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Cython typed columns

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This commit is contained in:
Celine Mercier
2017-04-06 14:40:44 +02:00
parent 381194194c
commit 0dfb1eb3e6
16 changed files with 1170 additions and 172 deletions
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53
python/obitools3/dms/column/bool.pxd
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@ -1,53 +0,0 @@
# #cython: language_level=3
#
# from cpython.bool cimport bool, PyBool_FromLong
#
# from ..capi.obitypes cimport index_t, \
# const_char_p, \
# OBIType_t, \
# obibool_t, \
# OBI_BOOL, \
# OBIBool_NA
#
# from ..capi.obiview cimport obi_get_bool_with_elt_name_and_col_p_in_view, \
# obi_get_bool_with_elt_idx_and_col_p_in_view, \
# obi_set_bool_with_elt_name_and_col_p_in_view, \
# obi_set_bool_with_elt_idx_and_col_p_in_view
#
# from ..capi.obidmscolumn cimport obi_column_get_obibool_with_elt_name, \
# obi_column_get_obibool_with_elt_idx, \
# obi_column_set_obibool_with_elt_name, \
# obi_column_set_obibool_with_elt_idx, \
# OBIDMS_column_p
#
# from ..capi.obierrno cimport obi_errno
#
# from .column cimport Column, \
# Column_line, \
# register_column_class
#
# from ..view.view cimport View
#
# from obitools3.utils cimport str2bytes, bytes2str
#
# cdef class Column_line_bool(Column_line) :
#
# @staticmethod
# cdef bool obibool_t2bool(obibool_t value)
#
# @staticmethod
# cdef bool2obibool_t(bool value)
#
# cpdef bool get_bool_item_by_name(self,bytes element_name)
# cpdef bool get_bool_item_by_idx(self,index_t index)
# cpdef set_bool_item_by_name(self,bytes element_name,bool value)
# cpdef set_bool_item_by_idx(self,index_t index,bool value)
#
#
# # cdef obibool_t [:] _data_view
#
# cdef class Column_bool(Column):
#
# cpdef object get_line(self, index_t line_nb)
# cpdef set_line(self, index_t line_nb, object value)

3
python/obitools3/dms/column/typed_column/__init__.py Normal file
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#from .bool import Column_bool
#from .int import Column_int
# TODO why is this needed?

44
python/obitools3/dms/column/typed_column/bool.pxd Normal file
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# #cython: language_level=3
from ...capi.obitypes cimport index_t
from ..column cimport Column, \
Column_multi_elts
cdef class Column_bool(Column) :
cpdef object get_line(self, index_t line_nb)
cpdef set_line(self, index_t line_nb, object value)
cdef class Column_multi_elts_bool(Column_multi_elts) :
cpdef object get_item(self, index_t line_nb, object elt_id)
cpdef object get_line(self, index_t line_nb)
cpdef set_item(self, index_t line_nb, object elt_id, object value)
# cdef class Column_line_bool(Column_line) :
#
# @staticmethod
# cdef bool obibool_t2bool(obibool_t value)
#
# @staticmethod
# cdef bool2obibool_t(bool value)
#
# cpdef bool get_bool_item_by_name(self,bytes element_name)
# cpdef bool get_bool_item_by_idx(self,index_t index)
# cpdef set_bool_item_by_name(self,bytes element_name,bool value)
# cpdef set_bool_item_by_idx(self,index_t index,bool value)
#
#
# # cdef obibool_t [:] _data_view
#

253
python/obitools3/dms/column/bool.pyx → python/obitools3/dms/column/typed_column/bool.pyx
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@ -1,21 +1,142 @@
#cython: language_level=3
from ..column cimport register_column_class
from ...view.view cimport View
from obitools3.utils cimport str2bytes, bytes2str, tobytes
from ...capi.obiview cimport obi_view_add_column, \
obi_get_bool_with_elt_name_and_col_p_in_view, \
obi_get_bool_with_elt_idx_and_col_p_in_view, \
obi_set_bool_with_elt_name_and_col_p_in_view, \
obi_set_bool_with_elt_idx_and_col_p_in_view
from ...capi.obierrno cimport obi_errno
from ...capi.obitypes cimport OBI_BOOL, OBIBool_NA, obibool_t, obitype_t
from cpython.bool cimport PyBool_FromLong
cdef class Column_bool(Column):
@staticmethod
def new(View view,
object column_name,
index_t nb_elements_per_line=1,
object elements_names=None,
object comments=b""):
return Column.new_column(view, column_name, OBI_BOOL,
nb_elements_per_line=nb_elements_per_line,
elements_names=elements_names,
comments=comments)
cpdef object get_line(self, index_t line_nb):
cdef obibool_t value
cdef object result
global obi_errno
value = obi_get_bool_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIBool_NA :
result = None
else :
result = PyBool_FromLong(value)
return result
cpdef set_line(self, index_t line_nb, object value):
if value is None :
value = OBIBool_NA
if obi_set_bool_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0, <obibool_t> value) < 0 :
raise Exception("Problem setting a value in a column")
cdef class Column_multi_elts_bool(Column_multi_elts):
cpdef object get_item(self, index_t line_nb, object elt_id) :
cdef obibool_t value
cdef object result
cdef bytes elt_name
if type(elt_id) == int :
value = obi_get_bool_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id)
else :
elt_name = tobytes(elt_id)
value = obi_get_bool_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name)
if obi_errno > 0 :
raise IndexError(line_nb, elt_id)
if value == OBIBool_NA :
result = None
else :
result = PyBool_FromLong(value)
return result
cpdef object get_line(self, index_t line_nb) :
cdef obibool_t value
cdef object value_in_result
cdef dict result
cdef index_t i
cdef bint all_NA
result = {}
all_NA = True
for i in range(self.nb_elements_per_line) :
value = obi_get_bool_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, i)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIBool_NA :
value_in_result = None
else :
value_in_result = PyBool_FromLong(value)
result[self.elements_names[i]] = value_in_result
if all_NA and (value_in_result is not None) :
all_NA = False
if all_NA :
result = None
return result
cpdef set_item(self, index_t line_nb, object elt_id, object value) :
cdef bytes elt_name
if value is None :
value = OBIBool_NA
if type(elt_id) == int :
if obi_set_bool_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id, <obibool_t> value) < 0 :
raise Exception("Problem setting a value in a column")
else :
elt_name = tobytes(elt_id)
if obi_set_bool_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name, <obibool_t> value) < 0 :
raise Exception("Problem setting a value in a column")
def register_class() :
register_column_class(OBI_BOOL, False, Column_bool, bool)
register_column_class(OBI_BOOL, True, Column_multi_elts_bool, bool)
# cdef class Column_line_bool(Column_line) :
#
# # cdef update_pointer(self):
# # """
# # Checks if the obicolumn address changed since the last call and update
# # if need the `_column_p` and `_data_view` data structure fields.
# # """
# # cdef OBIDMS_column_p* column_pp
# # column_pp = <OBIDMS_column_p*>self._pointer
# # cdef OBIDMS_column_p column_p = column_pp[0]
# #
# # if column_p != self._column_p:
# # self._column_p = column_p
# # # self._data_view = (<obibool_t*> (column_p.data)) + \
# # # self._index * column_p.header.nb_elements_per_line
# cdef update_pointer(self):
# """
# Checks if the obicolumn address changed since the last call and update
# if need the `_column_p` and `_data_view` data structure fields.
# """
# cdef OBIDMS_column_p* column_pp
# column_pp = <OBIDMS_column_p*>self._pointer
# cdef OBIDMS_column_p column_p = column_pp[0]
#
# if column_p != self._column_p:
# self._column_p = column_p
# self._data_view = (<obibool_t*> (column_p.data)) + \
# self._index * column_p.header.nb_elements_per_line
#
# @staticmethod
# cdef bool obibool_t2bool(obibool_t value):
@ -197,109 +318,3 @@
#
# def __len__(self):
# return self._len
# cdef class Column_bool(Column):
#
# @staticmethod
# def new(View view,
# object column_name,
# index_t nb_elements_per_line=1,
# object elements_names=None,
# object comments=b""):
#
# cdef bytes column_name_b = tobytes(column_name)
# cdef bytes comments_b
# cdef bytes elements_names_b
# cdef char* elements_names_p
# cdef Column new_column
#
# if comments is not None:
# comments_b = tobytes(comments)
# else:
# comments_b = b''
#
# if elements_names is not None:
# elements_names_b = b''.join([tobytes(x) for x in elements_names])
# elements_names_p = elements_names_b
# else:
# elements_names_p = NULL
#
# if (obi_view_add_column(view = view._pointer,
# column_name = column_name_b,
# version_number = -1,
# alias = NULL,
# data_type = OBI_BOOL,
# nb_lines = len(view),
# nb_elements_per_line = nb_elements_per_line,
# elements_names = elements_names_p,
# indexer_name = NULL,
# associated_column_name = NULL,
# associated_column_version = -1,
# comments = comments_b,
# create = True)<0):
# raise RuntimeError("Cannot create column %s in view %s" % (bytes2str(column_name),
# bytes2str(view.name)))
#
# view.__init_columns__()
# new_column = self._columns[column_name]
#
# return new_column
#
# def add_to_view(self,
# View view,
# object column_name=None,
# object comments=b""):
#
# cdef OBIDMS_column_p column_p = (<OBIDMS_column_p*>self._pointer)[0]
# cdef bytes alias
#
# if (column_name is None):
# alias = self._alias
# else:
# alias = tobytes(column_name)
#
# if (obi_view_add_column(view = view._ponter,
# column_name = column_p.header.name,
# version_number = column_p.header.version,
# alias = alias,
# data_type = OBI_BOOL,
# nb_lines = column_p.header.lines_used,
# nb_elements_per_line = column_p.header.nb_elements_per_line,
# elements_names = column_p.header.elements_names,
# indexer_name = NULL,
# associated_column_name = NULL,
# associated_column_version = NULL,
# comments = tobytes(comments),
# create = False) < 0):
# raise RuntimeError("Cannot insert column %s (%s@%d) into view %s" %
# ( bytes2str(alias),
# bytes2str(column_p.header.name),
# column_p.header.version,
# bytes2str(view.name)
# ))
#
# cpdef object get_line(self, index_t line_nb):
# cdef obibool_t value
# cdef object result
# global obi_errno
#
# value = obi_get_bool_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0)
# if obi_errno > 0 :
# raise IndexError(line_nb)
# if value == OBIBool_NA :
# result = None
# else :
# result = PyBool_FromLong(value)
# return result
#
# cpdef set_line(self, index_t line_nb, object value):
# if value is None :
# value = OBIBool_NA
# if obi_set_bool_with_elt_idx_and_col_p_in_view(<Obiview_p>self._view._pointer, (self._pointer)[0], line_nb, 0, <obibool_t> value) < 0:
# raise Exception("Problem setting a value in a column")
#
#
# register_column_class(OBI_BOOL, Column_bool, bool)

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python/obitools3/dms/column/typed_column/char.pxd Normal file
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# #cython: language_level=3
from ...capi.obitypes cimport index_t
from ..column cimport Column, \
Column_multi_elts
cdef class Column_char(Column) :
cpdef object get_line(self, index_t line_nb)
cpdef set_line(self, index_t line_nb, object value)
cdef class Column_multi_elts_char(Column_multi_elts) :
cpdef object get_item(self, index_t line_nb, object elt_id)
cpdef object get_line(self, index_t line_nb)
cpdef set_item(self, index_t line_nb, object elt_id, object value)

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python/obitools3/dms/column/typed_column/char.pyx Normal file
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#cython: language_level=3
from ..column cimport register_column_class
from ...view.view cimport View
from obitools3.utils cimport str2bytes, bytes2str, tobytes
from ...capi.obiview cimport obi_get_char_with_elt_name_and_col_p_in_view, \
obi_get_char_with_elt_idx_and_col_p_in_view, \
obi_set_char_with_elt_name_and_col_p_in_view, \
obi_set_char_with_elt_idx_and_col_p_in_view
from ...capi.obierrno cimport obi_errno
from ...capi.obitypes cimport OBI_CHAR, OBIChar_NA, obichar_t, obitype_t
cdef class Column_char(Column):
@staticmethod
def new(View view,
object column_name,
index_t nb_elements_per_line=1,
object elements_names=None,
object comments=b""):
return Column.new_column(view, column_name, OBI_CHAR,
nb_elements_per_line=nb_elements_per_line,
elements_names=elements_names,
comments=comments)
cpdef object get_line(self, index_t line_nb):
cdef obichar_t value
cdef object result
global obi_errno
value = obi_get_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIChar_NA :
result = None
else :
result = value # TODO return bytes or str?
return result
cpdef set_line(self, index_t line_nb, object value):
if value is None :
value = OBIChar_NA
if obi_set_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0, <obichar_t> tobytes(value)[0]) < 0:
raise Exception("Problem setting a value in a column")
cdef class Column_multi_elts_char(Column_multi_elts):
cpdef object get_item(self, index_t line_nb, object elt_id) :
cdef obichar_t value
cdef object result
cdef bytes elt_name
if type(elt_id) == int :
value = obi_get_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id)
else :
elt_name = tobytes(elt_id)
value = obi_get_char_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name)
if obi_errno > 0 :
raise IndexError(line_nb, elt_id)
if value == OBIChar_NA :
result = None
else :
result = value # TODO return bytes or str?
return result
cpdef object get_line(self, index_t line_nb) :
cdef obichar_t value
cdef object value_in_result
cdef dict result
cdef index_t i
cdef bint all_NA
result = {}
all_NA = True
for i in range(self.nb_elements_per_line) :
value = obi_get_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, i)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIChar_NA :
value_in_result = None
else :
value_in_result = value # TODO return bytes or str?
result[self.elements_names[i]] = value_in_result
if all_NA and (value_in_result is not None) :
all_NA = False
if all_NA :
result = None
return result
cpdef set_item(self, index_t line_nb, object elt_id, object value) :
cdef bytes elt_name
if value is None :
value = OBIChar_NA
if type(elt_id) == int :
if obi_set_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id, <obichar_t> tobytes(value)[0]) < 0 :
raise Exception("Problem setting a value in a column")
else :
elt_name = tobytes(elt_id)
if obi_set_char_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name, <obichar_t> tobytes(value)[0]) < 0 :
raise Exception("Problem setting a value in a column")
def register_class():
register_column_class(OBI_CHAR, False, Column_char, bytes) # TODO bytes or str?
register_column_class(OBI_CHAR, True, Column_multi_elts_char, bytes) # TODO bytes or str?

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python/obitools3/dms/column/typed_column/float.pxd Normal file
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# #cython: language_level=3
from ...capi.obitypes cimport index_t
from ..column cimport Column, \
Column_multi_elts
cdef class Column_float(Column) :
cpdef object get_line(self, index_t line_nb)
cpdef set_line(self, index_t line_nb, object value)
cdef class Column_multi_elts_float(Column_multi_elts) :
cpdef object get_item(self, index_t line_nb, object elt_id)
cpdef object get_line(self, index_t line_nb)
cpdef set_item(self, index_t line_nb, object elt_id, object value)

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python/obitools3/dms/column/typed_column/float.pyx Normal file
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#cython: language_level=3
from ..column cimport register_column_class
from ...view.view cimport View
from obitools3.utils cimport str2bytes, bytes2str, tobytes
from ...capi.obiview cimport obi_get_float_with_elt_name_and_col_p_in_view, \
obi_get_float_with_elt_idx_and_col_p_in_view, \
obi_set_float_with_elt_name_and_col_p_in_view, \
obi_set_float_with_elt_idx_and_col_p_in_view
from ...capi.obierrno cimport obi_errno
from ...capi.obitypes cimport OBI_FLOAT, OBIFloat_NA, obifloat_t, obitype_t
cdef class Column_float(Column):
@staticmethod
def new(View view,
object column_name,
index_t nb_elements_per_line=1,
object elements_names=None,
object comments=b""):
return Column.new_column(view, column_name, OBI_FLOAT,
nb_elements_per_line=nb_elements_per_line,
elements_names=elements_names,
comments=comments)
cpdef object get_line(self, index_t line_nb):
cdef obifloat_t value
cdef object result
global obi_errno
value = obi_get_float_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIFloat_NA :
result = None
else :
result = <double> value
return result
cpdef set_line(self, index_t line_nb, object value):
if value is None :
value = OBIFloat_NA
if obi_set_float_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0, <obifloat_t> value) < 0:
raise Exception("Problem setting a value in a column")
cdef class Column_multi_elts_float(Column_multi_elts):
cpdef object get_item(self, index_t line_nb, object elt_id) :
cdef obifloat_t value
cdef object result
cdef bytes elt_name
if type(elt_id) == int :
value = obi_get_float_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id)
else :
elt_name = tobytes(elt_id)
value = obi_get_float_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name)
if obi_errno > 0 :
raise IndexError(line_nb, elt_id)
if value == OBIFloat_NA :
result = None
else :
result = <double> value
return result
cpdef object get_line(self, index_t line_nb) :
cdef obifloat_t value
cdef object value_in_result
cdef dict result
cdef index_t i
cdef bint all_NA
result = {}
all_NA = True
for i in range(self.nb_elements_per_line) :
value = obi_get_float_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, i)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIFloat_NA :
value_in_result = None
else :
value_in_result = <double> value
result[self.elements_names[i]] = value_in_result
if all_NA and (value_in_result is not None) :
all_NA = False
if all_NA :
result = None
return result
cpdef set_item(self, index_t line_nb, object elt_id, object value) :
cdef bytes elt_name
if value is None :
value = OBIFloat_NA
if type(elt_id) == int :
if obi_set_float_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id, <obifloat_t> value) < 0 :
raise Exception("Problem setting a value in a column")
else :
elt_name = tobytes(elt_id)
if obi_set_float_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name, <obifloat_t> value) < 0 :
raise Exception("Problem setting a value in a column")
def register_class():
register_column_class(OBI_FLOAT, False, Column_float, float) # TODO why not double?
register_column_class(OBI_FLOAT, True, Column_multi_elts_float, float) # TODO why not double?

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python/obitools3/dms/column/typed_column/int.pxd Normal file
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# #cython: language_level=3
from ...capi.obitypes cimport index_t
from ..column cimport Column, \
Column_multi_elts
cdef class Column_int(Column) :
cpdef object get_line(self, index_t line_nb)
cpdef set_line(self, index_t line_nb, object value)
cdef class Column_multi_elts_int(Column_multi_elts) :
cpdef object get_item(self, index_t line_nb, object elt_id)
cpdef object get_line(self, index_t line_nb)
cpdef set_item(self, index_t line_nb, object elt_id, object value)

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python/obitools3/dms/column/typed_column/int.pyx Normal file
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#cython: language_level=3
from ..column cimport register_column_class
from ...view.view cimport View
from obitools3.utils cimport str2bytes, bytes2str, tobytes
from ...capi.obiview cimport obi_get_int_with_elt_name_and_col_p_in_view, \
obi_get_int_with_elt_idx_and_col_p_in_view, \
obi_set_int_with_elt_name_and_col_p_in_view, \
obi_set_int_with_elt_idx_and_col_p_in_view
from ...capi.obierrno cimport obi_errno
from ...capi.obitypes cimport OBI_INT, OBIInt_NA, obiint_t, obitype_t
from cpython.int cimport PyInt_FromLong
cdef class Column_int(Column):
@staticmethod
def new(View view,
object column_name,
index_t nb_elements_per_line=1,
object elements_names=None,
object comments=b""):
return Column.new_column(view, column_name, OBI_INT,
nb_elements_per_line=nb_elements_per_line,
elements_names=elements_names,
comments=comments)
cpdef object get_line(self, index_t line_nb):
cdef obiint_t value
cdef object result
global obi_errno
value = obi_get_int_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIInt_NA :
result = None
else :
result = PyInt_FromLong(value)
return result
cpdef set_line(self, index_t line_nb, object value):
if value is None :
value = OBIInt_NA
if obi_set_int_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0, <obiint_t> value) < 0:
raise Exception("Problem setting a value in a column")
cdef class Column_multi_elts_int(Column_multi_elts):
cpdef object get_item(self, index_t line_nb, object elt_id) :
cdef obiint_t value
cdef object result
cdef bytes elt_name
if type(elt_id) == int :
value = obi_get_int_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id)
else :
elt_name = tobytes(elt_id)
value = obi_get_int_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name)
if obi_errno > 0 :
raise IndexError(line_nb, elt_id)
if value == OBIInt_NA :
result = None
else :
result = PyInt_FromLong(value)
return result
cpdef object get_line(self, index_t line_nb) :
cdef obiint_t value
cdef object value_in_result
cdef dict result
cdef index_t i
cdef bint all_NA
result = {}
all_NA = True
for i in range(self.nb_elements_per_line) :
value = obi_get_int_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, i)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIInt_NA :
value_in_result = None
else :
value_in_result = PyInt_FromLong(value)
result[self.elements_names[i]] = value_in_result
if all_NA and (value_in_result is not None) :
all_NA = False
if all_NA :
result = None
return result
cpdef set_item(self, index_t line_nb, object elt_id, object value) :
cdef bytes elt_name
if value is None :
value = OBIInt_NA
if type(elt_id) == int :
if obi_set_int_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id, <obiint_t> value) < 0 :
raise Exception("Problem setting a value in a column")
else :
elt_name = tobytes(elt_id)
if obi_set_int_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name, <obiint_t> value) < 0 :
raise Exception("Problem setting a value in a column")
def register_class():
register_column_class(OBI_INT, False, Column_int, int)
register_column_class(OBI_INT, True, Column_multi_elts_int, int)

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python/obitools3/dms/column/typed_column/qual.pxd Normal file
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# #cython: language_level=3
from ...capi.obitypes cimport index_t
from ..column cimport Column, \
Column_multi_elts
cdef class Column_qual(Column) :
cpdef object get_line(self, index_t line_nb)
cpdef object get_str_line(self, index_t line_nb)
cpdef set_line(self, index_t line_nb, object value)
cpdef set_str_line(self, index_t line_nb, object value)
cdef class Column_multi_elts_qual(Column_multi_elts) :
cpdef object get_item(self, index_t line_nb, object elt_id)
cpdef object get_str_item(self, index_t line_nb, object elt_id)
cpdef object get_line(self, index_t line_nb)
cpdef object get_str_line(self, index_t line_nb)
cpdef set_item(self, index_t line_nb, object elt_id, object value)
cpdef set_str_item(self, index_t line_nb, object elt_id, object value)

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#cython: language_level=3
from ..column cimport register_column_class
from ...view.view cimport View
from obitools3.utils cimport str2bytes, bytes2str, tobytes
from ...capi.obiview cimport obi_get_qual_char_with_elt_name_and_col_p_in_view, \
obi_get_qual_char_with_elt_idx_and_col_p_in_view, \
obi_set_qual_char_with_elt_name_and_col_p_in_view, \
obi_set_qual_char_with_elt_idx_and_col_p_in_view, \
obi_get_qual_int_with_elt_name_and_col_p_in_view, \
obi_get_qual_int_with_elt_idx_and_col_p_in_view, \
obi_set_qual_int_with_elt_name_and_col_p_in_view, \
obi_set_qual_int_with_elt_idx_and_col_p_in_view
from ...capi.obierrno cimport obi_errno
from ...capi.obitypes cimport OBI_QUAL, OBIQual_char_NA, OBIQual_int_NA, const_char_p
from libc.stdlib cimport free
from libc.string cimport strcmp
from libc.stdint cimport uint8_t
from libc.stdlib cimport malloc
cdef class Column_qual(Column):
@staticmethod
def new(View view,
object column_name,
index_t nb_elements_per_line=1,
object elements_names=None,
object comments=b""):
return Column.new_column(view, column_name, OBI_QUAL,
nb_elements_per_line=nb_elements_per_line,
elements_names=elements_names,
comments=comments)
cpdef object get_line(self, index_t line_nb):
cdef const uint8_t* value
cdef int value_length
cdef object result
global obi_errno
value = obi_get_qual_int_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0, &value_length)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIQual_int_NA :
result = None
else :
result = []
for i in range(value_length) :
result.append(<int>value[i])
return result
cpdef object get_str_line(self, index_t line_nb):
cdef char* value
cdef object result
cdef int i
global obi_errno
value = obi_get_qual_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIQual_char_NA :
result = None
else : # TODO discuss
result = bytes2str(value)
free(value)
return result
cpdef set_line(self, index_t line_nb, object value):
cdef uint8_t* value_b
cdef int value_length
if value is None :
if obi_set_qual_int_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0, OBIQual_int_NA, 0) < 0:
raise Exception("Problem setting a value in a column")
else :
value_length = len(value)
value_b = <uint8_t*> malloc(value_length * sizeof(uint8_t))
for i in range(value_length) :
value_b[i] = <uint8_t>value[i]
if obi_set_qual_int_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0, value_b, value_length) < 0:
raise Exception("Problem setting a value in a column")
free(value_b)
cpdef set_str_line(self, index_t line_nb, object value):
cdef bytes value_b
if value is None :
if obi_set_qual_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0, OBIQual_char_NA) < 0:
raise Exception("Problem setting a value in a column")
else :
if type(value) == str:
value_b = str2bytes(value)
else :
value_b = value
if obi_set_qual_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0, value_b) < 0:
raise Exception("Problem setting a value in a column")
cdef class Column_multi_elts_qual(Column_multi_elts):
cpdef object get_item(self, index_t line_nb, object elt_id):
cdef const uint8_t* value
cdef int value_length
cdef object result
cdef int i
global obi_errno # TODO add everywhere
if type(elt_id) == int :
value = obi_get_qual_int_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id, &value_length)
else :
elt_name = tobytes(elt_id)
value = obi_get_qual_int_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name, &value_length)
if obi_errno > 0 :
raise IndexError(line_nb, elt_id)
if value == OBIQual_int_NA :
result = None
else :
result = []
for i in range(value_length) :
result.append(<int>value[i])
return result
cpdef object get_str_item(self, index_t line_nb, object elt_id):
cdef char* value
cdef object result
global obi_errno
if type(elt_id) == int :
value = obi_get_qual_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id)
else :
elt_name = tobytes(elt_id)
value = obi_get_qual_char_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name)
if obi_errno > 0 :
raise IndexError(line_nb, elt_name)
if value == OBIQual_char_NA :
result = None
else :
result = bytes2str(value) # TODO return bytes?
free(value)
return result
cpdef object get_line(self, index_t line_nb) :
cdef const uint8_t* value
cdef int value_length
cdef object value_in_result
cdef dict result
cdef index_t i
cdef int j
cdef bint all_NA
global obi_errno
result = {}
all_NA = True
for i in range(self.nb_elements_per_line) :
value = obi_get_qual_int_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, i, &value_length)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIQual_int_NA :
value_in_result = None
else :
value_in_result = []
for j in range(value_length) :
value_in_result.append(<int>value[j])
result[self.elements_names[i]] = value_in_result
if all_NA and (value_in_result is not None) :
all_NA = False
if all_NA :
result = None
return result
cpdef object get_str_line(self, index_t line_nb) :
cdef char* value
cdef object value_in_result
cdef dict result
cdef index_t i
cdef bint all_NA
global obi_errno
result = {}
all_NA = True
for i in range(self.nb_elements_per_line) :
value = obi_get_qual_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, i)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIQual_char_NA :
value_in_result = None
else :
value_in_result = bytes2str(value)
free(value)
result[self.elements_names[i]] = value_in_result
if all_NA and (value_in_result is not None) :
all_NA = False
if all_NA :
result = None
return result
cpdef set_item(self, index_t line_nb, object elt_id, object value):
cdef uint8_t* value_b
cdef int value_length
cdef bytes elt_name
if value is None :
value_b = OBIQual_int_NA
value_length = 0
else :
value_length = len(value)
value_b = <uint8_t*> malloc(value_length * sizeof(uint8_t))
for i in range(value_length) :
value_b[i] = <uint8_t>value[i]
if type(elt_id) == int :
if obi_set_qual_int_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id, value_b, value_length) < 0 :
raise Exception("Problem setting a value in a column")
else :
elt_name = tobytes(elt_id)
if obi_set_qual_int_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name, value_b, value_length) < 0:
raise Exception("Problem setting a value in a column")
if value is not None :
free(value_b)
cpdef set_str_item(self, index_t line_nb, object elt_id, object value):
cdef bytes value_b
cdef bytes elt_name
if value is None :
value_b = OBIQual_char_NA
else :
value_b = tobytes(value)
if type(elt_id) == int :
if obi_set_qual_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id, value_b) < 0 :
raise Exception("Problem setting a value in a column")
else :
elt_name = tobytes(elt_id)
if obi_set_qual_char_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name, value_b) < 0:
raise Exception("Problem setting a value in a column")
def register_class():
register_column_class(OBI_QUAL, False, Column_qual, bytes) # TODO str? int?
register_column_class(OBI_QUAL, True, Column_multi_elts_qual, bytes) # TODO str? int?

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# #cython: language_level=3
from ...capi.obitypes cimport index_t
from ..column cimport Column, \
Column_multi_elts
cdef class Column_seq(Column) :
cpdef object get_line(self, index_t line_nb)
cpdef set_line(self, index_t line_nb, object value)
cdef class Column_multi_elts_seq(Column_multi_elts) :
cpdef object get_item(self, index_t line_nb, object elt_id)
cpdef object get_line(self, index_t line_nb)
cpdef set_item(self, index_t line_nb, object elt_id, object value)

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#cython: language_level=3
from ..column cimport register_column_class
from ...view.view cimport View
from obitools3.utils cimport str2bytes, bytes2str, tobytes
from ...capi.obiview cimport obi_get_seq_with_elt_name_and_col_p_in_view, \
obi_get_seq_with_elt_idx_and_col_p_in_view, \
obi_set_seq_with_elt_name_and_col_p_in_view, \
obi_set_seq_with_elt_idx_and_col_p_in_view
from ...capi.obierrno cimport obi_errno
from ...capi.obitypes cimport OBI_SEQ, OBISeq_NA
from libc.stdlib cimport free
cdef class Column_seq(Column):
@staticmethod
def new(View view,
object column_name,
index_t nb_elements_per_line=1,
object elements_names=None,
object comments=b""):
return Column.new_column(view, column_name, OBI_SEQ,
nb_elements_per_line=nb_elements_per_line,
elements_names=elements_names,
comments=comments)
cpdef object get_line(self, index_t line_nb):
cdef char* value
cdef object result
global obi_errno
value = obi_get_seq_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBISeq_NA :
result = None
else : # TODO
try:
result = <bytes> value
finally:
free(value)
return result
cpdef set_line(self, index_t line_nb, object value):
cdef bytes value_b
if value is None :
value_b = OBISeq_NA
else :
value_b = tobytes(value)
if obi_set_seq_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0, value_b) < 0:
raise Exception("Problem setting a value in a column")
cdef class Column_multi_elts_seq(Column_multi_elts):
cpdef object get_item(self, index_t line_nb, object elt_id) :
cdef char* value
cdef object result
global obi_errno
if type(elt_id) == int :
value = obi_get_seq_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id)
else :
elt_name = tobytes(elt_id)
value = obi_get_seq_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name)
if obi_errno > 0 :
raise IndexError(line_nb, elt_id)
if value == OBISeq_NA :
result = None
else :
try:
result = <bytes> value
finally:
free(value)
return result
cpdef object get_line(self, index_t line_nb) :
cdef char* value
cdef object value_in_result
cdef dict result
cdef index_t i
cdef bint all_NA
global obi_errno
result = {}
all_NA = True
for i in range(self.nb_elements_per_line) :
value = obi_get_seq_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, i)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBISeq_NA :
value_in_result = None
else :
try:
value_in_result = <bytes> value
finally:
free(value)
result[self.elements_names[i]] = value_in_result
if all_NA and (value_in_result is not None) :
all_NA = False
if all_NA :
result = None
return result
cpdef set_item(self, index_t line_nb, object elt_id, object value):
cdef bytes value_b
cdef bytes elt_name
if value is None :
value_b = OBISeq_NA
else :
value_b = tobytes(value)
if type(elt_id) == int :
if obi_set_seq_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id, value_b) < 0:
raise Exception("Problem setting a value in a column")
else :
elt_name = tobytes(elt_id)
if obi_set_seq_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name, value_b) < 0:
raise Exception("Problem setting a value in a column")
def register_class():
register_column_class(OBI_SEQ, False, Column_seq, bytes) # TODO str?
register_column_class(OBI_SEQ, True, Column_multi_elts_seq, bytes) # TODO str?

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python/obitools3/dms/column/typed_column/str.pxd Normal file
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# #cython: language_level=3
from ...capi.obitypes cimport index_t
from ..column cimport Column, \
Column_multi_elts
cdef class Column_str(Column) :
cpdef object get_line(self, index_t line_nb)
cpdef set_line(self, index_t line_nb, object value)
cdef class Column_multi_elts_str(Column_multi_elts) :
cpdef object get_item(self, index_t line_nb, object elt_id)
cpdef object get_line(self, index_t line_nb)
cpdef set_item(self, index_t line_nb, object elt_id, object value)

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#cython: language_level=3
from ..column cimport register_column_class
from ...view.view cimport View
from obitools3.utils cimport str2bytes, bytes2str, tobytes
from ...capi.obiview cimport obi_get_str_with_elt_name_and_col_p_in_view, \
obi_get_str_with_elt_idx_and_col_p_in_view, \
obi_set_str_with_elt_name_and_col_p_in_view, \
obi_set_str_with_elt_idx_and_col_p_in_view
from ...capi.obierrno cimport obi_errno
from ...capi.obitypes cimport OBI_STR, OBIStr_NA
cdef class Column_str(Column):
@staticmethod
def new(View view,
object column_name,
index_t nb_elements_per_line=1,
object elements_names=None,
object comments=b""):
return Column.new_column(view, column_name, OBI_STR,
nb_elements_per_line=nb_elements_per_line,
elements_names=elements_names,
comments=comments)
cpdef object get_line(self, index_t line_nb):
cdef char* value
cdef object result
global obi_errno
value = obi_get_str_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIStr_NA :
result = None
else :
result = <bytes> value # NOTE: value is not freed because the pointer points to a mmapped region in an AVL data file.
return result
cpdef set_line(self, index_t line_nb, object value):
cdef bytes value_b
if value is None :
value_b = OBIStr_NA
else :
value_b = tobytes(value)
if obi_set_str_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0, value_b) < 0:
raise Exception("Problem setting a value in a column")
cdef class Column_multi_elts_str(Column_multi_elts):
cpdef object get_item(self, index_t line_nb, object elt_id) :
cdef char* value
cdef object result
global obi_errno
if type(elt_id) == int :
value = obi_get_str_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id)
else :
elt_name = tobytes(elt_id)
value = obi_get_str_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name)
if obi_errno > 0 :
raise IndexError(line_nb, elt_id)
if value == OBIStr_NA :
result = None
else :
result = <bytes> value # NOTE: value is not freed because the pointer points to a mmapped region in an AVL data file.
return result
cpdef object get_line(self, index_t line_nb) :
cdef char* value
cdef object value_in_result
cdef dict result
cdef index_t i
cdef bint all_NA
global obi_errno
result = {}
all_NA = True
for i in range(self.nb_elements_per_line) :
value = obi_get_str_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, i)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIStr_NA :
value_in_result = None
else :
value_in_result = <bytes> value
result[self.elements_names[i]] = value_in_result
if all_NA and (value_in_result is not None) :
all_NA = False
if all_NA :
result = None
return result
cpdef set_item(self, index_t line_nb, object elt_id, object value):
cdef bytes value_b
cdef bytes elt_name
if value is None :
value_b = OBIStr_NA
else :
value_b = tobytes(value)
if type(elt_id) == int :
if obi_set_str_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id, value_b) < 0:
raise Exception("Problem setting a value in a column")
else :
elt_name = tobytes(elt_id)
if obi_set_str_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name, value_b) < 0:
raise Exception("Problem setting a value in a column")
def register_class():
register_column_class(OBI_STR, False, Column_str, bytes) # TODO str?
register_column_class(OBI_STR, True, Column_multi_elts_str, bytes) # TODO str?