In OBI_CHAR columns, characters are now given and retrieved as decoded

(unicode) characters.

python/obitools3/obidms/_obidmscolumn_char.pxd

@@ -16,10 +16,10 @@ cdef class OBIDMS_column_char_writable(OBIDMS_column_char):
 cdef class OBIDMS_column_char_multi_elts(OBIDMS_column_char):
     cpdef object get_item(self, index_t line_nb, str element_name)
     cpdef object get_line(self, index_t line_nb)
-    cpdef set_item(self, index_t line_nb, str element_name, bytes value)
+    cpdef set_item(self, index_t line_nb, str element_name, str value)
     cpdef set_line(self, index_t line_nb, object values)
 
 cdef class OBIDMS_column_char_multi_elts_writable(OBIDMS_column_char_multi_elts):
-    cpdef set_item(self, index_t line_nb, str element_name, bytes value)
+    cpdef set_item(self, index_t line_nb, str element_name, str value)
     cpdef set_line(self, index_t line_nb, object values)
     cpdef close(self)

python/obitools3/obidms/_obidmscolumn_char.pyx

@@ -9,7 +9,7 @@ from .capi.obidmscolumn cimport obi_close_column,\
 from .capi.obierrno     cimport obi_errno
 from .capi.obitypes     cimport OBIChar_NA
 
-from obitools3.utils cimport str2bytes
+from obitools3.utils cimport str2bytes, bytes2str
 
 
 cdef class OBIDMS_column_char(OBIDMS_column):
@@ -23,7 +23,7 @@ cdef class OBIDMS_column_char(OBIDMS_column):
         if value == OBIChar_NA :
             result = None
         else :
-            result = <bytes> value
+            result = bytes2str(value)
         return result
 
     cpdef set_line(self, index_t line_nb, object value):
@@ -37,7 +37,7 @@ cdef class OBIDMS_column_char(OBIDMS_column):
 cdef class OBIDMS_column_char_writable(OBIDMS_column_char):     
 
     cpdef set_line(self, index_t line_nb, object value):
-        if obi_column_set_obichar_with_elt_idx(self.pointer, line_nb, 0, <bytes> value[0]) < 0:
+        if obi_column_set_obichar_with_elt_idx(self.pointer, line_nb, 0, str2bytes(value)[0]) < 0:
             raise Exception("Problem setting a value in a column")
 
     cpdef close(self):
@@ -56,7 +56,7 @@ cdef class OBIDMS_column_char_multi_elts(OBIDMS_column_char):
         if value == OBIChar_NA :
             result = None
         else :
-            result = <bytes> value
+            result = bytes2str(value)
         return result
     
     cpdef object get_line(self, index_t line_nb) :
@@ -70,14 +70,14 @@ cdef class OBIDMS_column_char_multi_elts(OBIDMS_column_char):
             value = obi_column_get_obichar_with_elt_idx(self.pointer, line_nb, i)
             if obi_errno > 0 :
                 raise IndexError(line_nb)           
-            result[self.elements_names[i]] = <bytes> value
+            result[self.elements_names[i]] = bytes2str(value)
             if all_NA and (value != OBIChar_NA) :
                 all_NA = False
         if all_NA :
             result = None
         return result
 
-    cpdef set_item(self, index_t line_nb, str element_name, bytes value):
+    cpdef set_item(self, index_t line_nb, str element_name, str value):
         raise Exception("Column is read-only")
 
     cpdef set_line(self, index_t line_nb, object values):
@@ -86,53 +86,17 @@ cdef class OBIDMS_column_char_multi_elts(OBIDMS_column_char):
 
 cdef class OBIDMS_column_char_multi_elts_writable(OBIDMS_column_char_multi_elts):     
 
-    cpdef set_item(self, index_t line_nb, str element_name, bytes value):
+    cpdef set_item(self, index_t line_nb, str element_name, str value):
-        if obi_column_set_obichar_with_elt_name(self.pointer, line_nb, str2bytes(element_name), value[0]) < 0:
+        if obi_column_set_obichar_with_elt_name(self.pointer, line_nb, str2bytes(element_name), str2bytes(value)[0]) < 0:
             raise Exception("Problem setting a value in a column")
     
     cpdef set_line(self, index_t line_nb, object values):
-        cdef bytes value
+        cdef str value
         for element_name in values :
-            value = <bytes> values[element_name]
+            value = values[element_name]
             self.set_item(line_nb, element_name, value)
 
     cpdef close(self):
         if obi_truncate_and_close_column(self.pointer) < 0 :
             raise Exception("Problem closing a column")
 
-
-
-
-
-# cdef class OBIDMS_column_char(OBIDMS_column) :
-#  
-#     cpdef object get_item(self, index_t line_nb, str element_name):
-#         cdef char value
-#         cdef object result
-#         value = obi_column_get_obichar_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
-#         if obi_errno > 0 :
-#             raise IndexError(line_nb, element_name)
-#         if value == OBIChar_NA :
-#             result = None
-#         else :
-#             result = <bytes> value
-#         return result
-# 
-#     cpdef set_item(self, index_t line_nb, str element_name, bytes value):
-#         raise Exception("Column is read-only")
-#  
-#     cpdef close(self):
-#         if obi_close_column(self.pointer) < 0 :
-#             raise Exception("Problem closing a column")
-#  
-#          
-# cdef class OBIDMS_column_char_writable(OBIDMS_column_char) :     
-#  
-#     cpdef set_item(self, index_t line_nb, str element_name, bytes value):
-#         if obi_column_set_obichar_with_elt_name(self.pointer, line_nb, str2bytes(element_name), value[0]) < 0:
-#             raise Exception("Problem setting a value in a column")
-#  
-#     cpdef close(self):
-#         if obi_truncate_and_close_column(self.pointer) < 0 :
-#             raise Exception("Problem closing a column")
-#       

python/obitools3/unit_tests.py

@@ -59,7 +59,7 @@ def random_obivalue(data_type):
         return randint(0,1)
     elif data_type == "OBI_CHAR" :
         nucs = 'atgc'
-        return bytes(nucs[randint(0,3)], 'utf-8')
+        return nucs[randint(0,3)]
     elif data_type == "OBI_IDX" :
         length = randint(1,500)
         randoms = ''.join(choice(string.ascii_lowercase) for i in range(length))