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obi arrays that don't work because of cython bug passing wrong pointers

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This commit is contained in:
Celine Mercier
2015-11-03 14:22:00 +01:00
parent ecb9d97adb
commit 456551ffeb
25 changed files with 1669 additions and 128 deletions
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77
src/obidmscolumn.c
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@ -16,6 +16,7 @@
#include <sys/types.h>
#include <dirent.h>
#include <unistd.h>
#include <time.h>
#include <fcntl.h>
#include <stdbool.h>
#include <math.h>
@ -28,6 +29,7 @@
#include "obierrno.h"
#include "obidebug.h"
#include "obilittlebigman.h"
#include "obiarray.h"
#define DEBUG_LEVEL 0 // TODO has to be defined somewhere else (cython compil flag?)
@ -151,35 +153,35 @@ static size_t get_line_count_per_page(OBIType_t data_type, size_t nb_elements_pe
************************************************************************/
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)
{
char *filename;
char* file_name;
// Build the database directory name
if (asprintf(&filename,"%s@%d.odc", column_name, version_number) < 0)
// Build the file name
if (asprintf(&file_name,"%s@%d.odc", column_name, version_number) < 0)
{
obi_set_errno(OBICOL_MEMORY_ERROR);
obidebug(1, "\nError building a column file name");
return NULL;
}
return filename;
return file_name;
}
static char *build_version_file_name(const char *column_name)
static char* build_version_file_name(const char* column_name)
{
char *filename;
char* file_name;
// Build the database directory name
if (asprintf(&filename,"%s.odv", column_name) < 0)
// Build the file name
if (asprintf(&file_name,"%s.odv", column_name) < 0)
{
obi_set_errno(OBICOL_MEMORY_ERROR);
obidebug(1, "\nError building a version file name");
return NULL;
}
return filename;
return file_name;
}
@ -602,11 +604,13 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
OBIType_t data_type,
size_t nb_lines,
size_t nb_elements_per_line,
const char* elements_names)
const char* elements_names,
const char* array_name)
{
OBIDMS_column_p new_column;
OBIDMS_column_directory_p column_directory;
OBIDMS_column_header_p header;
OBIDMS_array_p array;
size_t file_size;
obiversion_t version_number;
char* column_file_name;
@ -629,17 +633,23 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
obidebug(1, "\nCan't create column because of empty column name");
return NULL;
}
if ((data_type < 1) || (data_type > 4))
if ((data_type < 1) || (data_type > 5))
{
obidebug(1, "\nCan't create column because of invalid data type");
return NULL;
}
if ((data_type == 5) && (array_name == NULL))
{
obidebug(1, "\nCan't create column because of empty array name");
return NULL;
}
// The initial line count should be between the minimum (corresponding to the page size) and the maximum allowed
minimum_line_count = get_line_count_per_page(data_type, nb_elements_per_line);
if (nb_lines > MAXIMUM_LINE_COUNT)
{
obidebug(1, "\nCan't create column because of line count greater than the maximum allowed (%ld)", MAXIMUM_LINE_COUNT);
obidebug(1, "\nCan't create column because of line count greater than the maximum allowed (%d)", MAXIMUM_LINE_COUNT);
return NULL;
}
else if (nb_lines < minimum_line_count)
@ -800,6 +810,23 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
strncpy(header->name, column_name, OBIDMS_COLUMN_MAX_NAME);
// If the data type is OBI_IDX, the associated obi_array is opened or created
if (data_type == 5)
{
array = obi_array(dms, array_name);
if (array == NULL)
{
obidebug(1, "\nError opening or creating the array associated with a column");
munmap(new_column->header, header_size);
close(column_file_descriptor);
free(column_file_name);
free(new_column);
return NULL;
}
new_column->array = array;
strncpy(header->array_name, array_name, ARRAY_MAX_NAME);
}
// Fill the data with NA values
obi_ini_to_NA_values(new_column, 0, nb_lines);
@ -816,6 +843,7 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms,
{
OBIDMS_column_p column;
OBIDMS_column_directory_p column_directory;
OBIDMS_array_p array;
char* column_file_name;
int column_file_descriptor;
int column_dir_file_descriptor;
@ -931,6 +959,22 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms,
column->writable = false;
// If the data type is OBI_IDX, the associated obi_array is opened or created
if ((column->header)->data_type == 5)
{
array = obi_array(dms, (column->header)->array_name);
if (array == NULL)
{
obidebug(1, "\nError opening the array associated with a column");
munmap(column->header, header_size);
close(column_file_descriptor);
free(column_file_name);
free(column);
return NULL;
}
column->array = array;
}
free(column_file_name);
close(column_file_descriptor);
@ -972,7 +1016,8 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p dms,
data_type,
nb_lines,
nb_elements_per_line,
(column_to_clone->header)->elements_names);
(column_to_clone->header)->elements_names,
(column_to_clone->header)->array_name);
if (new_column == NULL)
{
@ -1170,7 +1215,7 @@ int obi_enlarge_column(OBIDMS_column_p column)
// Calculate the new file size
old_line_count = (column->header)->line_count;
new_line_count = old_line_count * GROWTH_FACTOR;
new_line_count = old_line_count * COLUMN_GROWTH_FACTOR;
if (new_line_count > MAXIMUM_LINE_COUNT)
{
@ -1181,7 +1226,7 @@ int obi_enlarge_column(OBIDMS_column_p column)
return -1;
}
old_data_size = obi_array_sizeof((column->header)->data_type, old_line_count, (column->header)->nb_elements_per_line);
new_data_size = old_data_size * GROWTH_FACTOR;
new_data_size = old_data_size * COLUMN_GROWTH_FACTOR;
header_size = (column->header)->header_size;
file_size = header_size + new_data_size;