* @param array_name The name of the array if there is one associated with the column.
*
* @returns A pointer on the newly created column structure.
* @retval NULL if an error occurred.
@ -180,8 +182,8 @@ size_t obi_get_platform_header_size();
OBIDMS_column_p obi_create_column(OBIDMS_p dms,
const char* column_name,
OBIType_t data_type,
size_t nb_lines,
size_t nb_elements_per_line,
index_t nb_lines,
index_t nb_elements_per_line,
const char* elements_names,
const char* array_name);
@ -287,7 +289,7 @@ int obi_truncate_and_close_column(OBIDMS_column_p column);
* @since August 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
void obi_ini_to_NA_values(OBIDMS_column_p column, size_t first_line_nb, size_t nb_lines); // TO make private?
void obi_ini_to_NA_values(OBIDMS_column_p column, index_t first_line_nb, index_t nb_lines); // TO make private?
/**
@ -333,7 +335,7 @@ int obi_unmap_header(OBIDMS_column_header_p header);
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
size_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const char* element_name);
index_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const char* element_name);
/**

16
src/obidmscolumn_bool.c
View File

@ -28,7 +28,7 @@
*
**********************************************************************/
int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obibool_t value)
int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, obibool_t value)
{
// Check that the line number is not greater than the maximum allowed
if (line_nb >= MAXIMUM_LINE_COUNT)
@ -57,7 +57,7 @@ int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column, size_t line_nb,
}
obibool_t obi_column_get_obibool_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx)
obibool_t obi_column_get_obibool_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
{
if ((line_nb+1) > (column->header)->lines_used)
{
@ -69,23 +69,23 @@ 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, const char* element_name, obibool_t value)
int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, obibool_t value)
{
size_t element_idx;
index_t element_idx;
element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == SIZE_MAX) //TODO
if (element_idx == OBIIdx_NA)
return -1;
obi_column_set_obibool_with_elt_idx(column, line_nb, element_idx, value);
return 0;
}
obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name)
obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
{
size_t element_idx;
index_t element_idx;
element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == SIZE_MAX) //TODO
if (element_idx == OBIIdx_NA)
return OBIBool_NA;
return obi_column_get_obibool_with_elt_idx(column, line_nb, element_idx);
}

10
src/obidmscolumn_bool.h
View File

@ -38,7 +38,7 @@
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obibool_t value);
int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column, index_t line_nb, size_t element_idx, obibool_t value);
/**
@ -54,7 +54,7 @@ int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column, size_t line_nb,
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
obibool_t obi_column_get_obibool_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx);
obibool_t obi_column_get_obibool_with_elt_idx(OBIDMS_column_p column, index_t line_nb, size_t element_idx);
/**
@ -66,7 +66,6 @@ obibool_t obi_column_get_obibool_with_elt_idx(OBIDMS_column_p column, size_t lin
* @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.
*
* @returns An integer value indicating the success of the operation.
@ -76,7 +75,7 @@ obibool_t obi_column_get_obibool_with_elt_idx(OBIDMS_column_p column, size_t lin
* @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, const char* element_name, obibool_t value);
int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, obibool_t value);
/**
@ -86,7 +85,6 @@ int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column, size_t line_nb,
* @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.
*
* @returns The recovered value.
* @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
@ -94,7 +92,7 @@ int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column, size_t line_nb,
* @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, const char* element_name);
obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
#endif /* OBIDMSCOLUMN_BOOL_H_ */

16
src/obidmscolumn_char.c
View File

@ -28,7 +28,7 @@
*
**********************************************************************/
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, index_t line_nb, index_t element_idx, obichar_t value)
{
// Check that the line number is not greater than the maximum allowed
if (line_nb >= MAXIMUM_LINE_COUNT)
@ -57,7 +57,7 @@ int obi_column_set_obichar_with_elt_idx(OBIDMS_column_p column, size_t line_nb,
}
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, index_t line_nb, index_t element_idx)
{
if ((line_nb+1) > (column->header)->lines_used)
{
@ -69,23 +69,23 @@ 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, const char* element_name, obichar_t value)
int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, obichar_t value)
{
size_t element_idx;
index_t element_idx;
element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == SIZE_MAX) //TODO
if (element_idx == OBIIdx_NA)
return -1;
obi_column_set_obichar_with_elt_idx(column, line_nb, element_idx, value);
return 0;
}
obichar_t obi_column_get_obichar_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name)
obichar_t obi_column_get_obichar_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
{
size_t element_idx;
index_t element_idx;
element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == SIZE_MAX) //TODO
if (element_idx == OBIIdx_NA)
return OBIChar_NA;
return obi_column_get_obichar_with_elt_idx(column, line_nb, element_idx);
}

10
src/obidmscolumn_char.h
View File

@ -38,7 +38,7 @@
* @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, index_t line_nb, index_t element_idx, obichar_t value);
/**
@ -54,7 +54,7 @@ int obi_column_set_obichar_with_elt_idx(OBIDMS_column_p column, size_t line_nb,
* @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, index_t line_nb, index_t element_idx);
/**
@ -66,7 +66,6 @@ obichar_t obi_column_get_obichar_with_elt_idx(OBIDMS_column_p column, size_t lin
* @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.
*
* @returns An integer value indicating the success of the operation.
@ -76,7 +75,7 @@ obichar_t obi_column_get_obichar_with_elt_idx(OBIDMS_column_p column, size_t lin
* @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, const char* element_name, obichar_t value);
int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, obichar_t value);
/**
@ -86,7 +85,6 @@ int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column, size_t line_nb,
* @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.
*
* @returns The recovered value.
* @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
@ -94,7 +92,7 @@ int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column, size_t line_nb,
* @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, const char* element_name);
obichar_t obi_column_get_obichar_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
#endif /* OBIDMSCOLUMN_CHAR_H_ */

16
src/obidmscolumn_float.c
View File

@ -28,7 +28,7 @@
*
**********************************************************************/
int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obifloat_t value)
int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, obifloat_t value)
{
// Check that the line number is not greater than the maximum allowed
if (line_nb >= MAXIMUM_LINE_COUNT)
@ -57,7 +57,7 @@ int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column, size_t line_nb,
}
obifloat_t obi_column_get_obifloat_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx)
obifloat_t obi_column_get_obifloat_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
{
if ((line_nb+1) > (column->header)->lines_used)
{
@ -69,23 +69,23 @@ 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, const char* element_name, obifloat_t value)
int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, obifloat_t value)
{
size_t element_idx;
index_t element_idx;
element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == SIZE_MAX) //TODO
if (element_idx == OBIIdx_NA)
return -1;
obi_column_set_obifloat_with_elt_idx(column, line_nb, element_idx, value);
return 0;
}
obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name)
obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
{
size_t element_idx;
index_t element_idx;
element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == SIZE_MAX) //TODO
if (element_idx == OBIIdx_NA)
return OBIFloat_NA;
return obi_column_get_obifloat_with_elt_idx(column, line_nb, element_idx);
}

10
src/obidmscolumn_float.h
View File

@ -38,7 +38,7 @@
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obifloat_t value);
int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, obifloat_t value);
/**
@ -54,7 +54,7 @@ int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column, size_t line_nb,
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
obifloat_t obi_column_get_obifloat_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx);
obifloat_t obi_column_get_obifloat_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx);
/**
@ -66,7 +66,6 @@ obifloat_t obi_column_get_obifloat_with_elt_idx(OBIDMS_column_p column, size_t l
* @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.
*
* @returns An integer value indicating the success of the operation.
@ -76,7 +75,7 @@ obifloat_t obi_column_get_obifloat_with_elt_idx(OBIDMS_column_p column, size_t l
* @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, const char* element_name, obifloat_t value);
int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, obifloat_t value);
/**
@ -86,7 +85,6 @@ int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, size_t line_nb
* @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.
*
* @returns The recovered value.
* @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
@ -94,7 +92,7 @@ int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, size_t line_nb
* @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, const char* element_name);
obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
#endif /* OBIDMSCOLUMN_FLOAT_H_ */

16
src/obidmscolumn_int.c
View File

@ -28,7 +28,7 @@
*
**********************************************************************/
int obi_column_set_obiint_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obiint_t value)
int obi_column_set_obiint_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, obiint_t value)
{
// Check that the line number is not greater than the maximum allowed
if (line_nb >= MAXIMUM_LINE_COUNT)
@ -57,7 +57,7 @@ int obi_column_set_obiint_with_elt_idx(OBIDMS_column_p column, size_t line_nb, s
}
obiint_t obi_column_get_obiint_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx)
obiint_t obi_column_get_obiint_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
{
if ((line_nb+1) > (column->header)->lines_used)
{
@ -69,23 +69,23 @@ 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, const char* element_name, obiint_t value)
int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, obiint_t value)
{
size_t element_idx;
index_t element_idx;
element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == SIZE_MAX) //TODO
if (element_idx == OBIIdx_NA)
return -1;
obi_column_set_obiint_with_elt_idx(column, line_nb, element_idx, value);
return 0;
}
obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name)
obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
{
size_t element_idx;
index_t element_idx;
element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == SIZE_MAX) //TODO
if (element_idx == OBIIdx_NA)
return OBIInt_NA;
return obi_column_get_obiint_with_elt_idx(column, line_nb, element_idx);
}

10
src/obidmscolumn_int.h
View File

@ -38,7 +38,7 @@
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_column_set_obiint_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obiint_t value);
int obi_column_set_obiint_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, obiint_t value);
/**
@ -54,7 +54,7 @@ int obi_column_set_obiint_with_elt_idx(OBIDMS_column_p column, size_t line_nb, s
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
obiint_t obi_column_get_obiint_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx);
obiint_t obi_column_get_obiint_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx);
/**
@ -66,7 +66,6 @@ obiint_t obi_column_get_obiint_with_elt_idx(OBIDMS_column_p column, size_t line_
* @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.
*
* @returns An integer value indicating the success of the operation.
@ -76,7 +75,7 @@ obiint_t obi_column_get_obiint_with_elt_idx(OBIDMS_column_p column, size_t line_
* @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, const char* element_name, obiint_t value);
int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, obiint_t value);
/**
@ -86,7 +85,6 @@ int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column, size_t line_nb,
* @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.
*
* @returns The recovered value.
* @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
@ -94,7 +92,7 @@ int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column, size_t line_nb,
* @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, const char* element_name);
obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
#endif /* OBIDMSCOLUMN_INT_H_ */

43
src/obidmscolumn_str.c
View File

@ -6,7 +6,7 @@
* @file obidsmcolumn_str.c
* @author Celine Mercier
* @date October 28th 2015
* @brief Functions handling OBIColumns containing data with the OBIType OBI_IDX.
* @brief Functions handling OBIColumns containing data in the form of indices referring to character strings.
*/
@ -29,7 +29,7 @@
*
**********************************************************************/
int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, char* value)
int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, char* value)
{
byte_t* value_b;
index_t idx;
@ -59,31 +59,24 @@ int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column, size_t line_nb, s
if (value_b == NULL)
return -1;
obidebug(1, "\nvalue=%s", value);
//obidebug(1, "\nbytes=%s", value_b+5);
// Add in the obiarray
idx = obi_array_add(column->array, value_b);
if (idx == -1)
return -1;
obidebug(1, "\nidx=%d", idx);
//obidebug(1, "\nbytes 2=%s", obi_array_get(column->array, idx)+5);
// Add the value's index in the column
*(((obiidx_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = idx;
*(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = idx;
// TODO free value_b probably
free(value_b);
return 0;
}
const char* obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx)
const char* obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
{
index_t idx;
byte_t* value_b;
const char* value;
if ((line_nb+1) > (column->header)->lines_used)
{
@ -92,32 +85,22 @@ const char* obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column, size_t li
return "\0"; // TODO
}
idx = *(((obiidx_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
idx = *(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
// Check NA
if (idx == OBIIdx_NA)
return "\0"; // TODO
obidebug(1, "\nwhy, idx = %d", idx);
value_b = obi_array_get(column->array, idx);
obidebug(1, "\nwhyyyy");
value = obi_obibytes_to_str(value_b);
obidebug(1, "\nwhyyyyyyyyyyyy, value=%s %p", value, value);
obidebug(1, "\nwhyyyyyyyyyyyy, len value=%d", strlen(value));
return value;
return obi_obibytes_to_str(value_b);
}
int obi_column_set_obistr_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name, char* value)
int obi_column_set_obistr_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, char* value)
{
size_t element_idx;
index_t element_idx;
element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == SIZE_MAX) //TODO
if (element_idx == OBIIdx_NA)
return -1;
if (obi_column_set_obistr_with_elt_idx(column, line_nb, element_idx, value) < 0)
return -1;
@ -125,12 +108,12 @@ int obi_column_set_obistr_with_elt_name(OBIDMS_column_p column, size_t line_nb,
}
const char* obi_column_get_obistr_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name)
const char* obi_column_get_obistr_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
{
size_t element_idx;
index_t element_idx;
element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == SIZE_MAX) //TODO
if (element_idx == OBIIdx_NA)
return "\0";
return obi_column_get_obistr_with_elt_idx(column, line_nb, element_idx);
}

48
src/obidmscolumn_str.h
View File

@ -1,17 +1,17 @@
/****************************************************************************
* OBIDMS_column_idx header file *
* OBIDMS_column_str header file *
****************************************************************************/
/**
* @file obidsmcolumn_idx.h
* @file obidsmcolumn_str.h
* @author Celine Mercier
* @date August 10th 2015
* @brief Header file for the functions handling OBIColumns containing data with the OBIType OBI_IDX.
* @date October 28th 2015
* @brief Header file for the functions handling OBIColumns containing data in the form of indices referring to character strings.
*/
#ifndef OBIDMSCOLUMN_IDX_H_
#define OBIDMSCOLUMN_IDX_H_
#ifndef OBIDMSCOLUMN_STR_H_
#define OBIDMSCOLUMN_STR_H_
#include <stdlib.h>
@ -22,7 +22,8 @@
/**
* @brief Sets a value in an OBIDMS column containing data with the type OBI_IDX, using the index of the element in the line.
* @brief Sets a value in an OBIDMS column containing data in the form of indices referring
* to character strings in an obiarray, using the index of the element in the line.
*
* @warning Pointers returned by obi_open_column() don't allow writing.
*
@ -35,66 +36,65 @@
* @retval 0 on success.
* @retval -1 if an error occurred.
*
* @since July 2015
* @since October 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_column_set_obiidx_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, void* value);
int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, char* value);
/**
* @brief Recovers a value in an OBIDMS column containing data with the type OBI_IDX.
* @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
* to character strings in an obiarray, using the index of the element in the line.
*
* @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.
*
* @returns The recovered value.
* @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
* @retval '\0' the NA value of the type if an error occurred and obi_errno is set.
*
* @since July 2015
* @since October 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
const char* obi_column_get_obiidx_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx);
const char* obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx);
/**
* @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 in the form of indices referring
* to character strings in an obiarray, using the name of the element in the line.
*
* @warning Pointers returned by obi_open_column() don't allow writing.
*
* @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.
*
* @returns An integer value indicating the success of the operation.
* @retval 0 on success.
* @retval -1 if an error occurred.
*
* @since August 2015
* @since October 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_column_set_obiidx_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name, void* value);
int obi_column_set_obistr_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, char* 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 in the form of indices referring
* to character strings in an obiarray, using the name of the element in the line.
*
* @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.
*
* @returns The recovered value.
* @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
* @retval '\0' the NA value of the type if an error occurred and obi_errno is set.
*
* @since August 2015
* @since October 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
const char* obi_column_get_obiidx_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name);
const char* obi_column_get_obistr_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
#endif /* OBIDMSCOLUMN_IDX_H_ */

2
src/obierrno.h
View File

@ -98,7 +98,7 @@ extern int obi_errno;
*/
#define OBICOL_ACCESS_ERROR (19) /**< Permission error trying to access an OBIDSM column directory
*/
#define OBI_ARRAY_ERROR (20) /** Error while handling a heap
#define OBI_ARRAY_ERROR (20) /** Error while handling an array
*/
/**@}*/

4
src/obitypes.c
View File

@ -40,7 +40,7 @@ size_t obi_sizeof(OBIType_t type)
case OBI_CHAR: size = sizeof(obichar_t);
break;
case OBI_IDX: size = sizeof(obiidx_t);
case OBI_IDX: size = sizeof(index_t);
break;
default: size = 0;
@ -50,7 +50,7 @@ size_t obi_sizeof(OBIType_t type)
}
size_t obi_array_sizeof(OBIType_t type, size_t nb_lines, size_t nb_elements_per_line)
size_t obi_array_sizeof(OBIType_t type, index_t nb_lines, index_t nb_elements_per_line)
{
size_t size;
size_t rsize;

8
src/obitypes.h
View File

@ -19,7 +19,7 @@
#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 OBIIdx_NA (INT64_MIN) /**< NA value for indices */
#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
@ -44,14 +44,14 @@ typedef enum OBIType {
OBI_FLOAT, /**< a floating value (C type : double) */
OBI_BOOL, /**< a boolean true/false value, see obibool_t enum */
OBI_CHAR, /**< a character (C type : char) */
OBI_IDX /**< an index in a data structure (C type : size_t) */
OBI_IDX /**< an index in a data structure (C type : int64_t) */
} OBIType_t, *OBIType_p;
typedef int64_t index_t;
typedef int32_t obiint_t;
typedef double obifloat_t;
typedef char obichar_t;
typedef size_t obiidx_t;
/**
@ -107,7 +107,7 @@ size_t obi_sizeof(OBIType_t type);
* @since May 2015
* @author Eric Coissac (eric.coissac@metabarcoding.org)
*/
size_t obi_array_sizeof(OBIType_t data_type, size_t nb_lines, size_t nb_elements_per_line);
size_t obi_array_sizeof(OBIType_t data_type, index_t nb_lines, index_t nb_elements_per_line);
/**