Cython typed columns

python/obitools3/dms/column/bool.pxd

@@ -1,53 +0,0 @@
-# #cython: language_level=3
-# 
-# from cpython.bool cimport bool, PyBool_FromLong
-# 
-# from ..capi.obitypes cimport index_t, \
-#                              const_char_p, \
-#                              OBIType_t, \
-#                              obibool_t, \
-#                              OBI_BOOL, \
-#                              OBIBool_NA
-#                              
-# from ..capi.obiview      cimport obi_get_bool_with_elt_name_and_col_p_in_view, \
-#                                  obi_get_bool_with_elt_idx_and_col_p_in_view, \
-#                                  obi_set_bool_with_elt_name_and_col_p_in_view, \
-#                                  obi_set_bool_with_elt_idx_and_col_p_in_view
-# 
-# from ..capi.obidmscolumn  cimport  obi_column_get_obibool_with_elt_name, \
-#                                    obi_column_get_obibool_with_elt_idx, \
-#                                    obi_column_set_obibool_with_elt_name, \
-#                                    obi_column_set_obibool_with_elt_idx, \
-#                                    OBIDMS_column_p 
-#                             
-# from ..capi.obierrno  cimport obi_errno
-# 
-# from .column  cimport Column, \
-#                       Column_line, \
-#                       register_column_class
-# 
-# from ..view.view cimport View
-# 
-# from obitools3.utils cimport str2bytes, bytes2str
-# 
-# cdef class Column_line_bool(Column_line) :
-#         
-#     @staticmethod
-#     cdef bool obibool_t2bool(obibool_t value)
-#     
-#     @staticmethod
-#     cdef bool2obibool_t(bool value)
-#     
-#     cpdef bool get_bool_item_by_name(self,bytes element_name)
-#     cpdef bool get_bool_item_by_idx(self,index_t index)
-#     cpdef set_bool_item_by_name(self,bytes element_name,bool value)
-#     cpdef set_bool_item_by_idx(self,index_t index,bool value)
-# 
-#       
-# #    cdef obibool_t [:]    _data_view
-# 
-# cdef class Column_bool(Column):
-# 
-#     cpdef object get_line(self, index_t line_nb)
-#     cpdef set_line(self, index_t line_nb, object value)
-

python/obitools3/dms/column/typed_column/__init__.py

@@ -0,0 +1,3 @@
+#from .bool import Column_bool
+#from .int import Column_int
+# TODO why is this needed?

python/obitools3/dms/column/typed_column/bool.pxd

@@ -0,0 +1,44 @@
+# #cython: language_level=3
+
+
+from ...capi.obitypes cimport index_t
+
+from ..column cimport Column, \
+                      Column_multi_elts
+
+
+cdef class Column_bool(Column) :
+
+    cpdef object get_line(self, index_t line_nb)
+    cpdef set_line(self, index_t line_nb, object value)
+
+
+cdef class Column_multi_elts_bool(Column_multi_elts) :
+
+    cpdef object get_item(self, index_t line_nb, object elt_id)
+    cpdef object get_line(self, index_t line_nb)
+    cpdef set_item(self, index_t line_nb, object elt_id, object value)
+    
+    
+    
+    
+    
+    
+    
+    
+# cdef class Column_line_bool(Column_line) :
+#         
+#     @staticmethod
+#     cdef bool obibool_t2bool(obibool_t value)
+#     
+#     @staticmethod
+#     cdef bool2obibool_t(bool value)
+#     
+#     cpdef bool get_bool_item_by_name(self,bytes element_name)
+#     cpdef bool get_bool_item_by_idx(self,index_t index)
+#     cpdef set_bool_item_by_name(self,bytes element_name,bool value)
+#     cpdef set_bool_item_by_idx(self,index_t index,bool value)
+# 
+#       
+# #    cdef obibool_t [:]    _data_view
+#

python/obitools3/dms/column/typed_column/bool.pyx

@@ -1,21 +1,142 @@
 #cython: language_level=3
+
+
+from ..column cimport register_column_class
+
+from ...view.view cimport View
+
+from obitools3.utils cimport str2bytes, bytes2str, tobytes
+
+from ...capi.obiview cimport obi_view_add_column, \
+                             obi_get_bool_with_elt_name_and_col_p_in_view, \
+                             obi_get_bool_with_elt_idx_and_col_p_in_view, \
+                             obi_set_bool_with_elt_name_and_col_p_in_view, \
+                             obi_set_bool_with_elt_idx_and_col_p_in_view
+
+from ...capi.obierrno     cimport obi_errno
+from ...capi.obitypes     cimport OBI_BOOL, OBIBool_NA, obibool_t, obitype_t
+
+from cpython.bool cimport PyBool_FromLong
+
+
+cdef class Column_bool(Column):
+
+    @staticmethod
+    def new(View    view,
+            object  column_name,
+            index_t nb_elements_per_line=1,
+            object  elements_names=None,
+            object  comments=b""):
+        
+        return Column.new_column(view, column_name, OBI_BOOL,
+                          nb_elements_per_line=nb_elements_per_line, 
+                          elements_names=elements_names, 
+                          comments=comments)
+                
+
+    cpdef object get_line(self, index_t line_nb):
+        cdef obibool_t value
+        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)
+        if obi_errno > 0 :
+            raise IndexError(line_nb)
+        if value == OBIBool_NA :
+            result = None
+        else :
+            result = PyBool_FromLong(value)
+        return result
+    
+    
+    cpdef set_line(self, index_t line_nb, object value):
+        if value is None :
+            value = OBIBool_NA
+        if obi_set_bool_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0, <obibool_t> value) < 0 :
+            raise Exception("Problem setting a value in a column")
+ 
+ 
+cdef class Column_multi_elts_bool(Column_multi_elts):
+ 
+    cpdef object get_item(self, index_t line_nb, object elt_id) :
+        cdef obibool_t value
+        cdef object    result
+        cdef bytes     elt_name
+        if type(elt_id) == int :
+            value = obi_get_bool_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id)
+        else :
+            elt_name = tobytes(elt_id)
+            value = obi_get_bool_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name)
+        if obi_errno > 0 :
+            raise IndexError(line_nb, elt_id)
+        if value == OBIBool_NA :
+            result = None
+        else :
+            result = PyBool_FromLong(value)
+        return result
+    
+    cpdef object get_line(self, index_t line_nb) :
+        cdef obibool_t value
+        cdef object value_in_result
+        cdef dict result
+        cdef index_t i
+        cdef bint all_NA
+        result = {}
+        all_NA = True
+        for i in range(self.nb_elements_per_line) :
+            value = obi_get_bool_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, i)
+            if obi_errno > 0 :
+                raise IndexError(line_nb)
+            if value == OBIBool_NA :
+                value_in_result = None
+            else :
+                value_in_result = PyBool_FromLong(value)   
+            result[self.elements_names[i]] = value_in_result
+            if all_NA and (value_in_result is not None) :
+                all_NA = False
+        if all_NA :
+            result = None
+        return result
+    
+    cpdef set_item(self, index_t line_nb, object elt_id, object value) :
+        cdef bytes elt_name
+        if value is None :
+            value = OBIBool_NA
+        if type(elt_id) == int :
+            if obi_set_bool_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id, <obibool_t> value) < 0 :
+                raise Exception("Problem setting a value in a column")
+        else :
+            elt_name = tobytes(elt_id)
+            if obi_set_bool_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name, <obibool_t> value) < 0 :
+                raise Exception("Problem setting a value in a column")
+
+
+def register_class() :
+    register_column_class(OBI_BOOL, False, Column_bool, bool)
+    register_column_class(OBI_BOOL, True, Column_multi_elts_bool, bool)
+
+
+
+
+
+
+
 
 # cdef class Column_line_bool(Column_line) :
 # 
-# #     cdef update_pointer(self):
+#     cdef update_pointer(self):
-# #         """
+#         """
-# #         Checks if the obicolumn address changed since the last call and update
+#         Checks if the obicolumn address changed since the last call and update
-# #         if need the `_column_p` and `_data_view` data structure fields.
+#         if need the `_column_p` and `_data_view` data structure fields.
-# #         """
+#         """
-# #         cdef OBIDMS_column_p* column_pp
+#         cdef OBIDMS_column_p* column_pp
-# #         column_pp = <OBIDMS_column_p*>self._pointer
+#         column_pp = <OBIDMS_column_p*>self._pointer
-# #         cdef OBIDMS_column_p column_p = column_pp[0]
+#         cdef OBIDMS_column_p column_p = column_pp[0]
-# #         
+#         
-# #         if column_p != self._column_p:
+#         if column_p != self._column_p:
-# #             self._column_p  = column_p
+#             self._column_p  = column_p
-# # #             self._data_view = (<obibool_t*> (column_p.data)) + \
+#             self._data_view = (<obibool_t*> (column_p.data)) + \
-# # #                               self._index * column_p.header.nb_elements_per_line
+#                               self._index * column_p.header.nb_elements_per_line
 #     
 #     @staticmethod                      
 #     cdef bool obibool_t2bool(obibool_t value):
@@ -197,109 +318,3 @@
 #     
 #     def __len__(self):
 #         return self._len
-
-
-
-# cdef class Column_bool(Column):
-# 
-#     @staticmethod
-#     def new(View view,
-#             object  column_name,
-#             index_t nb_elements_per_line=1,
-#             object  elements_names=None,
-#             object  comments=b""):
-#                             
-#         cdef bytes column_name_b = tobytes(column_name)
-#         cdef bytes comments_b
-#         cdef bytes elements_names_b
-#         cdef char* elements_names_p
-#         cdef Column new_column
-#         
-#         if comments is not None:
-#             comments_b  = tobytes(comments)
-#         else:
-#             comments_b  = b''
-# 
-#         if elements_names is not None:
-#             elements_names_b = b''.join([tobytes(x) for x in elements_names])
-#             elements_names_p = elements_names_b
-#         else:
-#             elements_names_p = NULL
-#                             
-#         if (obi_view_add_column(view                      = view._pointer,
-#                                 column_name               = column_name_b,
-#                                 version_number            = -1,
-#                                 alias                     = NULL,
-#                                 data_type                 = OBI_BOOL,
-#                                 nb_lines                  = len(view),
-#                                 nb_elements_per_line      = nb_elements_per_line,
-#                                 elements_names            = elements_names_p,
-#                                 indexer_name              = NULL,
-#                                 associated_column_name    = NULL,
-#                                 associated_column_version = -1,
-#                                 comments                  = comments_b,
-#                                 create                    = True)<0):
-#             raise RuntimeError("Cannot create column %s in view %s" % (bytes2str(column_name),
-#                                                                        bytes2str(view.name)))
-#         
-#         view.__init_columns__()
-#         new_column = self._columns[column_name]
-#         
-#         return new_column
-#                 
-#     def add_to_view(self,
-#                     View view,
-#                     object column_name=None,
-#                     object comments=b""):
-#                       
-#         cdef OBIDMS_column_p column_p = (<OBIDMS_column_p*>self._pointer)[0]
-#         cdef bytes alias
-#         
-#         if (column_name is None):
-#             alias = self._alias
-#         else:
-#             alias = tobytes(column_name)
-#                       
-#         if (obi_view_add_column(view                      = view._ponter,
-#                                 column_name               = column_p.header.name,
-#                                 version_number            = column_p.header.version,
-#                                 alias                     = alias,
-#                                 data_type                 = OBI_BOOL,
-#                                 nb_lines                  = column_p.header.lines_used,
-#                                 nb_elements_per_line      = column_p.header.nb_elements_per_line,
-#                                 elements_names            = column_p.header.elements_names,
-#                                 indexer_name              = NULL,
-#                                 associated_column_name    = NULL,
-#                                 associated_column_version = NULL,
-#                                 comments                  = tobytes(comments),
-#                                 create                    = False) < 0):
-#             raise RuntimeError("Cannot insert column %s (%s@%d) into view %s" %
-#                                ( bytes2str(alias),
-#                                  bytes2str(column_p.header.name),
-#                                  column_p.header.version,
-#                                  bytes2str(view.name)
-#                                ))
-# 
-#     cpdef object get_line(self, index_t line_nb):
-#         cdef obibool_t value
-#         cdef object result
-#         global obi_errno
-# 
-#         value = obi_get_bool_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0)
-#         if obi_errno > 0 :
-#             raise IndexError(line_nb)
-#         if value == OBIBool_NA :
-#             result = None
-#         else :
-#             result = PyBool_FromLong(value)
-#         return result
-#     
-#     cpdef set_line(self, index_t line_nb, object value):
-#         if value is None :
-#             value = OBIBool_NA
-#         if obi_set_bool_with_elt_idx_and_col_p_in_view(<Obiview_p>self._view._pointer, (self._pointer)[0], line_nb, 0, <obibool_t> value) < 0:
-#             raise Exception("Problem setting a value in a column")
-# 
-# 
-# register_column_class(OBI_BOOL, Column_bool, bool)
-

python/obitools3/dms/column/typed_column/char.pxd

@@ -0,0 +1,20 @@
+# #cython: language_level=3
+ 
+
+from ...capi.obitypes cimport index_t
+
+from ..column cimport Column, \
+                      Column_multi_elts
+
+
+cdef class Column_char(Column) :
+
+    cpdef object get_line(self, index_t line_nb)
+    cpdef set_line(self, index_t line_nb, object value)
+
+
+cdef class Column_multi_elts_char(Column_multi_elts) :
+
+    cpdef object get_item(self, index_t line_nb, object elt_id)
+    cpdef object get_line(self, index_t line_nb)
+    cpdef set_item(self, index_t line_nb, object elt_id, object value)

python/obitools3/dms/column/typed_column/char.pyx

@@ -0,0 +1,115 @@
+#cython: language_level=3
+
+
+from ..column cimport register_column_class
+
+from ...view.view cimport View
+
+from obitools3.utils cimport str2bytes, bytes2str, tobytes
+
+from ...capi.obiview cimport obi_get_char_with_elt_name_and_col_p_in_view, \
+                             obi_get_char_with_elt_idx_and_col_p_in_view, \
+                             obi_set_char_with_elt_name_and_col_p_in_view, \
+                             obi_set_char_with_elt_idx_and_col_p_in_view
+
+from ...capi.obierrno     cimport obi_errno
+from ...capi.obitypes     cimport OBI_CHAR, OBIChar_NA, obichar_t, obitype_t
+
+
+
+cdef class Column_char(Column):
+
+    @staticmethod
+    def new(View    view,
+            object  column_name,
+            index_t nb_elements_per_line=1,
+            object  elements_names=None,
+            object  comments=b""):
+        
+        return Column.new_column(view, column_name, OBI_CHAR,
+                                 nb_elements_per_line=nb_elements_per_line, 
+                                 elements_names=elements_names, 
+                                 comments=comments)
+
+
+    cpdef object get_line(self, index_t line_nb):
+        cdef obichar_t value
+        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)
+        if obi_errno > 0 :
+            raise IndexError(line_nb)
+        if value == OBIChar_NA :
+            result = None
+        else :
+            result = value  # TODO return bytes or str?
+        return result
+    
+    
+    cpdef set_line(self, index_t line_nb, object value):
+        if value is None :
+            value = OBIChar_NA
+        if obi_set_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0, <obichar_t> tobytes(value)[0]) < 0:
+            raise Exception("Problem setting a value in a column")
+ 
+ 
+cdef class Column_multi_elts_char(Column_multi_elts):
+ 
+    cpdef object get_item(self, index_t line_nb, object elt_id) :
+        cdef obichar_t value
+        cdef object    result
+        cdef bytes     elt_name
+        if type(elt_id) == int :
+            value = obi_get_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id)
+        else :
+            elt_name = tobytes(elt_id)
+            value = obi_get_char_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name)
+        if obi_errno > 0 :
+            raise IndexError(line_nb, elt_id)
+        if value == OBIChar_NA :
+            result = None
+        else :
+            result = value  # TODO return bytes or str?
+        return result
+    
+    cpdef object get_line(self, index_t line_nb) :
+        cdef obichar_t value
+        cdef object    value_in_result
+        cdef dict      result
+        cdef index_t   i
+        cdef bint      all_NA
+        result = {}
+        all_NA = True
+        for i in range(self.nb_elements_per_line) :
+            value = obi_get_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, i)
+            if obi_errno > 0 :
+                raise IndexError(line_nb)
+            if value == OBIChar_NA :
+                value_in_result = None
+            else :
+                value_in_result = value     # TODO return bytes or str?
+            result[self.elements_names[i]] = value_in_result
+            if all_NA and (value_in_result is not None) :
+                all_NA = False
+        if all_NA :
+            result = None
+        return result
+    
+    cpdef set_item(self, index_t line_nb, object elt_id, object value) :
+        cdef bytes elt_name
+        if value is None :
+            value = OBIChar_NA
+        if type(elt_id) == int :
+            if obi_set_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id, <obichar_t> tobytes(value)[0]) < 0 :
+                raise Exception("Problem setting a value in a column")
+        else :
+            elt_name = tobytes(elt_id)
+            if obi_set_char_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name, <obichar_t> tobytes(value)[0]) < 0 :
+                raise Exception("Problem setting a value in a column")
+
+
+def register_class():
+    register_column_class(OBI_CHAR, False, Column_char, bytes)  # TODO bytes or str?
+    register_column_class(OBI_CHAR, True, Column_multi_elts_char, bytes)  # TODO bytes or str?
+

python/obitools3/dms/column/typed_column/float.pxd

@@ -0,0 +1,21 @@
+# #cython: language_level=3
+ 
+
+from ...capi.obitypes cimport index_t
+
+from ..column cimport Column, \
+                      Column_multi_elts
+
+
+cdef class Column_float(Column) :
+
+    cpdef object get_line(self, index_t line_nb)
+    cpdef set_line(self, index_t line_nb, object value)
+
+
+cdef class Column_multi_elts_float(Column_multi_elts) :
+
+    cpdef object get_item(self, index_t line_nb, object elt_id)
+    cpdef object get_line(self, index_t line_nb)
+    cpdef set_item(self, index_t line_nb, object elt_id, object value)
+    

python/obitools3/dms/column/typed_column/float.pyx

@@ -0,0 +1,115 @@
+#cython: language_level=3
+
+
+from ..column cimport register_column_class
+
+from ...view.view cimport View
+
+from obitools3.utils cimport str2bytes, bytes2str, tobytes
+
+from ...capi.obiview cimport obi_get_float_with_elt_name_and_col_p_in_view, \
+                             obi_get_float_with_elt_idx_and_col_p_in_view, \
+                             obi_set_float_with_elt_name_and_col_p_in_view, \
+                             obi_set_float_with_elt_idx_and_col_p_in_view
+
+from ...capi.obierrno     cimport obi_errno
+from ...capi.obitypes     cimport OBI_FLOAT, OBIFloat_NA, obifloat_t, obitype_t
+
+
+
+cdef class Column_float(Column):
+
+    @staticmethod
+    def new(View    view,
+            object  column_name,
+            index_t nb_elements_per_line=1,
+            object  elements_names=None,
+            object  comments=b""):
+        
+        return Column.new_column(view, column_name, OBI_FLOAT,
+                                 nb_elements_per_line=nb_elements_per_line, 
+                                 elements_names=elements_names, 
+                                 comments=comments)
+
+
+    cpdef object get_line(self, index_t line_nb):
+        cdef obifloat_t value
+        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)
+        if obi_errno > 0 :
+            raise IndexError(line_nb)
+        if value == OBIFloat_NA :
+            result = None
+        else :
+            result = <double> value
+        return result
+    
+    
+    cpdef set_line(self, index_t line_nb, object value):
+        if value is None :
+            value = OBIFloat_NA
+        if obi_set_float_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0, <obifloat_t> value) < 0:
+            raise Exception("Problem setting a value in a column")
+ 
+ 
+cdef class Column_multi_elts_float(Column_multi_elts):
+ 
+    cpdef object get_item(self, index_t line_nb, object elt_id) :
+        cdef obifloat_t value
+        cdef object     result
+        cdef bytes      elt_name
+        if type(elt_id) == int :
+            value = obi_get_float_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id)
+        else :
+            elt_name = tobytes(elt_id)
+            value = obi_get_float_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name)
+        if obi_errno > 0 :
+            raise IndexError(line_nb, elt_id)
+        if value == OBIFloat_NA :
+            result = None
+        else :
+            result = <double> value
+        return result
+    
+    cpdef object get_line(self, index_t line_nb) :
+        cdef obifloat_t value
+        cdef object     value_in_result
+        cdef dict result
+        cdef index_t i
+        cdef bint all_NA
+        result = {}
+        all_NA = True
+        for i in range(self.nb_elements_per_line) :
+            value = obi_get_float_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, i)
+            if obi_errno > 0 :
+                raise IndexError(line_nb)
+            if value == OBIFloat_NA :
+                value_in_result = None
+            else :
+                value_in_result = <double> value   
+            result[self.elements_names[i]] = value_in_result
+            if all_NA and (value_in_result is not None) :
+                all_NA = False
+        if all_NA :
+            result = None
+        return result
+    
+    cpdef set_item(self, index_t line_nb, object elt_id, object value) :
+        cdef bytes elt_name
+        if value is None :
+            value = OBIFloat_NA
+        if type(elt_id) == int :
+            if obi_set_float_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id, <obifloat_t> value) < 0 :
+                raise Exception("Problem setting a value in a column")
+        else :
+            elt_name = tobytes(elt_id)
+            if obi_set_float_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name, <obifloat_t> value) < 0 :
+                raise Exception("Problem setting a value in a column")
+
+
+def register_class():
+    register_column_class(OBI_FLOAT, False, Column_float, float)    # TODO why not double?
+    register_column_class(OBI_FLOAT, True, Column_multi_elts_float, float)    # TODO why not double?
+

python/obitools3/dms/column/typed_column/int.pxd

@@ -0,0 +1,21 @@
+# #cython: language_level=3
+ 
+
+from ...capi.obitypes cimport index_t
+
+from ..column cimport Column, \
+                      Column_multi_elts
+
+
+cdef class Column_int(Column) :
+
+    cpdef object get_line(self, index_t line_nb)
+    cpdef set_line(self, index_t line_nb, object value)
+
+
+cdef class Column_multi_elts_int(Column_multi_elts) :
+
+    cpdef object get_item(self, index_t line_nb, object elt_id)
+    cpdef object get_line(self, index_t line_nb)
+    cpdef set_item(self, index_t line_nb, object elt_id, object value)
+    

python/obitools3/dms/column/typed_column/int.pyx

@@ -0,0 +1,116 @@
+#cython: language_level=3
+
+
+from ..column cimport register_column_class
+
+from ...view.view cimport View
+
+from obitools3.utils cimport str2bytes, bytes2str, tobytes
+
+from ...capi.obiview cimport obi_get_int_with_elt_name_and_col_p_in_view, \
+                             obi_get_int_with_elt_idx_and_col_p_in_view, \
+                             obi_set_int_with_elt_name_and_col_p_in_view, \
+                             obi_set_int_with_elt_idx_and_col_p_in_view
+
+from ...capi.obierrno     cimport obi_errno
+from ...capi.obitypes     cimport OBI_INT, OBIInt_NA, obiint_t, obitype_t
+
+from cpython.int cimport PyInt_FromLong
+
+
+cdef class Column_int(Column):
+
+    @staticmethod
+    def new(View    view,
+            object  column_name,
+            index_t nb_elements_per_line=1,
+            object  elements_names=None,
+            object  comments=b""):
+        
+        return Column.new_column(view, column_name, OBI_INT,
+                                 nb_elements_per_line=nb_elements_per_line, 
+                                 elements_names=elements_names, 
+                                 comments=comments)
+
+
+    cpdef object get_line(self, index_t line_nb):
+        cdef obiint_t value
+        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)
+        if obi_errno > 0 :
+            raise IndexError(line_nb)
+        if value == OBIInt_NA :
+            result = None
+        else :
+            result = PyInt_FromLong(value)
+        return result
+    
+    
+    cpdef set_line(self, index_t line_nb, object value):
+        if value is None :
+            value = OBIInt_NA
+        if obi_set_int_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0, <obiint_t> value) < 0:
+            raise Exception("Problem setting a value in a column")
+ 
+ 
+cdef class Column_multi_elts_int(Column_multi_elts):
+ 
+    cpdef object get_item(self, index_t line_nb, object elt_id) :
+        cdef obiint_t  value
+        cdef object    result
+        cdef bytes     elt_name
+        if type(elt_id) == int :
+            value = obi_get_int_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id)
+        else :
+            elt_name = tobytes(elt_id)
+            value = obi_get_int_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name)
+        if obi_errno > 0 :
+            raise IndexError(line_nb, elt_id)
+        if value == OBIInt_NA :
+            result = None
+        else :
+            result = PyInt_FromLong(value)
+        return result
+    
+    cpdef object get_line(self, index_t line_nb) :
+        cdef obiint_t value
+        cdef object   value_in_result
+        cdef dict result
+        cdef index_t i
+        cdef bint all_NA
+        result = {}
+        all_NA = True
+        for i in range(self.nb_elements_per_line) :
+            value = obi_get_int_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, i)
+            if obi_errno > 0 :
+                raise IndexError(line_nb)
+            if value == OBIInt_NA :
+                value_in_result = None
+            else :
+                value_in_result = PyInt_FromLong(value)   
+            result[self.elements_names[i]] = value_in_result
+            if all_NA and (value_in_result is not None) :
+                all_NA = False
+        if all_NA :
+            result = None
+        return result
+    
+    cpdef set_item(self, index_t line_nb, object elt_id, object value) :
+        cdef bytes elt_name
+        if value is None :
+            value = OBIInt_NA
+        if type(elt_id) == int :
+            if obi_set_int_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id, <obiint_t> value) < 0 :
+                raise Exception("Problem setting a value in a column")
+        else :
+            elt_name = tobytes(elt_id)
+            if obi_set_int_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name, <obiint_t> value) < 0 :
+                raise Exception("Problem setting a value in a column")
+
+
+def register_class():
+    register_column_class(OBI_INT, False, Column_int, int)
+    register_column_class(OBI_INT, True, Column_multi_elts_int, int)
+

python/obitools3/dms/column/typed_column/qual.pxd

@@ -0,0 +1,26 @@
+# #cython: language_level=3
+ 
+
+from ...capi.obitypes cimport index_t
+
+from ..column cimport Column, \
+                      Column_multi_elts
+
+
+cdef class Column_qual(Column) :
+
+    cpdef object get_line(self, index_t line_nb)
+    cpdef object get_str_line(self, index_t line_nb)
+    cpdef set_line(self, index_t line_nb, object value)
+    cpdef set_str_line(self, index_t line_nb, object value)
+
+
+cdef class Column_multi_elts_qual(Column_multi_elts) :
+
+    cpdef object get_item(self, index_t line_nb, object elt_id)
+    cpdef object get_str_item(self, index_t line_nb, object elt_id)
+    cpdef object get_line(self, index_t line_nb)
+    cpdef object get_str_line(self, index_t line_nb)
+    cpdef set_item(self, index_t line_nb, object elt_id, object value)
+    cpdef set_str_item(self, index_t line_nb, object elt_id, object value)
+    

python/obitools3/dms/column/typed_column/qual.pyx

@@ -0,0 +1,258 @@
+#cython: language_level=3
+
+
+from ..column cimport register_column_class
+
+from ...view.view cimport View
+
+from obitools3.utils cimport str2bytes, bytes2str, tobytes
+
+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_set_qual_char_with_elt_name_and_col_p_in_view, \
+                             obi_set_qual_char_with_elt_idx_and_col_p_in_view, \
+                             obi_get_qual_int_with_elt_name_and_col_p_in_view, \
+                             obi_get_qual_int_with_elt_idx_and_col_p_in_view, \
+                             obi_set_qual_int_with_elt_name_and_col_p_in_view, \
+                             obi_set_qual_int_with_elt_idx_and_col_p_in_view
+
+from ...capi.obierrno     cimport obi_errno
+from ...capi.obitypes     cimport OBI_QUAL, OBIQual_char_NA, OBIQual_int_NA, const_char_p
+
+from libc.stdlib cimport free
+from libc.string cimport strcmp
+from libc.stdint cimport uint8_t
+from libc.stdlib cimport malloc
+
+
+cdef class Column_qual(Column):
+
+    @staticmethod
+    def new(View    view,
+            object  column_name,
+            index_t nb_elements_per_line=1,
+            object  elements_names=None,
+            object  comments=b""):
+        
+        return Column.new_column(view, column_name, OBI_QUAL,
+                                 nb_elements_per_line=nb_elements_per_line, 
+                                 elements_names=elements_names, 
+                                 comments=comments)
+
+
+    cpdef object get_line(self, index_t line_nb):
+        cdef const uint8_t* value
+        cdef int            value_length
+        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)
+        if obi_errno > 0 :
+            raise IndexError(line_nb)
+        if value == OBIQual_int_NA :
+            result = None
+        else :
+            result = []
+            for i in range(value_length) :
+                result.append(<int>value[i])            
+        return result
+
+    
+    cpdef object get_str_line(self, index_t line_nb):
+        cdef char*  value
+        cdef object result
+        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)
+        if obi_errno > 0 :
+            raise IndexError(line_nb)
+        if value == OBIQual_char_NA :
+            result = None
+        else :  # TODO discuss
+            result = bytes2str(value)
+            free(value)
+        return result
+    
+    
+    cpdef set_line(self, index_t line_nb, object value):
+        cdef uint8_t* value_b
+        cdef int      value_length
+        if value is None :
+            if obi_set_qual_int_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0, OBIQual_int_NA, 0) < 0:
+                raise Exception("Problem setting a value in a column")
+        else :
+            value_length = len(value)
+            value_b = <uint8_t*> malloc(value_length * sizeof(uint8_t))
+            for i in range(value_length) :
+                value_b[i] = <uint8_t>value[i]
+            if obi_set_qual_int_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0, value_b, value_length) < 0:
+                raise Exception("Problem setting a value in a column")
+            free(value_b)
+ 
+ 
+    cpdef set_str_line(self, index_t line_nb, object value):
+        cdef bytes value_b        
+        if value is None :
+            if obi_set_qual_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0, OBIQual_char_NA) < 0:
+                raise Exception("Problem setting a value in a column")
+        else :
+            if type(value) == str:
+                value_b = str2bytes(value)
+            else :
+                value_b = value
+            if obi_set_qual_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0, value_b) < 0:
+                raise Exception("Problem setting a value in a column")
+
+ 
+cdef class Column_multi_elts_qual(Column_multi_elts):
+ 
+    cpdef object get_item(self, index_t line_nb, object elt_id):
+        cdef const uint8_t*  value
+        cdef int             value_length
+        cdef object          result
+        cdef int             i
+        global               obi_errno  # TODO add everywhere
+
+        if type(elt_id) == int :
+            value = obi_get_qual_int_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id, &value_length)
+        else :
+            elt_name = tobytes(elt_id)
+            value = obi_get_qual_int_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name, &value_length)
+        if obi_errno > 0 :
+            raise IndexError(line_nb, elt_id)
+        if value == OBIQual_int_NA :
+            result = None
+        else :
+            result = []
+            for i in range(value_length) :
+                result.append(<int>value[i])            
+        return result
+
+    
+    cpdef object get_str_item(self, index_t line_nb, object elt_id):
+        cdef char*  value
+        cdef object result
+        global      obi_errno
+        
+        if type(elt_id) == int :
+            value = obi_get_qual_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id)
+        else :
+            elt_name = tobytes(elt_id)
+            value = obi_get_qual_char_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name)
+        if obi_errno > 0 :
+            raise IndexError(line_nb, elt_name)
+        if value == OBIQual_char_NA :
+            result = None
+        else :
+            result = bytes2str(value)   # TODO return bytes?
+            free(value)
+        return result
+
+    
+    cpdef object get_line(self, index_t line_nb) :
+        cdef const uint8_t*  value
+        cdef int             value_length
+        cdef object          value_in_result
+        cdef dict            result
+        cdef index_t         i
+        cdef int             j
+        cdef bint            all_NA
+        global               obi_errno
+        
+        result = {}
+        all_NA = True
+        for i in range(self.nb_elements_per_line) :
+            value = obi_get_qual_int_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, i, &value_length)
+            if obi_errno > 0 :
+                raise IndexError(line_nb)
+            if value == OBIQual_int_NA :
+                value_in_result = None
+            else :
+                value_in_result = []
+                for j in range(value_length) :
+                    value_in_result.append(<int>value[j])            
+            result[self.elements_names[i]] = value_in_result
+            if all_NA and (value_in_result is not None) :
+                all_NA = False
+        if all_NA :
+            result = None
+        return result
+
+
+    cpdef object get_str_line(self, index_t line_nb) :
+        cdef char*   value
+        cdef object  value_in_result
+        cdef dict    result
+        cdef index_t i
+        cdef bint    all_NA
+        global       obi_errno
+        
+        result = {}
+        all_NA = True
+        for i in range(self.nb_elements_per_line) :
+            value = obi_get_qual_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, i)
+            if obi_errno > 0 :
+                raise IndexError(line_nb)
+            if value == OBIQual_char_NA :
+                value_in_result = None
+            else :
+                value_in_result = bytes2str(value)
+                free(value)
+            result[self.elements_names[i]] = value_in_result
+            if all_NA and (value_in_result is not None) :
+                all_NA = False
+        if all_NA :
+            result = None
+        return result
+    
+    
+    cpdef set_item(self, index_t line_nb, object elt_id, object value):
+        cdef uint8_t* value_b
+        cdef int      value_length
+        cdef bytes    elt_name
+        
+        if value is None :
+            value_b = OBIQual_int_NA
+            value_length = 0
+        else :
+            value_length = len(value)
+            value_b = <uint8_t*> malloc(value_length * sizeof(uint8_t))
+            for i in range(value_length) :
+                value_b[i] = <uint8_t>value[i]           
+   
+        if type(elt_id) == int :
+            if obi_set_qual_int_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id, value_b, value_length) < 0 :
+                raise Exception("Problem setting a value in a column")
+        else :
+            elt_name = tobytes(elt_id)
+            if obi_set_qual_int_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name, value_b, value_length) < 0:
+                raise Exception("Problem setting a value in a column")
+        
+        if value is not None :
+            free(value_b)
+    
+
+    cpdef set_str_item(self, index_t line_nb, object elt_id, object value):
+        cdef bytes value_b
+        cdef bytes elt_name
+        
+        if value is None :
+            value_b = OBIQual_char_NA
+        else :
+            value_b = tobytes(value)
+   
+        if type(elt_id) == int :
+            if obi_set_qual_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id, value_b) < 0 :
+                raise Exception("Problem setting a value in a column")
+        else :
+            elt_name = tobytes(elt_id)
+            if obi_set_qual_char_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name, value_b) < 0:
+                raise Exception("Problem setting a value in a column")
+
+
+
+def register_class():
+    register_column_class(OBI_QUAL, False, Column_qual, bytes)    # TODO str? int?
+    register_column_class(OBI_QUAL, True, Column_multi_elts_qual, bytes)    # TODO str? int?
+

python/obitools3/dms/column/typed_column/seq.pxd

@@ -0,0 +1,21 @@
+# #cython: language_level=3
+ 
+
+from ...capi.obitypes cimport index_t
+
+from ..column cimport Column, \
+                      Column_multi_elts
+
+
+cdef class Column_seq(Column) :
+
+    cpdef object get_line(self, index_t line_nb)
+    cpdef set_line(self, index_t line_nb, object value)
+
+
+cdef class Column_multi_elts_seq(Column_multi_elts) :
+
+    cpdef object get_item(self, index_t line_nb, object elt_id)
+    cpdef object get_line(self, index_t line_nb)
+    cpdef set_item(self, index_t line_nb, object elt_id, object value)
+    

python/obitools3/dms/column/typed_column/seq.pyx

@@ -0,0 +1,133 @@
+#cython: language_level=3
+
+
+from ..column cimport register_column_class
+
+from ...view.view cimport View
+
+from obitools3.utils cimport str2bytes, bytes2str, tobytes
+
+from ...capi.obiview cimport obi_get_seq_with_elt_name_and_col_p_in_view, \
+                             obi_get_seq_with_elt_idx_and_col_p_in_view, \
+                             obi_set_seq_with_elt_name_and_col_p_in_view, \
+                             obi_set_seq_with_elt_idx_and_col_p_in_view
+
+from ...capi.obierrno     cimport obi_errno
+from ...capi.obitypes     cimport OBI_SEQ, OBISeq_NA
+
+from libc.stdlib cimport free
+
+
+cdef class Column_seq(Column):
+
+    @staticmethod
+    def new(View    view,
+            object  column_name,
+            index_t nb_elements_per_line=1,
+            object  elements_names=None,
+            object  comments=b""):
+        
+        return Column.new_column(view, column_name, OBI_SEQ,
+                                 nb_elements_per_line=nb_elements_per_line, 
+                                 elements_names=elements_names, 
+                                 comments=comments)
+
+
+    cpdef object get_line(self, index_t line_nb):
+        cdef char*  value
+        cdef object result
+        global      obi_errno
+        value = obi_get_seq_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0)
+        if obi_errno > 0 :
+            raise IndexError(line_nb)
+        if value == OBISeq_NA :
+            result = None
+        else :   # TODO
+            try:
+                result = <bytes> value
+            finally:
+                free(value)
+        return result
+
+
+    cpdef set_line(self, index_t line_nb, object value):
+        cdef bytes value_b
+        if value is None :
+            value_b = OBISeq_NA
+        else :
+            value_b = tobytes(value)
+        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")
+ 
+ 
+cdef class Column_multi_elts_seq(Column_multi_elts):
+ 
+    cpdef object get_item(self, index_t line_nb, object elt_id) :
+        cdef char*  value
+        cdef object result
+        global      obi_errno
+        if type(elt_id) == int :
+            value = obi_get_seq_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id)
+        else :
+            elt_name = tobytes(elt_id)
+            value = obi_get_seq_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name)
+        if obi_errno > 0 :
+            raise IndexError(line_nb, elt_id)
+        if value == OBISeq_NA :
+            result = None
+        else :
+            try:
+                result = <bytes> value
+            finally:
+                free(value)
+        return result
+
+
+    cpdef object get_line(self, index_t line_nb) :
+        cdef char*   value
+        cdef object  value_in_result
+        cdef dict    result
+        cdef index_t i
+        cdef bint    all_NA
+        global      obi_errno
+        result = {}
+        all_NA = True
+        for i in range(self.nb_elements_per_line) :
+            value = obi_get_seq_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, i)
+            if obi_errno > 0 :
+                raise IndexError(line_nb)
+            if value == OBISeq_NA :
+                value_in_result = None
+            else :
+                try:
+                    value_in_result = <bytes> value
+                finally:
+                    free(value)    
+            result[self.elements_names[i]] = value_in_result
+            if all_NA and (value_in_result is not None) :
+                all_NA = False
+        if all_NA :
+            result = None
+        return result
+
+
+    cpdef set_item(self, index_t line_nb, object elt_id, object value):
+        cdef bytes value_b
+        cdef bytes elt_name
+        if value is None :
+            value_b = OBISeq_NA
+        else :
+            value_b = tobytes(value)
+        if type(elt_id) == int :
+            if obi_set_seq_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id, value_b) < 0:
+                raise Exception("Problem setting a value in a column")
+        else :
+            elt_name = tobytes(elt_id)
+            if obi_set_seq_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name, value_b) < 0:
+                raise Exception("Problem setting a value in a column")
+
+
+def register_class():
+    register_column_class(OBI_SEQ, False, Column_seq, bytes)    # TODO str?
+    register_column_class(OBI_SEQ, True, Column_multi_elts_seq, bytes)    # TODO str?
+

python/obitools3/dms/column/typed_column/str.pxd

@@ -0,0 +1,21 @@
+# #cython: language_level=3
+ 
+
+from ...capi.obitypes cimport index_t
+
+from ..column cimport Column, \
+                      Column_multi_elts
+
+
+cdef class Column_str(Column) :
+
+    cpdef object get_line(self, index_t line_nb)
+    cpdef set_line(self, index_t line_nb, object value)
+
+
+cdef class Column_multi_elts_str(Column_multi_elts) :
+
+    cpdef object get_item(self, index_t line_nb, object elt_id)
+    cpdef object get_line(self, index_t line_nb)
+    cpdef set_item(self, index_t line_nb, object elt_id, object value)
+    

python/obitools3/dms/column/typed_column/str.pyx

@@ -0,0 +1,122 @@
+#cython: language_level=3
+
+
+from ..column cimport register_column_class
+
+from ...view.view cimport View
+
+from obitools3.utils cimport str2bytes, bytes2str, tobytes
+
+from ...capi.obiview cimport obi_get_str_with_elt_name_and_col_p_in_view, \
+                             obi_get_str_with_elt_idx_and_col_p_in_view, \
+                             obi_set_str_with_elt_name_and_col_p_in_view, \
+                             obi_set_str_with_elt_idx_and_col_p_in_view
+
+from ...capi.obierrno     cimport obi_errno
+from ...capi.obitypes     cimport OBI_STR, OBIStr_NA
+
+
+cdef class Column_str(Column):
+
+    @staticmethod
+    def new(View    view,
+            object  column_name,
+            index_t nb_elements_per_line=1,
+            object  elements_names=None,
+            object  comments=b""):
+        
+        return Column.new_column(view, column_name, OBI_STR,
+                                 nb_elements_per_line=nb_elements_per_line, 
+                                 elements_names=elements_names, 
+                                 comments=comments)
+
+
+    cpdef object get_line(self, index_t line_nb):
+        cdef char*  value
+        cdef object result
+        global      obi_errno
+        value = obi_get_str_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0)
+        if obi_errno > 0 :
+            raise IndexError(line_nb)
+        if value == OBIStr_NA :
+            result = None
+        else :
+            result = <bytes> value      # NOTE: value is not freed because the pointer points to a mmapped region in an AVL data file.
+        return result
+
+
+    cpdef set_line(self, index_t line_nb, object value):
+        cdef bytes value_b
+        if value is None :
+            value_b = OBIStr_NA
+        else :
+            value_b = tobytes(value)
+        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")
+ 
+ 
+cdef class Column_multi_elts_str(Column_multi_elts):
+ 
+    cpdef object get_item(self, index_t line_nb, object elt_id) :
+        cdef char*  value
+        cdef object result
+        global      obi_errno
+        if type(elt_id) == int :
+            value = obi_get_str_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id)
+        else :
+            elt_name = tobytes(elt_id)
+            value = obi_get_str_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name)
+        if obi_errno > 0 :
+            raise IndexError(line_nb, elt_id)
+        if value == OBIStr_NA :
+            result = None
+        else :
+            result = <bytes> value      # NOTE: value is not freed because the pointer points to a mmapped region in an AVL data file.
+        return result
+
+
+    cpdef object get_line(self, index_t line_nb) :
+        cdef char*   value
+        cdef object  value_in_result
+        cdef dict    result
+        cdef index_t i
+        cdef bint    all_NA
+        global      obi_errno
+        result = {}
+        all_NA = True
+        for i in range(self.nb_elements_per_line) :
+            value = obi_get_str_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, i)
+            if obi_errno > 0 :
+                raise IndexError(line_nb)
+            if value == OBIStr_NA :
+                value_in_result = None
+            else :
+                value_in_result = <bytes> value    
+            result[self.elements_names[i]] = value_in_result
+            if all_NA and (value_in_result is not None) :
+                all_NA = False
+        if all_NA :
+            result = None
+        return result
+
+
+    cpdef set_item(self, index_t line_nb, object elt_id, object value):
+        cdef bytes value_b
+        cdef bytes elt_name
+        if value is None :
+            value_b = OBIStr_NA
+        else :
+            value_b = tobytes(value)
+        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:
+                raise Exception("Problem setting a value in a column")
+        else :
+            elt_name = tobytes(elt_id)
+            if obi_set_str_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name, value_b) < 0:
+                raise Exception("Problem setting a value in a column")
+
+
+def register_class():
+    register_column_class(OBI_STR, False, Column_str, bytes)    # TODO str?
+    register_column_class(OBI_STR, True, Column_multi_elts_str, bytes)    # TODO str?
+