diff --git a/python/obitools3/dms/column/column_idx.pyx b/python/obitools3/dms/column/column_idx.pyx index 76a68ac..da1bb06 100755 --- a/python/obitools3/dms/column/column_idx.pyx +++ b/python/obitools3/dms/column/column_idx.pyx @@ -30,7 +30,7 @@ cdef class Column_idx(Column): cdef index_t value cdef object result value = obi_get_index_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0) - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=None, error_message="Problem getting a value from a column") + obi_errno_to_exception(line_nb=line_nb, elt_id=None, error_message="Problem getting a value from a column") if value == OBIIdx_NA : result = None else : @@ -42,7 +42,7 @@ cdef class Column_idx(Column): if value is None : value = OBIIdx_NA if obi_set_index_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0, value) < 0: - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=None, error_message="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_idx(Column_multi_elts): @@ -57,7 +57,7 @@ cdef class Column_multi_elts_idx(Column_multi_elts): else : elt_name = tobytes(elt_id) value = obi_get_index_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name) - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=elt_id, error_message="Problem getting a value from a column") + obi_errno_to_exception(line_nb=line_nb, elt_id=elt_id, error_message="Problem getting a value from a column") if value == OBIIdx_NA : result = None else : @@ -81,7 +81,7 @@ cdef class Column_multi_elts_idx(Column_multi_elts): elements_names = self._elements_names 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) - 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(line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column") if value != OBIIdx_NA : value_in_result = PyLong_FromLongLong(value) result[elements_names[i]] = value_in_result @@ -98,11 +98,11 @@ cdef class Column_multi_elts_idx(Column_multi_elts): value = OBIIdx_NA if type(elt_id) == int : if obi_set_index_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id, value) < 0 : - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=elt_id, error_message="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_index_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name, value) < 0 : - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=elt_id, error_message="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") cpdef set_line_idx(self, index_t line_nb, object values): if values is None : diff --git a/python/obitools3/dms/column/typed_column/bool.pyx b/python/obitools3/dms/column/typed_column/bool.pyx index 2b1e541..54377fd 100755 --- a/python/obitools3/dms/column/typed_column/bool.pyx +++ b/python/obitools3/dms/column/typed_column/bool.pyx @@ -51,7 +51,7 @@ cdef class Column_bool(Column): 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) - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=None, error_message="Problem getting a value from a column") + 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 : @@ -63,7 +63,7 @@ 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, value) < 0 : - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=None, error_message="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): @@ -78,7 +78,7 @@ cdef class Column_multi_elts_bool(Column_multi_elts): 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) - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=elt_id, error_message="Problem getting a value from a column") + 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 : @@ -102,7 +102,7 @@ cdef class Column_multi_elts_bool(Column_multi_elts): elements_names = self._elements_names 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) - 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(line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column") if value != OBIBool_NA : value_in_result = PyBool_FromLong(value) result[elements_names[i]] = value_in_result @@ -119,11 +119,11 @@ cdef class Column_multi_elts_bool(Column_multi_elts): 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, value) < 0 : - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=elt_id, error_message="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, value) < 0 : - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=elt_id, error_message="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") cdef class Column_tuples_bool(Column): @@ -140,7 +140,7 @@ cdef class Column_tuples_bool(Column): result = [] array = obi_get_array_with_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, &value_length) - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=None, error_message="Problem getting a value from a column") + obi_errno_to_exception(line_nb=line_nb, elt_id=None, error_message="Problem getting a value from a column") if array == OBITuple_NA : return None @@ -179,7 +179,7 @@ cdef class Column_tuples_bool(Column): j+=1 if obi_set_array_with_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, array, sizeof(obibool_t)*8, value_length) < 0 : - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=None, error_message="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") if array != OBITuple_NA: free(array) diff --git a/python/obitools3/dms/column/typed_column/char.pyx b/python/obitools3/dms/column/typed_column/char.pyx index 6c95024..1ba7e89 100755 --- a/python/obitools3/dms/column/typed_column/char.pyx +++ b/python/obitools3/dms/column/typed_column/char.pyx @@ -50,7 +50,7 @@ cdef class Column_char(Column): 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) - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=None, error_message="Problem getting a value from a column") + 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 : @@ -65,7 +65,7 @@ cdef class Column_char(Column): else : value_b = 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: - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=None, error_message="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): @@ -80,7 +80,7 @@ cdef class Column_multi_elts_char(Column_multi_elts): 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) - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=elt_id, error_message="Problem getting a value from a column") + 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 : @@ -104,7 +104,7 @@ cdef class Column_multi_elts_char(Column_multi_elts): elements_names = self._elements_names 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) - 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(line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column") if value != OBIChar_NA : value_in_result = value result[elements_names[i]] = value_in_result @@ -124,11 +124,11 @@ cdef class Column_multi_elts_char(Column_multi_elts): value_b = 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 : - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=elt_id, error_message="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 : - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=elt_id, error_message="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") cdef class Column_tuples_char(Column): @@ -145,7 +145,7 @@ cdef class Column_tuples_char(Column): result = [] array = obi_get_array_with_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, &value_length) - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=None, error_message="Problem getting a value from a column") + obi_errno_to_exception(line_nb=line_nb, elt_id=None, error_message="Problem getting a value from a column") if array == OBITuple_NA : return None @@ -186,7 +186,7 @@ cdef class Column_tuples_char(Column): j+=1 if obi_set_array_with_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, array, sizeof(obichar_t)*8, value_length) < 0 : - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=None, error_message="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") if array != OBITuple_NA: free(array) diff --git a/python/obitools3/dms/column/typed_column/float.pyx b/python/obitools3/dms/column/typed_column/float.pyx index 1b13134..3a0702b 100755 --- a/python/obitools3/dms/column/typed_column/float.pyx +++ b/python/obitools3/dms/column/typed_column/float.pyx @@ -50,7 +50,7 @@ cdef class Column_float(Column): cdef obifloat_t value cdef object result value = obi_get_float_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0) - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=None, error_message="Problem getting a value from a column") + 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 : @@ -62,7 +62,7 @@ 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, value) < 0: - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=None, error_message="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): @@ -77,7 +77,7 @@ 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) - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=elt_id, error_message="Problem getting a value from a column") + 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 : @@ -101,7 +101,7 @@ cdef class Column_multi_elts_float(Column_multi_elts): elements_names = self._elements_names 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) - 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(line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column") if value != OBIFloat_NA : value_in_result = value result[elements_names[i]] = value_in_result @@ -118,11 +118,11 @@ 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, value) < 0 : - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=elt_id, error_message="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, value) < 0 : - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=elt_id, error_message="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") cdef class Column_tuples_float(Column): @@ -139,7 +139,7 @@ cdef class Column_tuples_float(Column): result = [] array = obi_get_array_with_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, &value_length) - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=None, error_message="Problem getting a value from a column") + obi_errno_to_exception(line_nb=line_nb, elt_id=None, error_message="Problem getting a value from a column") if array == OBITuple_NA : return None @@ -178,7 +178,7 @@ cdef class Column_tuples_float(Column): j+=1 if obi_set_array_with_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, array, sizeof(obifloat_t)*8, value_length) < 0 : - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=None, error_message="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") if array != OBITuple_NA: free(array) diff --git a/python/obitools3/dms/column/typed_column/int.pyx b/python/obitools3/dms/column/typed_column/int.pyx index 1fcbf21..5d9150e 100755 --- a/python/obitools3/dms/column/typed_column/int.pyx +++ b/python/obitools3/dms/column/typed_column/int.pyx @@ -53,7 +53,7 @@ cdef class Column_int(Column): cdef obiint_t value cdef object result value = obi_get_int_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0) - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=None, error_message="Problem getting a value from a column") + 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 : @@ -66,7 +66,7 @@ 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, value) < 0: - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=None, error_message="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): @@ -81,7 +81,7 @@ 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) - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=elt_id, error_message="Problem getting a value from a column") + 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 : @@ -105,7 +105,7 @@ cdef class Column_multi_elts_int(Column_multi_elts): elements_names = self._elements_names 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) - 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(line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column") if value != OBIInt_NA : value_in_result = PyInt_FromLong(value) result[elements_names[i]] = value_in_result @@ -122,11 +122,11 @@ 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, value) < 0 : - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=elt_id, error_message="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, value) < 0 : - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=elt_id, error_message="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") cdef class Column_tuples_int(Column): @@ -143,7 +143,7 @@ cdef class Column_tuples_int(Column): result = [] array = obi_get_array_with_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, &value_length) - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=None, error_message="Problem getting a value from a column") + obi_errno_to_exception(line_nb=line_nb, elt_id=None, error_message="Problem getting a value from a column") if array == OBITuple_NA : return None @@ -182,7 +182,7 @@ cdef class Column_tuples_int(Column): j+=1 if obi_set_array_with_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, array, sizeof(obiint_t)*8, value_length) < 0 : - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=None, error_message="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") if array != OBITuple_NA: free(array) diff --git a/python/obitools3/dms/column/typed_column/qual.pyx b/python/obitools3/dms/column/typed_column/qual.pyx index 4af9e34..7670f3a 100755 --- a/python/obitools3/dms/column/typed_column/qual.pyx +++ b/python/obitools3/dms/column/typed_column/qual.pyx @@ -57,7 +57,7 @@ cdef class Column_qual(Column_idx): cdef int value_length 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) - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=None, error_message="Problem getting a value from a column") + 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 : @@ -73,7 +73,7 @@ cdef class Column_qual(Column_idx): 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, offset) - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=None, error_message="Problem getting a value from a column") + 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 : @@ -88,14 +88,14 @@ cdef class Column_qual(Column_idx): 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: - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=None, error_message="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 = malloc(value_length * sizeof(uint8_t)) for i in range(value_length) : value_b[i] = 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: - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=None, error_message="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) @@ -104,11 +104,11 @@ cdef class Column_qual(Column_idx): 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, offset) < 0: - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=None, error_message="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, offset) < 0: - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=None, error_message="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_idx): @@ -124,7 +124,7 @@ cdef class Column_multi_elts_qual(Column_multi_elts_idx): 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) - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=elt_id, error_message="Problem getting a value from a column") + 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 : @@ -143,7 +143,7 @@ cdef class Column_multi_elts_qual(Column_multi_elts_idx): 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, offset) - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=elt_id, error_message="Problem getting a value from a column") + 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 : @@ -171,7 +171,7 @@ cdef class Column_multi_elts_qual(Column_multi_elts_idx): elements_names = self._elements_names 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) - 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(line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column") if value != OBIQual_int_NA : value_in_result = [] for j in range(value_length) : @@ -201,7 +201,7 @@ cdef class Column_multi_elts_qual(Column_multi_elts_idx): elements_names = self._elements_names 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) - 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(line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column") if value != OBIQual_char_NA : value_in_result = value free(value) @@ -230,11 +230,11 @@ cdef class Column_multi_elts_qual(Column_multi_elts_idx): 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 : - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=elt_id, error_message="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: - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=elt_id, error_message="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) @@ -252,11 +252,11 @@ cdef class Column_multi_elts_qual(Column_multi_elts_idx): 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, offset) < 0 : - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=elt_id, error_message="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, offset) < 0: - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=elt_id, error_message="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(): diff --git a/python/obitools3/dms/column/typed_column/seq.pyx b/python/obitools3/dms/column/typed_column/seq.pyx index 79f2359..e77e076 100755 --- a/python/obitools3/dms/column/typed_column/seq.pyx +++ b/python/obitools3/dms/column/typed_column/seq.pyx @@ -54,7 +54,7 @@ cdef class Column_seq(Column_idx): cdef char* value cdef object result value = obi_get_seq_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0) - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=None, error_message="Problem getting a value from a column") + 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 @@ -77,7 +77,7 @@ cdef class Column_seq(Column_idx): value_b = 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: - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=None, error_message="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_idx): @@ -91,7 +91,7 @@ cdef class Column_multi_elts_seq(Column_multi_elts_idx): 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) - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=elt_id, error_message="Problem getting a value from a column") + 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 : @@ -119,7 +119,7 @@ cdef class Column_multi_elts_seq(Column_multi_elts_idx): elements_names = self._elements_names 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) - 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(line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column") if value != OBISeq_NA : try: value_in_result = value @@ -147,12 +147,12 @@ cdef class Column_multi_elts_seq(Column_multi_elts_idx): 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: - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=elt_id, error_message="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: - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=elt_id, error_message="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") cdef class Column_tuples_seq(Column_idx): @@ -169,7 +169,7 @@ cdef class Column_tuples_seq(Column_idx): result = [] array = obi_get_array_with_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, &value_length) - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=None, error_message="Problem getting a value from a column") + obi_errno_to_exception(line_nb=line_nb, elt_id=None, error_message="Problem getting a value from a column") if array == OBITuple_NA : return None @@ -217,7 +217,7 @@ cdef class Column_tuples_seq(Column_idx): i = i + len(elt_b) + 1 if obi_set_array_with_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, array, sizeof(char)*8, value_length) < 0 : - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=None, error_message="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") if array != OBITuple_NA: free(array) diff --git a/python/obitools3/dms/column/typed_column/str.pyx b/python/obitools3/dms/column/typed_column/str.pyx index 9c12fa8..412d86b 100755 --- a/python/obitools3/dms/column/typed_column/str.pyx +++ b/python/obitools3/dms/column/typed_column/str.pyx @@ -53,7 +53,7 @@ cdef class Column_str(Column_idx): cdef const_char_p value cdef object result value = obi_get_str_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0) - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=None, error_message="Problem getting a value from a column") + 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 # For columns containing character strings that should be evaluated: @@ -76,7 +76,7 @@ cdef class Column_str(Column_idx): value_b = 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: - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=None, error_message="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_idx): @@ -90,7 +90,7 @@ cdef class Column_multi_elts_str(Column_multi_elts_idx): 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) - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=elt_id, error_message="Problem getting a value from a column") + 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 : @@ -115,7 +115,7 @@ cdef class Column_multi_elts_str(Column_multi_elts_idx): elements_names = self._elements_names 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) - 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(line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column") if value != OBIStr_NA : value_in_result = value result[elements_names[i]] = value_in_result @@ -140,11 +140,11 @@ cdef class Column_multi_elts_str(Column_multi_elts_idx): 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: - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=elt_id, error_message="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, value_b) < 0: - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=elt_id, error_message="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") cdef class Column_tuples_str(Column_idx): @@ -161,7 +161,7 @@ cdef class Column_tuples_str(Column_idx): result = [] array = obi_get_array_with_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, &value_length) - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=None, error_message="Problem getting a value from a column") + obi_errno_to_exception(line_nb=line_nb, elt_id=None, error_message="Problem getting a value from a column") if array == OBITuple_NA : return None @@ -209,7 +209,7 @@ cdef class Column_tuples_str(Column_idx): i = i + len(elt_b) + 1 if obi_set_array_with_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, array, sizeof(char)*8, value_length) < 0 : - obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=None, error_message="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") if array != OBITuple_NA: free(array) diff --git a/python/obitools3/utils.pxd b/python/obitools3/utils.pxd index cc4e38b..53d3765 100755 --- a/python/obitools3/utils.pxd +++ b/python/obitools3/utils.pxd @@ -5,7 +5,7 @@ from obitools3.dms.capi.obitypes cimport obitype_t, index_t cpdef bytes format_separator(bytes format) cpdef int count_entries(file, bytes format) -cdef obi_errno_to_exception(int obi_errno, index_t line_nb=*, object elt_id=*, str error_message=*) +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) diff --git a/python/obitools3/utils.pyx b/python/obitools3/utils.pyx index 1699419..d3a1526 100755 --- a/python/obitools3/utils.pyx +++ b/python/obitools3/utils.pyx @@ -12,8 +12,8 @@ from obitools3.dms.capi.obitypes cimport is_a_DNA_seq, \ index_t from obitools3.dms.capi.obierrno cimport OBI_LINE_IDX_ERROR, \ - OBI_ELT_IDX_ERROR - #obi_errno # TODO + OBI_ELT_IDX_ERROR, \ + obi_errno import re import mmap @@ -83,7 +83,7 @@ cpdef int count_entries(file, bytes format): # TODO RollbackException? -cdef obi_errno_to_exception(int obi_errno, index_t line_nb=-1, object elt_id=None, str error_message=None) : +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 :