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Cython API: compiling but not working

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This commit is contained in:
Celine Mercier
2017-03-06 16:07:02 +01:00
parent 778acc48cd
commit 381194194c
19 changed files with 1404 additions and 1531 deletions
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4
python/obitools3/dms/capi/obialign.pxd
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@ -1,7 +1,7 @@
#cython: language_level=3
from obitools3.obidms.capi.obidms cimport OBIDMS_p
from obitools3.obidms.capi.obitypes cimport const_char_p
from obitools3.dms.capi.obidms cimport OBIDMS_p
from obitools3.dms.capi.obitypes cimport const_char_p
cdef extern from "obi_align.h" nogil:

25
python/obitools3/dms/column.pxd
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@ -1,25 +0,0 @@
#cython: language_level=3
from .capi.obitypes cimport index_t, \
obitype_t
from .capi.obidmscolumn cimport OBIDMS_column_p
from .view cimport View
cdef class Column:
cdef OBIDMS_column_p* _pointer
cdef View _view
cpdef close(self)
cdef class Column_line:
cdef Column _column
cdef index_t _index
cpdef update(self, data)
cdef register_column_class(obitype_t obitype,
type classe,
type python)

180
python/obitools3/dms/column.pyx
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@ -1,180 +0,0 @@
#cython: language_level=3
from .capi.obitypes cimport name_data_type
from .capi.obidmscolumn cimport OBIDMS_column_header_p, \
obi_close_column, \
obi_column_prepare_to_get_value
from .capi.obiutils cimport obi_format_date
from .dms cimport __OBIDMS_COLUMN_CLASS__
from obitools3.utils cimport bytes2str
cdef class Column :
"""
The obitools3.dms.column.Column class wraps a C instance of a column in the context of a View
"""
# Note: should only be initialized through a subclass
def __init__(self,
View view,
int __internalCall__):
'''
Creates a new OBDMS column objected referring to a already created column
in the context of a view.
This constructor is normally only called by subclass constructor.
@param view: The view object containing the column.
@type view: OBIView
'''
cdef OBIDMS_column_p* column_pp
if __internalCall__!=987654:
raise RuntimeError('OBIView constructor cannot be called directly')
# Check that the class is only created as a subclass instance
if type(self)==Column or not isinstance(self, Column):
raise RuntimeError('OBIDMS.Column constructor cannot be called directly')
# Fill structure
self._pointer = NULL
self._view = view
def __len__(self):
'''
Implements the len() function for the Column class
@rtype: `int`
'''
return self.lines_used
def __sizeof__(self):
'''
returns the size of the C object wrapped by the Column instance
'''
cdef OBIDMS_column_header_p header = self._pointer[0].header
return header.header_size + header.data_size
def __iter__(self):
cdef index_t line_nb
for line_nb in range(self.lines_used):
yield self[line_nb]
def __str__(self) :
cdef str to_print
to_print = ''
for line in self :
to_print = to_print + str(line) + "\n"
return to_print
def __repr__(self) :
return b"%s, original name: %s, version %d, data type: %d" % (
self._alias,
self.original_name,
self.version,
self.data_type
)
cpdef close(self):
if self._pointer != NULL:
if obi_close_column(self._pointer[0]) < 0 :
raise Exception("Problem closing column %s" % bytes2str(self.name))
# Column alias property getter and setter
@property
def name(self):
return self._alias
@name.setter
def name(self, new_alias): # @DuplicatedSignature
self._view.change_column_alias(self._alias, new_alias)
# elements_names property getter
@property
def elements_names(self):
return (((self._pointer)[0].header).elements_names).split(b';')
# nb_elements_per_line property getter
@property
def nb_elements_per_line(self):
return ((self._pointer)[0].header).nb_elements_per_line
# data_type property getter
@property
def data_type(self):
return name_data_type(((self._pointer)[0].header).returned_data_type)
# original_name property getter
@property
def original_name(self):
return ((self._pointer)[0].header).name
# version property getter
@property
def version(self):
return ((self._pointer)[0].header).version
# lines_used property getter
@property
def lines_used(self):
return (self._pointer)[0].header.lines_used
# comments property getter
@property
def comments(self):
return (self._pointer)[0].header.comments
# creation_date property getter
@property
def creation_date(self):
return obi_format_date((self._pointer)[0].header.creation_date)
######################################################################################################
cdef class Column_line :
def __init__(self, Column column, index_t line_nb) :
self._index = line_nb
self._column = column
if obi_column_prepare_to_get_value(self._column._pointer[0],line_nb) < 0:
raise IndexError("Cannot access to the line %d" % line_nb)
def __contains__(self, str element_name):
pass
#return (element_name in self._column.elements_names)
def __repr__(self) :
return str(self._column.get_line(self._index))
cpdef update(self, data):
if isinstance(data, dict):
data=data.items()
for key,value in data:
if key in self:
self[key]=value
######################################################################################################
cdef register_column_class(obitype_t obitype,
type classe,
type python):
"""
Each sub class of `OBIDMS_column` needs to be registered after its declaration
to declare its relationship with an `OBIType_t`
"""
global __OBIDMS_COLUMN_CLASS__
assert issubclass(classe,Column)
__OBIDMS_COLUMN_CLASS__[obitype]=(classe,python)

107
python/obitools3/dms/column/bool.pxd
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@ -1,56 +1,53 @@
#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 obitools3.utils cimport str2bytes, bytes2str
cdef class Column_line_bool(OBIDMS_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(OBIDMS_column):
cdef Column _new(OBIView view,
bytes column_name,
index_t nb_elements_per_line=1,
object elements_names=None,
bytes comments=b""):
cpdef object get_line(self, index_t line_nb)
cpdef set_line(self, index_t line_nb, object value)
# #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)

585
python/obitools3/dms/column/bool.pyx
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@ -1,294 +1,305 @@
#cython: language_level=3
cdef class OBIDMS_column_line_bool(OBIDMS_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_p = self._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):
cdef bool result
if value == OBIBool_NA :
result = None
else :
result = PyBool_FromLong(value)
return result
@staticmethod
cdef bool2obibool_t(bool value):
cdef obibool_t result
if value is None:
result=OBIBool_NA
else:
result= <obibool_t> <int> value
return result
def __init__(self, OBIDMS_column column, index_t line_nb) :
"""
Creates a new `OBIDMS_column_line_bool`
@param column: an OBIDMS_column instance
@param line_nb: the line in the column
"""
OBIDMS_column_line.__init__(self,column,line_nb)
self.update_pointer()
cpdef bool get_bool_item_by_name(self,bytes element_name):
"""
Returns the value associated to the name `element_name` of the current line
@param element_name: a `bytes` instance containing the name of the element
@return: the `bool` value corresponding to the name
"""
cdef char* cname = element_name
cdef obibool_t value
global obi_errno
self.update_pointer()
value = obi_column_get_obibool_with_elt_name(self._column_p,
self._index,
cname)
if obi_errno > 0 :
obi_errno = 0
raise KeyError("Cannot access to key %s" % bytes2str(element_name))
return OBIDMS_column_line_bool.obibool_t2bool(value)
cpdef bool get_bool_item_by_idx(self,index_t index):
"""
Returns the value associated to the name `element_name` of the current line
@param index: a `int` instance containing the index of the element
@return: the `bool` value corresponding to the name
"""
cdef obibool_t value # @DuplicatedSignature
global obi_errno
self.update_pointer()
value = obi_column_get_obibool_with_elt_idx(self._column_p,
self._index,
index)
if obi_errno > 0 :
obi_errno = 0
raise IndexError("Cannot access to element %d" % index)
return OBIDMS_column_line_bool.obibool_t2bool(value)
def __getitem__(self, object element_name) :
cdef bytes name
cdef int cindex
cdef obibool_t value
cdef type typearg = type(element_name)
cdef bool result
if typearg == int:
cindex=element_name
if cindex < 0:
cindex = self._len - cindex
result=self.get_bool_item_by_idx(cindex)
elif typearg == bytes:
result=self.get_bool_item_by_name(element_name)
elif typearg == str:
name = str2bytes(element_name)
result=self.get_bool_item_by_name(name)
return result
cpdef set_bool_item_by_name(self,bytes element_name,bool value):
"""
Sets the value associated to the name `element_name` of the current line
@param element_name: a `bytes` instance containing the name of the element
@param value: a `bool` instance of the new value
@return: the `bool` value corresponding to the name
"""
cdef char* cname = element_name
cdef obibool_t cvalue
self.update_pointer()
cvalue = OBIDMS_column_line_bool.bool2obibool_t(value)
if ( obi_column_set_obibool_with_elt_name(self._column_p,
self._index,
cname,
cvalue) < 0 ):
raise KeyError("Cannot access to key %s" % bytes2str(element_name))
cpdef set_bool_item_by_idx(self,index_t index,bool value):
"""
Sets the value associated to the name `element_name` of the current line
@param index: a `int` instance containing the index of the element
@param value: a `bool` instance of the new value
@return: the `bool` value corresponding to the name
"""
cdef obibool_t cvalue # @DuplicatedSignature
self.update_pointer()
cvalue = OBIDMS_column_line_bool.bool2obibool_t(value)
if ( obi_column_set_obibool_with_elt_idx(self._column_p,
self._index,
index,
cvalue) < 0 ):
raise IndexError("Cannot access to item index %d" % index)
def __setitem__(self, object element_name, object value):
cdef bytes name
cdef int cindex
cdef type typearg = type(element_name)
cdef bool result
if typearg == int:
cindex=element_name
if cindex < 0:
cindex = self._len - cindex
self.set_bool_item_by_idx(cindex,value)
elif typearg == bytes:
self.set_bool_item_by_name(element_name,value)
elif typearg == str:
name = str2bytes(element_name)
self.set_bool_item_by_name(name,value)
def __repr__(self) :
return str(self._column.get_line(self._index))
def __len__(self):
return self._len
# 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
#
# @staticmethod
# cdef bool obibool_t2bool(obibool_t value):
# cdef bool result
#
# if value == OBIBool_NA :
# result = None
# else :
# result = PyBool_FromLong(value)
#
# return result
#
# @staticmethod
# cdef bool2obibool_t(bool value):
# cdef obibool_t result
#
# if value is None:
# result=OBIBool_NA
# else:
# result= <obibool_t> <int> value
#
# return result
#
#
# def __init__(self, Column column, index_t line_nb) :
# """
# Creates a new `OBIDMS_column_line_bool`
#
# @param column: an OBIDMS_column instance
# @param line_nb: the line in the column
# """
#
# Column_line.__init__(self, column, line_nb)
# self.update_pointer()
#
#
#
# cpdef bool get_bool_item_by_name(self, bytes element_name) :
# """
# Returns the value associated to the name `element_name` of the current line
#
# @param element_name: a `bytes` instance containing the name of the element
#
# @return: the `bool` value corresponding to the name
# """
# cdef char* cname = element_name
# cdef obibool_t value
# global obi_errno
#
# self.update_pointer()
#
# cdef OBIDMS_column_p* column_pp
# column_pp = <OBIDMS_column_p*>self._pointer
# cdef OBIDMS_column_p column_p = column_pp[0]
#
# value = obi_column_get_obibool_with_elt_name(column_p,
# self._index,
# cname)
#
# if obi_errno > 0 :
# obi_errno = 0
# raise KeyError("Cannot access to key %s" % bytes2str(element_name))
#
# return Column_line_bool.obibool_t2bool(value)
#
#
# cpdef bool get_bool_item_by_idx(self,index_t index):
# """
# Returns the value associated to the name `element_name` of the current line
#
# @param index: a `int` instance containing the index of the element
#
# @return: the `bool` value corresponding to the name
# """
# cdef obibool_t value # @DuplicatedSignature
# global obi_errno
#
# cdef OBIDMS_column_p* column_pp
# column_pp = <OBIDMS_column_p*>self._pointer
# cdef OBIDMS_column_p column_p = column_pp[0]
#
# self.update_pointer()
#
# value = obi_column_get_obibool_with_elt_idx(column_p,
# self._index,
# index)
#
# if obi_errno > 0 :
# obi_errno = 0
# raise IndexError("Cannot access to element %d" % index)
#
# return Column_line_bool.obibool_t2bool(value)
#
#
# def __getitem__(self, object element_name) :
# cdef bytes name
# cdef int cindex
# cdef obibool_t value
# cdef type typearg = type(element_name)
# cdef bool result
#
#
# if typearg == int:
# cindex=element_name
# if cindex < 0:
# cindex = self._len - cindex
# result=self.get_bool_item_by_idx(cindex)
# elif typearg == bytes:
# result=self.get_bool_item_by_name(element_name)
# elif typearg == str:
# name = str2bytes(element_name)
# result=self.get_bool_item_by_name(name)
#
# return result
#
# cpdef set_bool_item_by_name(self,bytes element_name,bool value):
# """
# Sets the value associated to the name `element_name` of the current line
#
# @param element_name: a `bytes` instance containing the name of the element
# @param value: a `bool` instance of the new value
#
# @return: the `bool` value corresponding to the name
# """
# cdef char* cname = element_name
# cdef obibool_t cvalue
#
# self.update_pointer()
# cvalue = OBIDMS_column_line_bool.bool2obibool_t(value)
#
# if ( obi_column_set_obibool_with_elt_name((<OBIDMS_column_p*>self._pointer)[0],
# self._index,
# cname,
# cvalue) < 0 ):
# raise KeyError("Cannot access to key %s" % bytes2str(element_name))
#
# cpdef set_bool_item_by_idx(self,index_t index,bool value):
# """
# Sets the value associated to the name `element_name` of the current line
#
# @param index: a `int` instance containing the index of the element
# @param value: a `bool` instance of the new value
#
# @return: the `bool` value corresponding to the name
# """
# cdef obibool_t cvalue # @DuplicatedSignature
#
# self.update_pointer()
# cvalue = OBIDMS_column_line_bool.bool2obibool_t(value)
#
# if ( obi_column_set_obibool_with_elt_idx((<OBIDMS_column_p*>self._pointer)[0],
# self._index,
# index,
# cvalue) < 0 ):
# raise IndexError("Cannot access to item index %d" % index)
#
#
#
# def __setitem__(self, object element_name, object value):
# cdef bytes name
# cdef int cindex
# cdef type typearg = type(element_name)
# cdef bool result
#
#
# if typearg == int:
# cindex=element_name
# if cindex < 0:
# cindex = self._len - cindex
# self.set_bool_item_by_idx(cindex,value)
# elif typearg == bytes:
# self.set_bool_item_by_name(element_name,value)
# elif typearg == str:
# name = str2bytes(element_name)
# self.set_bool_item_by_name(name,value)
#
# def __repr__(self) :
# return str(self._column.get_line(self._index))
#
# def __len__(self):
# return self._len
cdef class Column_bool(Column):
# 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)
@staticmethod
def new(OBIView 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 OBIDMS_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,
OBIView view,
object column_name=None,
object comments=b""):
cdef OBIDMS_column_p column_p = self._column_pp[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(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)

40
python/obitools3/dms/column/column.pxd
View File

@ -1,26 +1,34 @@
#cython: language_level=3
from ..capi.obitypes cimport index_t, \
obitype_t
from ..capi.obidmscolumn cimport OBIDMS_column_p
from ..view cimport View
from ..view.view cimport View
from ..object cimport OBIWrapper
cdef class Column:
cdef OBIDMS_column_p* _pointer
cdef View _view
cdef class Column(OBIWrapper) :
cdef View _view
cpdef close(self)
cdef class Column_line:
@staticmethod
cdef type get_column_class(obitype_t obitype)
cdef Column _column
cdef index_t _index
cpdef update(self, data)
#
# cdef class Column_line:
#
# cdef Column _column
# cdef index_t _index
#
# cpdef update(self, data)
#
#
cdef register_column_class(obitype_t obitype,
type classe,
type matrix,
type python)

426
python/obitools3/dms/column/column.pyx
View File

@ -1,23 +1,22 @@
#cython: language_level=3
from .capi.obitypes cimport name_data_type
from .capi.obidmscolumn cimport OBIDMS_column_header_p, \
obi_close_column, \
obi_column_prepare_to_get_value
from .capi.obiutils cimport obi_format_date
from .dms cimport __OBIDMS_COLUMN_CLASS__
from ..capi.obitypes cimport name_data_type
from ..capi.obidmscolumn cimport OBIDMS_column_header_p, \
obi_close_column
from ..capi.obiutils cimport obi_format_date
from ..dms cimport __OBIDMS_COLUMN_CLASS__
from obitools3.utils cimport bytes2str
cdef class Column :
cdef class Column(OBIWrapper) :
"""
The obitools3.dms.column.Column class wraps a c instance of a column in the context of a View
The obitools3.dms.column.Column class wraps a C instance of a column in the context of a View
"""
# Note: should only be initialized through a subclass
def __init__(self,
View view,
@ -25,192 +24,235 @@ cdef class Column :
'''
Create a new OBDMS column objected referring to a already created column
in the context of a view.
This constructor is normally only called by subclass constructor.
@param view: The view object containing the column.
@type view: OBIView
'''
cdef OBIDMS_column_p* column_pp
if __internalCall__!=987654:
if __internalCall__ != 987654:
raise RuntimeError('OBIView constructor cannot be called directly')
OBIWrapper.__init__(self)
# Check that the class is only created as a subclass instance
if type(self)==Column or not isinstance(self, Column):
raise RuntimeError('OBIDMS.Column constructor cannot be called directly')
# Fill structure
self._pointer = NULL
self._view = view
self._pointer = NULL
self._view = view
@staticmethod
def new(OBIView 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 OBIDMS_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 = self.pointer.header.returned_data_type,
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 __len__(self):
'''
implements the len() function for the Column class
@rtype: `int`
'''
return self.lines_used
def __sizeof__(self):
'''
returns the size of the C object wrapped by the Column instance
'''
cdef OBIDMS_column_header_p header = self._pointer[0].header
return header.header_size + header.data_size
def __iter__(self):
cdef index_t line_nb
for line_nb in range(self.lines_used):
yield self[line_nb]
def __str__(self) :
cdef str to_print
to_print = ''
for line in self :
to_print = to_print + str(line) + "\n"
return to_print
def __repr__(self) :
return b"%s, original name: %s, version %d, data type: %d" % (
self._alias,
self.original_name,
self.version,
self.data_type
)
cpdef close(self):
if self._pointer != NULL:
if obi_close_column(self._pointer[0]) < 0 :
raise Exception("Problem closing column %s" % bytes2str(self.name))
# Column alias property getter and setter
@property
def name(self):
return self._alias
@name.setter
def name(self, new_alias): # @DuplicatedSignature
self._view.change_column_alias(self._alias, new_alias)
# elements_names property getter
@property
def elements_names(self):
return (((self._pointer)[0].header).elements_names).split(b';')
# nb_elements_per_line property getter
@property
def nb_elements_per_line(self):
return ((self._pointer)[0].header).nb_elements_per_line
# data_type property getter
@property
def data_type(self):
return name_data_type(((self._pointer)[0].header).returned_data_type)
# original_name property getter
@property
def original_name(self):
return ((self._pointer)[0].header).name
# version property getter
@property
def version(self):
return ((self._pointer)[0].header).version
# lines_used property getter
@property
def lines_used(self):
return (self._pointer)[0].header.lines_used
# comments property getter
@property
def comments(self):
return (self._pointer)[0].header.comments
# creation_date property getter
@property
def creation_date(self):
return obi_format_date((self._pointer)[0].header.creation_date)
######################################################################################################
cdef class Column_line :
def __init__(self, Column column, index_t line_nb) :
self._index = line_nb
self._column = column
if obi_column_prepare_to_get_value(self._column._pointer[0],line_nb) < 0:
raise IndexError("Cannot access to the line %d" % line_nb)
def __contains__(self, str element_name):
pass
#return (element_name in self._column.elements_names)
def __repr__(self) :
return str(self._column.get_line(self._index))
cpdef update(self, data):
if isinstance(data, dict):
data=data.items()
for key,value in data:
if key in self:
self[key]=value
######################################################################################################
cdef type get_column_class(obitype_t obitype):
"""
Internal function returning the python class representing
a column for a given obitype.
"""
return __OBIDMS_COLUMN_CLASS__[obitype][0]
# @staticmethod
# def new(OBIView 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 OBIDMS_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 = self.pointer.header.returned_data_type,
# 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)))
#
# return Column.open(view,column_name)
#
#
# @staticmethod
# def open(OBIView view,
# object column_name):
# cdef bytes column_name_b = tobytes(column_name)
# cdef OBIDMS_column_p* column_pp
# cdef OBIDMS_column_p column_p
# cdef Column column
# cdef obitype_t column_type
#
# column_pp = obi_view_get_pointer_on_column_in_view(view._pointer,
# column_name_b)
#
# if column_pp == NULL:
# raise KeyError("Cannot access to column %s in view %s" % (
# bytes2str(column_name_b),
# bytes2str(self.name)
# ))
#
# column_p = column_pp[0]
# column_type = column_p.header.returned_data_type
#
# column = DMS.get_column_class(column_type)(view, 987654)
# column._pointer = column_pp
#
# return column
#
#
# def __len__(self):
# '''
# implements the len() function for the Column class
#
# @rtype: `int`
# '''
# return self.lines_used
#
#
# def __sizeof__(self):
# '''
# returns the size of the C object wrapped by the Column instance
# '''
# cdef OBIDMS_column_header_p header = self._pointer[0].header
# return header.header_size + header.data_size
#
#
# def __iter__(self):
# cdef index_t line_nb
#
# for line_nb in range(self.lines_used):
# yield self[line_nb]
#
#
# def __str__(self) :
# cdef str to_print
# to_print = ''
# for line in self :
# to_print = to_print + str(line) + "\n"
# return to_print
#
#
# def __repr__(self) :
# return b"%s, original name: %s, version %d, data type: %d" % (
# self._alias,
# self.original_name,
# self.version,
# self.data_type
# )
#
#
# cpdef close(self):
# if self._pointer != NULL:
# if obi_close_column(self._pointer[0]) < 0 :
# raise Exception("Problem closing column %s" % bytes2str(self.name))
#
#
# # Column alias property getter and setter
# @property
# def name(self):
# return self._alias
# @name.setter
# def name(self, new_alias): # @DuplicatedSignature
# self._view.change_column_alias(self._alias, new_alias)
#
# # elements_names property getter
# @property
# def elements_names(self):
# return (((self._pointer)[0].header).elements_names).split(b';')
#
# # nb_elements_per_line property getter
# @property
# def nb_elements_per_line(self):
# return ((self._pointer)[0].header).nb_elements_per_line
#
# # data_type property getter
# @property
# def data_type(self):
# return name_data_type(((self._pointer)[0].header).returned_data_type)
#
# # original_name property getter
# @property
# def original_name(self):
# return ((self._pointer)[0].header).name
#
# # version property getter
# @property
# def version(self):
# return ((self._pointer)[0].header).version
#
# # lines_used property getter
# @property
# def lines_used(self):
# return (self._pointer)[0].header.lines_used
#
# # comments property getter
# @property
# def comments(self):
# return (self._pointer)[0].header.comments
#
# # creation_date property getter
# @property
# def creation_date(self):
# return obi_format_date((self._pointer)[0].header.creation_date)
#
#
# ######################################################################################################
#
#
# cdef class Column_line :
#
# def __init__(self, Column column, index_t line_nb) :
# self._index = line_nb
# self._column = column
#
# if obi_column_prepare_to_get_value(self._column._pointer[0],line_nb) < 0:
# raise IndexError("Cannot access to the line %d" % line_nb)
#
#
# def __contains__(self, str element_name):
# pass
# #return (element_name in self._column.elements_names)
#
#
# def __repr__(self) :
# return str(self._column.get_line(self._index))
#
#
# cpdef update(self, data):
# if isinstance(data, dict):
# data=data.items()
# for key,value in data:
# if key in self:
# self[key]=value
#
#
# ######################################################################################################
#
#
cdef register_column_class(obitype_t obitype,
type classe,
type python):
@ -219,7 +261,7 @@ cdef register_column_class(obitype_t obitype,
to declare its relationship with an `OBIType_t`
"""
global __OBIDMS_COLUMN_CLASS__
assert issubclass(classe,Column)
__OBIDMS_COLUMN_CLASS__[obitype]=(classe,python)

18
python/obitools3/dms/dms.pxd
View File

@ -5,21 +5,21 @@ from .capi.obitypes cimport obiversion_t, \
obitype_t, \
index_t
from .object cimport OBIObject
from .object cimport OBIWrapper
cdef dict __OBIDMS_COLUMN_CLASS__
cdef dict __OBIDMS_VIEW_CLASS__
cdef class DMS(OBIObject):
cdef OBIDMS_p _pointer
@staticmethod
cdef type get_column_class(obitype_t obitype)
cdef class DMS(OBIWrapper):
@staticmethod
cdef type get_python_type(obitype_t obitype)
@staticmethod
cdef DMS new(object dms_name)
cpdef close(self)
cpdef int view_count(self)
cpdef bint is_view_writable(self, object view_name)

96
python/obitools3/dms/dms.pyx
View File

@ -20,18 +20,9 @@ from pathlib import Path
__OBIDMS_COLUMN_CLASS__ = {}
__OBIDMS_VIEW_CLASS__= {}
cdef class DMS(OBIObject):
@staticmethod
cdef type get_column_class(obitype_t obitype):
"""
Internal function returning the python class representing
a column for a given obitype.
"""
return __OBIDMS_COLUMN_CLASS__[obitype][0]
cdef class DMS(OBIWrapper):
@staticmethod
cdef type get_python_type(obitype_t obitype):
@ -40,31 +31,31 @@ cdef class DMS(OBIObject):
an instance for a given obitype.
"""
return __OBIDMS_COLUMN_CLASS__[obitype][1]
@staticmethod
cdef type get_view_class(bytes viewtype):
return __OBIDMS_VIEW_CLASS__[viewtype]
def __init__(self, object dms_name) :
'''
Constructor of a obitools3.dms.DMS instance.
@param dms_name: The name of the DMS
@type dms_name: a `str` or a `bytes` instance
'''
OBIObject.__init__(self)
# Declarations
# def __init__(self, size_t pointer) :
# '''
# Constructor of a obitools3.dms.DMS instance.
#
# @param dms_name: The name of the DMS
# @type dms_name: a `str` or a `bytes` instance
# '''
#
# print("hmmmm")
@staticmethod
cdef DMS new(object dms_name) :
cdef OBIDMS_p pointer
cdef DMS dms
cdef bytes dms_name_b = tobytes(dms_name)
# Fill structure and create or open the DMS
self._pointer = obi_dms(<const_char_p> dms_name_b)
if self._pointer == NULL :
pointer = obi_dms(<const_char_p> dms_name_b)
if pointer == NULL :
raise Exception("Failed opening or creating an OBIDMS")
dms = OBIWrapper.new_wrapper(DMS, pointer)
return dms
# name property getter
@property
def name(self):
@ -73,27 +64,32 @@ cdef class DMS(OBIObject):
@rtype: bytes
"""
return <bytes> self._pointer.dms_name
cdef OBIDMS_p pointer = <OBIDMS_p>(self._pointer)
return <bytes> pointer.dms_name
def close(self) :
"""
Closes the DNS instance and free the associated memory
Closes the DMS instance and free the associated memory
the `close` method is automatically called by the object destructor.
The `close` method is automatically called by the object destructor.
"""
cdef OBIDMS_p pointer = self._pointer
cdef OBIDMS_p pointer = <OBIDMS_p>(self._pointer)
OBIObject.close(self)
self._pointer=NULL
if pointer!=NULL:
OBIWrapper.close(self)
if (obi_close_dms(pointer)) < 0 :
raise Exception("Problem closing an OBIDMS")
self._pointer=NULL
else:
raise OBIObjectClosedInstance()
def keys(self):
cdef const_char_p path = obi_dms_get_full_path(self._pointer,
cdef OBIDMS_p pointer = <OBIDMS_p>(self._pointer)
cdef const_char_p path = obi_dms_get_full_path(pointer,
b"VIEWS"
)
@ -106,12 +102,14 @@ cdef class DMS(OBIObject):
for v in p.glob("*.obiview"):
yield str2bytes(v.stem)
def values(self):
cdef bytes view_name
for view_name in self.keys():
yield self.get_view(view_name)
def items(self):
cdef bytes view_name
@ -119,9 +117,14 @@ cdef class DMS(OBIObject):
for view_name in self.keys():
yield (view_name,self.get_view(view_name))
def __contains__(self,key):
def __contains__(self, key):
cdef OBIDMS_p pointer = <OBIDMS_p>(self._pointer)
cdef str key_s = tostr(key)
cdef const_char_p path = obi_dms_get_full_path(self._pointer,
cdef const_char_p path = obi_dms_get_full_path(pointer,
b"VIEWS"
)
p = Path(bytes2str(path),key_s)
@ -130,23 +133,28 @@ cdef class DMS(OBIObject):
return p.with_suffix(".obiview").is_file()
cpdef int view_count(self):
return PyList_Size(list(self.keys()))
def get_view(self):
raise NotImplemented
def __len__(self):
return self.view_count()
def __getitem__(self, object view_name):
return self.get_view(view_name)
def __iter__(self):
return self.keys()
cpdef bint is_view_writable(self, object view_name):
raise NotImplemented

21
python/obitools3/dms/object.pxd
View File

@ -1,13 +1,28 @@
#cython: language_level=3
cdef dict __c_cython_mapping__
cdef class OBIObject:
cdef dict _dependent_object
cpdef register(self, OBIObject object)
cpdef unregister(self, OBIObject object)
cdef register(self, OBIObject object)
cdef unregister(self, OBIObject object)
cpdef close(self)
cdef class OBIWrapper(OBIObject):
cdef void* _pointer
cdef size_t cid(self)
cpdef bint active(self)
@staticmethod
cdef object new_wrapper(type constructor, void* pointer)
cdef class OBIObjectClosedInstance(Exception):
pass

72
python/obitools3/dms/object.pyx
View File

@ -1,29 +1,63 @@
#cython: language_level=3
__c_cython_mapping__={}
cdef class OBIObject:
cpdef register(self, OBIObject object):
cdef register(self, OBIObject object):
self._dependent_object[id(object)]=object
cpdef unregister(self, OBIObject object):
cdef unregister(self, OBIObject object):
del self._dependent_object[id(object)]
def close(self):
cpdef close(self):
cdef OBIObject object
cdef list toclose = list(self._dependent_object.values())
for object in toclose:
object.close()
assert len(dependent_object.values)==0
def __init__(self):
assert len(self._dependent_object.values)==0
def __init__(self, __internalCall__):
if __internalCall__ != 987654 :
raise RuntimeError('OBIObject constructor can not be called directly')
if type(self) == OBIObject or type(self) == OBIWrapper or not isinstance(self, OBIObject) :
raise RuntimeError('OBIObject constructor can not be called directly')
self._dependent_object={}
cdef class OBIWrapper(OBIObject):
"""
The OBIWrapper class enables to wrap a C object representing a DMS or an element from a DMS
"""
cdef size_t cid(self) :
return <size_t>(self._pointer)
cpdef close(self):
if (self._pointer != NULL):
OBIObject.close(self)
self._pointer = NULL
assert len(self._dependent_object.values) == 0
cpdef bint active(self):
return self._pointer != NULL
def __dealloc__(self):
"""
Destructor of any OBI instance.
@ -31,9 +65,23 @@ cdef class OBIObject:
The destructor automatically calls the `close` method and
therefore frees all the associated memory.
"""
self.close()
cdef class OBIObjectClosedInstance(Exception):
@staticmethod
cdef object new_wrapper(type constructor, void* pointer):
cdef object o
if (<size_t>pointer in __c_cython_mapping__):
return __c_cython_mapping__[<size_t>pointer]
else:
o = constructor(<size_t>pointer, 987654)
o._pointer = <size_t>pointer
__c_cython_mapping__[<size_t>pointer] = o
return o
cdef class OBIDeactivatedInstanceError(Exception):
pass

22
python/obitools3/dms/view/view.pxd
View File

@ -4,18 +4,18 @@ from ..capi.obiview cimport Obiview_p
from ..capi.obitypes cimport index_t, \
obitype_t
from ..object cimport OBIObject
from ..object cimport OBIWrapper
from ..dms cimport DMS
from ..column.column cimport Column
cdef class View(OBIObject):
cdef class View(OBIWrapper):
cdef DMS _dms
cdef Obiview_p _pointer
cdef DMS _dms
cdef inline Obiview_p pointer(self)
cpdef delete_column(self,
object column_name)
@ -23,8 +23,16 @@ cdef class View(OBIObject):
object current_name,
object new_name)
cpdef View_line_selection new_selection(self,
list lines=*)
cpdef Line_selection new_selection(self,
list lines=*)
@staticmethod
cdef type get_view_class(bytes viewtype)
@staticmethod
cdef register_view_class(bytes viewtype,
type classe)
cdef class Line_selection(list):

222
python/obitools3/dms/view/view.pyx
View File

@ -2,6 +2,9 @@
from libc.stdlib cimport malloc
cdef dict __VIEW_CLASS__= {}
from ..capi.obiview cimport Alias_column_pair_p, \
obi_new_view, \
obi_open_view, \
@ -11,8 +14,7 @@ from ..capi.obiview cimport Alias_column_pair_p, \
obi_view_create_column_alias
from ..capi.obidmscolumn cimport OBIDMS_column_p
from .dms cimport __OBIDMS_VIEW_CLASS__
from ..capi.obidms cimport OBIDMS_p
from obitools3.utils cimport tobytes, \
bytes2str
@ -20,19 +22,77 @@ from obitools3.utils cimport tobytes, \
from ..object cimport OBIObjectClosedInstance
cdef class View(OBIObject) :
cdef class View(OBIWrapper) :
cdef inline Obiview_p pointer(self):
return <Obiview_p>(self.pointer)
@staticmethod
cdef register_view_class(bytes viewtype,
type classe):
"""
Each sub class of `dms.View` needs to be registered after its declaration
to declare its relationship with an `OBIType_t`
"""
global __VIEW_CLASS__
assert issubclass(classe,View)
__VIEW_CLASS__[viewtype]=classe
@staticmethod
cdef type get_view_class(bytes viewtype):
global __VIEW_CLASS__
return __VIEW_CLASS__.get(viewtype,View)
def __init__(self,dms,int __internalCall__):
OBIObject.__init__(self)
OBIWrapper.__init__(self,__internalCall__)
if __internalCall__!=987654:
raise RuntimeError('OBIView constructor cannot be called directly')
self._dms = dms
self._pointer = NULL
@staticmethod
def new(DMS dms,
object view_name,
object comments=None,
type viewclass=View):
cdef bytes view_name_b = tobytes(view_name)
cdef bytes comments_b
cdef str message
cdef void* pointer
cdef View view # @DuplicatedSignature
if comments is not None:
comments_b = tobytes(comments)
else:
comments_b = b''
pointer = <void*>obi_new_view(<OBIDMS_p>dms._pointer,
view_name_b,
NULL,
NULL,
comments_b)
if pointer == NULL :
message = "Error : Cannot create view %s" % bytes2str(view_name_b)
raise RuntimeError(message)
view = OBIWrapper.new_wrapper(viewclass, pointer)
view._dms = dms
dms.register(view)
return view
def clone(self,
object view_name,
object comments=None):
@ -40,95 +100,69 @@ cdef class View(OBIObject) :
cdef bytes view_name_b = tobytes(view_name)
cdef bytes comments_b
cdef View view = View(self._dms,
987654)
cdef void* pointer
cdef View
if comments is not None:
comments_b = tobytes(comments)
else:
comments_b = b''
view._pointer = obi_new_view(self._pointer.dms,
view_name_b,
self._pointer,
NULL,
comments_b)
pointer = <void*> obi_new_view(<OBIDMS_p>(self._dms._pointer),
view_name_b,
<Obiview_p>self._pointer,
NULL,
comments_b)
if view._pointer == NULL :
if pointer == NULL :
raise RuntimeError("Error : Cannot clone view %s into view %s"
% (str(self.name),
bytes2str(view_name_b))
)
view = OBIWrapper.new_wrapper(type(self),pointer)
view._dms = self._dms
self._dms.register(view)
return view
@staticmethod
def new(DMS dms,
object view_name,
object comments=None):
cdef bytes view_name_b = tobytes(view_name)
cdef bytes comments_b
cdef str message
cdef View view = View(dms,
987654) # @DuplicatedSignature
if comments is not None:
comments_b = tobytes(comments)
else:
comments_b = b''
view._pointer = obi_new_view(dms._pointer,
view_name_b,
NULL,
NULL,
comments_b)
if view._pointer == NULL :
message = "Error : Cannot create view %s" % bytes2str(view_name_b)
raise RuntimeError(message)
dms.register(view)
return view
@staticmethod
def open(DMS dms, # @ReservedAssignment
object view_name):
cdef bytes view_name_b = tobytes(view_name)
cdef View view = View(dms,
987654) # @DuplicatedSignature
view._pointer = obi_open_view(dms._pointer,
view_name_b)
cdef void* pointer
cdef View view
pointer = <void*> obi_open_view(<OBIDMS_p>dms._pointer,
view_name_b)
if view._pointer == NULL :
if pointer == NULL :
raise RuntimeError("Error : Cannot open view %s" % bytes2str(view_name_b))
view = OBIWrapper.new_wrapper(View.get_view_class((<Obiview_p>pointer).infos.view_type),
pointer)
view._dms = dms
dms.register(view)
return view
def close(self):
cdef Obiview_p pointer = self._pointer
cpdef close(self):
cdef Obiview_p pointer = <Obiview_p>self._pointer
if (pointer != NULL):
self._dms.unregister(self)
OBIObject.close(self)
self._pointer = NULL
if obi_save_and_close_view(self._pointer) < 0 :
OBIWrapper.close(self)
if obi_save_and_close_view(pointer) < 0 :
raise Exception("Problem closing view %s" %
bytes2str(self.name))
else:
raise OBIObjectClosedInstance()
def __repr__(self) :
cdef str s = "{name:s}\n{comments:s}\n{line_count:d} lines\n".format(name = str(self.name),
comments = str(self.comments),
@ -138,16 +172,19 @@ cdef class View(OBIObject) :
# s = s + repr(self._columns[column_name]) + '\n'
return s
def keys(self):
cdef int i
cdef int nb_column = self._pointer.infos.column_count
cdef Alias_column_pair_p column_p = self._pointer.infos.column_references
cdef Obiview_p pointer = self.pointer()
cdef int nb_column = pointer.infos.column_count
cdef Alias_column_pair_p column_p = pointer.infos.column_references
for i in range(nb_column) :
col_alias = bytes2str(self._pointer.infos.column_references[i].alias)
col_alias = bytes2str(pointer.infos.column_references[i].alias)
yield col_alias
def get_column(self,
object column_name):
cdef bytes column_name_b = tobytes(column_name)
@ -155,8 +192,9 @@ cdef class View(OBIObject) :
cdef OBIDMS_column_p column_p
cdef Column column
cdef obitype_t column_type
cdef Obiview_p pointer = self.pointer()
column_pp = obi_view_get_pointer_on_column_in_view(self._pointer,
column_pp = obi_view_get_pointer_on_column_in_view(pointer,
column_name_b)
if column_pp == NULL:
@ -173,16 +211,16 @@ cdef class View(OBIObject) :
return column
cpdef delete_column(self,
object column_name) :
cdef bytes column_name_b = tobytes(column_name)
if obi_view_delete_column(self._pointer, column_name_b) < 0 :
if obi_view_delete_column(self.pointer(), column_name_b) < 0 :
raise Exception("Problem deleting column %s from a view",
bytes2str(column_name_b))
cpdef rename_column(self,
object current_name,
@ -192,7 +230,7 @@ cdef class View(OBIObject) :
cdef bytes current_name_b = tobytes(current_name)
cdef bytes new_name_b = tobytes(new_name)
if (obi_view_create_column_alias(self._pointer,
if (obi_view_create_column_alias(self.pointer(),
tobytes(current_name_b),
tobytes(new_name_b)) < 0) :
raise Exception("Problem in renaming column %s to %s" % (
@ -200,15 +238,16 @@ cdef class View(OBIObject) :
bytes2str(new_name_b)))
cpdef View_line_selection new_selection(self,list lines=None):
return View_line_selection(self,lines)
cpdef Line_selection new_selection(self,list lines=None):
return Line_selection(self,lines)
def __iter__(self):
# Iteration on each line of all columns
# Declarations
cdef index_t line_nb
cdef View_line line
cdef Line line
# Yield each line
for line_nb in range(self.line_count) :
@ -220,7 +259,7 @@ cdef class View(OBIObject) :
if type(item) == str :
return (self._columns)[item]
elif type(item) == int :
return View_line(self, item)
return Line(self, item)
def __contains__(self, str column_name):
@ -232,7 +271,7 @@ cdef class View(OBIObject) :
def __str__(self) :
cdef View_line line
cdef Line line
cdef str to_print
to_print = ""
for line in self :
@ -244,25 +283,29 @@ cdef class View(OBIObject) :
def dms(self):
return self._dms
# line_count property getter
@property
def line_count(self):
return self._pointer.infos.line_count
return (<Obiview_p>self._pointer).infos.line_count
# name property getter
@property
def name(self):
return <bytes> self._pointer.infos.name
return <bytes> (<Obiview_p>self._pointer).infos.name
# view type property getter
@property
def type(self): # @ReservedAssignment
return <bytes> self._pointer.infos.view_type
return <bytes> (<Obiview_p>self._pointer).infos.view_type
# comments property getter
@property
def comments(self):
return <bytes> self._pointer.infos.comments
return <bytes> (<Obiview_p>self._pointer).infos.comments
# TODO setter that concatenates new comments?
@ -277,6 +320,7 @@ cdef class Line_selection(list):
if lines is not None:
self.extend(lines)
def extend(self, iterable):
cdef index_t i
cdef index_t max_i = self._view.line_count
@ -290,6 +334,7 @@ cdef class Line_selection(list):
)
list.append(self,i)
def append(self, index_t idx) :
if idx >= self._view.line_count :
raise IndexError("Error: trying to select line %d beyond the line count %d of view %s" %
@ -299,6 +344,7 @@ cdef class Line_selection(list):
)
list.append(self,idx)
cdef index_t* __build_binary_list__(self):
cdef index_t* line_selection_p = NULL
cdef int i
@ -311,6 +357,7 @@ cdef class Line_selection(list):
return line_selection_p
cpdef View materialize(self,
object view_name,
object comments=""):
@ -318,9 +365,9 @@ cdef class Line_selection(list):
cdef View view = View(987654)
cdef bytes view_name_b=tobytes(view_name)
view._pointer = obi_new_view(self._view._pointer.dms,
view._pointer = obi_new_view(<OBIDMS_p>self.view._dms.pointer,
view_name_b,
self._view._pointer,
<Obiview_p>self._view._pointer,
self.__build_binary_list__(),
tobytes(comments))
@ -339,6 +386,7 @@ cdef class Line :
self._index = line_nb
self._view = view
def __getitem__(self, str column_name) :
return ((self._view)._columns)[column_name][self._index]
@ -429,15 +477,3 @@ cdef class Line :
# return view_infos_d
cdef register_view_class(bytes viewtype,
type classe):
"""
Each sub class of `dms.View` needs to be registered after its declaration
to declare its relationship with an `OBIType_t`
"""
global __OBIDMS_VIEW_CLASS__
assert issubclass(classe,View)
__OBIDMS_VIEW_CLASS__[viewtype]=classe