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Better handling and tracing of Index Errors between C and Cython

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This commit is contained in:
Celine Mercier
2017-07-05 14:45:43 +02:00
parent f6631f3857
commit 1d2996c6c0
12 changed files with 236 additions and 147 deletions
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3
python/obitools3/dms/capi/obierrno.pxd
View File

@ -3,3 +3,6 @@
cdef extern from "obierrno.h":
int obi_errno
extern int OBI_LINE_IDX_ERROR
extern int OBI_ELT_IDX_ERROR

45
python/obitools3/dms/column/typed_column/bool.pyx
View File

@ -5,15 +5,14 @@ from ..column cimport register_column_class
from ...view.view cimport View
from obitools3.utils cimport tobytes
from obitools3.utils cimport tobytes, \
obi_errno_to_exception
from ...capi.obiview cimport obi_get_bool_with_elt_name_and_col_p_in_view, \
obi_get_bool_with_elt_idx_and_col_p_in_view, \
obi_set_bool_with_elt_name_and_col_p_in_view, \
obi_set_bool_with_elt_idx_and_col_p_in_view
from ...capi.obierrno cimport obi_errno
from ...capi.obitypes cimport OBI_BOOL, OBIBool_NA, obibool_t
from cpython.bool cimport PyBool_FromLong
@ -27,7 +26,6 @@ cdef class Column_bool(Column):
index_t nb_elements_per_line=1,
object elements_names=None,
object comments=b""):
return Column.new_column(view, column_name, OBI_BOOL,
nb_elements_per_line=nb_elements_per_line,
elements_names=elements_names,
@ -35,13 +33,10 @@ cdef class Column_bool(Column):
cpdef object get_line(self, index_t line_nb):
cdef obibool_t value
cdef object result
global obi_errno
cdef obibool_t value
cdef object result
value = obi_get_bool_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0)
if obi_errno > 0 :
raise IndexError(line_nb)
obi_errno_to_exception(line_nb=line_nb, elt_id=None, error_message="Problem getting a value from a column")
if value == OBIBool_NA :
result = None
else :
@ -53,22 +48,21 @@ cdef class Column_bool(Column):
if value is None :
value = OBIBool_NA
if obi_set_bool_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0, <obibool_t> value) < 0 :
raise Exception("Problem setting a value in a column")
obi_errno_to_exception(line_nb=line_nb, elt_id=None, error_message="Problem setting a value in a column")
cdef class Column_multi_elts_bool(Column_multi_elts):
cpdef object get_item(self, index_t line_nb, object elt_id) :
cdef obibool_t value
cdef object result
cdef bytes elt_name
cdef obibool_t value
cdef object result
cdef bytes elt_name
if type(elt_id) == int :
value = obi_get_bool_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id)
else :
elt_name = tobytes(elt_id)
value = obi_get_bool_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name)
if obi_errno > 0 :
raise IndexError(line_nb, elt_id)
obi_errno_to_exception(line_nb=line_nb, elt_id=elt_id, error_message="Problem getting a value from a column")
if value == OBIBool_NA :
result = None
else :
@ -76,17 +70,16 @@ cdef class Column_multi_elts_bool(Column_multi_elts):
return result
cpdef object get_line(self, index_t line_nb) :
cdef obibool_t value
cdef object value_in_result
cdef dict result
cdef index_t i
cdef bint all_NA
cdef obibool_t value
cdef object value_in_result
cdef dict result
cdef index_t i
cdef bint all_NA
result = {}
all_NA = True
for i in range(self.nb_elements_per_line) :
value = obi_get_bool_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, i)
if obi_errno > 0 :
raise IndexError(line_nb)
obi_errno_to_exception(line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column")
if value == OBIBool_NA :
value_in_result = None
else :
@ -99,16 +92,16 @@ cdef class Column_multi_elts_bool(Column_multi_elts):
return result
cpdef set_item(self, index_t line_nb, object elt_id, object value) :
cdef bytes elt_name
cdef bytes elt_name
if value is None :
value = OBIBool_NA
if type(elt_id) == int :
if obi_set_bool_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id, <obibool_t> value) < 0 :
raise Exception("Problem setting a value in a column")
obi_errno_to_exception(line_nb=line_nb, elt_id=elt_id, error_message="Problem setting a value in a column")
else :
elt_name = tobytes(elt_id)
if obi_set_bool_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name, <obibool_t> value) < 0 :
raise Exception("Problem setting a value in a column")
obi_errno_to_exception(line_nb=line_nb, elt_id=elt_id, error_message="Problem setting a value in a column")
def register_class() :

34
python/obitools3/dms/column/typed_column/char.pyx
View File

@ -5,15 +5,14 @@ from ..column cimport register_column_class
from ...view.view cimport View
from obitools3.utils cimport tobytes
from obitools3.utils cimport tobytes, \
obi_errno_to_exception
from ...capi.obiview cimport obi_get_char_with_elt_name_and_col_p_in_view, \
obi_get_char_with_elt_idx_and_col_p_in_view, \
obi_set_char_with_elt_name_and_col_p_in_view, \
obi_set_char_with_elt_idx_and_col_p_in_view
from ...capi.obierrno cimport obi_errno
from ...capi.obitypes cimport OBI_CHAR, OBIChar_NA, obichar_t
@ -33,13 +32,10 @@ cdef class Column_char(Column):
comments=comments)
cpdef object get_line(self, index_t line_nb):
cdef obichar_t value
cdef object result
global obi_errno
cdef obichar_t value
cdef object result
value = obi_get_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0)
if obi_errno > 0 :
raise IndexError(line_nb)
obi_errno_to_exception(line_nb=line_nb, elt_id=None, error_message="Problem getting a value from a column")
if value == OBIChar_NA :
result = None
else :
@ -47,28 +43,27 @@ cdef class Column_char(Column):
return result
cpdef set_line(self, index_t line_nb, object value):
cdef obichar_t value_b
cdef obichar_t value_b
if value is None :
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")
obi_errno_to_exception(line_nb=line_nb, elt_id=None, error_message="Problem setting a value in a column")
cdef class Column_multi_elts_char(Column_multi_elts):
cpdef object get_item(self, index_t line_nb, object elt_id) :
cdef obichar_t value
cdef object result
cdef bytes elt_name
cdef obichar_t value
cdef object result
cdef bytes elt_name
if type(elt_id) == int :
value = obi_get_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id)
else :
elt_name = tobytes(elt_id)
value = obi_get_char_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name)
if obi_errno > 0 :
raise IndexError(line_nb, elt_id)
obi_errno_to_exception(line_nb=line_nb, elt_id=elt_id, error_message="Problem getting a value from a column")
if value == OBIChar_NA :
result = None
else :
@ -85,8 +80,7 @@ cdef class Column_multi_elts_char(Column_multi_elts):
all_NA = True
for i in range(self.nb_elements_per_line) :
value = obi_get_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, i)
if obi_errno > 0 :
raise IndexError(line_nb)
obi_errno_to_exception(line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column")
if value == OBIChar_NA :
value_in_result = None
else :
@ -107,11 +101,11 @@ cdef class Column_multi_elts_char(Column_multi_elts):
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, value_b) < 0 :
raise Exception("Problem setting a value in a column")
obi_errno_to_exception(line_nb=line_nb, elt_id=elt_id, error_message="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, value_b) < 0 :
raise Exception("Problem setting a value in a column")
obi_errno_to_exception(line_nb=line_nb, elt_id=elt_id, error_message="Problem setting a value in a column")
def register_class():

24
python/obitools3/dms/column/typed_column/float.pyx
View File

@ -5,15 +5,14 @@ from ..column cimport register_column_class
from ...view.view cimport View
from obitools3.utils cimport tobytes
from obitools3.utils cimport tobytes, \
obi_errno_to_exception
from ...capi.obiview cimport obi_get_float_with_elt_name_and_col_p_in_view, \
obi_get_float_with_elt_idx_and_col_p_in_view, \
obi_set_float_with_elt_name_and_col_p_in_view, \
obi_set_float_with_elt_idx_and_col_p_in_view
from ...capi.obierrno cimport obi_errno
from ...capi.obitypes cimport OBI_FLOAT, OBIFloat_NA, obifloat_t
@ -35,12 +34,9 @@ cdef class Column_float(Column):
cpdef object get_line(self, index_t line_nb):
cdef obifloat_t value
cdef object result
global obi_errno
cdef object result
value = obi_get_float_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0)
if obi_errno > 0 :
raise IndexError(line_nb)
obi_errno_to_exception(line_nb=line_nb, elt_id=None, error_message="Problem getting a value from a column")
if value == OBIFloat_NA :
result = None
else :
@ -52,7 +48,7 @@ cdef class Column_float(Column):
if value is None :
value = OBIFloat_NA
if obi_set_float_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0, <obifloat_t> value) < 0:
raise Exception("Problem setting a value in a column")
obi_errno_to_exception(line_nb=line_nb, elt_id=None, error_message="Problem setting a value in a column")
cdef class Column_multi_elts_float(Column_multi_elts):
@ -66,8 +62,7 @@ cdef class Column_multi_elts_float(Column_multi_elts):
else :
elt_name = tobytes(elt_id)
value = obi_get_float_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name)
if obi_errno > 0 :
raise IndexError(line_nb, elt_id)
obi_errno_to_exception(line_nb=line_nb, elt_id=elt_id, error_message="Problem getting a value from a column")
if value == OBIFloat_NA :
result = None
else :
@ -84,8 +79,7 @@ cdef class Column_multi_elts_float(Column_multi_elts):
all_NA = True
for i in range(self.nb_elements_per_line) :
value = obi_get_float_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, i)
if obi_errno > 0 :
raise IndexError(line_nb)
obi_errno_to_exception(line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column")
if value == OBIFloat_NA :
value_in_result = None
else :
@ -103,11 +97,11 @@ cdef class Column_multi_elts_float(Column_multi_elts):
value = OBIFloat_NA
if type(elt_id) == int :
if obi_set_float_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id, <obifloat_t> value) < 0 :
raise Exception("Problem setting a value in a column")
obi_errno_to_exception(line_nb=line_nb, elt_id=elt_id, error_message="Problem setting a value in a column")
else :
elt_name = tobytes(elt_id)
if obi_set_float_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name, <obifloat_t> value) < 0 :
raise Exception("Problem setting a value in a column")
obi_errno_to_exception(line_nb=line_nb, elt_id=elt_id, error_message="Problem setting a value in a column")
def register_class():

23
python/obitools3/dms/column/typed_column/int.pyx
View File

@ -5,14 +5,14 @@ from ..column cimport register_column_class
from ...view.view cimport View
from obitools3.utils cimport tobytes
from obitools3.utils cimport tobytes, \
obi_errno_to_exception
from ...capi.obiview cimport obi_get_int_with_elt_name_and_col_p_in_view, \
obi_get_int_with_elt_idx_and_col_p_in_view, \
obi_set_int_with_elt_name_and_col_p_in_view, \
obi_set_int_with_elt_idx_and_col_p_in_view
from ...capi.obierrno cimport obi_errno
from ...capi.obitypes cimport OBI_INT, OBIInt_NA, obiint_t
from cpython.int cimport PyInt_FromLong
@ -35,12 +35,9 @@ cdef class Column_int(Column):
cpdef object get_line(self, index_t line_nb):
cdef obiint_t value
cdef object result
global obi_errno
cdef object result
value = obi_get_int_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0)
if obi_errno > 0 :
raise IndexError(line_nb)
obi_errno_to_exception(line_nb=line_nb, elt_id=None, error_message="Problem getting a value from a column")
if value == OBIInt_NA :
result = None
else :
@ -52,7 +49,7 @@ cdef class Column_int(Column):
if value is None :
value = OBIInt_NA
if obi_set_int_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0, <obiint_t> value) < 0:
raise Exception("Problem setting a value in a column")
obi_errno_to_exception(line_nb=line_nb, elt_id=None, error_message="Problem setting a value in a column")
cdef class Column_multi_elts_int(Column_multi_elts):
@ -66,8 +63,7 @@ cdef class Column_multi_elts_int(Column_multi_elts):
else :
elt_name = tobytes(elt_id)
value = obi_get_int_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name)
if obi_errno > 0 :
raise IndexError(line_nb, elt_id)
obi_errno_to_exception(line_nb=line_nb, elt_id=elt_id, error_message="Problem getting a value from a column")
if value == OBIInt_NA :
result = None
else :
@ -84,8 +80,7 @@ cdef class Column_multi_elts_int(Column_multi_elts):
all_NA = True
for i in range(self.nb_elements_per_line) :
value = obi_get_int_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, i)
if obi_errno > 0 :
raise IndexError(line_nb)
obi_errno_to_exception(line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column")
if value == OBIInt_NA :
value_in_result = None
else :
@ -103,11 +98,11 @@ cdef class Column_multi_elts_int(Column_multi_elts):
value = OBIInt_NA
if type(elt_id) == int :
if obi_set_int_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id, <obiint_t> value) < 0 :
raise Exception("Problem setting a value in a column")
obi_errno_to_exception(line_nb=line_nb, elt_id=elt_id, error_message="Problem setting a value in a column")
else :
elt_name = tobytes(elt_id)
if obi_set_int_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name, <obiint_t> value) < 0 :
raise Exception("Problem setting a value in a column")
obi_errno_to_exception(line_nb=line_nb, elt_id=elt_id, error_message="Problem setting a value in a column")
def register_class():

59
python/obitools3/dms/column/typed_column/qual.pyx
View File

@ -5,7 +5,8 @@ from ..column cimport register_column_class
from ...view.view cimport View
from obitools3.utils cimport tobytes, bytes2str
from obitools3.utils cimport tobytes, bytes2str, \
obi_errno_to_exception
from ...capi.obiview cimport obi_get_qual_char_with_elt_name_and_col_p_in_view, \
obi_get_qual_char_with_elt_idx_and_col_p_in_view, \
@ -16,8 +17,6 @@ from ...capi.obiview cimport obi_get_qual_char_with_elt_name_and_col_p_in_view,
obi_set_qual_int_with_elt_name_and_col_p_in_view, \
obi_set_qual_int_with_elt_idx_and_col_p_in_view
from ...capi.obierrno cimport obi_errno
from ...capi.obitypes cimport OBI_QUAL, OBIQual_char_NA, OBIQual_int_NA, const_char_p
from libc.stdlib cimport free
@ -43,12 +42,9 @@ cdef class Column_qual(Column):
cpdef object get_line(self, index_t line_nb):
cdef const uint8_t* value
cdef int value_length
cdef object result
global obi_errno
cdef object result
value = obi_get_qual_int_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0, &value_length)
if obi_errno > 0 :
raise IndexError(line_nb)
obi_errno_to_exception(line_nb=line_nb, elt_id=None, error_message="Problem getting a value from a column")
if value == OBIQual_int_NA :
result = None
else :
@ -59,14 +55,11 @@ cdef class Column_qual(Column):
cpdef object get_str_line(self, index_t line_nb):
cdef char* value
cdef object result
cdef int i
global obi_errno
cdef char* value
cdef object result
cdef int i
value = obi_get_qual_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0)
if obi_errno > 0 :
raise IndexError(line_nb)
obi_errno_to_exception(line_nb=line_nb, elt_id=None, error_message="Problem getting a value from a column")
if value == OBIQual_char_NA :
result = None
else : # TODO discuss
@ -80,14 +73,14 @@ cdef class Column_qual(Column):
cdef int value_length
if value is None :
if obi_set_qual_int_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0, OBIQual_int_NA, 0) < 0:
raise Exception("Problem setting a value in a column")
obi_errno_to_exception(line_nb=line_nb, elt_id=None, error_message="Problem setting a value in a column")
else :
value_length = len(value)
value_b = <uint8_t*> malloc(value_length * sizeof(uint8_t))
for i in range(value_length) :
value_b[i] = <uint8_t>value[i]
if obi_set_qual_int_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0, value_b, value_length) < 0:
raise Exception("Problem setting a value in a column")
obi_errno_to_exception(line_nb=line_nb, elt_id=None, error_message="Problem setting a value in a column")
free(value_b)
@ -95,11 +88,11 @@ cdef class Column_qual(Column):
cdef bytes value_b
if value is None :
if obi_set_qual_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0, OBIQual_char_NA) < 0:
raise Exception("Problem setting a value in a column")
obi_errno_to_exception(line_nb=line_nb, elt_id=None, error_message="Problem setting a value in a column")
else :
value_b = tobytes(value)
if obi_set_qual_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")
obi_errno_to_exception(line_nb=line_nb, elt_id=None, error_message="Problem setting a value in a column")
cdef class Column_multi_elts_qual(Column_multi_elts):
@ -109,15 +102,12 @@ cdef class Column_multi_elts_qual(Column_multi_elts):
cdef int value_length
cdef object result
cdef int i
global obi_errno # TODO add everywhere
if type(elt_id) == int :
value = obi_get_qual_int_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id, &value_length)
else :
elt_name = tobytes(elt_id)
value = obi_get_qual_int_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name, &value_length)
if obi_errno > 0 :
raise IndexError(line_nb, elt_id)
obi_errno_to_exception(line_nb=line_nb, elt_id=elt_id, error_message="Problem getting a value from a column")
if value == OBIQual_int_NA :
result = None
else :
@ -130,15 +120,12 @@ cdef class Column_multi_elts_qual(Column_multi_elts):
cpdef object get_str_item(self, index_t line_nb, object elt_id):
cdef char* value
cdef object result
global obi_errno
if type(elt_id) == int :
value = obi_get_qual_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id)
else :
elt_name = tobytes(elt_id)
value = obi_get_qual_char_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name)
if obi_errno > 0 :
raise IndexError(line_nb, elt_name)
obi_errno_to_exception(line_nb=line_nb, elt_id=elt_id, error_message="Problem getting a value from a column")
if value == OBIQual_char_NA :
result = None
else :
@ -155,14 +142,11 @@ cdef class Column_multi_elts_qual(Column_multi_elts):
cdef index_t i
cdef int j
cdef bint all_NA
global obi_errno
result = {}
all_NA = True
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)
if obi_errno > 0 :
raise IndexError(line_nb)
obi_errno_to_exception(line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column")
if value == OBIQual_int_NA :
value_in_result = None
else :
@ -183,14 +167,11 @@ cdef class Column_multi_elts_qual(Column_multi_elts):
cdef dict result
cdef index_t i
cdef bint all_NA
global obi_errno
result = {}
all_NA = True
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)
if obi_errno > 0 :
raise IndexError(line_nb)
obi_errno_to_exception(line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column")
if value == OBIQual_char_NA :
value_in_result = None
else :
@ -220,11 +201,11 @@ cdef class Column_multi_elts_qual(Column_multi_elts):
if type(elt_id) == int :
if obi_set_qual_int_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id, value_b, value_length) < 0 :
raise Exception("Problem setting a value in a column")
obi_errno_to_exception(line_nb=line_nb, elt_id=elt_id, error_message="Problem setting a value in a column")
else :
elt_name = tobytes(elt_id)
if obi_set_qual_int_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name, value_b, value_length) < 0:
raise Exception("Problem setting a value in a column")
obi_errno_to_exception(line_nb=line_nb, elt_id=elt_id, error_message="Problem setting a value in a column")
if value is not None :
free(value_b)
@ -241,11 +222,11 @@ cdef class Column_multi_elts_qual(Column_multi_elts):
if type(elt_id) == int :
if obi_set_qual_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")
obi_errno_to_exception(line_nb=line_nb, elt_id=elt_id, error_message="Problem setting a value in a column")
else :
elt_name = tobytes(elt_id)
if obi_set_qual_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")
obi_errno_to_exception(line_nb=line_nb, elt_id=elt_id, error_message="Problem setting a value in a column")

23
python/obitools3/dms/column/typed_column/seq.pyx
View File

@ -5,15 +5,14 @@ from ..column cimport register_column_class
from ...view.view cimport View
from obitools3.utils cimport tobytes
from obitools3.utils cimport tobytes, \
obi_errno_to_exception
from ...capi.obiview cimport obi_get_seq_with_elt_name_and_col_p_in_view, \
obi_get_seq_with_elt_idx_and_col_p_in_view, \
obi_set_seq_with_elt_name_and_col_p_in_view, \
obi_set_seq_with_elt_idx_and_col_p_in_view
from ...capi.obierrno cimport obi_errno
from ...capi.obitypes cimport OBI_SEQ, OBISeq_NA
from libc.stdlib cimport free
@ -37,10 +36,8 @@ cdef class Column_seq(Column):
cpdef object get_line(self, index_t line_nb):
cdef char* value
cdef object result
global obi_errno
value = obi_get_seq_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0)
if obi_errno > 0 :
raise IndexError(line_nb)
obi_errno_to_exception(line_nb=line_nb, elt_id=None, error_message="Problem getting a value from a column")
if value == OBISeq_NA :
result = None
else : # TODO
@ -62,7 +59,7 @@ cdef class Column_seq(Column):
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")
obi_errno_to_exception(line_nb=line_nb, elt_id=None, error_message="Problem setting a value in a column")
cdef class Column_multi_elts_seq(Column_multi_elts):
@ -70,14 +67,12 @@ cdef class Column_multi_elts_seq(Column_multi_elts):
cpdef object get_item(self, index_t line_nb, object elt_id) :
cdef char* value
cdef object result
global obi_errno
if type(elt_id) == int :
value = obi_get_seq_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id)
else :
elt_name = tobytes(elt_id)
value = obi_get_seq_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name)
if obi_errno > 0 :
raise IndexError(line_nb, elt_id)
obi_errno_to_exception(line_nb=line_nb, elt_id=elt_id, error_message="Problem getting a value from a column")
if value == OBISeq_NA :
result = None
else :
@ -94,13 +89,11 @@ cdef class Column_multi_elts_seq(Column_multi_elts):
cdef dict result
cdef index_t i
cdef bint all_NA
global obi_errno
result = {}
all_NA = True
for i in range(self.nb_elements_per_line) :
value = obi_get_seq_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, i)
if obi_errno > 0 :
raise IndexError(line_nb)
obi_errno_to_exception(line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column")
if value == OBISeq_NA :
value_in_result = None
else :
@ -130,12 +123,12 @@ cdef class Column_multi_elts_seq(Column_multi_elts):
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")
obi_errno_to_exception(line_nb=line_nb, elt_id=elt_id, error_message="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:
raise Exception("Problem setting a value in a column")
obi_errno_to_exception(line_nb=line_nb, elt_id=elt_id, error_message="Problem setting a value in a column")
def register_class():

25
python/obitools3/dms/column/typed_column/str.pyx
View File

@ -5,14 +5,14 @@ from ..column cimport register_column_class
from ...view.view cimport View
from obitools3.utils cimport tobytes
from obitools3.utils cimport tobytes, \
obi_errno_to_exception
from ...capi.obiview cimport obi_get_str_with_elt_name_and_col_p_in_view, \
obi_get_str_with_elt_idx_and_col_p_in_view, \
obi_set_str_with_elt_name_and_col_p_in_view, \
obi_set_str_with_elt_idx_and_col_p_in_view
from ...capi.obierrno cimport obi_errno
from ...capi.obitypes cimport OBI_STR, OBIStr_NA, const_char_p
@ -34,11 +34,8 @@ cdef class Column_str(Column):
cpdef object get_line(self, index_t line_nb):
cdef const_char_p value
cdef object result
global obi_errno
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)
obi_errno_to_exception(line_nb=line_nb, elt_id=None, error_message="Problem getting a value from a column")
if value == OBIStr_NA :
result = None
else :
@ -57,7 +54,7 @@ cdef class Column_str(Column):
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")
obi_errno_to_exception(line_nb=line_nb, elt_id=None, error_message="Problem setting a value in a column")
cdef class Column_multi_elts_str(Column_multi_elts):
@ -65,15 +62,12 @@ cdef class Column_multi_elts_str(Column_multi_elts):
cpdef object get_item(self, index_t line_nb, object elt_id) :
cdef const_char_p value
cdef object result
global obi_errno
if type(elt_id) == int :
value = obi_get_str_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id)
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)
obi_errno_to_exception(line_nb=line_nb, elt_id=elt_id, error_message="Problem getting a value from a column")
if value == OBIStr_NA :
result = None
else :
@ -87,14 +81,11 @@ cdef class Column_multi_elts_str(Column_multi_elts):
cdef dict result
cdef index_t i
cdef bint all_NA
global obi_errno
result = {}
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)
obi_errno_to_exception(line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column")
if value == OBIStr_NA :
value_in_result = None
else :
@ -120,11 +111,11 @@ cdef class Column_multi_elts_str(Column_multi_elts):
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, <char*>value_b) < 0:
raise Exception("Problem setting a value in a column")
obi_errno_to_exception(line_nb=line_nb, elt_id=elt_id, error_message="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, <char*>value_b) < 0:
raise Exception("Problem setting a value in a column")
obi_errno_to_exception(line_nb=line_nb, elt_id=elt_id, error_message="Problem setting a value in a column")
def register_class():

33
python/obitools3/utils.cfiles Normal file
View File

@ -0,0 +1,33 @@
../../src/bloom.c
../../src/char_str_indexer.c
../../src/crc64.c
../../src/dna_seq_indexer.c
../../src/encode.c
../../src/hashtable.c
../../src/linked_list.c
../../src/murmurhash2.c
../../src/obi_align.c
../../src/obiavl.c
../../src/obiblob_indexer.c
../../src/obiblob.c
../../src/obidms_taxonomy.c
../../src/obidms.c
../../src/obidmscolumn_blob.c
../../src/obidmscolumn_bool.c
../../src/obidmscolumn_char.c
../../src/obidmscolumn_float.c
../../src/obidmscolumn_idx.c
../../src/obidmscolumn_int.c
../../src/obidmscolumn_qual.c
../../src/obidmscolumn_seq.c
../../src/obidmscolumn_str.c
../../src/obidmscolumn.c
../../src/obidmscolumndir.c
../../src/obierrno.c
../../src/obilittlebigman.c
../../src/obitypes.c
../../src/obiview.c
../../src/sse_banded_LCS_alignment.c
../../src/uint8_indexer.c
../../src/upperband.c
../../src/utils.c

10
python/obitools3/utils.pxd
View File

@ -1,7 +1,15 @@
#cython: language_level=3
from obitools3.dms.capi.obitypes cimport obitype_t, index_t
cdef obi_errno_to_exception(index_t line_nb=*, object elt_id=*, str error_message=*)
cdef bytes str2bytes(str string)
cdef str bytes2str(bytes string)
cdef bytes tobytes(object string)
cdef str tostr(object string)
cdef str tostr(object string)
cdef obitype_t get_obitype_single_value(object value)
cdef obitype_t update_obitype(obitype_t obitype, object new_value)
cdef obitype_t get_obitype_iterable_value(object value)
cdef obitype_t get_obitype(object value)

99
python/obitools3/utils.pyx
View File

@ -1,5 +1,32 @@
#cython: language_level=3
from obitools3.dms.capi.obitypes cimport is_a_DNA_seq, \
OBI_VOID, \
OBI_BOOL, \
OBI_CHAR, \
OBI_FLOAT, \
OBI_INT, \
OBI_QUAL, \
OBI_SEQ, \
OBI_STR, \
index_t
from obitools3.dms.capi.obierrno cimport obi_errno, \
OBI_LINE_IDX_ERROR, \
OBI_ELT_IDX_ERROR
cdef obi_errno_to_exception(index_t line_nb=-1, object elt_id=None, str error_message=None) :
global obi_errno
if obi_errno > 0 :
if obi_errno == OBI_LINE_IDX_ERROR :
raise IndexError(line_nb, None or error_message)
elif obi_errno == OBI_ELT_IDX_ERROR :
raise IndexError(elt_id, None or error_message)
else :
raise Exception(None or error_message)
cdef bytes str2bytes(str string):
"""
Short cut to convert ascii encoded python string (str) to bytes
@ -52,3 +79,75 @@ cdef str tostr(object string):
return string
return bytes2str(string)
cdef obitype_t get_obitype_single_value(object value) :
cdef type value_type
cdef obitype_t value_obitype
if value is None :
return OBI_VOID
value_type = type(value)
value_obitype = OBI_VOID
if value_type == int :
value_obitype = OBI_INT
elif value_type == float :
value_obitype = OBI_FLOAT
elif value_type == bool :
value_obitype = OBI_BOOL
elif value_type == str or value_type == bytes :
if is_a_DNA_seq(tobytes(value)) :
value_obitype = OBI_SEQ
elif len(value) == 1 :
value_obitype = OBI_CHAR
elif (len(value) > 1) :
value_obitype = OBI_STR
else :
value_obitype = OBI_VOID
return value_obitype
cdef obitype_t update_obitype(obitype_t obitype, object new_value) :
cdef type new_type
new_type = type(new_value)
if obitype == OBI_INT :
if new_type == float :
return OBI_FLOAT
# TODO BOOL vers INT/FLOAT
elif new_type == str or new_type == bytes :
if obitype == OBI_SEQ and is_a_DNA_seq(tobytes(new_value)) :
pass
else :
return OBI_STR
return obitype
cdef obitype_t get_obitype_iterable_value(object value) :
cdef obitype_t value_obitype
value_obitype = OBI_VOID
for k in value :
if value_obitype == OBI_VOID :
value_obitype = get_obitype_single_value(value[k])
else :
value_obitype = update_obitype(value_obitype, value[k])
return value_obitype
cdef obitype_t get_obitype(object value) :
if type(value) == dict or type(value) == list or type(value) == tuple :
return get_obitype_iterable_value(value)
else :
return get_obitype_single_value(value)

5
src/obierrno.h
View File

@ -118,6 +118,11 @@ extern int obi_errno;
*/
#define OBI_ALIGN_ERROR (29) /** Error while aligning sequences
*/
#define OBI_LINE_IDX_ERROR (30) /** Error setting or getting a value at a forbidden line index (greater than the line count of the view or the column)
*/
#define OBI_ELT_IDX_ERROR (31) /** Error setting or getting a value at a non-existent element index or with a non-existent element name
*/
/**@}*/
#endif /* OBIERRNO_H_ */