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C sources modified to add the handling of OBIDM columns with the type

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OBI_INT, and the handling of multiple types in general
This commit is contained in:
celinemercier
2015-07-31 18:03:48 +02:00
parent a6abc74500
commit 5f62cd8526
6 changed files with 684 additions and 10 deletions
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48
src/obidms.c
View File

@ -14,6 +14,10 @@
#include "obidms.h"
#include "obierrno.h"
#include "obidebug.h"
#include "obidmscolumn.h"
#define DEBUG_LEVEL 0
/**************************************************************************
@ -148,6 +152,7 @@ OBIDMS_p obi_open_dms(const char* dms_name)
directory = opendir(directory_name);
if (directory == NULL)
{
obidebug(1, "Can't open DMS");
switch (errno)
{
case ENOENT:
@ -206,6 +211,49 @@ OBIDMS_p obi_dms(const char* dms_name)
}
int obi_list_columns(OBIDMS_p dms)
{
DIR *d;
struct dirent *dir;
char* dir_name;
char* extension;
OBIType_t data_type;
obiversion_t latest_version;
d = dms->directory;
dir = readdir(d);
fprintf(stderr, "Column name\tData type\tLatest version");
while (dir != NULL)
{
dir_name = strdup(dir->d_name);
if (dir_name == NULL)
{
obidebug(1, "\nError strdup-ing a directory name");
return -1;
}
dir_name = strtok(dir_name, ".");
extension = strtok(NULL, ".");
if ((extension != NULL) && (strcmp("obicol", extension) == 0))
// Found a column directory
{
data_type = obi_column_get_data_type_from_name(dms, dir_name);
latest_version = obi_column_get_latest_version_from_name(dms, dir_name);
fprintf(stderr, "\n%s\t%d\t%d", dir_name, data_type, latest_version);
}
dir = readdir(d);
}
rewinddir(d);
return(0);
}
int obi_close_dms(OBIDMS_p dms)
{
if (dms != NULL)

17
src/obidms.h
View File

@ -126,6 +126,23 @@ OBIDMS_p obi_open_dms(const char *dms_name);
OBIDMS_p obi_dms(const char *dms_name);
/**
* @brief Lists all the column directories in the OBIDMS, their data type and
* their latest version.
*
* @param dms a pointer as returned by obi_create_dms() or obi_open_dms().
*
* @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.
*
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_list_columns(OBIDMS_p dms);
/**
* @brief Closes an opened OBITools Data Management instance (OBIDMS).
*

379
src/obidmscolumn.c
View File

@ -3,7 +3,7 @@
****************************************************************************/
/**
* @file OBIDMS_column.h
* @file obidmscolumn.c
* @author Celine Mercier
* @date 22 May 2015
* @brief Functions for the shared elements of all the OBIColumn structures.
@ -12,6 +12,7 @@
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <sys/types.h>
#include <dirent.h>
#include <unistd.h>
@ -27,6 +28,11 @@
#include "obidebug.h"
#include "obilittlebigman.h"
#include "obidmscolumn_int.h"
#define DEBUG_LEVEL 0
/**************************************************************************
*
@ -115,13 +121,28 @@ static obiversion_t obi_get_new_version_number(OBIDMS_column_directory_p column_
static int create_version_file(OBIDMS_column_directory_p column_directory);
/**
* @brief Internal function setting the elements names of the lines of a
* column in the header of the OBIDMS column structure.
*
* @param column a pointer as returned by obi_create_column()
* @param elements_names the names of the elements with ';' as separator
*
* @return 0 if the operation was successfully completed
* @retvalue -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);
/************************************************************************
*
* D E F I N I T I O N O F T H E P R I V A T E F U N C T I O N S
*
************************************************************************/
#define DEBUG_LEVEL 0
static char *build_column_file_name(const char *column_name, obiversion_t version_number)
{
@ -423,6 +444,16 @@ static int create_version_file(OBIDMS_column_directory_p column_directory)
}
int obi_column_set_elements_names(OBIDMS_column_p column, const char* elements_names)
{
(column->header)->elements_names = malloc(strlen(elements_names)*sizeof(char) + 1);
if ((column->header)->elements_names == NULL)
return -1;
strcpy((column->header)->elements_names, elements_names);
return 0;
}
/**********************************************************************
*
* D E F I N I T I O N O F T H E P U B L I C F U N C T I O N S
@ -521,6 +552,32 @@ obiversion_t obi_get_latest_version_number(OBIDMS_column_directory_p column_dire
}
obiversion_t obi_column_get_latest_version_from_name(OBIDMS_p dms, const char* column_name)
{
OBIDMS_column_directory_p column_directory;
obiversion_t latest_version;
// Get the column directory structure associated to the column
column_directory = obi_open_column_directory(dms, column_name);
if (column_directory == NULL)
{
obidebug(1, "\nProblem opening column directory");
return -1;
}
// Get the latest version number
latest_version = obi_get_latest_version_number(column_directory);
if (latest_version < 0)
{
obidebug(1, "\nProblem getting the latest version number");
obi_close_column_directory(column_directory);
return -1;
}
return latest_version;
}
size_t obi_get_platform_header_size()
{
return getpagesize() * 1;
@ -547,6 +604,8 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
new_column = NULL;
// TODO check that informations are not NULL/invalid
// Get the column directory structure associated to the column
column_directory = obi_column_directory(dms, column_name);
if (column_directory == NULL)
@ -673,8 +732,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
header->version = version_number;
header->comments[0] = 0x0;
header->elements_names = malloc(strlen(elements_names)*sizeof(char) + 1);
strcpy(header->elements_names, elements_names);
obi_column_set_elements_names(new_column, elements_names);
strncpy(header->name, column_name, OBIDMS_MAX_COLNAME);
@ -683,3 +741,316 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
return new_column;
}
OBIDMS_column_p obi_open_column(OBIDMS_p dms, const char* column_name, obiversion_t version_number)
{
OBIDMS_column_p column;
OBIDMS_column_directory_p column_directory;
char* column_file_name;
int column_file_descriptor;
int column_dir_file_descriptor;
size_t header_size;
size_t data_size;
column = NULL;
// Get the column directory structure associated to the column
column_directory = obi_open_column_directory(dms, column_name);
if (column_directory == NULL)
{
obidebug(1, "\nProblem opening column directory");
return NULL;
}
// Get the file descriptor associated to the column directory
column_dir_file_descriptor = dirfd(column_directory->directory);
if (column_dir_file_descriptor < 0)
{
obidebug(1, "\nProblem opening column directory");
obi_set_errno(OBICOLDIR_UNKNOWN_ERROR);
obi_close_column_directory(column_directory);
return NULL;
}
// Calculate the header size
header_size = obi_get_platform_header_size();
// Get the latest version number if it has the value -1 (not given by user)
if (version_number == -1)
{
version_number = obi_get_latest_version_number(column_directory);
if (version_number < 0)
{
obidebug(1, "\nProblem getting the latest version number");
obi_close_column_directory(column_directory);
close(column_dir_file_descriptor);
return NULL;
}
}
// Get the column file name
column_file_name = build_column_file_name(column_name, version_number);
if (column_file_name == NULL)
{
obidebug(1, "Problem building column file name");
obi_close_column_directory(column_directory);
close(column_dir_file_descriptor);
return NULL;
}
// Open the column file, ALWAYS READ-ONLY
column_file_descriptor = openat(column_dir_file_descriptor, column_file_name, O_RDONLY);
if (column_file_descriptor < 0)
{
obidebug(1, "\nCan't open column file");
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obi_close_column_directory(column_directory);
close(column_dir_file_descriptor);
free(column_file_name);
return NULL;
}
// Allocate the memory for the column structure
column = (OBIDMS_column_p) malloc(sizeof(OBIDMS_column_t));
if (column == NULL)
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obi_close_column_directory(column_directory);
close(column_dir_file_descriptor);
close(column_file_descriptor);
free(column_file_name);
return NULL;
}
// Fill the column structure
column->dms = dms;
column->column_directory = column_directory;
column->header = mmap(NULL,
header_size,
PROT_READ,
MAP_SHARED,
column_file_descriptor,
0
);
if (column->header == MAP_FAILED)
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obi_close_column_directory(column_directory);
close(column_dir_file_descriptor);
close(column_file_descriptor);
free(column_file_name);
free(column);
return NULL;
}
// Check endianness?
// Compute data size from the informations in the header
data_size = ((column->header)->line_count) * sizeof((column->header)->data_type); // TODO line_count for tests, change to lines_used later
column->data = mmap(NULL,
data_size,
PROT_READ,
MAP_SHARED,
column_file_descriptor,
header_size
);
if (column->data == MAP_FAILED)
{
munmap(column->header, header_size);
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obi_close_column_directory(column_directory);
close(column_dir_file_descriptor);
close(column_file_descriptor);
free(column_file_name);
free(column);
return NULL;
}
column->writable = false;
free(column_file_name);
close(column_file_descriptor);
return column;
}
int obi_close_column(OBIDMS_column_p column)
{
//munmap?
free(column);
return 0;
}
void obi_column_make_unwritable(OBIDMS_column_p column)
{
column->writable = false;
}
size_t obi_column_get_line_count(OBIDMS_column_p column)
{
return (column->header)->line_count;
}
OBIType_t obi_column_get_data_type(OBIDMS_column_p column)
{
return (column->header)->data_type;
}
OBIType_t obi_column_get_data_type_from_name(OBIDMS_p dms, const char* column_name)
{
OBIDMS_column_header_p header;
OBIDMS_column_directory_p column_directory;
char* column_file_name;
int column_file_descriptor;
int column_dir_file_descriptor;
size_t header_size;
OBIType_t data_type;
obiversion_t version_number;
// Get the column directory structure associated to the column
column_directory = obi_open_column_directory(dms, column_name);
if (column_directory == NULL)
{
obidebug(1, "\nProblem opening column directory");
return -1;
}
// Get the file descriptor associated to the column directory
column_dir_file_descriptor = dirfd(column_directory->directory);
if (column_dir_file_descriptor < 0)
{
obidebug(1, "\nProblem opening column directory");
obi_set_errno(OBICOLDIR_UNKNOWN_ERROR);
obi_close_column_directory(column_directory);
return -1;
}
// Calculate the header size
header_size = obi_get_platform_header_size();
// Get the latest version number
version_number = obi_get_latest_version_number(column_directory);
if (version_number < 0)
{
obidebug(1, "\nProblem getting the latest version number");
obi_close_column_directory(column_directory);
close(column_dir_file_descriptor);
return -1;
}
// Get the column file name
column_file_name = build_column_file_name(column_name, version_number);
if (column_file_name == NULL)
{
obidebug(1, "Problem building column file name");
obi_close_column_directory(column_directory);
close(column_dir_file_descriptor);
return -1;
}
// Open the column file (READ-ONLY)
column_file_descriptor = openat(column_dir_file_descriptor, column_file_name, O_RDONLY);
if (column_file_descriptor < 0)
{
obidebug(1, "\nCan't open column file");
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obi_close_column_directory(column_directory);
close(column_dir_file_descriptor);
free(column_file_name);
return -1;
}
// Fill the header structure
header = mmap(NULL,
header_size,
PROT_READ,
MAP_SHARED,
column_file_descriptor,
0
);
if (header == MAP_FAILED)
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obi_close_column_directory(column_directory);
close(column_dir_file_descriptor);
close(column_file_descriptor);
free(column_file_name);
free(header);
return -1;
}
// Check endianness?
data_type = header->data_type;
free(column_file_name);
close(column_file_descriptor);
munmap(header, header_size);
return data_type;
}
const char* obi_column_get_elements_names(OBIDMS_column_p column)
{
return (column->header)->elements_names;
}
// 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)
{
char* elements_names;
char* name;
size_t element_index;
elements_names = strdup((column->header)->elements_names);
if (elements_names == NULL)
{
obidebug(1, "\nError strdup-ing the elements names");
return -1;
}
element_index = 0;
name = strtok (elements_names, ";"); // not thread safe, see strtok_r maybe
if (strcmp(element_name, name) == 0)
{
free(elements_names);
return element_index;
}
element_index++;
while (name != NULL)
{
name = strtok (NULL, ";"); // not thread safe, see strtok_r maybe
if (strcmp(element_name, name) == 0)
{
free(elements_names);
return element_index;
}
element_index++;
}
obidebug(1, "\nCan't find element name");
free(elements_names);
return -1;
}
size_t obi_column_get_nb_elements_per_line(OBIDMS_column_p column)
{
return (column->header)->nb_elements_per_line;
}

142
src/obidmscolumn.h
View File

@ -86,6 +86,28 @@ typedef struct OBIDMS_column {
} OBIDMS_column_t, *OBIDMS_column_p;
/**
* @brief Returns the latest version of a column in a column directory
*
* @param column_directory
*
* @return the latest version number kept in the version file
* @return -1 if an error occurred
*/
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
*
* @param column_name
*
* @return the latest version number kept in the version file
* @return -1 if an error occurred
*/
obiversion_t obi_column_get_latest_version_from_name(OBIDMS_p dms, const char* column_name);
/**
* @brief Returns the header size in bytes of a column on this platform.
*
@ -103,7 +125,7 @@ size_t obi_get_platform_header_size();
/**
* @brief Creates a column.
*
* @param dms a pointer on an OBIDMS 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_elements the number of elements to be stored
@ -120,15 +142,123 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
/**
* @brief Returns the latest column version in the `dms` database
* @brief Opens a column in read-only mode.
*
* @param dms a pointer as returned by obi_create_dms() or obi_open_dms()
* @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
*
* @return the bigger version number used for this column
* @return -1 if the column does not exist
* @return a pointer to the opened column
*
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
obiversion_t obi_get_latest_version_number(OBIDMS_column_directory_p column_directory);
OBIDMS_column_p obi_open_column(OBIDMS_p dms, const char* column_name, obiversion_t version_number);
/**
* @brief Closes a column.
*
* @param column a pointer on an OBIDMS column
*
* @return 0 if the operation was successfully completed
* @return -1 if an error occurred
*
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_close_column(OBIDMS_column_p column);
/**
* @brief Sets the 'writable' header attribute of an OBIDMS column to False.
*
* @param column a pointer on an OBIDMS column
*
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
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
*
* @return the line count of the column
*
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
size_t obi_column_get_line_count(OBIDMS_column_p column);
/**
* @brief Recovers the data type of an OBIDMS column.
*
* @param column a pointer on an OBIDMS column
*
* @return the data type of the column
*
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
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
*
* @return the data type of the column
*
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
OBIType_t obi_column_get_data_type_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
*
* @return the elements names
*
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
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.
*
* @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
*
* @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);
/**
* @brief Recovers the number of elements per line in an OBIDMS column.
*
* @param column a pointer on an OBIDMS column
*
* @return the number of elements per line
*
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
size_t obi_column_get_nb_elements_per_line(OBIDMS_column_p column);
#endif /* OBIDMSCOLUMN_H_ */

49
src/obidmscolumn_int.c Normal file
View File

@ -0,0 +1,49 @@
/****************************************************************************
* OBIDMS_column_int functions *
****************************************************************************/
/**
* @file obidsmcolumn_int.c
* @author Celine Mercier
* @date July 21st 2015
* @brief Functions handling OBIColumns containing data with the OBIType OBI_INT.
*/
#include <stdlib.h>
#include <stdio.h>
#include "obidmscolumn.h"
#include "obitypes.h"
#include "obierrno.h"
#include "obidebug.h"
/**********************************************************************
*
* 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
*
**********************************************************************/
int obi_column_set_int(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obiint_t value)
{
// check if can write?
size_t nb_elements_per_line = -1;
nb_elements_per_line = (column->header)->nb_elements_per_line;
*(((obiint_t*) (column->data)) + (line_nb * nb_elements_per_line) + element_idx) = value;
return 0;
}
obiint_t obi_column_get_int(OBIDMS_column_p column, size_t line_nb, size_t element_idx)
{
size_t nb_elements_per_line = -1;
nb_elements_per_line = (column->header)->nb_elements_per_line;
return *(((obiint_t*) (column->data)) + (line_nb * nb_elements_per_line) + element_idx);
}
//obiint_t* obi_column_get_line_address_int(OBIDMS_column_p column, size_t nb_elements_per_line, size_t line_nb)
//{
// return (((obiint_t*) (column->data)) + (line_nb * nb_elements_per_line));
//}

59
src/obidmscolumn_int.h Normal file
View File

@ -0,0 +1,59 @@
/****************************************************************************
* OBIDMS_column_int header file *
****************************************************************************/
/**
* @file obidsmcolumn_int.h
* @author Celine Mercier
* @date July 21st 2015
* @brief Header file for the functions handling OBIColumns containing data with the OBIType OBI_INT.
*/
#include <stdlib.h>
#include <stdio.h>
#include "obidmscolumn.h"
#include "obitypes.h"
/**
* @brief Sets a value in an OBIDMS column containing data with the type OBI_INT.
*
* @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 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.
*
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_column_set_int(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obiint_t value);
/**
* @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 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
*
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
obiint_t obi_column_get_int(OBIDMS_column_p column, size_t line_nb, size_t element_idx);