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Reorganized the code to have less functions, and the functions to get

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and format the creation date of a column are now working.
This commit is contained in:
Celine Mercier
2015-10-15 15:12:45 +02:00
parent 0eaa5aa784
commit ecb9d97adb
6 changed files with 48 additions and 291 deletions
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2
python/obitools3/obidms/_obidms.pxd
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@ -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)

48
python/obitools3/obidms/_obidms.pyx
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@ -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)
# cpdef str get_creation_date(self):
# return bytes2str(obi_column_get_formatted_creation_date(self.pointer))
cpdef size_t get_nb_lines_used(self):
return self.pointer.header.lines_used
cpdef str get_creation_date(self):
return bytes2str(obi_column_format_date(self.pointer.header.creation_date))
cpdef close(self):
raise NotImplementedError

31
python/obitools3/obidms/capi/obidmscolumn.pxd
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@ -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,

2
python/obitools3/unit_tests.py
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@ -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()