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OBITools3
Commit ecb9d97a authored by Celine Mercier's avatar Celine Mercier
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Reorganized the code to have less functions, and the functions to get 

and format the creation date of a column are now working.
parent 0eaa5aa7
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Showing with 47 additions and 290 deletions
python/obitools3/obidms/_obidms.pxd
View file @ ecb9d97a
......@@ -41,6 +41,6 @@ cdef class OBIDMS_column:
cpdef list get_elements_names(self)
cpdef str get_data_type(self)
cpdef size_t get_nb_lines_used(self)
# cpdef str get_creation_date(self)
cpdef str get_creation_date(self)
cpdef close(self)
python/obitools3/obidms/_obidms.pyx
View file @ ecb9d97a
......@@ -6,17 +6,15 @@ from obitools3.utils cimport bytes2str, str2bytes
from .capi.obidms cimport obi_dms, \
obi_close_dms
from .capi.obidmscolumn cimport obi_column_get_nb_lines_used, \
obi_column_get_elements_names, \
obi_column_get_header_from_name, \
from .capi.obidmscolumn cimport obi_column_get_header_from_name, \
obi_unmap_header, \
obi_column_get_latest_version_from_name, \
obi_create_column, \
obi_clone_column, \
obi_open_column, \
obi_close_column, \
obi_column_format_date, \
OBIDMS_column_header_p
#obi_column_get_formatted_creation_date
from .capi.obitypes cimport const_char_p, \
name_data_type
......@@ -28,7 +26,7 @@ from ._obidmscolumn_int cimport OBIDMS_column_int, \
OBIDMS_column_int_writable, \
OBIDMS_column_int_multi_elts, \
OBIDMS_column_int_multi_elts_writable
from ._obidmscolumn_float cimport OBIDMS_column_float, \
OBIDMS_column_float_writable, \
OBIDMS_column_float_multi_elts, \
......@@ -87,11 +85,11 @@ cdef class OBIDMS :
p = Path(self.dms_name+'.obidms')
print("{:<25} {:<25} {:<25} {:<25}".format('-Column name-',
print("{:<30} {:<12} {:<25} {:<30} {:<40}".format('-Column name-',
'-Data type-',
'-Latest version number-',
'-Line count of latest version-'))
#'-Creation date of latest version-'))
'-Line count of latest version-',
'-Creation date of latest version-'))
for entry in p.iterdir():
if entry.suffix == ".obicol":
column_name = entry.stem
......@@ -100,18 +98,16 @@ cdef class OBIDMS :
header = obi_column_get_header_from_name(self.pointer, column_name_b)
data_type = bytes2str(name_data_type(header.data_type))
line_count = header.line_count
creation_date = bytes2str(obi_column_format_date(header.creation_date))
obi_unmap_header(header) # TODO check if error? but C will already warn and there's nothing to do
latest_version = obi_column_get_latest_version_from_name(self.pointer, column_name_b)
# creation_date = bytes2str(obi_column_get_formatted_creation_date_from_name(self.pointer, column_name_b)) #TODO (deprecated, use header)
# print(creation_date)
dms[column_name]['data_type'] = data_type
dms[column_name]['latest_version'] = latest_version
dms[column_name]['line_count'] = line_count
# dms[column_name]['creation_date'] = creation_date
print("{:<25} {:<25} {:<25} {:<25}".format(column_name, data_type, latest_version, line_count))
dms[column_name]['creation_date'] = creation_date
# TODO : actually get all the informations in the header
print("{:<30} {:<12} {:<25} {:<30} {:<40}".format(column_name, data_type, latest_version, line_count, creation_date))
obi_unmap_header(header) # TODO check if error? but C will already warn and there's nothing to do
return dms
......@@ -272,7 +268,7 @@ cdef class OBIDMS_column :
self.pointer = obi_clone_column(self.dms.pointer, column_name_b, version_number, clone_data)
else :
self.pointer = obi_open_column(self.dms.pointer, column_name_b, version_number)
def __iter__(self):
......@@ -281,34 +277,44 @@ cdef class OBIDMS_column :
cdef size_t line_nb
# Yield each line
lines_used = obi_column_get_nb_lines_used(self.pointer)
lines_used = self.pointer.header.lines_used
for line_nb in range(lines_used):
yield self.get_line(line_nb)
def __setitem__(self, size_t line_nb, object value):
self.set_line(line_nb, value)
def __getitem__(self, size_t line_nb):
return self.get_line(line_nb)
# cpdef object get_item(self, size_t line_nb, str element_name): TODO
# raise NotImplementedError
# cpdef set_item(self, size_t line_nb, str element_name, object value): TODO
# raise NotImplementedError
cpdef list get_elements_names(self):
return self.elements_names
cpdef str get_data_type(self):
return self.data_type
cpdef size_t get_nb_lines_used(self):
return obi_column_get_nb_lines_used(self.pointer)
return self.pointer.header.lines_used
cpdef str get_creation_date(self):
return bytes2str(obi_column_format_date(self.pointer.header.creation_date))
# cpdef str get_creation_date(self):
# return bytes2str(obi_column_get_formatted_creation_date(self.pointer))
cpdef close(self):
raise NotImplementedError
python/obitools3/obidms/capi/obidmscolumn.pxd
View file @ ecb9d97a
......@@ -13,11 +13,6 @@ from ..capi.obitypes cimport const_char_p, \
cdef extern from "obidmscolumn.h" nogil:
struct OBIDMS_column_t:
pass
ctypedef OBIDMS_column_t* OBIDMS_column_p
struct OBIDMS_column_header_t:
bint little_endian
......@@ -35,25 +30,22 @@ cdef extern from "obidmscolumn.h" nogil:
ctypedef OBIDMS_column_header_t* OBIDMS_column_header_p
struct OBIDMS_column_t:
OBIDMS_column_header_p header
ctypedef OBIDMS_column_t* OBIDMS_column_p
OBIDMS_column_p obi_create_column(OBIDMS_p dms,
const_char_p column_name,
OBIType_t type,
size_t nb_lines,
size_t nb_elements_per_line,
const_char_p elements_names)
size_t obi_column_get_nb_lines_used(OBIDMS_column_p column)
const_char_p obi_column_get_elements_names(OBIDMS_column_p column)
void obi_column_make_unwritable(OBIDMS_column_p column)
OBIDMS_column_p obi_open_column(OBIDMS_p dms,
const_char_p column_name,
obiversion_t version_number)
OBIType_t obi_column_get_type(OBIDMS_column_p column)
int obi_close_column(OBIDMS_column_p column)
OBIDMS_column_p obi_clone_column(OBIDMS_p dms,
......@@ -70,12 +62,9 @@ cdef extern from "obidmscolumn.h" nogil:
const_char_p column_name)
int obi_unmap_header(OBIDMS_column_header_p header)
# char* obi_column_get_formatted_creation_date(OBIDMS_column_p column)
# char* obi_column_get_formatted_creation_date_from_name(OBIDMS_p dms,
# const_char_p column_name)
char* obi_column_format_date(time_t date)
cdef extern from "obidmscolumn_int.h" nogil:
int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column,
......
python/obitools3/unit_tests.py
View file @ ecb9d97a
......@@ -25,7 +25,7 @@ def create_test_column(dms, data_type_code, multiple_elements_per_line=False):
data_types = DATA_TYPES
data_type_code = data_type_code
data_type_str = data_types[data_type_code-1]
col_name = "test_col_"+data_type_str
col_name = "unit_test_"+data_type_str
if multiple_elements_per_line :
elts_names = elements_names()
......
src/obidmscolumn.c
View file @ ecb9d97a
......@@ -1317,31 +1317,7 @@ void obi_ini_to_NA_values(OBIDMS_column_p column,
}
void obi_column_make_unwritable(OBIDMS_column_p column) // TODO this might be irrelevant
{
column->writable = false;
}
size_t obi_column_get_line_count(OBIDMS_column_p column)
{
return (column->header)->line_count;
}
size_t obi_column_get_nb_lines_used(OBIDMS_column_p column)
{
return (column->header)->lines_used;
}
OBIType_t obi_column_get_data_type(OBIDMS_column_p column)
{
return (column->header)->data_type;
}
OBIDMS_column_header_p obi_column_get_header_from_name(OBIDMS_p dms, const char* column_name)
OBIDMS_column_header_p obi_column_get_header_from_name(OBIDMS_p dms, const char* column_name) // ADD VERSION ARGUMENT
{
OBIDMS_column_header_p header;
OBIDMS_column_directory_p column_directory;
......@@ -1436,12 +1412,6 @@ int obi_unmap_header(OBIDMS_column_header_p header)
}
const char* obi_column_get_elements_names(OBIDMS_column_p column)
{
return (column->header)->elements_names;
}
// 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)
{
......@@ -1483,146 +1453,28 @@ size_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const char
}
size_t obi_column_get_nb_elements_per_line(OBIDMS_column_p column)
{
// TODO check that column is not NULL?
return (column->header)->nb_elements_per_line;
}
char* obi_column_get_formatted_creation_date(OBIDMS_column_p column) // TODO
char* obi_column_format_date(time_t date)
{
char* formatted_time;
struct tm* tmp;
formatted_time = (char*) malloc(FORMATTED_TIME_LENGTH*sizeof(char));
tmp = localtime(&((column->header)->creation_date));
tmp = localtime(&date);
if (tmp == NULL)
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError formatting the creation date of a column");
obidebug(1, "\nError formatting a date");
return NULL;
}
if (strftime(formatted_time, FORMATTED_TIME_LENGTH, "%c", tmp) == 0)
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError formatting the creation date of a column");
obidebug(1, "\nError formatting a date");
return NULL;
}
return formatted_time;
}
char* obi_column_get_formatted_creation_date_from_name(OBIDMS_p dms, const char* column_name) // TODO
{
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;
obiversion_t version_number;
char* formatted_time;
struct tm* tmp;
// Get the column directory structure associated to the column
column_directory = obi_open_column_directory(dms, column_name);
if (column_directory == NULL)
{
obidebug(1, "\nError opening a column directory structure");
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)
{
obi_set_errno(OBICOLDIR_UNKNOWN_ERROR);
obidebug(1, "\nError getting the file descriptor of a column directory");
obi_close_column_directory(column_directory);
return NULL;
}
// 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, "\nError getting the latest version number in a column directory");
return NULL;
}
// Get the column file name
column_file_name = build_column_file_name(column_name, version_number);
if (column_file_name == NULL)
{
return NULL;
}
// 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, "\nError opening a column file");
obi_set_errno(OBICOL_UNKNOWN_ERROR);
free(column_file_name);
return NULL;
}
// 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);
obidebug(1, "\nError mmapping the header of a column");
close(column_file_descriptor);
free(column_file_name);
return NULL;
}
// TODO Check endianness?
// Format time
formatted_time = (char*) malloc(FORMATTED_TIME_LENGTH*sizeof(char));
tmp = localtime(&(header->creation_date));
if (tmp == NULL)
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError formatting the creation date of a column");
close(column_file_descriptor);
free(column_file_name);
return NULL;
}
if (strftime(formatted_time, FORMATTED_TIME_LENGTH, "%c", tmp) == 0)
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError formatting the creation date of a column");
close(column_file_descriptor);
free(column_file_name);
return NULL;
}
// Munmap header
if (munmap(header, header->header_size) < 0)
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError munmapping header after getting the creation date of a column");
}
free(column_file_name);
close(column_file_descriptor);
return formatted_time;
}
src/obidmscolumn.h
View file @ ecb9d97a
......@@ -283,56 +283,6 @@ 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); // TO make private?
/**
* @brief Sets the 'writable' header attribute of an OBIDMS column to False. // TODO delete?
*
* @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.
*
* @returns 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 number of lines used in an OBIDMS column.
*
* @param column A pointer on an OBIDMS column.
*
* @returns The number of lines used in the column.
*
* @since August 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
size_t obi_column_get_nb_lines_used(OBIDMS_column_p column);
/**
* @brief Recovers the data type of an OBIDMS column.
*
* @param column A pointer on an OBIDMS column.
*
* @returns 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 header of an OBIDMS column from the column name.
*
......@@ -364,19 +314,6 @@ OBIDMS_column_header_p obi_column_get_header_from_name(OBIDMS_p dms, const char*
int obi_unmap_header(OBIDMS_column_header_p header);
/**
* @brief Recovers the elements names of an OBIDMS column.
*
* @param column A pointer on an OBIDMS column.
*
* @returns 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 the element's name.
*
......@@ -393,43 +330,16 @@ size_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const char
/**
* @brief Recovers the number of elements per line in an OBIDMS column.
* @brief Formats a date in a way that is easy to read.
*
* @param column A pointer on an OBIDMS column.
*
* @returns 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);
/**
* @brief Recovers the creation date of an OBIDMS column.
*
* @param column A pointer on an OBIDMS column.
*
* @returns The creation date of the column.
*
* @since October 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
char* obi_column_get_formatted_creation_date(OBIDMS_column_p column);
/**
* @brief Recovers the creation date of an OBIDMS column from the column name.
*
* @param dms A pointer on an OBIDMS.
* @param column_name The name of an OBIDMS column.
* @param date A date.
*
* @returns The creation date of the column.
* @returns The date formatted in a way that is easy to read.
*
* @since October 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
char* obi_column_get_get_formatted_creation_date_from_name(OBIDMS_p dms, const char* column_name);
char* obi_column_format_date(time_t date);
#endif /* OBIDMSCOLUMN_H_ */
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