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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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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