Cython API: added a Column subclass to allow direct access to indexes
for columns that store indexes referring to other data
This commit is contained in:
Celine Mercier
21
python/obitools3/dms/column/column_idx.pxd
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21
python/obitools3/dms/column/column_idx.pxd
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# #cython: language_level=3
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from ..capi.obitypes cimport index_t
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from .column cimport Column, \
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Column_multi_elts
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cdef class Column_idx(Column) :
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cpdef object get_line_idx(self, index_t line_nb)
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cpdef set_line_idx(self, index_t line_nb, object value)
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cdef class Column_multi_elts_idx(Column_multi_elts) :
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cpdef object get_item_idx(self, index_t line_nb, object elt_id)
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cpdef object get_line_idx(self, index_t line_nb)
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cpdef set_item_idx(self, index_t line_nb, object elt_id, object value)
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cpdef set_line_idx(self, index_t line_nb, object values)
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114
python/obitools3/dms/column/column_idx.pyx
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114
python/obitools3/dms/column/column_idx.pyx
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#cython: language_level=3
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from obitools3.dms.capi.obierrno cimport obi_errno
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from ..view.view cimport View
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from obitools3.utils cimport tobytes, \
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obi_errno_to_exception
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from ..capi.obiview cimport obi_get_index_with_elt_name_and_col_p_in_view, \
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obi_get_index_with_elt_idx_and_col_p_in_view, \
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obi_set_index_with_elt_name_and_col_p_in_view, \
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obi_set_index_with_elt_idx_and_col_p_in_view, \
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Obiview_p
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from ..capi.obidmscolumn cimport OBIDMS_column_p
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from ..capi.obitypes cimport OBI_IDX, OBIIdx_NA, index_t
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from cpython.long cimport PyLong_FromLongLong
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# TODO overwrite other functions from Column and Column_multi_elts
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cdef class Column_idx(Column):
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cpdef object get_line_idx(self, index_t line_nb):
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global obi_errno
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cdef index_t value
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cdef object result
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value = obi_get_index_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0)
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obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=None, error_message="Problem getting a value from a column")
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if value == OBIIdx_NA :
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result = None
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else :
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result = PyLong_FromLongLong(value)
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return result
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cpdef set_line_idx(self, index_t line_nb, object value):
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global obi_errno
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if value is None :
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value = OBIIdx_NA
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if obi_set_index_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0, <index_t> value) < 0:
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obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=None, error_message="Problem setting a value in a column")
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cdef class Column_multi_elts_idx(Column_multi_elts):
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cpdef object get_item_idx(self, index_t line_nb, object elt_id) :
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global obi_errno
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cdef int value
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cdef object result
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cdef bytes elt_name
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if type(elt_id) == int :
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value = obi_get_index_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id)
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else :
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elt_name = tobytes(elt_id)
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value = obi_get_index_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name)
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obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=elt_id, error_message="Problem getting a value from a column")
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if value == OBIIdx_NA :
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result = None
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else :
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result = PyLong_FromLongLong(value)
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return result
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cpdef object get_line_idx(self, index_t line_nb) :
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global obi_errno
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cdef index_t value
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cdef int value_in_result
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cdef dict result
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cdef index_t i
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cdef bint all_NA
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cdef list elements_names
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cdef Obiview_p view_p
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cdef OBIDMS_column_p column_p
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result = {}
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all_NA = True
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view_p = self._view.pointer()
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column_p = self.pointer()
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elements_names = self.elements_names
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for i in range(self.nb_elements_per_line) :
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value = obi_get_index_with_elt_idx_and_col_p_in_view(view_p, column_p, line_nb, i)
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obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column")
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if value != OBIIdx_NA :
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value_in_result = PyLong_FromLongLong(value)
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result[elements_names[i]] = value_in_result
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if all_NA :
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all_NA = False
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if all_NA :
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result = None
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return result
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cpdef set_item_idx(self, index_t line_nb, object elt_id, object value) :
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global obi_errno
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cdef bytes elt_name
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if value is None :
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value = OBIIdx_NA
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if type(elt_id) == int :
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if obi_set_index_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id, <index_t> value) < 0 :
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obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=elt_id, error_message="Problem setting a value in a column")
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else :
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elt_name = tobytes(elt_id)
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if obi_set_index_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name, <index_t> value) < 0 :
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obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=elt_id, error_message="Problem setting a value in a column")
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cpdef set_line_idx(self, index_t line_nb, object values):
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if values is None :
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for element_name in self.elements_names :
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self.set_item_idx(line_nb, element_name, None)
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else :
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for element_name in values :
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self.set_item_idx(line_nb, element_name, values[element_name])
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@ -3,17 +3,17 @@
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from ...capi.obitypes cimport index_t
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from ..column cimport Column, \
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Column_multi_elts
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from ..column_idx cimport Column_idx, \
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Column_multi_elts_idx
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cdef class Column_seq(Column) :
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cdef class Column_seq(Column_idx) :
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cpdef object get_line(self, index_t line_nb)
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cpdef set_line(self, index_t line_nb, object value)
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cdef class Column_multi_elts_seq(Column_multi_elts) :
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cdef class Column_multi_elts_seq(Column_multi_elts_idx) :
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cpdef object get_item(self, index_t line_nb, object elt_id)
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cpdef object get_line(self, index_t line_nb)
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@ -6,6 +6,8 @@ from ..column cimport register_column_class
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from ...view.view cimport View
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from ..column cimport Column
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from obitools3.utils cimport tobytes, \
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obi_errno_to_exception
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@ -22,7 +24,7 @@ from ...capi.obitypes cimport OBI_SEQ, OBISeq_NA
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from libc.stdlib cimport free
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cdef class Column_seq(Column):
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cdef class Column_seq(Column_idx):
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@staticmethod
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def new(View view,
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@ -68,7 +70,7 @@ cdef class Column_seq(Column):
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obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=None, error_message="Problem setting a value in a column")
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cdef class Column_multi_elts_seq(Column_multi_elts):
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cdef class Column_multi_elts_seq(Column_multi_elts_idx):
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cpdef object get_item(self, index_t line_nb, object elt_id) :
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global obi_errno
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@ -3,17 +3,17 @@
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from ...capi.obitypes cimport index_t
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from ..column cimport Column, \
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Column_multi_elts
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from ..column_idx cimport Column_idx, \
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Column_multi_elts_idx
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cdef class Column_str(Column) :
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cdef class Column_str(Column_idx) :
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cpdef object get_line(self, index_t line_nb)
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cpdef set_line(self, index_t line_nb, object value)
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cdef class Column_multi_elts_str(Column_multi_elts) :
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cdef class Column_multi_elts_str(Column_multi_elts_idx) :
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cpdef object get_item(self, index_t line_nb, object elt_id)
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cpdef object get_line(self, index_t line_nb)
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@ -6,6 +6,8 @@ from ..column cimport register_column_class
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from ...view.view cimport View
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from ..column cimport Column
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from obitools3.utils cimport tobytes, \
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obi_errno_to_exception
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@ -20,7 +22,7 @@ from ...capi.obidmscolumn cimport OBIDMS_column_p
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from ...capi.obitypes cimport OBI_STR, OBIStr_NA, const_char_p
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cdef class Column_str(Column):
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cdef class Column_str(Column_idx):
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@staticmethod
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def new(View view,
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@ -63,7 +65,7 @@ cdef class Column_str(Column):
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obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=None, error_message="Problem setting a value in a column")
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cdef class Column_multi_elts_str(Column_multi_elts):
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cdef class Column_multi_elts_str(Column_multi_elts_idx):
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cpdef object get_item(self, index_t line_nb, object elt_id) :
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global obi_errno
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