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entirely reworked cython wrapper

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This commit is contained in:
Celine Mercier
2015-09-28 13:51:35 +02:00
parent 9aaf2d264a
commit 72155c3b73
48 changed files with 698 additions and 488 deletions
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1
python/obitools3/obidms/_obidms.c
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@ -1 +0,0 @@
#error Do not use this file, it is the result of a failed Cython compilation.

21
python/obitools3/obidms/_obidms.pxd
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@ -1,5 +1,8 @@
from .capi.obidms cimport OBIDMS_p
from .capi.obitypes cimport obiversion_t, OBIType_t
#cython: language_level=3
from .capi.obidms cimport OBIDMS_p
from .capi.obidmscolumn cimport OBIDMS_column_p
from .capi.obitypes cimport obiversion_t, OBIType_t
cdef class OBIDMS_column
@ -19,3 +22,17 @@ cdef class OBIDMS:
size_t nb_lines=*,
size_t nb_elements_per_line=*,
str elements_names=*)
cdef class OBIDMS_column:
cdef OBIDMS_column_p pointer
cdef OBIDMS dms
cdef str data_type # TODO keep as OBIType_t? both?
cdef str dms_name
cdef str column_name
cpdef object get_item(self, size_t line_nb, str element_name)
cpdef list get_elements_names(self)
cpdef str get_data_type(self)
cpdef size_t get_nb_lines_used(self)

195
python/obitools3/obidms/_obidms.pyx
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@ -1,31 +1,44 @@
#cython: language_level=3
from obitools3.utils cimport bytes2str, str2bytes
from obitools3.obidms.obidmscolumn._obidmscolumn cimport OBIDMS_column
from pathlib import Path
# from obitools3.obidms.obidmscolumn.capidmscolumn cimport OBIDMS_column
# from obitools3.obidms.obidmscolumn.capidmscolumn cimport obiversion_t # TODO pourquoi je peux pas les declarer dans le pxd?
# from obitools3.obidms.obidmscolumn.capidmscolumn cimport name_data_type
# from obitools3.obidms.obidmscolumn.capidmscolumn cimport obi_column_get_data_type_from_name
# from obitools3.obidms.obidmscolumn.capidmscolumn cimport obi_column_get_latest_version_from_name
# from obitools3.obidms.obidmscolumn.capidmscolumn cimport obi_column_get_line_count_from_name
#
from obitools3.obidms.obidmscolumn.obidmscolumn_int.capidmscolumn_int cimport OBIDMS_column_int_writable # TODO pourquoi pas cimport?
from obitools3.obidms.obidmscolumn.obidmscolumn_int.capidmscolumn_int cimport OBIDMS_column_int_read
from obitools3.obidms.obidmscolumn.obidmscolumn_float.capidmscolumn_float cimport OBIDMS_column_float_writable
from obitools3.obidms.obidmscolumn.obidmscolumn_float.capidmscolumn_float cimport OBIDMS_column_float_read
from obitools3.obidms.obidmscolumn.obidmscolumn_bool.capidmscolumn_bool cimport OBIDMS_column_bool_writable
from obitools3.obidms.obidmscolumn.obidmscolumn_bool.capidmscolumn_bool cimport OBIDMS_column_bool_read
from obitools3.obidms.obidmscolumn.obidmscolumn_char.capidmscolumn_char cimport OBIDMS_column_char_writable
from obitools3.obidms.obidmscolumn.obidmscolumn_char.capidmscolumn_char cimport OBIDMS_column_char_read
from obitools3.obidms.obidmscolumn.obidmscolumn_idx.capidmscolumn_idx cimport OBIDMS_column_idx_writable
from obitools3.obidms.obidmscolumn.obidmscolumn_idx.capidmscolumn_idx cimport OBIDMS_column_idx_read
from obitools3.utils cimport bytes2str, str2bytes
from .capi.obidms cimport obi_dms
from .capi.obidmscolumn cimport obi_column_get_data_type_from_name, \
obi_column_get_latest_version_from_name, \
obi_column_get_line_count_from_name, \
obi_column_get_nb_lines_used, \
obi_column_get_elements_names, \
obi_create_column, \
obi_clone_column, \
obi_open_column, \
obi_close_column
from .capi.obitypes cimport const_char_p, name_data_type
from ._obidms cimport OBIDMS
from ._obidms cimport OBIDMS_column
from ._obidmscolumn_int cimport OBIDMS_column_int, \
OBIDMS_column_int_writable
from ._obidmscolumn_float cimport OBIDMS_column_float, \
OBIDMS_column_float_writable
from ._obidmscolumn_bool cimport OBIDMS_column_bool, \
OBIDMS_column_bool_writable
from ._obidmscolumn_char cimport OBIDMS_column_char, \
OBIDMS_column_char_writable
from ._obidmscolumn_idx cimport OBIDMS_column_idx, \
OBIDMS_column_idx_writable
cdef class OBIDMS :
def __init__(self, str dms_name) : # TODO
def __init__(self, str dms_name) :
# Declarations
cdef bytes dms_name_b
@ -61,7 +74,7 @@ cdef class OBIDMS :
column_name = entry.stem
column_name_b = str2bytes(column_name)
dms[column_name] = {}
data_type = bytes2str((name_data_type(obi_column_get_data_type_from_name(self.pointer, column_name_b)))
data_type = bytes2str(name_data_type(obi_column_get_data_type_from_name(self.pointer, column_name_b)))
latest_version = obi_column_get_latest_version_from_name(self.pointer, column_name_b)
line_count = obi_column_get_line_count_from_name(self.pointer, column_name_b)
dms[column_name]['data_type'] = data_type
@ -71,18 +84,18 @@ cdef class OBIDMS :
return dms
cpdef OBIDMS_column open_column(self, # TODO j'arrive pas a le passer en cpdef
str column_name, # TODO
bint create=False,
bint clone=False, bint clone_data=True,
obiversion_t version_number=-1,
OBIType_t data_type=0, # TODO
size_t nb_lines=0,
size_t nb_elements_per_line=1,
str elements_names=None):
cpdef OBIDMS_column open_column(self,
str column_name,
bint create=False,
bint clone=False, bint clone_data=True,
obiversion_t version_number=-1,
OBIType_t data_type= <OBIType_t> 0,
size_t nb_lines=0,
size_t nb_elements_per_line=1,
str elements_names=None):
# Declarations
cdef OBIDMS_column column # TODO not sure object
cdef OBIDMS_column column
cdef bytes column_name_b
# Format the character string to send to C function
@ -104,7 +117,7 @@ cdef class OBIDMS :
nb_lines, nb_elements_per_line,
elements_names)
else :
column = OBIDMS_column_int_read(self, column_name,
column = OBIDMS_column_int(self, column_name,
create, clone, clone_data,
version_number, data_type,
nb_lines, nb_elements_per_line,
@ -118,7 +131,7 @@ cdef class OBIDMS :
nb_lines, nb_elements_per_line,
elements_names)
else :
column = OBIDMS_column_float_read(self, column_name,
column = OBIDMS_column_float(self, column_name,
create, clone, clone_data,
version_number, data_type,
nb_lines, nb_elements_per_line,
@ -132,7 +145,7 @@ cdef class OBIDMS :
nb_lines, nb_elements_per_line,
elements_names)
else :
column = OBIDMS_column_bool_read(self, column_name,
column = OBIDMS_column_bool(self, column_name,
create, clone, clone_data,
version_number, data_type,
nb_lines, nb_elements_per_line,
@ -146,13 +159,125 @@ cdef class OBIDMS :
nb_lines, nb_elements_per_line,
elements_names)
else :
column = OBIDMS_column_char_read(self, column_name,
column = OBIDMS_column_char(self, column_name,
create, clone, clone_data,
version_number, data_type,
nb_lines, nb_elements_per_line,
elements_names)
# elif data_type == 5 :
# if (create or clone) :
# column = OBIDMS_column_idx_writable(self, column_name,
# create, clone, clone_data,
# version_number, data_type,
# nb_lines, nb_elements_per_line,
# elements_names)
# else :
# column = OBIDMS_column_idx(self, column_name,
# create, clone, clone_data,
# version_number, data_type,
# nb_lines, nb_elements_per_line,
# elements_names)
else :
raise Exception("Problem with the data type")
return column
cdef class OBIDMS_column :
# Should only be initialized through a subclass
def __init__(self,
OBIDMS dms,
str column_name,
bint create,
bint clone, bint clone_data,
obiversion_t version_number,
OBIType_t type,
size_t nb_lines,
size_t nb_elements_per_line,
str elements_names):
# Declarations
cdef bytes column_name_b
cdef bytes dms_name_b
cdef bytes elements_names_b
# Fill structure
self.dms = dms
self.data_type = bytes2str(name_data_type(type))
self.column_name = column_name
# Format the character strings to send them to C functions
column_name_b = str2bytes(column_name)
dms_name_b = str2bytes(self.dms.dms_name)
# Create, clone or open column
if create :
if elements_names == None :
elements_names_b = column_name_b
else :
elements_names_b = str2bytes(elements_names)
self.pointer = obi_create_column(self.dms.pointer, column_name_b, type, nb_lines, nb_elements_per_line, elements_names_b)
else :
if clone :
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):
# Declarations
cdef list elements_names
cdef str element_name
cdef bint multiple_elements
cdef object line # TODO
cdef size_t lines_used
cdef size_t line_nb
# Check if there are multiple elements per line anf if yes, get their names
elements_names = self.get_elements_names()
if len(elements_names) > 1 :
multiple_elements = True
else :
element_name = elements_names[0]
# Yield each line
lines_used = obi_column_get_nb_lines_used(self.pointer)
for line_nb in xrange(lines_used):
if multiple_elements :
line = []
for element_name in elements_names :
line.append(self.get_item(line_nb, element_name))
else :
line = self.get_item(line_nb, element_name)
yield line
def __setitem__(self, size_t line_nb, object value):
self.set_item(line_nb, "", value)
def __getitem__(self, size_t line_nb):
return self.get_item(line_nb, "")
cpdef object get_item(self, size_t line_nb, str element_name):
raise NotImplementedError
cpdef list get_elements_names(self):
cdef bytes elements_names
elements_names = obi_column_get_elements_names(self.pointer)
return (bytes2str(elements_names)).split(';')
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)

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python/obitools3/obidms/_obidmscolumn_bool.cfiles Normal file
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../../../src/obidmscolumn_bool.c
../../../src/obidmscolumn_bool.h
../../../src/obidmscolumn.h
../../../src/obidmscolumn.c
../../../src/obidmscolumndir.h
../../../src/obidmscolumndir.c
../../../src/obidms.h
../../../src/obidms.c
../../../src/obierrno.h
../../../src/obierrno.c
../../../src/obilittlebigman.h
../../../src/obilittlebigman.c
../../../src/obitypes.h
../../../src/obitypes.c
../../../src/private_at_functions.h
../../../src/private_at_functions.c

17
python/obitools3/obidms/_obidmscolumn_bool.pxd Normal file
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@ -0,0 +1,17 @@
#cython: language_level=3
from .capi.obitypes cimport obibool_t
from .capi.obidmscolumn cimport OBIDMS_column_p
from ._obidms cimport OBIDMS_column
cdef class OBIDMS_column_bool(OBIDMS_column):
cpdef object get_item(self, size_t line_nb, str element_name)
cpdef set_item(self, size_t line_nb, str element_name, obibool_t value)
cpdef close(self)
cdef class OBIDMS_column_bool_writable(OBIDMS_column_bool):
cpdef set_item(self, size_t line_nb, str element_name, obibool_t value)
cpdef close(self)

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python/obitools3/obidms/_obidmscolumn_bool.pyx Normal file
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@ -0,0 +1,46 @@
#cython: language_level=3
from .capi.obidmscolumn cimport obi_close_column,\
obi_truncate_and_close_column, \
obi_column_get_obibool_with_elt_name, \
obi_column_set_obibool_with_elt_name
from .capi.obierrno cimport obi_errno
from .capi.obitypes cimport OBIBool_NA
from obitools3.utils cimport str2bytes
from cpython.bool cimport PyBool_FromLong
cdef class OBIDMS_column_bool(OBIDMS_column):
cpdef object get_item(self, size_t line_nb, str element_name):
cdef obibool_t value
cdef object result
value = obi_column_get_obibool_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
if obi_errno > 0 :
raise IndexError(line_nb, element_name)
if value == OBIBool_NA :
result = None
else :
result = PyBool_FromLong(value)
return result
cpdef set_item(self, size_t line_nb, str element_name, obibool_t value):
raise Exception("Column is read-only")
cpdef close(self):
if obi_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")
cdef class OBIDMS_column_bool_writable(OBIDMS_column_bool):
cpdef set_item(self, size_t line_nb, str element_name, obibool_t value):
if obi_column_set_obibool_with_elt_name(self.pointer, line_nb, str2bytes(element_name), value) < 0 :
raise Exception("Problem setting a value in a column")
cpdef close(self):
if obi_truncate_and_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")

16
python/obitools3/obidms/_obidmscolumn_char.cfiles Normal file
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@ -0,0 +1,16 @@
../../../src/obidmscolumn_char.c
../../../src/obidmscolumn_char.h
../../../src/obidmscolumn.h
../../../src/obidmscolumn.c
../../../src/obidmscolumndir.h
../../../src/obidmscolumndir.c
../../../src/obidms.h
../../../src/obidms.c
../../../src/obierrno.h
../../../src/obierrno.c
../../../src/obilittlebigman.h
../../../src/obilittlebigman.c
../../../src/obitypes.h
../../../src/obitypes.c
../../../src/private_at_functions.h
../../../src/private_at_functions.c

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python/obitools3/obidms/_obidmscolumn_char.pxd Normal file
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@ -0,0 +1,17 @@
#cython: language_level=3
from .capi.obitypes cimport obichar_t
from .capi.obidmscolumn cimport OBIDMS_column_p
from ._obidms cimport OBIDMS_column
cdef class OBIDMS_column_char(OBIDMS_column):
cpdef object get_item(self, size_t line_nb, str element_name)
cpdef set_item(self, size_t line_nb, str element_name, bytes value)
cpdef close(self)
cdef class OBIDMS_column_char_writable(OBIDMS_column_char):
cpdef set_item(self, size_t line_nb, str element_name, bytes value)
cpdef close(self)

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python/obitools3/obidms/_obidmscolumn_char.pyx Normal file
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@ -0,0 +1,44 @@
#cython: language_level=3
from .capi.obidmscolumn cimport obi_close_column,\
obi_truncate_and_close_column, \
obi_column_get_obichar_with_elt_name, \
obi_column_set_obichar_with_elt_name
from .capi.obierrno cimport obi_errno
from .capi.obitypes cimport OBIChar_NA
from obitools3.utils cimport str2bytes
cdef class OBIDMS_column_char(OBIDMS_column) :
cpdef object get_item(self, size_t line_nb, str element_name):
cdef char value
cdef object result
value = obi_column_get_obichar_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
if obi_errno > 0 :
raise IndexError(line_nb, element_name)
if value == OBIChar_NA :
result = None
else :
result = <bytes> value
return result
cpdef set_item(self, size_t line_nb, str element_name, bytes value):
raise Exception("Column is read-only")
cpdef close(self):
if obi_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")
cdef class OBIDMS_column_char_writable(OBIDMS_column_char) :
cpdef set_item(self, size_t line_nb, str element_name, bytes value):
if obi_column_set_obichar_with_elt_name(self.pointer, line_nb, str2bytes(element_name), value[0]) < 0:
raise Exception("Problem setting a value in a column")
cpdef close(self):
if obi_truncate_and_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")

16
python/obitools3/obidms/_obidmscolumn_float.cfiles Normal file
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@ -0,0 +1,16 @@
../../../src/obidmscolumn_float.c
../../../src/obidmscolumn_float.h
../../../src/obidmscolumn.h
../../../src/obidmscolumn.c
../../../src/obidmscolumndir.h
../../../src/obidmscolumndir.c
../../../src/obidms.h
../../../src/obidms.c
../../../src/obierrno.h
../../../src/obierrno.c
../../../src/obilittlebigman.h
../../../src/obilittlebigman.c
../../../src/obitypes.h
../../../src/obitypes.c
../../../src/private_at_functions.h
../../../src/private_at_functions.c

16
python/obitools3/obidms/_obidmscolumn_float.pxd Normal file
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@ -0,0 +1,16 @@
#cython: language_level=3
from .capi.obitypes cimport obifloat_t
from .capi.obidmscolumn cimport OBIDMS_column_p
from ._obidms cimport OBIDMS_column
cdef class OBIDMS_column_float(OBIDMS_column):
cpdef object get_item(self, size_t line_nb, str element_name)
cpdef set_item(self, size_t line_nb, str element_name, obifloat_t value)
cpdef close(self)
cdef class OBIDMS_column_float_writable(OBIDMS_column_float):
cpdef set_item(self, size_t line_nb, str element_name, obifloat_t value)
cpdef close(self)

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python/obitools3/obidms/_obidmscolumn_float.pyx Normal file
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@ -0,0 +1,44 @@
#cython: language_level=3
from .capi.obidmscolumn cimport obi_close_column,\
obi_truncate_and_close_column, \
obi_column_get_obifloat_with_elt_name, \
obi_column_set_obifloat_with_elt_name
from .capi.obierrno cimport obi_errno
from .capi.obitypes cimport OBIFloat_NA
from obitools3.utils cimport str2bytes
cdef class OBIDMS_column_float(OBIDMS_column):
cpdef object get_item(self, size_t line_nb, str element_name):
cdef obifloat_t value
cdef object result
value = obi_column_get_obifloat_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
if obi_errno > 0 :
raise IndexError(line_nb, element_name)
if value == OBIFloat_NA :
result = None
else :
result = <float> value
return result
cpdef set_item(self, size_t line_nb, str element_name, obifloat_t value):
raise Exception("Column is read-only")
cpdef close(self):
if obi_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")
cdef class OBIDMS_column_float_writable(OBIDMS_column_float):
cpdef set_item(self, size_t line_nb, str element_name, obifloat_t value):
if obi_column_set_obifloat_with_elt_name(self.pointer, line_nb, str2bytes(element_name), value) < 0:
raise Exception("Problem setting a value in a column")
cpdef close(self):
if obi_truncate_and_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")

16
python/obitools3/obidms/_obidmscolumn_idx.cfiles Normal file
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@ -0,0 +1,16 @@
../../../src/obidmscolumn_idx.c
../../../src/obidmscolumn_idx.h
../../../src/obidmscolumn.h
../../../src/obidmscolumn.c
../../../src/obidmscolumndir.h
../../../src/obidmscolumndir.c
../../../src/obidms.h
../../../src/obidms.c
../../../src/obierrno.h
../../../src/obierrno.c
../../../src/obilittlebigman.h
../../../src/obilittlebigman.c
../../../src/obitypes.h
../../../src/obitypes.c
../../../src/private_at_functions.h
../../../src/private_at_functions.c

16
python/obitools3/obidms/_obidmscolumn_idx.pxd Normal file
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@ -0,0 +1,16 @@
#cython: language_level=3
from .capi.obitypes cimport obiidx_t
from .capi.obidmscolumn cimport OBIDMS_column_p
from ._obidms cimport OBIDMS_column
cdef class OBIDMS_column_idx(OBIDMS_column):
cpdef object get_item(self, size_t line_nb, str element_name)
cpdef set_item(self, size_t line_nb, str element_name, obiidx_t value)
cpdef close(self)
cdef class OBIDMS_column_idx_writable(OBIDMS_column_idx):
cpdef set_item(self, size_t line_nb, str element_name, obiidx_t value)
cpdef close(self)

46
python/obitools3/obidms/_obidmscolumn_idx.pyx Normal file
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@ -0,0 +1,46 @@
#cython: language_level=3
from .capi.obidmscolumn cimport obi_close_column,\
obi_truncate_and_close_column, \
obi_column_get_obiidx_with_elt_name, \
obi_column_set_obiidx_with_elt_name
from .capi.obierrno cimport obi_errno
from .capi.obitypes cimport OBIIdx_NA
from obitools3.utils cimport str2bytes
from cpython.int cimport PyInt_FromSsize_t
cdef class OBIDMS_column_idx(OBIDMS_column):
cpdef object get_item(self, size_t line_nb, str element_name):
cdef obiidx_t value
cdef object result
value = obi_column_get_obiidx_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
if obi_errno > 0 :
raise IndexError(line_nb, element_name)
if value == OBIIdx_NA :
result = None
else :
result = PyInt_FromSsize_t(value)
return result
cpdef set_item(self, size_t line_nb, str element_name, obiidx_t value):
raise Exception("Column is read-only")
cpdef close(self):
if obi_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")
cdef class OBIDMS_column_idx_writable(OBIDMS_column_idx):
cpdef set_item(self, size_t line_nb, str element_name, obiidx_t value):
if obi_column_set_obiidx_with_elt_name(self.pointer, line_nb, str2bytes(element_name), value) < 0:
raise Exception("Problem setting a value in a column")
cpdef close(self):
if obi_truncate_and_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")

16
python/obitools3/obidms/_obidmscolumn_int.cfiles Normal file
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@ -0,0 +1,16 @@
../../../src/obidmscolumn_int.c
../../../src/obidmscolumn_int.h
../../../src/obidmscolumn.h
../../../src/obidmscolumn.c
../../../src/obidmscolumndir.h
../../../src/obidmscolumndir.c
../../../src/obidms.h
../../../src/obidms.c
../../../src/obierrno.h
../../../src/obierrno.c
../../../src/obilittlebigman.h
../../../src/obilittlebigman.c
../../../src/obitypes.h
../../../src/obitypes.c
../../../src/private_at_functions.h
../../../src/private_at_functions.c

16
python/obitools3/obidms/_obidmscolumn_int.pxd Normal file
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@ -0,0 +1,16 @@
#cython: language_level=3
from .capi.obitypes cimport obiint_t
from .capi.obidmscolumn cimport OBIDMS_column_p
from ._obidms cimport OBIDMS_column
cdef class OBIDMS_column_int(OBIDMS_column):
cpdef object get_item(self, size_t line_nb, str element_name)
cpdef set_item(self, size_t line_nb, str element_name, obiint_t value)
cpdef close(self)
cdef class OBIDMS_column_int_writable(OBIDMS_column_int):
cpdef set_item(self, size_t line_nb, str element_name, obiint_t value)
cpdef close(self)

48
python/obitools3/obidms/_obidmscolumn_int.pyx Normal file
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@ -0,0 +1,48 @@
#cython: language_level=3
from .capi.obidmscolumn cimport obi_close_column,\
obi_truncate_and_close_column, \
obi_column_get_obiint_with_elt_name, \
obi_column_set_obiint_with_elt_name
from .capi.obierrno cimport obi_errno
from .capi.obitypes cimport OBIInt_NA
from obitools3.utils cimport str2bytes
from cpython.int cimport PyInt_FromLong
from ._obidms cimport OBIDMS_column
cdef class OBIDMS_column_int(OBIDMS_column):
cpdef object get_item(self, size_t line_nb, str element_name):
cdef obiint_t value
cdef object result
value = obi_column_get_obiint_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
if obi_errno > 0 :
raise IndexError(line_nb, element_name)
if value == OBIInt_NA :
result = None
else :
result = PyInt_FromLong(value)
return result
cpdef set_item(self, size_t line_nb, str element_name, obiint_t value):
raise Exception("Column is read-only")
cpdef close(self):
if obi_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")
cdef class OBIDMS_column_int_writable(OBIDMS_column_int):
cpdef set_item(self, size_t line_nb, str element_name, obiint_t value):
if obi_column_set_obiint_with_elt_name(self.pointer, line_nb, str2bytes(element_name), value) < 0:
raise Exception("Problem setting a value in a column")
cpdef close(self):
if obi_truncate_and_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")

4
python/obitools3/obidms/capi/obidms.pxd
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@ -1,3 +1,7 @@
#cython: language_level=3
from .obitypes cimport const_char_p
cdef extern from "obidms.h" nogil:
struct OBIDMS_t:
pass

110
python/obitools3/obidms/capi/obidmscolumn.pxd
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@ -1,19 +1,113 @@
#cython: language_level=3
from ..capi.obidms cimport OBIDMS_p
from ..capi.obitypes cimport const_char_p, \
OBIType_t, \
obiversion_t, \
obiint_t, \
obibool_t, \
obichar_t, \
obifloat_t, \
obiidx_t
cdef extern from "obidmscolumn.h" nogil:
struct OBIDMS_column_t:
pass
ctypedef OBIDMS_column_t* OBIDMS_column_p
OBIDMS_column_p obi_create_column(OBIDMS_p dms, const char* column_name, OBIType_t type, size_t nb_lines, size_t nb_elements_per_line, const char* elements_names)
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* obi_column_get_elements_names(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* column_name, obiversion_t version_number)
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)
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)
OBIType_t obi_column_get_data_type_from_name(OBIDMS_p dms,
const_char_p column_name)
OBIDMS_column_p obi_clone_column(OBIDMS_p dms,
const_char_p column_name,
obiversion_t version_number,
bint clone_data)
int obi_truncate_and_close_column(OBIDMS_column_p column)
obiversion_t obi_column_get_latest_version_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)
size_t obi_column_get_line_count_from_name(OBIDMS_p dms, const char* column_name)
obiversion_t obi_column_get_latest_version_from_name(OBIDMS_p dms,
const_char_p column_name)
OBIType_t obi_column_get_data_type_from_name(OBIDMS_p dms,
const_char_p column_name)
size_t obi_column_get_line_count_from_name(OBIDMS_p dms,
const_char_p column_name)
cdef extern from "obidmscolumn_int.h" nogil:
int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column,
size_t line_nb,
const_char_p element_name,
obiint_t value)
obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column,
size_t line_nb,
const_char_p element_name)
cdef extern from "obidmscolumn_bool.h" nogil:
int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column,
size_t line_nb,
const_char_p element_name,
obibool_t value)
obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column,
size_t line_nb,
const_char_p element_name)
cdef extern from "obidmscolumn_char.h" nogil:
int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column,
size_t line_nb,
const_char_p element_name,
obichar_t value)
obichar_t obi_column_get_obichar_with_elt_name(OBIDMS_column_p column,
size_t line_nb,
const_char_p element_name)
cdef extern from "obidmscolumn_float.h" nogil:
int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column,
size_t line_nb,
const_char_p element_name,
obifloat_t value)
obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column,
size_t line_nb,
const_char_p element_name)
cdef extern from "obidmscolumn_idx.h" nogil:
int obi_column_set_obiidx_with_elt_name(OBIDMS_column_p column,
size_t line_nb,
const_char_p element_name,
obiidx_t value)
obiidx_t obi_column_get_obiidx_with_elt_name(OBIDMS_column_p column,
size_t line_nb,
const_char_p element_name)

4
python/obitools3/obidms/capi/obierrno.pxd
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@ -1,3 +1,5 @@
#cython: language_level=3
cdef extern from "obierrno.h" nogil:
extern int obi_errno

12
python/obitools3/obidms/capi/obitypes.pxd
View File

@ -1,13 +1,18 @@
#cython: language_level=3
from libc.stdint cimport int32_t
cdef extern from *:
ctypedef char* const_char_p "const char*"
cdef extern from "obidmscolumn.h" nogil:
ctypedef int32_t obiversion_t
cdef extern from "obitypes.h" nogil:
enum OBIType: # TODO je sais pas si ça sert de declarer le contenu de l'enum
@ -20,7 +25,6 @@ cdef extern from "obitypes.h" nogil:
ctypedef OBIType OBIType_t
enum OBIBool:
pass
@ -30,4 +34,10 @@ cdef extern from "obitypes.h" nogil:
ctypedef char obichar_t
ctypedef size_t obiidx_t
extern obiint_t OBIInt_NA
extern obiidx_t OBIIdx_NA
extern obifloat_t OBIFloat_NA
extern obichar_t OBIChar_NA
extern obibool_t OBIBool_NA
char* name_data_type(int data_type)

0
python/obitools3/obidms/obidmscolumn/__init__.py
View File

20
python/obitools3/obidms/obidmscolumn/_obidmscolumn.pxd
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@ -1,20 +0,0 @@
from obitools3.obidms.capi.obidms cimport OBIDMS_p
from obitools3.obidms.capi.obierrno cimport obi_errno
from obitools3.obidms.capi.obidmscolumn cimport OBIDMS_column_p
cdef class OBIDMS
cdef class OBIDMS_column:
cdef OBIDMS_column_p pointer
cdef OBIDMS dms
cdef str data_type # TODO keep as OBIType_t? both?
cdef str dms_name
cdef str column_name
cpdef object get_item(self, size_t line_nb, str element_name)
cpdef list get_elements_names(self)
cpdef str get_data_type(self)
cpdef size_t get_nb_lines_used(self)

16
python/obitools3/obidms/obidmscolumn/capidmscolumn.cfiles
View File

@ -1,16 +0,0 @@
../../../../src/obidmscolumn_int.c
../../../../src/obidmscolumn_int.h
../../../../src/obidmscolumn.h
../../../../src/obidmscolumn.c
../../../../src/obidmscolumndir.h
../../../../src/obidmscolumndir.c
../../../../src/obidms.h
../../../../src/obidms.c
../../../../src/obierrno.h
../../../../src/obierrno.c
../../../../src/obilittlebigman.h
../../../../src/obilittlebigman.c
../../../../src/obitypes.h
../../../../src/obitypes.c
../../../../src/private_at_functions.h
../../../../src/private_at_functions.c

98
python/obitools3/obidms/obidmscolumn/capidmscolumn.pyx
View File

@ -1,98 +0,0 @@
#cython: language_level=3
cdef class OBIDMS_column:
# Should only be initialized through a subclass
def __init__(self,
OBIDMS dms,
object column_name, # TODO
bint create,
bint clone, bint clone_data,
obiversion_t version_number,
OBIType_t type,
size_t nb_lines,
size_t nb_elements_per_line,
str elements_names):
# Declarations
cpdef bytes column_name_b
cpdef bytes dms_name_b
cpdef bytes elements_names_b
# Fill structure
self.dms = dms
self.data_type = (name_data_type(type)).decode('UTF-8')
self.column_name = column_name
# Format the character strings to send them to C functions
column_name_b = column_name.encode(encoding='UTF-8')
dms_name_b = self.dms.dms_name.encode(encoding='UTF-8')
# Create, clone or open column
if create :
if elements_names == None :
elements_names_b = column_name_b
else :
elements_names_b = elements_names.encode(encoding='UTF-8')
self.pointer = obi_create_column(self.dms.pointer, column_name_b, type, nb_lines, nb_elements_per_line, elements_names_b)
else :
if clone :
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):
# Declarations
cpdef list elements_names
cpdef str element_name
cpdef bint multiple_elements
cpdef object line # TODO
cdef size_t lines_used
cdef size_t line_nb
# Check if there are multiple elements per line anf if yes, get their names
elements_names = self.get_elements_names()
if len(elements_names) > 1 :
multiple_elements = True
else :
element_name = elements_names[0]
# Yield each line
lines_used = obi_column_get_nb_lines_used(self.pointer)
for line_nb in xrange(lines_used):
if multiple_elements :
line = []
for element_name in elements_names :
line.append(self.get_item(line_nb, element_name))
else :
line = self.get_item(line_nb, element_name)
yield line
def __setitem__(self, size_t line_nb, object value):
self.set_item(line_nb, "", value)
def __getitem__(self, size_t line_nb):
return self.get_item(line_nb, "")
cpdef object get_item(self, line_nb, element_name):
raise NotImplementedError
cpdef get_elements_names(self):
cpdef bytes elements_names
elements_names = obi_column_get_elements_names(self.pointer)
return (elements_names.decode('UTF-8')).split(';')
cpdef get_data_type(self):
return self.data_type
cpdef get_nb_lines_used(self):
return obi_column_get_nb_lines_used(self.pointer)

0
python/obitools3/obidms/obidmscolumn/obidmscolumn_bool/__init__.py
View File

16
python/obitools3/obidms/obidmscolumn/obidmscolumn_bool/capidmscolumn_bool.cfiles
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@ -1,16 +0,0 @@
../../../../../src/obidmscolumn_bool.c
../../../../../src/obidmscolumn_bool.h
../../../../../src/obidmscolumn.h
../../../../../src/obidmscolumn.c
../../../../../src/obidmscolumndir.h
../../../../../src/obidmscolumndir.c
../../../../../src/obidms.h
../../../../../src/obidms.c
../../../../../src/obierrno.h
../../../../../src/obierrno.c
../../../../../src/obilittlebigman.h
../../../../../src/obilittlebigman.c
../../../../../src/obitypes.h
../../../../../src/obitypes.c
../../../../../src/private_at_functions.h
../../../../../src/private_at_functions.c

7
python/obitools3/obidms/obidmscolumn/obidmscolumn_bool/capidmscolumn_bool.pxd
View File

@ -1,7 +0,0 @@
from obitools3.obidms.obidmscolumn.capidmscolumn cimport *
cdef extern from "obidmscolumn_bool.h" nogil:
int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obibool_t value);
obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);

35
python/obitools3/obidms/obidmscolumn/obidmscolumn_bool/capidmscolumn_bool.pyx
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@ -1,35 +0,0 @@
#cython: language_level=3
from .capidmscolumn_bool cimport *
cdef class OBIDMS_column_bool(OBIDMS_column) :
def get_item(self, line_nb, element_name):
value = obi_column_get_obibool_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'))
if obi_errno > 0 :
raise IndexError(line_nb, element_name)
return value
cdef class OBIDMS_column_bool_read(OBIDMS_column_bool) :
def set_item(self, line_nb, element_name, value):
raise Exception('Column is read-only')
def close(self):
if obi_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")
cdef class OBIDMS_column_bool_writable(OBIDMS_column_bool) :
def set_item(self, line_nb, element_name, value):
return obi_column_set_obibool_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'), value)
def close(self):
if obi_truncate_and_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")

0
python/obitools3/obidms/obidmscolumn/obidmscolumn_char/__init__.py
View File

16
python/obitools3/obidms/obidmscolumn/obidmscolumn_char/capidmscolumn_char.cfiles
View File

@ -1,16 +0,0 @@
../../../../../src/obidmscolumn_char.c
../../../../../src/obidmscolumn_char.h
../../../../../src/obidmscolumn.h
../../../../../src/obidmscolumn.c
../../../../../src/obidmscolumndir.h
../../../../../src/obidmscolumndir.c
../../../../../src/obidms.h
../../../../../src/obidms.c
../../../../../src/obierrno.h
../../../../../src/obierrno.c
../../../../../src/obilittlebigman.h
../../../../../src/obilittlebigman.c
../../../../../src/obitypes.h
../../../../../src/obitypes.c
../../../../../src/private_at_functions.h
../../../../../src/private_at_functions.c

7
python/obitools3/obidms/obidmscolumn/obidmscolumn_char/capidmscolumn_char.pxd
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@ -1,7 +0,0 @@
from obitools3.obidms.obidmscolumn.capidmscolumn cimport *
cdef extern from "obidmscolumn_char.h" nogil:
int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obichar_t value)
obichar_t obi_column_get_obichar_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name)

33
python/obitools3/obidms/obidmscolumn/obidmscolumn_char/capidmscolumn_char.pyx
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@ -1,33 +0,0 @@
#cython: language_level=3
from .capidmscolumn_char cimport *
cdef class OBIDMS_column_char(OBIDMS_column) :
def get_item(self, line_nb, element_name):
cdef char value = obi_column_get_obichar_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'))
if obi_errno > 0 :
raise IndexError(line_nb, element_name)
return <bytes> value
cdef class OBIDMS_column_char_read(OBIDMS_column_char) :
def set_item(self, line_nb, element_name, value):
raise Exception('Column is read-only')
cpdef close(self):
if obi_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")
cdef class OBIDMS_column_char_writable(OBIDMS_column_char) :
def set_item(self, line_nb, element_name, bytes value):
return obi_column_set_obichar_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'), value[0])
def close(self):
if obi_truncate_and_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")

0
python/obitools3/obidms/obidmscolumn/obidmscolumn_float/__init__.py
View File

16
python/obitools3/obidms/obidmscolumn/obidmscolumn_float/capidmscolumn_float.cfiles
View File

@ -1,16 +0,0 @@
../../../../../src/obidmscolumn_float.c
../../../../../src/obidmscolumn_float.h
../../../../../src/obidmscolumn.h
../../../../../src/obidmscolumn.c
../../../../../src/obidmscolumndir.h
../../../../../src/obidmscolumndir.c
../../../../../src/obidms.h
../../../../../src/obidms.c
../../../../../src/obierrno.h
../../../../../src/obierrno.c
../../../../../src/obilittlebigman.h
../../../../../src/obilittlebigman.c
../../../../../src/obitypes.h
../../../../../src/obitypes.c
../../../../../src/private_at_functions.h
../../../../../src/private_at_functions.c

7
python/obitools3/obidms/obidmscolumn/obidmscolumn_float/capidmscolumn_float.pxd
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@ -1,7 +0,0 @@
from obitools3.obidms.obidmscolumn.capidmscolumn cimport *
cdef extern from "obidmscolumn_float.h" nogil:
int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obifloat_t value);
obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);

34
python/obitools3/obidms/obidmscolumn/obidmscolumn_float/capidmscolumn_float.pyx
View File

@ -1,34 +0,0 @@
#cython: language_level=3
from .capidmscolumn_float cimport *
cdef class OBIDMS_column_float(OBIDMS_column) :
def get_item(self, line_nb, element_name):
value = obi_column_get_obifloat_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'))
if obi_errno > 0 :
raise IndexError(line_nb, element_name)
return value
cdef class OBIDMS_column_float_read(OBIDMS_column_float) :
def set_item(self, line_nb, element_name, value):
raise Exception('Column is read-only')
def close(self):
if obi_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")
cdef class OBIDMS_column_float_writable(OBIDMS_column_float) :
def set_item(self, line_nb, element_name, value):
return obi_column_set_obifloat_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'), value)
def close(self):
if obi_truncate_and_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")

0
python/obitools3/obidms/obidmscolumn/obidmscolumn_idx/__init__.py
View File

16
python/obitools3/obidms/obidmscolumn/obidmscolumn_idx/capidmscolumn_idx.cfiles
View File

@ -1,16 +0,0 @@
../../../../../src/obidmscolumn_idx.c
../../../../../src/obidmscolumn_idx.h
../../../../../src/obidmscolumn.h
../../../../../src/obidmscolumn.c
../../../../../src/obidmscolumndir.h
../../../../../src/obidmscolumndir.c
../../../../../src/obidms.h
../../../../../src/obidms.c
../../../../../src/obierrno.h
../../../../../src/obierrno.c
../../../../../src/obilittlebigman.h
../../../../../src/obilittlebigman.c
../../../../../src/obitypes.h
../../../../../src/obitypes.c
../../../../../src/private_at_functions.h
../../../../../src/private_at_functions.c

7
python/obitools3/obidms/obidmscolumn/obidmscolumn_idx/capidmscolumn_idx.pxd
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@ -1,7 +0,0 @@
from obitools3.obidms.obidmscolumn.capidmscolumn cimport *
cdef extern from "obidmscolumn_idx.h" nogil:
int obi_column_set_obiidx_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obiidx_t value);
obiidx_t obi_column_get_obiidx_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);

33
python/obitools3/obidms/obidmscolumn/obidmscolumn_idx/capidmscolumn_idx.pyx
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@ -1,33 +0,0 @@
#cython: language_level=3
from .capidmscolumn_idx cimport *
cdef class OBIDMS_column_idx(OBIDMS_column) :
def get_item(self, line_nb, element_name):
value = obi_column_get_obiidx_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'))
if obi_errno > 0 :
raise IndexError(line_nb, element_name)
return value
cdef class OBIDMS_column_idx_read(OBIDMS_column_idx) :
def set_item(self, line_nb, element_name, value):
raise Exception('Column is read-only')
def close(self):
if obi_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")
cdef class OBIDMS_column_idx_writable(OBIDMS_column_idx) :
def set_item(self, line_nb, element_name, value):
return obi_column_set_obiidx_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'), value)
def close(self):
if obi_truncate_and_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")

0
python/obitools3/obidms/obidmscolumn/obidmscolumn_int/__init__.py
View File

16
python/obitools3/obidms/obidmscolumn/obidmscolumn_int/capidmscolumn_int.cfiles
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@ -1,16 +0,0 @@
../../../../../src/obidmscolumn_int.c
../../../../../src/obidmscolumn_int.h
../../../../../src/obidmscolumn.h
../../../../../src/obidmscolumn.c
../../../../../src/obidmscolumndir.h
../../../../../src/obidmscolumndir.c
../../../../../src/obidms.h
../../../../../src/obidms.c
../../../../../src/obierrno.h
../../../../../src/obierrno.c
../../../../../src/obilittlebigman.h
../../../../../src/obilittlebigman.c
../../../../../src/obitypes.h
../../../../../src/obitypes.c
../../../../../src/private_at_functions.h
../../../../../src/private_at_functions.c

21
python/obitools3/obidms/obidmscolumn/obidmscolumn_int/capidmscolumn_int.pxd
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from obitools3.obidms.capitypes cimport obiint_t
from obitools3.obidms.obidmscolumn.capidmscolumn cimport OBIDMS_column_p
from obitools3.obidms.obidmscolumn.capidmscolumn cimport OBIDMS_column
cdef extern from "obidmscolumn_int.h" nogil:
int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obiint_t value);
obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);
cdef class OBIDMS_column_int(OBIDMS_column):
#cpdef get_item(self, size_t line_nb, str element_name)
cdef class OBIDMS_column_int_read(OBIDMS_column_int):
# cpdef set_item(self, size_t line_nb, str element_name, obiint_t value)
# cpdef close(self)
cdef class OBIDMS_column_int_writable(OBIDMS_column_int):
# cpdef set_item(self, size_t line_nb, str element_name, obiint_t value)
# cpdef close(self)

37
python/obitools3/obidms/obidmscolumn/obidmscolumn_int/capidmscolumn_int.pyx
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#cython: language_level=3
from obitools3.obidms.obidmscolumn.capidmscolumn cimport obi_close_column
from obitools3.obidms.obidmscolumn.capidmscolumn cimport obi_truncate_and_close_column
from obitools3.obidms.capidms cimport obi_errno
from cpython.int cimport PyInt_FromLong
cdef class OBIDMS_column_int(OBIDMS_column) :
def object get_item(self, size_t line_nb, str element_name):
cdef obiint_t value
value = obi_column_get_obiint_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'))
if obi_errno > 0 :
raise IndexError(line_nb, element_name)
return PyInt_FromLong(value)
cdef class OBIDMS_column_int_read(OBIDMS_column_int) :
def set_item(self, size_t line_nb, str element_name, obiint_t value):
raise Exception('Column is read-only')
def close(self):
if obi_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")
cdef class OBIDMS_column_int_writable(OBIDMS_column_int) :
def set_item(self, size_t line_nb, str element_name, obiint_t value):
return obi_column_set_obiint_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'), value)
def close(self):
if obi_truncate_and_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")

2
python/obitools3/utils.pxd
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#cython: language_level=3
cdef bytes str2bytes(str string)
cdef str bytes2str(bytes string)

2
python/obitools3/utils.pyx
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#cython: language_level=3
cdef bytes str2bytes(str string):
return string.encode('ascii')