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Branch to refactor and debug (AVLs bugged)

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This commit is contained in:
Celine Mercier
2016-04-08 15:38:57 +02:00
parent edc4fd7b3e
commit 019dfc01b4
32 changed files with 1553 additions and 812 deletions
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31
python/obitools3/obidms/_obidmscolumn_str.pyx
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@ -10,19 +10,22 @@ from .capi.obitypes cimport OBIStr_NA, const_char_p
from obitools3.utils cimport str2bytes, bytes2str
from libc.string cimport strcmp
cdef class OBIDMS_column_str(OBIDMS_column):
cpdef object get_line(self, index_t line_nb):
cdef bytes value
cdef char* value
cdef object result
value = <bytes> obi_column_get_obistr_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0)
value = obi_column_get_obistr_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIStr_NA : # TODO
if strcmp(value, OBIStr_NA) == 0 :
result = None
else :
result = bytes2str(value)
# NOTE: value is not freed because the pointer points to a mmapped region in an AVL data file. (TODO discuss)
return result
cpdef set_line(self, index_t line_nb, object value):
@ -38,33 +41,35 @@ cdef class OBIDMS_column_str(OBIDMS_column):
cdef class OBIDMS_column_multi_elts_str(OBIDMS_column_multi_elts):
cpdef object get_item(self, index_t line_nb, str element_name):
cdef bytes value
cdef char* value
cdef object result
value = <bytes> obi_column_get_obistr_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name))
value = obi_column_get_obistr_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name))
if obi_errno > 0 :
raise IndexError(line_nb, element_name)
if value == OBIStr_NA :
if strcmp(value, OBIStr_NA) == 0 :
result = None
else :
result = bytes2str(value)
# NOTE: value is not freed because the pointer points to a mmapped region in an AVL data file. (TODO discuss)
return result
cpdef object get_line(self, index_t line_nb) :
cdef bytes value
cdef object value_in_result
cdef dict result
cdef char* value
cdef object value_in_result
cdef dict result
cdef index_t i
cdef bint all_NA
cdef bint all_NA
result = {}
all_NA = True
for i in range(self.nb_elements_per_line) :
value = <bytes> obi_column_get_obistr_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, i)
value = obi_column_get_obistr_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, i)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIStr_NA :
if strcmp(value, OBIStr_NA) == 0 :
value_in_result = None
else :
value_in_result = bytes2str(value)
value_in_result = bytes2str(value)
# NOTE: value is not freed because the pointer points to a mmapped region in an AVL data file. (TODO discuss)
result[self.elements_names[i]] = value_in_result
if all_NA and (value_in_result is not None) :
all_NA = False