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Cython View API

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This commit is contained in:
Celine Mercier
2017-04-06 14:41:58 +02:00
parent 08be4e231d
commit 255f3c92ae
3 changed files with 216 additions and 205 deletions
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6
python/obitools3/dms/view/__init__.py
View File

@ -1,3 +1,3 @@
from .view import View # @UnresolvedImport #from .view import View # @UnresolvedImport
from .view import Line_selection # @UnresolvedImport #from .view import Line_selection # @UnresolvedImport
from .view import Line # @UnresolvedImport #from .view import Line # @UnresolvedImport

15
python/obitools3/dms/view/view.pxd
View File

@ -1,13 +1,16 @@
#cython: language_level=3 #cython: language_level=3
from ..capi.obiview cimport Obiview_p from ..capi.obiview cimport Obiview_p
from ..capi.obitypes cimport index_t, \
obitype_t from ..capi.obitypes cimport index_t
from ..object cimport OBIWrapper from ..object cimport OBIWrapper
from ..dms cimport DMS from ..dms cimport DMS
from ..column.column cimport Column
cdef dict __OBIDMS_VIEW_CLASS__
cdef class View(OBIWrapper): cdef class View(OBIWrapper):
@ -37,13 +40,15 @@ cdef class View(OBIWrapper):
cdef class Line_selection(list): cdef class Line_selection(list):
cdef View _view cdef View _view
cdef bytes _view_name
cdef index_t* __build_binary_list__(self) cdef index_t* __build_binary_list__(self)
cpdef View materialize(self, cpdef View materialize(self,
object view_name, object view_name,
object comments=*) object comments=*)
cdef class Line : cdef class Line :
cdef index_t _index cdef index_t _index

400
python/obitools3/dms/view/view.pyx
View File

@ -1,10 +1,11 @@
#cython: language_level=3 #cython: language_level=3
from libc.stdlib cimport malloc
cdef dict __VIEW_CLASS__= {} cdef dict __VIEW_CLASS__= {}
from libc.stdlib cimport malloc
from ..capi.obiview cimport Alias_column_pair_p, \ from ..capi.obiview cimport Alias_column_pair_p, \
obi_new_view, \ obi_new_view, \
obi_open_view, \ obi_open_view, \
@ -15,54 +16,57 @@ from ..capi.obiview cimport Alias_column_pair_p, \
from ..capi.obidmscolumn cimport OBIDMS_column_p from ..capi.obidmscolumn cimport OBIDMS_column_p
from ..capi.obidms cimport OBIDMS_p from ..capi.obidms cimport OBIDMS_p
from ..capi.obitypes cimport obitype_t
from obitools3.utils cimport tobytes, \ from obitools3.utils cimport tobytes, \
str2bytes, \
bytes2str bytes2str
from ..object cimport OBIObjectClosedInstance from ..object cimport OBIObjectClosedInstance
from ..column.column cimport Column
from ..capi.obitypes cimport only_ATGC, \
OBI_BOOL, \
OBI_CHAR, \
OBI_FLOAT, \
OBI_INT, \
OBI_QUAL, \
OBI_SEQ, \
OBI_STR
cdef class View(OBIWrapper) : cdef class View(OBIWrapper) :
cdef inline Obiview_p pointer(self): cdef inline Obiview_p pointer(self) :
return <Obiview_p>(self.pointer) return <Obiview_p>(self._pointer)
@staticmethod @staticmethod
cdef register_view_class(bytes viewtype, cdef register_view_class(bytes view_type_name,
type classe): type view_class):
""" '''
Each sub class of `dms.View` needs to be registered after its declaration Each sub class of `dms.View` needs to be registered after its declaration
to declare its relationship with an `OBIType_t` to declare its relationship with an `OBIType_t`
""" '''
global __VIEW_CLASS__ global __VIEW_CLASS__
assert issubclass(classe,View) assert issubclass(view_class, View)
__VIEW_CLASS__[viewtype]=classe __VIEW_CLASS__[view_type_name] = view_class
@staticmethod @staticmethod
cdef type get_view_class(bytes viewtype): cdef type get_view_class(bytes view_type):
global __VIEW_CLASS__ global __VIEW_CLASS__
return __VIEW_CLASS__.get(viewtype,View) return __VIEW_CLASS__.get(view_type, View)
def __init__(self,dms,int __internalCall__):
OBIWrapper.__init__(self,__internalCall__)
if __internalCall__!=987654:
raise RuntimeError('OBIView constructor cannot be called directly')
self._pointer = NULL
@staticmethod @staticmethod
def new(DMS dms, def new(DMS dms,
object view_name, object view_name,
object comments=None, object comments=None,
type viewclass=View): type view_class=View):
cdef bytes view_name_b = tobytes(view_name) cdef bytes view_name_b = tobytes(view_name)
cdef bytes comments_b cdef bytes comments_b
@ -86,8 +90,8 @@ cdef class View(OBIWrapper) :
message = "Error : Cannot create view %s" % bytes2str(view_name_b) message = "Error : Cannot create view %s" % bytes2str(view_name_b)
raise RuntimeError(message) raise RuntimeError(message)
view = OBIWrapper.new_wrapper(viewclass, pointer) view = OBIWrapper.new(view_class, pointer)
view._dms = dms view._dms = dms
dms.register(view) dms.register(view)
return view return view
@ -101,16 +105,19 @@ cdef class View(OBIWrapper) :
cdef bytes view_name_b = tobytes(view_name) cdef bytes view_name_b = tobytes(view_name)
cdef bytes comments_b cdef bytes comments_b
cdef void* pointer cdef void* pointer
cdef View cdef View view
if not self.active() :
raise OBIObjectClosedInstance()
if comments is not None: if comments is not None:
comments_b = tobytes(comments) comments_b = tobytes(comments)
else: else:
comments_b = b'' comments_b = b''
pointer = <void*> obi_new_view(<OBIDMS_p>(self._dms._pointer), pointer = <void*> obi_new_view(self._dms.pointer(),
view_name_b, view_name_b,
<Obiview_p>self._pointer, self.pointer(),
NULL, NULL,
comments_b) comments_b)
@ -120,9 +127,8 @@ cdef class View(OBIWrapper) :
bytes2str(view_name_b)) bytes2str(view_name_b))
) )
view = OBIWrapper.new_wrapper(type(self),pointer) view = OBIWrapper.new(type(self), pointer)
view._dms = self._dms view._dms = self._dms
self._dms.register(view) self._dms.register(view)
return view return view
@ -134,52 +140,59 @@ cdef class View(OBIWrapper) :
cdef bytes view_name_b = tobytes(view_name) cdef bytes view_name_b = tobytes(view_name)
cdef void* pointer cdef void* pointer
cdef View view cdef View view
cdef type view_class
pointer = <void*> obi_open_view(<OBIDMS_p>dms._pointer, pointer = <void*> obi_open_view(dms.pointer(),
view_name_b) view_name_b)
if pointer == NULL : if pointer == NULL :
raise RuntimeError("Error : Cannot open view %s" % bytes2str(view_name_b)) 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), view_class = View.get_view_class((<Obiview_p>pointer).infos.view_type)
pointer) view = OBIWrapper.new(view_class, pointer)
view._dms = dms view._dms = dms
dms.register(view) dms.register(view)
return view return view
cpdef close(self): cpdef close(self):
cdef Obiview_p pointer = <Obiview_p>self._pointer cdef Obiview_p pointer = self.pointer()
if (pointer != NULL): if self.active() :
self._dms.unregister(self) self._dms.unregister(self)
OBIWrapper.close(self) OBIWrapper.close(self)
if obi_save_and_close_view(pointer) < 0 : if obi_save_and_close_view(pointer) < 0 :
raise Exception("Problem closing view %s" % raise Exception("Problem closing view %s" %
bytes2str(self.name)) bytes2str(self.name))
def __repr__(self) : def __repr__(self) :
# TODO check everywhere
if not self.active() :
raise OBIObjectClosedInstance()
cdef str s = "{name:s}\n{comments:s}\n{line_count:d} lines\n".format(name = str(self.name), cdef str s = "{name:s}\n{comments:s}\n{line_count:d} lines\n".format(name = str(self.name),
comments = str(self.comments), comments = str(self.comments),
line_count = self.line_count) line_count = self.line_count)
#for column_name in self._columns : for column_name in self.keys() :
# s = s + repr(self._columns[column_name]) + '\n' s = s + repr(self[column_name]) + '\n'
return s return s
def keys(self): def keys(self):
cdef int i cdef int i
cdef Obiview_p pointer = self.pointer() cdef Obiview_p pointer = self.pointer()
cdef int nb_column = pointer.infos.column_count cdef int nb_column = pointer.infos.column_count
cdef Alias_column_pair_p column_p = pointer.infos.column_references cdef Alias_column_pair_p column_p = pointer.infos.column_references
if not self.active() :
raise OBIObjectClosedInstance()
for i in range(nb_column) : for i in range(nb_column) :
col_alias = bytes2str(pointer.infos.column_references[i].alias) col_alias = bytes2str(pointer.infos.column_references[i].alias)
yield col_alias yield col_alias
@ -187,36 +200,21 @@ cdef class View(OBIWrapper) :
def get_column(self, def get_column(self,
object column_name): 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
cdef Obiview_p pointer = self.pointer()
column_pp = obi_view_get_pointer_on_column_in_view(pointer,
column_name_b)
if column_pp == NULL: if not self.active() :
raise KeyError("Cannot access to column %s in view %s" % ( raise OBIObjectClosedInstance()
bytes2str(column_name_b),
bytes2str(self.name) return Column.open(self, column_name)
))
column_p = column_pp[0]
column_type = column_p.header.returned_data_type
column = DMS.get_column_class(column_type)(self)
column._pointer = column_pp
return column
cpdef delete_column(self, cpdef delete_column(self,
object column_name) : object column_name) :
if not self.active() :
raise OBIObjectClosedInstance()
cdef bytes column_name_b = tobytes(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", raise Exception("Problem deleting column %s from a view",
bytes2str(column_name_b)) bytes2str(column_name_b))
@ -230,6 +228,9 @@ cdef class View(OBIWrapper) :
cdef bytes current_name_b = tobytes(current_name) cdef bytes current_name_b = tobytes(current_name)
cdef bytes new_name_b = tobytes(new_name) cdef bytes new_name_b = tobytes(new_name)
if not self.active() :
raise OBIObjectClosedInstance()
if (obi_view_create_column_alias(self.pointer(), if (obi_view_create_column_alias(self.pointer(),
tobytes(current_name_b), tobytes(current_name_b),
tobytes(new_name_b)) < 0) : tobytes(new_name_b)) < 0) :
@ -239,15 +240,15 @@ cdef class View(OBIWrapper) :
cpdef Line_selection new_selection(self,list lines=None): cpdef Line_selection new_selection(self,list lines=None):
return Line_selection(self,lines) return Line_selection(self, lines)
def __iter__(self): def __iter__(self):
# Iteration on each line of all columns # Iteration on each line of all columns
# Declarations # Declarations
cdef index_t line_nb cdef index_t line_nb
cdef Line line cdef Line line
# Yield each line # Yield each line
for line_nb in range(self.line_count) : for line_nb in range(self.line_count) :
@ -257,13 +258,13 @@ cdef class View(OBIWrapper) :
def __getitem__(self, object item) : def __getitem__(self, object item) :
if type(item) == str : if type(item) == str :
return (self._columns)[item] return self.get_column(item) # TODO hyper lent dans la pratique
elif type(item) == int : elif type(item) == int :
return Line(self, item) return Line(self, item)
def __contains__(self, str column_name): def __contains__(self, str column_name):
return (column_name in self._columns) return (column_name in self.keys())
def __len__(self): def __len__(self):
@ -287,99 +288,28 @@ cdef class View(OBIWrapper) :
# line_count property getter # line_count property getter
@property @property
def line_count(self): def line_count(self):
return (<Obiview_p>self._pointer).infos.line_count return self.pointer().infos.line_count
# name property getter # name property getter
@property @property
def name(self): def name(self):
return <bytes> (<Obiview_p>self._pointer).infos.name return <bytes> self.pointer().infos.name
# view type property getter # view type property getter
@property @property
def type(self): # @ReservedAssignment def type(self): # @ReservedAssignment
return <bytes> (<Obiview_p>self._pointer).infos.view_type return <bytes> self.pointer().infos.view_type
# comments property getter # comments property getter
@property @property
def comments(self): def comments(self):
return <bytes> (<Obiview_p>self._pointer).infos.comments return <bytes> self.pointer().infos.comments
# TODO setter that concatenates new comments? # TODO setter that concatenates new comments?
cdef class Line_selection(list):
def __init__(self, View view, lines=None) :
if view._pointer == NULL:
raise Exception("Error: trying to create a line selection with an invalidated view")
self._view = view
self._view_name = view.name
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
for i in iterable:
if i > max_i:
raise RuntimeError("Error: trying to select line %d beyond the line count %d of view %s" %
(i,
max_i,
self._view_name)
)
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" %
(idx,
self._view.line_count,
bytes2str(self.name))
)
list.append(self,idx)
cdef index_t* __build_binary_list__(self):
cdef index_t* line_selection_p = NULL
cdef int i
cdef size_t l_selection = len(self)
line_selection_p = <index_t*> malloc((l_selection + 1) * sizeof(index_t)) # +1 for the -1 flagging the end of the array
for i in range(l_selection) :
line_selection_p[i] = self[i]
line_selection_p[l_selection] = -1 # flagging the end of the array
return line_selection_p
cpdef View materialize(self,
object view_name,
object comments=""):
cdef View view = View(987654)
cdef bytes view_name_b=tobytes(view_name)
view._pointer = obi_new_view(<OBIDMS_p>self.view._dms.pointer,
view_name_b,
<Obiview_p>self._view._pointer,
self.__build_binary_list__(),
tobytes(comments))
if view._pointer == NULL :
raise RuntimeError("Error : Cannot clone view %s into view %s"
% (str(self.name),
view_name)
)
return view
cdef class Line : cdef class Line :
def __init__(self, View view, index_t line_nb) : def __init__(self, View view, index_t line_nb) :
@ -388,55 +318,60 @@ cdef class Line :
def __getitem__(self, str column_name) : def __getitem__(self, str column_name) :
return ((self._view)._columns)[column_name][self._index] return (self._view)[column_name][self._index]
# def __setitem__(self, str column_name, object value):
# # TODO detect multiple elements (dict type)? put somewhere else? but more risky (in get) def __setitem__(self, str column_name, object value): # TODO discuss
# # TODO OBI_QUAL ? # TODO detect multiple elements (dict type)? put somewhere else? but more risky (in get)
# cdef type value_type # TODO OBI_QUAL ?
# cdef str value_obitype cdef type value_type
# cdef bytes value_b cdef obitype_t value_obitype
# cdef bytes value_b
# if column_name not in self._view :
# if value == None : if column_name not in self._view :
# raise Exception("Trying to create a column from a None value (can't guess type)") if value == None :
# value_type = type(value) raise Exception("Trying to create a column from a None value (can't guess type)")
# if value_type == int : value_type = type(value)
# value_obitype = 'OBI_INT' if value_type == int :
# elif value_type == float : value_obitype = OBI_INT
# value_obitype = 'OBI_FLOAT' elif value_type == float :
# elif value_type == bool : value_obitype = OBI_FLOAT
# value_obitype = 'OBI_BOOL' elif value_type == bool :
# elif value_type == str or value_type == bytes : value_obitype = OBI_BOOL
# if value_type == str : elif value_type == str or value_type == bytes :
# value_b = str2bytes(value) if value_type == str :
# else : value_b = str2bytes(value)
# value_b = value else :
# if only_ATGC(value_b) : # TODO detect IUPAC value_b = value
# value_obitype = 'OBI_SEQ' if only_ATGC(value_b) : # TODO detect IUPAC
# elif len(value) == 1 : value_obitype = OBI_SEQ
# value_obitype = 'OBI_CHAR' elif len(value) == 1 :
# elif (len(value) > 1) : value_obitype = OBI_CHAR
# value_obitype = 'OBI_STR' elif (len(value) > 1) :
# else : value_obitype = OBI_STR
# raise Exception("Could not guess the type of a value to create a new column") else :
# self._view.add_column(column_name, type=value_obitype) raise Exception("Could not guess the type of a value to create a new column")
#
# (((self._view)._columns)[column_name]).set_line(self._index, value) Column.new_column(self._view, column_name, value_obitype)
#
# def __iter__(self): (self._view)[column_name][self._index] = value
# for column_name in ((self._view)._columns) :
# yield column_name
# def __iter__(self):
# def __contains__(self, str column_name): for column_name in (self._view).keys() :
# return (column_name in self._view._columns) yield self[column_name]
def __contains__(self, str column_name):
return (column_name in self._view.keys())
def __repr__(self): def __repr__(self):
cdef dict line cdef dict line
cdef str column_name cdef str column_name
line = {} line = {}
# for column_name in self._view._columns : for column_name in self._view.keys() :
# line[column_name] = self[column_name] line[column_name] = self[column_name]
return str(line) return str(line)
@ -477,3 +412,74 @@ cdef class Line :
# return view_infos_d # return view_infos_d
cdef class Line_selection(list):
def __init__(self, View view, lines=None) :
if view._pointer == NULL:
raise Exception("Error: trying to create a line selection with an invalidated view")
self._view = view
self._view_name = view.name
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
for i in iterable: # TODO this is already checked in C
if i > max_i:
raise RuntimeError("Error: trying to select line %d beyond the line count %d of view %s" %
(i,
max_i,
self._view_name)
)
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" %
(idx,
self._view.line_count,
bytes2str(self.name))
)
list.append(self,idx)
cdef index_t* __build_binary_list__(self):
cdef index_t* line_selection_p = NULL
cdef int i
cdef size_t l_selection = len(self)
line_selection_p = <index_t*> malloc((l_selection + 1) * sizeof(index_t)) # +1 for the -1 flagging the end of the array
for i in range(l_selection) :
line_selection_p[i] = self[i]
line_selection_p[l_selection] = -1 # flagging the end of the array
return line_selection_p
cpdef View materialize(self,
object view_name,
object comments=""):
cdef View view = View(987654)
cdef bytes view_name_b=tobytes(view_name)
view._pointer = obi_new_view(self._view._dms.pointer(),
view_name_b,
self._view.pointer(),
self.__build_binary_list__(),
tobytes(comments))
if view._pointer == NULL :
raise RuntimeError("Error : Cannot clone view %s into view %s"
% (str(self._view_name),
view_name)
)
return view