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Added the possibility to clone a column, with or without its data

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This commit is contained in:
Celine Mercier
2015-08-26 10:29:07 +02:00
parent e6d96d999a
commit 9ad31fddff
4 changed files with 110 additions and 35 deletions
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3
python/obitools3/obidms/obidmscolumn/capidmscolumn.pxd
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@ -35,7 +35,8 @@ cdef extern from "obidmscolumn.h" nogil:
OBIType_t obi_column_get_type(OBIDMS_column_p column) OBIType_t obi_column_get_type(OBIDMS_column_p column)
int obi_close_column(OBIDMS_column_p column) int obi_close_column(OBIDMS_column_p column)
OBIType_t obi_column_get_data_type_from_name(OBIDMS_p dms, const char* column_name) OBIType_t obi_column_get_data_type_from_name(OBIDMS_p dms, const char* column_name)
OBIDMS_column_p obi_clone_column(OBIDMS_p dms, const char* column_name, obiversion_t version_number, bint clone_data)
cdef class OBIDMS_column: cdef class OBIDMS_column:
cdef OBIDMS_column_p pointer cdef OBIDMS_column_p pointer

66
python/obitools3/obidms/obidmscolumn/capidmscolumn.pyx
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@ -12,9 +12,10 @@ cdef class OBIDMS_column:
#Should only be initialized through a subclass (or open()) #Should only be initialized through a subclass (or open())
def __init__(self, dms_name, column_name, def __init__(self, dms_name, column_name,
create, version_number, create, clone, clone_data,
type, nb_elements, version_number, type,
nb_elements_per_line, elements_names): nb_elements, nb_elements_per_line,
elements_names):
column_name_b = column_name.encode(encoding='UTF-8') column_name_b = column_name.encode(encoding='UTF-8')
dms_name_b = dms_name.encode(encoding='UTF-8') dms_name_b = dms_name.encode(encoding='UTF-8')
self.dms_name = dms_name self.dms_name = dms_name
@ -31,13 +32,10 @@ cdef class OBIDMS_column:
else : else :
dms = obi_open_dms(dms_name_b) dms = obi_open_dms(dms_name_b)
self.dms = dms self.dms = dms
self.pointer = obi_open_column(self.dms, column_name_b, version_number) if clone :
self.pointer = obi_clone_column(self.dms, column_name_b, version_number, clone_data)
def create(self, dms_name, column_name, type, nb_elements, nb_elements_per_line=1, elements_names=None): else :
if elements_names == None : self.pointer = obi_open_column(self.dms, column_name_b, version_number)
elements_names = column_name
self.dms = obi_dms(dms_name)
self.pointer = obi_create_column(self.dms, column_name, type, nb_elements, nb_elements_per_line, elements_names)
def __iter__(self): def __iter__(self):
elements_names = self.get_elements_names() elements_names = self.get_elements_names()
@ -78,9 +76,10 @@ cdef class OBIDMS_column:
@staticmethod @staticmethod
def open(dms_name, column_name, def open(dms_name, column_name,
create=False, version_number=-1, create=False, clone=False, clone_data=True,
type=None, nb_elements=None, version_number=-1, type=None,
nb_elements_per_line=1, elements_names=None): nb_elements=None, nb_elements_per_line=1,
elements_names=None):
column_name_b = column_name.encode(encoding='UTF-8') column_name_b = column_name.encode(encoding='UTF-8')
dms_name_b = dms_name.encode(encoding='UTF-8') dms_name_b = dms_name.encode(encoding='UTF-8')
@ -94,39 +93,44 @@ cdef class OBIDMS_column:
if type == 1 : if type == 1 :
column = OBIDMS_column_int(dms_name, column_name, column = OBIDMS_column_int(dms_name, column_name,
create, version_number, create, clone, clone_data,
type, nb_elements, version_number, type,
nb_elements_per_line, elements_names) nb_elements, nb_elements_per_line,
elements_names)
elif type == 2 : elif type == 2 :
column = OBIDMS_column_float(dms_name, column_name, column = OBIDMS_column_float(dms_name, column_name,
create, version_number, create, clone, clone_data,
type, nb_elements, version_number, type,
nb_elements_per_line, elements_names) nb_elements, nb_elements_per_line,
elements_names)
elif type == 3 : elif type == 3 :
column = OBIDMS_column_bool(dms_name, column_name, column = OBIDMS_column_bool(dms_name, column_name,
create, version_number, create, clone, clone_data,
type, nb_elements, version_number, type,
nb_elements_per_line, elements_names) nb_elements, nb_elements_per_line,
elements_names)
# elif type == 4 : # elif type == 4 :
# column = OBIDMS_column_char(dms_name, column_name, # column = OBIDMS_column_char(dms_name, column_name,
# create, version_number, # create, clone, clone_data,
# type, nb_elements, # version_number, type,
# nb_elements_per_line, elements_names) # nb_elements, nb_elements_per_line,
# elements_names)
elif type == 5 : elif type == 5 :
column = OBIDMS_column_idx(dms_name, column_name, column = OBIDMS_column_idx(dms_name, column_name,
create, version_number, create, clone, clone_data,
type, nb_elements, version_number, type,
nb_elements_per_line, elements_names) nb_elements, nb_elements_per_line,
elements_names)
else : else :
"Problem with the data type" "Problem with the data type"
return column return column

55
src/obidmscolumn.c
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@ -723,6 +723,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
header->data_type = type; header->data_type = type;
header->creation_date = time(NULL); header->creation_date = time(NULL);
header->version = version_number; header->version = version_number;
header->cloned_from = -1;
header->comments[0] = 0x0; header->comments[0] = 0x0;
obi_column_set_elements_names(new_column, elements_names); obi_column_set_elements_names(new_column, elements_names);
@ -813,7 +814,7 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms, const char* column_name, obiversio
column->header = mmap(NULL, column->header = mmap(NULL,
header_size, header_size,
PROT_READ, PROT_READ,
MAP_SHARED, MAP_PRIVATE,
column_file_descriptor, column_file_descriptor,
0 0
); );
@ -836,7 +837,7 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms, const char* column_name, obiversio
column->data = mmap(NULL, column->data = mmap(NULL,
data_size, data_size,
PROT_READ, PROT_READ,
MAP_SHARED, MAP_PRIVATE,
column_file_descriptor, column_file_descriptor,
header_size header_size
); );
@ -861,9 +862,59 @@ 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 column_to_clone;
OBIDMS_column_p new_column;
size_t nb_lines;
size_t nb_elements_per_line;
OBIType_t data_type;
column_to_clone = obi_open_column(dms, column_name, version_number);
if (column_to_clone == NULL)
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError opening the column to clone");
return NULL;
}
if (clone_data)
nb_lines = (column_to_clone->header)->line_count;
else
nb_lines = INITIAL_LINE_COUNT;
nb_elements_per_line = (column_to_clone->header)->nb_elements_per_line;
data_type = (column_to_clone->header)->data_type;
new_column = obi_create_column(dms,
column_name,
data_type,
nb_lines,
nb_elements_per_line,
(column_to_clone->header)->elements_names);
if (new_column == NULL)
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError creating the new column when cloning a column");
// TODO the new file should be deleted
return NULL;
}
(new_column->header)->cloned_from = version_number;
// TODO copy header->comments?
if (clone_data)
memcpy(new_column->data, column_to_clone->data, nb_lines*nb_elements_per_line*sizeof(data_type));
return new_column;
}
int obi_close_column(OBIDMS_column_p column) int obi_close_column(OBIDMS_column_p column)
{ {
//munmap? TODO //munmap? TODO
//truncate to lines used TODO
free(column); free(column);
return 0; return 0;
} }

21
src/obidmscolumn.h
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@ -17,6 +17,7 @@
#include <unistd.h> #include <unistd.h>
#include <stdbool.h> #include <stdbool.h>
#include <time.h> #include <time.h>
#include <stdbool.h>
#include "obidms.h" #include "obidms.h"
#include "obitypes.h" #include "obitypes.h"
@ -25,6 +26,7 @@
#include "obidmscolumndir.h" #include "obidmscolumndir.h"
#define ELEMENTS_NAMES_MAX (2048) #define ELEMENTS_NAMES_MAX (2048)
#define INITIAL_LINE_COUNT (1000)
typedef int32_t obiversion_t; /**< Used to store the column version number typedef int32_t obiversion_t; /**< Used to store the column version number
@ -49,6 +51,7 @@ typedef struct OBIDMS_column_header {
OBIType_t data_type; /**< type of the data */ OBIType_t data_type; /**< type of the data */
time_t creation_date; /**< date of creation of the file */ time_t creation_date; /**< date of creation of the file */
obiversion_t version; /**< version of the OBIColumn */ 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 char name[OBIDMS_MAX_COLNAME+1]; /**< The column name as a NULL
* terminated string. * terminated string.
*/ */
@ -148,7 +151,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
* *
* @param dms a pointer on an OBIDMS * @param dms a pointer on an OBIDMS
* @param column_name the name of the column * @param column_name the name of the column
* @param version_number the version of the column that should be opened * @param version_number the version of the column that should be opened (if -1, the latest version number is retrieved)
* *
* @return a pointer to the opened column * @return a pointer to the opened column
* *
@ -158,6 +161,22 @@ 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);
/**
* @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
*
* @return a pointer to the created column
*
* @since August 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
OBIDMS_column_p obi_clone_column(OBIDMS_p dms, const char* column_name, obiversion_t version_number, bool clone_data);
/** /**
* @brief Closes a column. * @brief Closes a column.
* *