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Cython API: fixed conversion bugs when setting and getting values

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(especially NA values) in OBI_CHAR, OBI_STR and OBI_SEQ columns
This commit is contained in:
Celine Mercier
2017-04-14 16:07:23 +02:00
parent a3fad27190
commit 693859eec2
3 changed files with 49 additions and 24 deletions
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24
python/obitools3/dms/column/typed_column/char.pyx
View File

@ -31,7 +31,6 @@ cdef class Column_char(Column):
elements_names=elements_names,
comments=comments)
cpdef object get_line(self, index_t line_nb):
cdef obichar_t value
cdef object result
@ -43,14 +42,16 @@ cdef class Column_char(Column):
if value == OBIChar_NA :
result = None
else :
result = value # TODO return bytes or str?
result = <bytes>value # TODO return bytes or str?
return result
cpdef set_line(self, index_t line_nb, object value):
cdef obichar_t value_b
if value is None :
value = OBIChar_NA
if obi_set_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0, <obichar_t> tobytes(value)[0]) < 0:
value_b = OBIChar_NA
else :
value_b = <obichar_t> tobytes(value)[0]
if obi_set_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0, value_b) < 0:
raise Exception("Problem setting a value in a column")
@ -70,7 +71,7 @@ cdef class Column_multi_elts_char(Column_multi_elts):
if value == OBIChar_NA :
result = None
else :
result = value # TODO return bytes or str?
result = <bytes>value # TODO return bytes or str?
return result
cpdef object get_line(self, index_t line_nb) :
@ -88,7 +89,7 @@ cdef class Column_multi_elts_char(Column_multi_elts):
if value == OBIChar_NA :
value_in_result = None
else :
value_in_result = value # TODO return bytes or str?
value_in_result = <bytes>value # TODO return bytes or str?
result[self.elements_names[i]] = value_in_result
if all_NA and (value_in_result is not None) :
all_NA = False
@ -98,14 +99,17 @@ cdef class Column_multi_elts_char(Column_multi_elts):
cpdef set_item(self, index_t line_nb, object elt_id, object value) :
cdef bytes elt_name
cdef obichar_t value_b
if value is None :
value = OBIChar_NA
value_b = OBIChar_NA
else :
value_b = <obichar_t> tobytes(value)[0]
if type(elt_id) == int :
if obi_set_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id, <obichar_t> tobytes(value)[0]) < 0 :
if obi_set_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id, value_b) < 0 :
raise Exception("Problem setting a value in a column")
else :
elt_name = tobytes(elt_id)
if obi_set_char_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name, <obichar_t> tobytes(value)[0]) < 0 :
if obi_set_char_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name, value_b) < 0 :
raise Exception("Problem setting a value in a column")

22
python/obitools3/dms/column/typed_column/seq.pyx
View File

@ -51,11 +51,15 @@ cdef class Column_seq(Column):
cpdef set_line(self, index_t line_nb, object value):
cdef bytes value_b
cdef char* value_b
cdef bytes value_bytes
if value is None :
value_b = OBISeq_NA
value_b = <char*>OBISeq_NA
else :
value_b = tobytes(value)
value_bytes = tobytes(value)
value_b = <char*>value_bytes
if obi_set_seq_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0, value_b) < 0:
raise Exception("Problem setting a value in a column")
@ -112,15 +116,21 @@ cdef class Column_multi_elts_seq(Column_multi_elts):
cpdef set_item(self, index_t line_nb, object elt_id, object value):
cdef bytes value_b
cdef bytes elt_name
cdef char* value_b
cdef bytes value_bytes
if value is None :
value_b = OBISeq_NA
value_b = <char*>OBISeq_NA
else :
value_b = tobytes(value)
value_bytes = tobytes(value)
value_b = <char*>value_bytes
if type(elt_id) == int :
if obi_set_seq_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id, value_b) < 0:
raise Exception("Problem setting a value in a column")
else :
elt_name = tobytes(elt_id)
if obi_set_seq_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name, value_b) < 0:

27
python/obitools3/dms/column/typed_column/str.pyx
View File

@ -38,6 +38,7 @@ cdef class Column_str(Column):
value = obi_get_str_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0)
if obi_errno > 0 :
raise IndexError(line_nb)
print(value == NULL)
if value == OBIStr_NA :
result = None
else :
@ -46,11 +47,15 @@ cdef class Column_str(Column):
cpdef set_line(self, index_t line_nb, object value):
cdef bytes value_b
cdef char* value_b
cdef bytes value_bytes
if value is None :
value_b = OBIStr_NA
value_b = <char*>OBIStr_NA
else :
value_b = tobytes(value)
value_bytes = tobytes(value)
value_b = <char*>value_bytes
if obi_set_str_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0, value_b) < 0:
raise Exception("Problem setting a value in a column")
@ -66,6 +71,7 @@ cdef class Column_multi_elts_str(Column_multi_elts):
else :
elt_name = tobytes(elt_id)
value = obi_get_str_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name)
print(value == NULL)
if obi_errno > 0 :
raise IndexError(line_nb, elt_id)
if value == OBIStr_NA :
@ -86,6 +92,7 @@ cdef class Column_multi_elts_str(Column_multi_elts):
all_NA = True
for i in range(self.nb_elements_per_line) :
value = obi_get_str_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, i)
print(value == NULL)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIStr_NA :
@ -101,18 +108,22 @@ cdef class Column_multi_elts_str(Column_multi_elts):
cpdef set_item(self, index_t line_nb, object elt_id, object value):
cdef bytes value_b
cdef bytes elt_name
cdef char* value_b
cdef bytes value_bytes
if value is None :
value_b = OBIStr_NA
value_b = <char*>OBIStr_NA
else :
value_b = tobytes(value)
value_bytes = tobytes(value)
value_b = <char*>value_bytes
if type(elt_id) == int :
if obi_set_str_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id, value_b) < 0:
if obi_set_str_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id, <char*>value_b) < 0:
raise Exception("Problem setting a value in a column")
else :
elt_name = tobytes(elt_id)
if obi_set_str_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name, value_b) < 0:
if obi_set_str_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name, <char*>value_b) < 0:
raise Exception("Problem setting a value in a column")