Cython API: various improvements and checks
This commit is contained in:
Celine Mercier
@ -23,7 +23,7 @@ from obitools3.utils cimport tobytes, \
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bytes2str, \
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tostr
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from ..object cimport OBIObjectClosedInstance
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from ..object cimport OBIDeactivatedInstanceError
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from obitools3.dms.view import typed_view
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@ -92,14 +92,13 @@ cdef class View(OBIWrapper) :
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object view_name,
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object comments=None):
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cdef bytes view_name_b = tobytes(view_name)
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cdef bytes comments_b
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cdef void* pointer
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cdef View view
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if not self.active() :
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raise OBIObjectClosedInstance()
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raise OBIDeactivatedInstanceError()
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if comments is not None:
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comments_b = tobytes(comments)
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@ -149,7 +148,7 @@ cdef class View(OBIWrapper) :
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return view
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cpdef close(self):
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def close(self):
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cdef Obiview_p pointer = self.pointer()
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if self.active() :
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@ -160,34 +159,29 @@ cdef class View(OBIWrapper) :
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bytes2str(self.name))
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def __repr__(self) :
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# TODO check everywhere
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if not self.active() :
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raise OBIObjectClosedInstance()
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@OBIWrapper.checkIsActive
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def __repr__(self) :
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cdef str s = "{name:s}\n{comments:s}\n{line_count:d} lines\n".format(name = str(self.name),
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comments = str(self.comments),
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line_count = self.line_count)
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for column_name in self.keys() :
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s = s + repr(self[column_name]) + '\n'
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return s
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def keys(self):
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cdef str col_alias
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cdef bytes col_alias
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cdef int i
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cdef Obiview_p pointer = self.pointer()
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cdef int nb_column = pointer.infos.column_count
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cdef Alias_column_pair_p column_p = pointer.infos.column_references
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if not self.active() :
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raise OBIObjectClosedInstance()
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raise OBIDeactivatedInstanceError()
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for i in range(nb_column) :
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col_alias = bytes2str(column_p[i].alias)
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col_alias = column_p[i].alias
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yield col_alias
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@ -195,9 +189,9 @@ cdef class View(OBIWrapper) :
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object column_name):
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if not self.active() :
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raise OBIObjectClosedInstance()
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raise OBIDeactivatedInstanceError()
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return Column.open(self, column_name)
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return Column.open(self, tobytes(column_name))
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def get_column_with_idx(self,
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@ -207,24 +201,24 @@ cdef class View(OBIWrapper) :
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cdef int nb_column = pointer.infos.column_count
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if not self.active() :
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raise OBIObjectClosedInstance()
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raise OBIDeactivatedInstanceError()
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if column_idx > nb_column :
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raise IndexError(column_idx, "No column with this index")
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return Column.open(self, pointer.infos.column_references[column_idx].alias)
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cpdef delete_column(self,
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object column_name) :
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cdef bytes column_name_b = tobytes(column_name)
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if not self.active() :
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raise OBIObjectClosedInstance()
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raise OBIDeactivatedInstanceError()
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# Close the cython instance first
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col = self[column_name]
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col = self[column_name_b]
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col.close()
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# Remove the column from the view which closes the C structure
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@ -242,7 +236,7 @@ cdef class View(OBIWrapper) :
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cdef bytes new_name_b = tobytes(new_name)
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if not self.active() :
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raise OBIObjectClosedInstance()
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raise OBIDeactivatedInstanceError()
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if (obi_view_create_column_alias(self.pointer(),
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tobytes(current_name_b),
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@ -262,8 +256,12 @@ cdef class View(OBIWrapper) :
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cdef Column old_column
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cdef Column new_column
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cdef index_t length = len(self)
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old_column = self.get_column(column_name)
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cdef column_name_b = tobytes(column_name)
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if not self.active() :
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raise OBIDeactivatedInstanceError()
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old_column = self.get_column(column_name_b)
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if new_data_type == 0 :
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new_data_type = old_column.data_type
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@ -276,24 +274,27 @@ cdef class View(OBIWrapper) :
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new_column = Column.new_column(self, old_column.pointer().header.name, new_data_type,
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nb_elements_per_line=new_nb_elements_per_line, elements_names=new_elements_names,
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comments=old_column.comments, alias=tobytes(column_name)+tobytes('___new___'))
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comments=old_column.comments, alias=column_name_b+tobytes('___new___'))
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for i in range(length) :
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new_column[i] = old_column[i]
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# Remove old column from view
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self.delete_column(column_name)
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self.delete_column(column_name_b)
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# Rename new
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new_column.name = column_name
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new_column.name = column_name_b
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return new_column
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cpdef Line_selection new_selection(self,list lines=None):
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cpdef Line_selection new_selection(self, list lines=None):
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if not self.active() :
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raise OBIDeactivatedInstanceError()
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return Line_selection(self, lines)
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@OBIWrapper.checkIsActive
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def __iter__(self):
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# Iteration on each line of all columns
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@ -304,14 +305,17 @@ cdef class View(OBIWrapper) :
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for line_nb in range(self.line_count) :
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yield Line(self, line_nb)
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# TODO test time gain without
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@OBIWrapper.checkIsActive
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def __getitem__(self, object ref) :
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if type(ref) == int :
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return Line(self, ref)
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else : # TODO assume str or bytes for optimization (discuss)
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return self.get_column(ref) # TODO hyper lent dans la pratique
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@OBIWrapper.checkIsActive
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def __setitem__(self, index_t idx, object item) :
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cdef Column col
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line = self[idx]
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@ -329,15 +333,18 @@ cdef class View(OBIWrapper) :
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)
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line[k] = item[k]
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def __contains__(self, str column_name):
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return (column_name in self.keys())
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@OBIWrapper.checkIsActive
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def __contains__(self, object column_name):
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return (tobytes(column_name) in self.keys())
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@OBIWrapper.checkIsActive
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def __len__(self):
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return(self.line_count)
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@OBIWrapper.checkIsActive
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def __str__(self) :
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cdef Line line
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cdef str to_print
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@ -350,36 +357,48 @@ cdef class View(OBIWrapper) :
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# Width (column count) property getter
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@property
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def width(self):
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if not self.active() :
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raise OBIDeactivatedInstanceError()
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return self.pointer().infos.column_count
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# DMS property getter
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@property
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def dms(self):
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if not self.active() :
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raise OBIDeactivatedInstanceError()
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return self._dms
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# line_count property getter
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@property
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def line_count(self):
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if not self.active() :
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raise OBIDeactivatedInstanceError()
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return self.pointer().infos.line_count
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# name property getter
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@property
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def name(self):
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if not self.active() :
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raise OBIDeactivatedInstanceError()
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return <bytes> self.pointer().infos.name
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# view type property getter
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@property
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def type(self): # @ReservedAssignment
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if not self.active() :
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raise OBIDeactivatedInstanceError()
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return <bytes> self.pointer().infos.view_type
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# comments property getter
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@property
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def comments(self):
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if not self.active() :
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raise OBIDeactivatedInstanceError()
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return <bytes> self.pointer().infos.comments
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# TODO setter that concatenates new comments?
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@ -391,20 +410,21 @@ cdef class Line :
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self._view = view
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def __getitem__(self, str column_name) :
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return (self._view).get_column(column_name)[self._index]
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def __getitem__(self, object column_name) :
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return (self._view).get_column(tobytes(column_name))[self._index]
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def __setitem__(self, object column_name_, object value): # TODO discuss
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def __setitem__(self, object column_name, object value): # TODO discuss
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# TODO detect multiple elements (dict type)? put somewhere else? but more risky (in get)
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# TODO OBI_QUAL ?
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cdef type value_type
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cdef obitype_t value_obitype
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cdef bytes value_b
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cdef bytes column_name_b
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column_name = tostr(column_name_) # TODO
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column_name_b = tobytes(column_name)
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if column_name not in self._view :
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if column_name_b not in self._view :
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if value == None :
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raise Exception("Trying to create a column from a None value (can't guess type)")
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value_type = type(value)
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@ -428,27 +448,33 @@ cdef class Line :
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else :
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raise Exception("Could not guess the type of a value to create a new column")
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Column.new_column(self._view, column_name, value_obitype)
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Column.new_column(self._view, column_name_b, value_obitype)
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(self._view).get_column(column_name).set_line(self._index, value)
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(self._view).get_column(column_name_b).set_line(self._index, value)
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def __iter__(self):
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cdef bytes column_name
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for column_name in (self._view).keys() :
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yield column_name
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def keys(self):
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return self._view.keys()
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def __contains__(self, str column_name):
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return (column_name in self.keys())
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def __contains__(self, object column_name):
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return (tobytes(column_name) in self.keys())
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def __repr__(self):
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cdef dict line
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cdef str column_name
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cdef dict line
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cdef bytes column_name_b
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cdef str column_name_str
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line = {}
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for column_name in self._view.keys() :
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line[column_name] = self[column_name]
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for column_name_b in self._view.keys() :
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column_name_str = bytes2str(column_name_b)
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line[column_name_str] = self[column_name_str]
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return str(line)
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# View property getter
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@ -559,7 +585,7 @@ cdef class Line_selection(list):
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cdef View view
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if not self._view.active() :
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raise OBIObjectClosedInstance()
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raise OBIDeactivatedInstanceError()
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if comments is not None:
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comments_b = tobytes(comments)
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@ -568,7 +594,7 @@ cdef class Line_selection(list):
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pointer = obi_clone_view(self._view._dms.pointer(),
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self._view.pointer(),
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view_name_b,
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view_name_b,
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self.__build_binary_list__(),
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comments_b)
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@ -589,7 +615,7 @@ cdef class Line_selection(list):
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cdef register_view_class(bytes view_type_name,
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type view_class):
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type view_class):
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'''
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Each subclass of `dms.view` needs to be registered after its declaration
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'''
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