obi arrays that don't work because of cython bug passing wrong pointers

python/obitools3/obidms/_obidmscolumn_str.pyx

@@ -0,0 +1,121 @@
+#cython: language_level=3
+ 
+from .capi.obidmscolumn cimport obi_close_column,\
+                                obi_truncate_and_close_column, \
+                                obi_column_get_obistr_with_elt_name, \
+                                obi_column_get_obistr_with_elt_idx, \
+                                obi_column_set_obistr_with_elt_name, \
+                                obi_column_set_obistr_with_elt_idx
+from .capi.obierrno     cimport obi_errno
+from .capi.obitypes     cimport OBIIdx_NA, const_char_p
+
+
+from libc.string cimport strlen
+
+from obitools3.utils cimport str2bytes, bytes2str
+
+from cpython.int cimport PyInt_FromSsize_t
+
+
+cdef class OBIDMS_column_str(OBIDMS_column):
+
+    cpdef object get_line(self, size_t line_nb):
+        cdef const_char_p cvalue 
+        cdef bytes value
+        cdef object result
+        
+        cvalue = obi_column_get_obistr_with_elt_idx(self.pointer, line_nb, 0)
+        
+        print('test 1')
+        
+        print(hex(<int> cvalue))
+        
+        
+        print(strlen(cvalue))
+        print("test")
+        value = <bytes> cvalue
+        print(value)
+        if obi_errno > 0 :
+            raise IndexError(line_nb)
+        if value == OBIIdx_NA :
+            result = None
+        else :
+            print(value)
+            result = bytes2str(value)
+        return result
+
+    cpdef set_line(self, size_t line_nb, object 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_str_writable(OBIDMS_column_str):     
+
+    cpdef set_line(self, size_t line_nb, object value):
+        if obi_column_set_obistr_with_elt_idx(self.pointer, line_nb, 0, str2bytes(value)) < 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")
+
+
+cdef class OBIDMS_column_str_multi_elts(OBIDMS_column_str):
+
+    cpdef object get_item(self, size_t line_nb, str element_name):
+        cdef bytes value
+        cdef object result
+        value = obi_column_get_obistr_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
+        if obi_errno > 0 :
+            raise IndexError(line_nb, element_name)
+        if value == OBIIdx_NA :
+            result = None
+        else :
+            result = bytes2str(value)
+        return result
+    
+    cpdef object get_line(self, size_t line_nb) :
+        cdef bytes value
+        cdef object result
+        cdef size_t i
+        cdef bint all_NA
+        result = {}
+        all_NA = True
+        for i in range(self.nb_elements_per_line) :
+            value = obi_column_get_obistr_with_elt_idx(self.pointer, line_nb, i)
+            if obi_errno > 0 :
+                raise IndexError(line_nb)           
+            result[self.elements_names[i]] = bytes2str(value)
+            if all_NA and (value != OBIIdx_NA) :
+                all_NA = False
+        if all_NA :
+            result = None
+        return result
+
+    cpdef set_item(self, size_t line_nb, str element_name, str value):
+        raise Exception("Column is read-only")
+
+    cpdef set_line(self, size_t line_nb, object values):
+        raise Exception("Column is read-only")
+
+
+cdef class OBIDMS_column_str_multi_elts_writable(OBIDMS_column_str_multi_elts):     
+
+    cpdef set_item(self, size_t line_nb, str element_name, str value):
+        if obi_column_set_obistr_with_elt_name(self.pointer, line_nb, str2bytes(element_name), str2bytes(value)) < 0:
+            raise Exception("Problem setting a value in a column")
+    
+    cpdef set_line(self, size_t line_nb, object values):
+        cdef str value
+        for element_name in values :
+            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")
+
+