obitools/obitools3
2
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases 66 Wiki Activity

Better handling of elements names in Cython

Browse Source
This commit is contained in:
Celine Mercier
2017-12-13 23:12:14 +01:00
parent e9e7fac999
commit b7b8ba7e5a
11 changed files with 36 additions and 31 deletions
Download Patch File Download Diff File Expand all files Collapse all files

5
python/obitools3/dms/column/column.pxd
View File

@ -18,10 +18,11 @@ cdef class Column(OBIWrapper) :
cdef View _view cdef View _view
cdef bytes _alias cdef bytes _alias
cdef list elements_names cdef list _elements_names
cdef inline OBIDMS_column_p pointer(self) cdef inline OBIDMS_column_p pointer(self)
cdef read_elements_names(self)
@staticmethod @staticmethod
cdef type get_column_class(obitype_t obitype, bint multi_elts, bint tuples) cdef type get_column_class(obitype_t obitype, bint multi_elts, bint tuples)

38
python/obitools3/dms/column/column.pyx
View File

@ -160,7 +160,7 @@ cdef class Column(OBIWrapper) :
column._view = view column._view = view
column._alias = column_name_b column._alias = column_name_b
column.elements_names = column._elements_names column._elements_names = column.read_elements_names()
view.register(column) view.register(column)
return column return column
@ -274,6 +274,19 @@ cdef class Column(OBIWrapper) :
# raise Exception("Problem closing column %s" % bytes2str(self.name)) # raise Exception("Problem closing column %s" % bytes2str(self.name))
cdef read_elements_names(self):
cdef char* elts_names_b
cdef list elts_names_list
if not self.active() :
raise OBIDeactivatedInstanceError()
elts_names_b = obi_get_elements_names(self.pointer())
if elts_names_b == NULL:
raise Exception("Error reading the elements names of a column")
elts_names_list = elts_names_b.split(b';')
free(elts_names_b)
return elts_names_list
# Column alias property getter and setter # Column alias property getter and setter
@property @property
def name(self): def name(self):
@ -285,20 +298,11 @@ cdef class Column(OBIWrapper) :
if not self.active() : if not self.active() :
raise OBIDeactivatedInstanceError() raise OBIDeactivatedInstanceError()
self._view.rename_column(self._alias, new_alias) self._view.rename_column(self._alias, new_alias)
# elements_names property getter # elements_names property getter
@property @property
def _elements_names(self): def elements_names(self):
cdef char* elts_names_b return self._elements_names
cdef list elts_names_list
if not self.active() :
raise OBIDeactivatedInstanceError()
elts_names_b = obi_get_elements_names(self.pointer())
if elts_names_b == NULL:
raise Exception("Error reading the elements names of a column")
elts_names_list = elts_names_b.split(b';')
free(elts_names_b)
return elts_names_list
# nb_elements_per_line property getter # nb_elements_per_line property getter
@property @property
@ -386,7 +390,7 @@ cdef class Column_multi_elts(Column) :
if not self.active() : if not self.active() :
raise OBIDeactivatedInstanceError() raise OBIDeactivatedInstanceError()
if values is None or len(values) == 0 : if values is None or len(values) == 0 :
for element_name in self.elements_names : for element_name in self._elements_names :
self.set_item(line_nb, element_name, None) self.set_item(line_nb, element_name, None)
else : else :
values_iter = xrange(len(values)) if isinstance(values, list) else values values_iter = xrange(len(values)) if isinstance(values, list) else values
@ -427,7 +431,7 @@ cdef class Column_line :
if type(elt_id) == int: if type(elt_id) == int:
return elt_id < self._column.nb_elements_per_line return elt_id < self._column.nb_elements_per_line
else: else:
return (tobytes(elt_id) in self._column.elements_names) return (tobytes(elt_id) in self._column._elements_names)
def __repr__(self) : def __repr__(self) :
@ -437,13 +441,13 @@ cdef class Column_line :
def __iter__(self) : def __iter__(self) :
cdef list elements_names cdef list elements_names
cdef bytes element_name cdef bytes element_name
elements_names = self._column.elements_names elements_names = self._column._elements_names
for element_name in elements_names : for element_name in elements_names :
yield element_name yield element_name
def keys(self): # TODO Discuss if keys with None values should be returned too def keys(self): # TODO Discuss if keys with None values should be returned too
return self._column.elements_names return self._column._elements_names
# column property getter # column property getter

4
python/obitools3/dms/column/column_idx.pyx
View File

@ -78,7 +78,7 @@ cdef class Column_multi_elts_idx(Column_multi_elts):
all_NA = True all_NA = True
view_p = self._view.pointer() view_p = self._view.pointer()
column_p = self.pointer() column_p = self.pointer()
elements_names = self.elements_names elements_names = self._elements_names
for i in range(self.nb_elements_per_line) : for i in range(self.nb_elements_per_line) :
value = obi_get_index_with_elt_idx_and_col_p_in_view(view_p, column_p, line_nb, i) value = obi_get_index_with_elt_idx_and_col_p_in_view(view_p, column_p, line_nb, i)
obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column") obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column")
@ -106,7 +106,7 @@ cdef class Column_multi_elts_idx(Column_multi_elts):
cpdef set_line_idx(self, index_t line_nb, object values): cpdef set_line_idx(self, index_t line_nb, object values):
if values is None : if values is None :
for element_name in self.elements_names : for element_name in self._elements_names :
self.set_item_idx(line_nb, element_name, None) self.set_item_idx(line_nb, element_name, None)
else : else :
for element_name in values : for element_name in values :

2
python/obitools3/dms/column/typed_column/bool.pyx
View File

@ -99,7 +99,7 @@ cdef class Column_multi_elts_bool(Column_multi_elts):
all_NA = True all_NA = True
view_p = self._view.pointer() view_p = self._view.pointer()
column_p = self.pointer() column_p = self.pointer()
elements_names = self.elements_names elements_names = self._elements_names
for i in range(self.nb_elements_per_line) : for i in range(self.nb_elements_per_line) :
value = obi_get_bool_with_elt_idx_and_col_p_in_view(view_p, column_p, line_nb, i) value = obi_get_bool_with_elt_idx_and_col_p_in_view(view_p, column_p, line_nb, i)
obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column") obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column")

2
python/obitools3/dms/column/typed_column/char.pyx
View File

@ -101,7 +101,7 @@ cdef class Column_multi_elts_char(Column_multi_elts):
all_NA = True all_NA = True
view_p = self._view.pointer() view_p = self._view.pointer()
column_p = self.pointer() column_p = self.pointer()
elements_names = self.elements_names elements_names = self._elements_names
for i in range(self.nb_elements_per_line) : for i in range(self.nb_elements_per_line) :
value = obi_get_char_with_elt_idx_and_col_p_in_view(view_p, column_p, line_nb, i) value = obi_get_char_with_elt_idx_and_col_p_in_view(view_p, column_p, line_nb, i)
obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column") obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column")

2
python/obitools3/dms/column/typed_column/float.pyx
View File

@ -98,7 +98,7 @@ cdef class Column_multi_elts_float(Column_multi_elts):
all_NA = True all_NA = True
view_p = self._view.pointer() view_p = self._view.pointer()
column_p = self.pointer() column_p = self.pointer()
elements_names = self.elements_names elements_names = self._elements_names
for i in range(self.nb_elements_per_line) : for i in range(self.nb_elements_per_line) :
value = obi_get_float_with_elt_idx_and_col_p_in_view(view_p, column_p, line_nb, i) value = obi_get_float_with_elt_idx_and_col_p_in_view(view_p, column_p, line_nb, i)
obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column") obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column")

2
python/obitools3/dms/column/typed_column/int.pyx
View File

@ -102,7 +102,7 @@ cdef class Column_multi_elts_int(Column_multi_elts):
all_NA = True all_NA = True
view_p = self._view.pointer() view_p = self._view.pointer()
column_p = self.pointer() column_p = self.pointer()
elements_names = self.elements_names elements_names = self._elements_names
for i in range(self.nb_elements_per_line) : for i in range(self.nb_elements_per_line) :
value = obi_get_int_with_elt_idx_and_col_p_in_view(view_p, column_p, line_nb, i) value = obi_get_int_with_elt_idx_and_col_p_in_view(view_p, column_p, line_nb, i)
obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column") obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column")

4
python/obitools3/dms/column/typed_column/qual.pyx
View File

@ -164,7 +164,7 @@ cdef class Column_multi_elts_qual(Column_multi_elts_idx):
all_NA = True all_NA = True
view_p = self._view.pointer() view_p = self._view.pointer()
column_p = self.pointer() column_p = self.pointer()
elements_names = self.elements_names elements_names = self._elements_names
for i in range(self.nb_elements_per_line) : for i in range(self.nb_elements_per_line) :
value = obi_get_qual_int_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, i, &value_length) value = obi_get_qual_int_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, i, &value_length)
obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column") obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column")
@ -194,7 +194,7 @@ cdef class Column_multi_elts_qual(Column_multi_elts_idx):
all_NA = True all_NA = True
view_p = self._view.pointer() view_p = self._view.pointer()
column_p = self.pointer() column_p = self.pointer()
elements_names = self.elements_names elements_names = self._elements_names
for i in range(self.nb_elements_per_line) : for i in range(self.nb_elements_per_line) :
value = obi_get_qual_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, i, offset) value = obi_get_qual_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, i, offset)
obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column") obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column")

2
python/obitools3/dms/column/typed_column/seq.pyx
View File

@ -116,7 +116,7 @@ cdef class Column_multi_elts_seq(Column_multi_elts_idx):
all_NA = True all_NA = True
view_p = self._view.pointer() view_p = self._view.pointer()
column_p = self.pointer() column_p = self.pointer()
elements_names = self.elements_names elements_names = self._elements_names
for i in range(self.nb_elements_per_line) : for i in range(self.nb_elements_per_line) :
value = obi_get_seq_with_elt_idx_and_col_p_in_view(view_p, column_p, line_nb, i) value = obi_get_seq_with_elt_idx_and_col_p_in_view(view_p, column_p, line_nb, i)
obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column") obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column")

2
python/obitools3/dms/column/typed_column/str.pyx
View File

@ -112,7 +112,7 @@ cdef class Column_multi_elts_str(Column_multi_elts_idx):
all_NA = True all_NA = True
view_p = self._view.pointer() view_p = self._view.pointer()
column_p = self.pointer() column_p = self.pointer()
elements_names = self.elements_names elements_names = self._elements_names
for i in range(self.nb_elements_per_line) : for i in range(self.nb_elements_per_line) :
value = obi_get_str_with_elt_idx_and_col_p_in_view(view_p, column_p, line_nb, i) value = obi_get_str_with_elt_idx_and_col_p_in_view(view_p, column_p, line_nb, i)
obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column") obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column")

4
python/obitools3/dms/view/view.pyx
View File

@ -279,7 +279,7 @@ cdef class View(OBIWrapper) :
new_nb_elements_per_line = old_column.nb_elements_per_line new_nb_elements_per_line = old_column.nb_elements_per_line
if new_elements_names is None : if new_elements_names is None :
new_elements_names = old_column.elements_names new_elements_names = old_column._elements_names
new_column = Column.new_column(self, old_column.pointer().header.name, new_data_type, new_column = Column.new_column(self, old_column.pointer().header.name, new_data_type,
nb_elements_per_line=new_nb_elements_per_line, elements_names=new_elements_names, nb_elements_per_line=new_nb_elements_per_line, elements_names=new_elements_names,
@ -337,7 +337,7 @@ cdef class View(OBIWrapper) :
col.original_name, col.original_name,
col.data_type_int, col.data_type_int,
nb_elements_per_line = col.nb_elements_per_line, nb_elements_per_line = col.nb_elements_per_line,
elements_names = col.elements_names, elements_names = col._elements_names,
tuples = col.tuples, tuples = col.tuples,
to_eval = col.to_eval, to_eval = col.to_eval,
comments = col.comments, comments = col.comments,