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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
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@ -3,3 +3,6 @@
cdef extern from "obierrno.h": cdef extern from "obierrno.h":
int obi_errno 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 ...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, \ 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_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_name_and_col_p_in_view, \
obi_set_bool_with_elt_idx_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 ...capi.obitypes cimport OBI_BOOL, OBIBool_NA, obibool_t
from cpython.bool cimport PyBool_FromLong from cpython.bool cimport PyBool_FromLong
@ -27,7 +26,6 @@ cdef class Column_bool(Column):
index_t nb_elements_per_line=1, index_t nb_elements_per_line=1,
object elements_names=None, object elements_names=None,
object comments=b""): object comments=b""):
return Column.new_column(view, column_name, OBI_BOOL, return Column.new_column(view, column_name, OBI_BOOL,
nb_elements_per_line=nb_elements_per_line, nb_elements_per_line=nb_elements_per_line,
elements_names=elements_names, elements_names=elements_names,
@ -35,13 +33,10 @@ cdef class Column_bool(Column):
cpdef object get_line(self, index_t line_nb): cpdef object get_line(self, index_t line_nb):
cdef obibool_t value cdef obibool_t value
cdef object result cdef object result
global obi_errno
value = obi_get_bool_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0) value = obi_get_bool_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0)
if obi_errno > 0 : obi_errno_to_exception(line_nb=line_nb, elt_id=None, error_message="Problem getting a value from a column")
raise IndexError(line_nb)
if value == OBIBool_NA : if value == OBIBool_NA :
result = None result = None
else : else :
@ -53,22 +48,21 @@ cdef class Column_bool(Column):
if value is None : if value is None :
value = OBIBool_NA 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 : 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): cdef class Column_multi_elts_bool(Column_multi_elts):
cpdef object get_item(self, index_t line_nb, object elt_id) : cpdef object get_item(self, index_t line_nb, object elt_id) :
cdef obibool_t value cdef obibool_t value
cdef object result cdef object result
cdef bytes elt_name cdef bytes elt_name
if type(elt_id) == int : 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) value = obi_get_bool_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id)
else : else :
elt_name = tobytes(elt_id) 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) 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 : obi_errno_to_exception(line_nb=line_nb, elt_id=elt_id, error_message="Problem getting a value from a column")
raise IndexError(line_nb, elt_id)
if value == OBIBool_NA : if value == OBIBool_NA :
result = None result = None
else : else :
@ -76,17 +70,16 @@ cdef class Column_multi_elts_bool(Column_multi_elts):
return result return result
cpdef object get_line(self, index_t line_nb) : cpdef object get_line(self, index_t line_nb) :
cdef obibool_t value cdef obibool_t value
cdef object value_in_result cdef object value_in_result
cdef dict result cdef dict result
cdef index_t i cdef index_t i
cdef bint all_NA cdef bint all_NA
result = {} result = {}
all_NA = True all_NA = True
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(self._view.pointer(), self.pointer(), line_nb, i) value = obi_get_bool_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, i)
if obi_errno > 0 : obi_errno_to_exception(line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column")
raise IndexError(line_nb)
if value == OBIBool_NA : if value == OBIBool_NA :
value_in_result = None value_in_result = None
else : else :
@ -99,16 +92,16 @@ cdef class Column_multi_elts_bool(Column_multi_elts):
return result return result
cpdef set_item(self, index_t line_nb, object elt_id, object value) : 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 : if value is None :
value = OBIBool_NA value = OBIBool_NA
if type(elt_id) == int : 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 : 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 : else :
elt_name = tobytes(elt_id) 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 : 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() : 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 ...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, \ 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_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_name_and_col_p_in_view, \
obi_set_char_with_elt_idx_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 from ...capi.obitypes cimport OBI_CHAR, OBIChar_NA, obichar_t
@ -33,13 +32,10 @@ cdef class Column_char(Column):
comments=comments) comments=comments)
cpdef object get_line(self, index_t line_nb): cpdef object get_line(self, index_t line_nb):
cdef obichar_t value cdef obichar_t value
cdef object result cdef object result
global obi_errno
value = obi_get_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0) value = obi_get_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0)
if obi_errno > 0 : obi_errno_to_exception(line_nb=line_nb, elt_id=None, error_message="Problem getting a value from a column")
raise IndexError(line_nb)
if value == OBIChar_NA : if value == OBIChar_NA :
result = None result = None
else : else :
@ -47,28 +43,27 @@ cdef class Column_char(Column):
return result return result
cpdef set_line(self, index_t line_nb, object value): cpdef set_line(self, index_t line_nb, object value):
cdef obichar_t value_b cdef obichar_t value_b
if value is None : if value is None :
value_b = OBIChar_NA value_b = OBIChar_NA
else : else :
value_b = <obichar_t> tobytes(value)[0] 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: 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): cdef class Column_multi_elts_char(Column_multi_elts):
cpdef object get_item(self, index_t line_nb, object elt_id) : cpdef object get_item(self, index_t line_nb, object elt_id) :
cdef obichar_t value cdef obichar_t value
cdef object result cdef object result
cdef bytes elt_name cdef bytes elt_name
if type(elt_id) == int : 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) value = obi_get_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id)
else : else :
elt_name = tobytes(elt_id) 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) 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 : obi_errno_to_exception(line_nb=line_nb, elt_id=elt_id, error_message="Problem getting a value from a column")
raise IndexError(line_nb, elt_id)
if value == OBIChar_NA : if value == OBIChar_NA :
result = None result = None
else : else :
@ -85,8 +80,7 @@ cdef class Column_multi_elts_char(Column_multi_elts):
all_NA = True all_NA = True
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(self._view.pointer(), self.pointer(), line_nb, i) value = obi_get_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, i)
if obi_errno > 0 : obi_errno_to_exception(line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column")
raise IndexError(line_nb)
if value == OBIChar_NA : if value == OBIChar_NA :
value_in_result = None value_in_result = None
else : else :
@ -107,11 +101,11 @@ cdef class Column_multi_elts_char(Column_multi_elts):
value_b = <obichar_t> tobytes(value)[0] value_b = <obichar_t> tobytes(value)[0]
if type(elt_id) == int : 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 : 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 : else :
elt_name = tobytes(elt_id) 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 : 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(): 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 ...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, \ 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_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_name_and_col_p_in_view, \
obi_set_float_with_elt_idx_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 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): cpdef object get_line(self, index_t line_nb):
cdef obifloat_t value cdef obifloat_t value
cdef object result cdef object result
global obi_errno
value = obi_get_float_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0) value = obi_get_float_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0)
if obi_errno > 0 : obi_errno_to_exception(line_nb=line_nb, elt_id=None, error_message="Problem getting a value from a column")
raise IndexError(line_nb)
if value == OBIFloat_NA : if value == OBIFloat_NA :
result = None result = None
else : else :
@ -52,7 +48,7 @@ cdef class Column_float(Column):
if value is None : if value is None :
value = OBIFloat_NA 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: 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): cdef class Column_multi_elts_float(Column_multi_elts):
@ -66,8 +62,7 @@ cdef class Column_multi_elts_float(Column_multi_elts):
else : else :
elt_name = tobytes(elt_id) 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) 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 : obi_errno_to_exception(line_nb=line_nb, elt_id=elt_id, error_message="Problem getting a value from a column")
raise IndexError(line_nb, elt_id)
if value == OBIFloat_NA : if value == OBIFloat_NA :
result = None result = None
else : else :
@ -84,8 +79,7 @@ cdef class Column_multi_elts_float(Column_multi_elts):
all_NA = True all_NA = True
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(self._view.pointer(), self.pointer(), line_nb, i) value = obi_get_float_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, i)
if obi_errno > 0 : obi_errno_to_exception(line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column")
raise IndexError(line_nb)
if value == OBIFloat_NA : if value == OBIFloat_NA :
value_in_result = None value_in_result = None
else : else :
@ -103,11 +97,11 @@ cdef class Column_multi_elts_float(Column_multi_elts):
value = OBIFloat_NA value = OBIFloat_NA
if type(elt_id) == int : 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 : 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 : else :
elt_name = tobytes(elt_id) 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 : 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(): 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 ...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, \ 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_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_name_and_col_p_in_view, \
obi_set_int_with_elt_idx_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 ...capi.obitypes cimport OBI_INT, OBIInt_NA, obiint_t
from cpython.int cimport PyInt_FromLong from cpython.int cimport PyInt_FromLong
@ -35,12 +35,9 @@ cdef class Column_int(Column):
cpdef object get_line(self, index_t line_nb): cpdef object get_line(self, index_t line_nb):
cdef obiint_t value cdef obiint_t value
cdef object result cdef object result
global obi_errno
value = obi_get_int_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0) value = obi_get_int_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0)
if obi_errno > 0 : obi_errno_to_exception(line_nb=line_nb, elt_id=None, error_message="Problem getting a value from a column")
raise IndexError(line_nb)
if value == OBIInt_NA : if value == OBIInt_NA :
result = None result = None
else : else :
@ -52,7 +49,7 @@ cdef class Column_int(Column):
if value is None : if value is None :
value = OBIInt_NA 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: 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): cdef class Column_multi_elts_int(Column_multi_elts):
@ -66,8 +63,7 @@ cdef class Column_multi_elts_int(Column_multi_elts):
else : else :
elt_name = tobytes(elt_id) 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) 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 : obi_errno_to_exception(line_nb=line_nb, elt_id=elt_id, error_message="Problem getting a value from a column")
raise IndexError(line_nb, elt_id)
if value == OBIInt_NA : if value == OBIInt_NA :
result = None result = None
else : else :
@ -84,8 +80,7 @@ cdef class Column_multi_elts_int(Column_multi_elts):
all_NA = True all_NA = True
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(self._view.pointer(), self.pointer(), line_nb, i) value = obi_get_int_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, i)
if obi_errno > 0 : obi_errno_to_exception(line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column")
raise IndexError(line_nb)
if value == OBIInt_NA : if value == OBIInt_NA :
value_in_result = None value_in_result = None
else : else :
@ -103,11 +98,11 @@ cdef class Column_multi_elts_int(Column_multi_elts):
value = OBIInt_NA value = OBIInt_NA
if type(elt_id) == int : 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 : 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 : else :
elt_name = tobytes(elt_id) 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 : 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(): 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 ...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, \ 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, \ 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_name_and_col_p_in_view, \
obi_set_qual_int_with_elt_idx_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 ...capi.obitypes cimport OBI_QUAL, OBIQual_char_NA, OBIQual_int_NA, const_char_p
from libc.stdlib cimport free from libc.stdlib cimport free
@ -43,12 +42,9 @@ cdef class Column_qual(Column):
cpdef object get_line(self, index_t line_nb): cpdef object get_line(self, index_t line_nb):
cdef const uint8_t* value cdef const uint8_t* value
cdef int value_length cdef int value_length
cdef object result cdef object result
global obi_errno
value = obi_get_qual_int_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0, &value_length) 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 : obi_errno_to_exception(line_nb=line_nb, elt_id=None, error_message="Problem getting a value from a column")
raise IndexError(line_nb)
if value == OBIQual_int_NA : if value == OBIQual_int_NA :
result = None result = None
else : else :
@ -59,14 +55,11 @@ cdef class Column_qual(Column):
cpdef object get_str_line(self, index_t line_nb): cpdef object get_str_line(self, index_t line_nb):
cdef char* value cdef char* value
cdef object result cdef object result
cdef int i cdef int i
global obi_errno
value = obi_get_qual_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0) 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 : obi_errno_to_exception(line_nb=line_nb, elt_id=None, error_message="Problem getting a value from a column")
raise IndexError(line_nb)
if value == OBIQual_char_NA : if value == OBIQual_char_NA :
result = None result = None
else : # TODO discuss else : # TODO discuss
@ -80,14 +73,14 @@ cdef class Column_qual(Column):
cdef int value_length cdef int value_length
if value is None : 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: 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 : else :
value_length = len(value) value_length = len(value)
value_b = <uint8_t*> malloc(value_length * sizeof(uint8_t)) value_b = <uint8_t*> malloc(value_length * sizeof(uint8_t))
for i in range(value_length) : for i in range(value_length) :
value_b[i] = <uint8_t>value[i] 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: 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) free(value_b)
@ -95,11 +88,11 @@ cdef class Column_qual(Column):
cdef bytes value_b cdef bytes value_b
if value is None : 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: 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 : else :
value_b = tobytes(value) 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: 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): 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 int value_length
cdef object result cdef object result
cdef int i cdef int i
global obi_errno # TODO add everywhere
if type(elt_id) == int : 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) 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 : else :
elt_name = tobytes(elt_id) 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) 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 : obi_errno_to_exception(line_nb=line_nb, elt_id=elt_id, error_message="Problem getting a value from a column")
raise IndexError(line_nb, elt_id)
if value == OBIQual_int_NA : if value == OBIQual_int_NA :
result = None result = None
else : 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): cpdef object get_str_item(self, index_t line_nb, object elt_id):
cdef char* value cdef char* value
cdef object result cdef object result
global obi_errno
if type(elt_id) == int : 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) value = obi_get_qual_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id)
else : else :
elt_name = tobytes(elt_id) 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) 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 : obi_errno_to_exception(line_nb=line_nb, elt_id=elt_id, error_message="Problem getting a value from a column")
raise IndexError(line_nb, elt_name)
if value == OBIQual_char_NA : if value == OBIQual_char_NA :
result = None result = None
else : else :
@ -155,14 +142,11 @@ cdef class Column_multi_elts_qual(Column_multi_elts):
cdef index_t i cdef index_t i
cdef int j cdef int j
cdef bint all_NA cdef bint all_NA
global obi_errno
result = {} result = {}
all_NA = True all_NA = True
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)
if obi_errno > 0 : obi_errno_to_exception(line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column")
raise IndexError(line_nb)
if value == OBIQual_int_NA : if value == OBIQual_int_NA :
value_in_result = None value_in_result = None
else : else :
@ -183,14 +167,11 @@ cdef class Column_multi_elts_qual(Column_multi_elts):
cdef dict result cdef dict result
cdef index_t i cdef index_t i
cdef bint all_NA cdef bint all_NA
global obi_errno
result = {} result = {}
all_NA = True all_NA = True
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) 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 : obi_errno_to_exception(line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column")
raise IndexError(line_nb)
if value == OBIQual_char_NA : if value == OBIQual_char_NA :
value_in_result = None value_in_result = None
else : else :
@ -220,11 +201,11 @@ cdef class Column_multi_elts_qual(Column_multi_elts):
if type(elt_id) == int : 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 : 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 : else :
elt_name = tobytes(elt_id) 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: 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 : if value is not None :
free(value_b) free(value_b)
@ -241,11 +222,11 @@ cdef class Column_multi_elts_qual(Column_multi_elts):
if type(elt_id) == int : 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 : 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 : else :
elt_name = tobytes(elt_id) 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: 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 ...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, \ 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_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_name_and_col_p_in_view, \
obi_set_seq_with_elt_idx_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 ...capi.obitypes cimport OBI_SEQ, OBISeq_NA
from libc.stdlib cimport free from libc.stdlib cimport free
@ -37,10 +36,8 @@ cdef class Column_seq(Column):
cpdef object get_line(self, index_t line_nb): cpdef object get_line(self, index_t line_nb):
cdef char* value cdef char* value
cdef object result 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) value = obi_get_seq_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0)
if obi_errno > 0 : obi_errno_to_exception(line_nb=line_nb, elt_id=None, error_message="Problem getting a value from a column")
raise IndexError(line_nb)
if value == OBISeq_NA : if value == OBISeq_NA :
result = None result = None
else : # TODO else : # TODO
@ -62,7 +59,7 @@ cdef class Column_seq(Column):
value_b = <char*>value_bytes 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: 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): 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) : cpdef object get_item(self, index_t line_nb, object elt_id) :
cdef char* value cdef char* value
cdef object result cdef object result
global obi_errno
if type(elt_id) == int : 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) value = obi_get_seq_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id)
else : else :
elt_name = tobytes(elt_id) 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) 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 : obi_errno_to_exception(line_nb=line_nb, elt_id=elt_id, error_message="Problem getting a value from a column")
raise IndexError(line_nb, elt_id)
if value == OBISeq_NA : if value == OBISeq_NA :
result = None result = None
else : else :
@ -94,13 +89,11 @@ cdef class Column_multi_elts_seq(Column_multi_elts):
cdef dict result cdef dict result
cdef index_t i cdef index_t i
cdef bint all_NA cdef bint all_NA
global obi_errno
result = {} result = {}
all_NA = True all_NA = True
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(self._view.pointer(), self.pointer(), line_nb, i) value = obi_get_seq_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, i)
if obi_errno > 0 : obi_errno_to_exception(line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column")
raise IndexError(line_nb)
if value == OBISeq_NA : if value == OBISeq_NA :
value_in_result = None value_in_result = None
else : else :
@ -130,12 +123,12 @@ cdef class Column_multi_elts_seq(Column_multi_elts):
if type(elt_id) == int : 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: 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 : else :
elt_name = tobytes(elt_id) 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: 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(): 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 ...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, \ 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_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_name_and_col_p_in_view, \
obi_set_str_with_elt_idx_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 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): cpdef object get_line(self, index_t line_nb):
cdef const_char_p value cdef const_char_p value
cdef object result 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) value = obi_get_str_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0)
if obi_errno > 0 : obi_errno_to_exception(line_nb=line_nb, elt_id=None, error_message="Problem getting a value from a column")
raise IndexError(line_nb)
print(value == NULL)
if value == OBIStr_NA : if value == OBIStr_NA :
result = None result = None
else : else :
@ -57,7 +54,7 @@ cdef class Column_str(Column):
value_b = <char*>value_bytes 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: 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): 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) : cpdef object get_item(self, index_t line_nb, object elt_id) :
cdef const_char_p value cdef const_char_p value
cdef object result cdef object result
global obi_errno
if type(elt_id) == int : 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) value = obi_get_str_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id)
else : else :
elt_name = tobytes(elt_id) 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) value = obi_get_str_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name)
print(value == NULL) obi_errno_to_exception(line_nb=line_nb, elt_id=elt_id, error_message="Problem getting a value from a column")
if obi_errno > 0 :
raise IndexError(line_nb, elt_id)
if value == OBIStr_NA : if value == OBIStr_NA :
result = None result = None
else : else :
@ -87,14 +81,11 @@ cdef class Column_multi_elts_str(Column_multi_elts):
cdef dict result cdef dict result
cdef index_t i cdef index_t i
cdef bint all_NA cdef bint all_NA
global obi_errno
result = {} result = {}
all_NA = True all_NA = True
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(self._view.pointer(), self.pointer(), line_nb, i) value = obi_get_str_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, i)
print(value == NULL) obi_errno_to_exception(line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column")
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIStr_NA : if value == OBIStr_NA :
value_in_result = None value_in_result = None
else : else :
@ -120,11 +111,11 @@ cdef class Column_multi_elts_str(Column_multi_elts):
if type(elt_id) == int : 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: 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 : else :
elt_name = tobytes(elt_id) 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: 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(): 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 #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 bytes str2bytes(str string)
cdef str bytes2str(bytes string) cdef str bytes2str(bytes string)
cdef bytes tobytes(object 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 #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): cdef bytes str2bytes(str string):
""" """
Short cut to convert ascii encoded python string (str) to bytes Short cut to convert ascii encoded python string (str) to bytes
@ -52,3 +79,75 @@ cdef str tostr(object string):
return string return string
return bytes2str(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_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_ */ #endif /* OBIERRNO_H_ */