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OBITools3
Commit 9d042f7b authored by Celine Mercier's avatar Celine Mercier
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Refactored and relocated the set and get functions of all column types, 

both within and out of the context of a view
parent 5ec2d884
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Showing with 1081 additions and 1322 deletions
python/obitools3/obidms/_obidms.cfiles
View file @ 9d042f7b
......@@ -37,3 +37,15 @@
../../../src/obiview.c
../../../src/utils.h
../../../src/utils.c
../../../src/obidmscolumn_bool.c
../../../src/obidmscolumn_bool.h
../../../src/obidmscolumn_char.c
../../../src/obidmscolumn_char.h
../../../src/obidmscolumn_float.c
../../../src/obidmscolumn_float.h
../../../src/obidmscolumn_int.c
../../../src/obidmscolumn_int.h
../../../src/obidmscolumn_seq.c
../../../src/obidmscolumn_seq.h
../../../src/obidmscolumn_str.c
../../../src/obidmscolumn_str.h
python/obitools3/obidms/_obidmscolumn_bool.pyx
View file @ 9d042f7b
#cython: language_level=3
from .capi.obidmscolumn cimport obi_truncate_and_close_column, \
obi_column_get_obibool_with_elt_name_in_view, \
from .capi.obidmscolumn cimport obi_truncate_and_close_column
from .capi.obiview cimport obi_column_get_obibool_with_elt_name_in_view, \
obi_column_get_obibool_with_elt_idx_in_view, \
obi_column_set_obibool_with_elt_name_in_view, \
obi_column_set_obibool_with_elt_idx_in_view
......
python/obitools3/obidms/_obidmscolumn_char.pyx
View file @ 9d042f7b
#cython: language_level=3
from .capi.obidmscolumn cimport obi_truncate_and_close_column, \
obi_column_get_obichar_with_elt_name_in_view, \
from .capi.obidmscolumn cimport obi_truncate_and_close_column
from .capi.obiview cimport obi_column_get_obichar_with_elt_name_in_view, \
obi_column_get_obichar_with_elt_idx_in_view, \
obi_column_set_obichar_with_elt_name_in_view, \
obi_column_set_obichar_with_elt_idx_in_view
......
python/obitools3/obidms/_obidmscolumn_float.pyx
View file @ 9d042f7b
#cython: language_level=3
from .capi.obidmscolumn cimport obi_truncate_and_close_column,\
obi_column_get_obifloat_with_elt_name_in_view, \
from .capi.obidmscolumn cimport obi_truncate_and_close_column
from .capi.obiview cimport obi_column_get_obifloat_with_elt_name_in_view, \
obi_column_get_obifloat_with_elt_idx_in_view, \
obi_column_set_obifloat_with_elt_name_in_view, \
obi_column_set_obifloat_with_elt_idx_in_view
......
python/obitools3/obidms/_obidmscolumn_int.pyx
View file @ 9d042f7b
#cython: language_level=3
from .capi.obidmscolumn cimport obi_truncate_and_close_column, \
obi_column_get_obiint_with_elt_name_in_view, \
from .capi.obidmscolumn cimport obi_truncate_and_close_column
from .capi.obiview cimport obi_column_get_obiint_with_elt_name_in_view, \
obi_column_get_obiint_with_elt_idx_in_view, \
obi_column_set_obiint_with_elt_name_in_view, \
obi_column_set_obiint_with_elt_idx_in_view
......
python/obitools3/obidms/_obidmscolumn_seq.pyx
View file @ 9d042f7b
#cython: language_level=3
from .capi.obidmscolumn cimport obi_truncate_and_close_column, \
obi_column_get_obiseq_with_elt_name_in_view, \
from .capi.obidmscolumn cimport obi_truncate_and_close_column
from .capi.obiview cimport obi_column_get_obiseq_with_elt_name_in_view, \
obi_column_get_obiseq_with_elt_idx_in_view, \
obi_column_set_obiseq_with_elt_name_in_view, \
obi_column_set_obiseq_with_elt_idx_in_view
......
python/obitools3/obidms/_obidmscolumn_str.pyx
View file @ 9d042f7b
#cython: language_level=3
from .capi.obidmscolumn cimport obi_truncate_and_close_column, \
obi_column_get_obistr_with_elt_name_in_view, \
from .capi.obidmscolumn cimport obi_truncate_and_close_column
from .capi.obiview cimport obi_column_get_obistr_with_elt_name_in_view, \
obi_column_get_obistr_with_elt_idx_in_view, \
obi_column_set_obistr_with_elt_name_in_view, \
obi_column_set_obistr_with_elt_idx_in_view
......@@ -16,8 +16,8 @@ from libc.string cimport strcmp
cdef class OBIDMS_column_str(OBIDMS_column):
cpdef object get_line(self, index_t line_nb):
cdef char* value
cdef object result
cdef const_char_p value
cdef object result
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)
......@@ -41,8 +41,8 @@ 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 char* value
cdef object result
cdef const_char_p value
cdef object result
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)
......@@ -54,11 +54,11 @@ cdef class OBIDMS_column_multi_elts_str(OBIDMS_column_multi_elts):
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
cdef const_char_p 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) :
......
python/obitools3/obidms/capi/obidmscolumn.pxd
View file @ 9d042f7b
......@@ -76,30 +76,7 @@ cdef extern from "obidmscolumn.h" nogil:
int obi_select(OBIDMS_column_p line_selection_column, index_t line_to_grep)
from ..capi.obiview cimport Obiview_p # TODO
cdef extern from "obidmscolumn_int.h" nogil:
int obi_column_set_obiint_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name,
obiint_t value)
int obi_column_set_obiint_with_elt_idx_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
index_t element_idx,
obiint_t value)
obiint_t obi_column_get_obiint_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name)
obiint_t obi_column_get_obiint_with_elt_idx_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
index_t element_idx)
int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column,
index_t line_nb,
......@@ -121,28 +98,6 @@ cdef extern from "obidmscolumn_int.h" nogil:
cdef extern from "obidmscolumn_bool.h" nogil:
int obi_column_set_obibool_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name,
obibool_t value)
int obi_column_set_obibool_with_elt_idx_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
index_t element_idx,
obibool_t value)
obibool_t obi_column_get_obibool_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name)
obibool_t obi_column_get_obibool_with_elt_idx_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
index_t element_idx)
int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name,
......@@ -163,28 +118,6 @@ cdef extern from "obidmscolumn_bool.h" nogil:
cdef extern from "obidmscolumn_char.h" nogil:
int obi_column_set_obichar_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name,
obichar_t value)
int obi_column_set_obichar_with_elt_idx_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
index_t element_idx,
obichar_t value)
obichar_t obi_column_get_obichar_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name)
obichar_t obi_column_get_obichar_with_elt_idx_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
index_t element_idx)
int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name,
......@@ -205,83 +138,39 @@ cdef extern from "obidmscolumn_char.h" nogil:
cdef extern from "obidmscolumn_float.h" nogil:
int obi_column_set_obifloat_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name,
obifloat_t value)
int obi_column_set_obifloat_with_elt_idx_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
index_t element_idx,
obifloat_t value)
obifloat_t obi_column_get_obifloat_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name)
obifloat_t obi_column_get_obifloat_with_elt_idx_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
index_t element_idx)
int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name,
obifloat_t value)
index_t line_nb,
const_char_p element_name,
obifloat_t value)
int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column,
index_t line_nb,
index_t element_idx,
obifloat_t value)
index_t line_nb,
index_t element_idx,
obifloat_t value)
obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name)
index_t line_nb,
const_char_p element_name)
obifloat_t obi_column_get_obifloat_with_elt_idx(OBIDMS_column_p column,
index_t line_nb,
index_t element_idx)
cdef extern from "obidmscolumn_str.h" nogil:
int obi_column_set_obistr_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name,
char* value)
index_t element_idx)
int obi_column_set_obistr_with_elt_idx_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
index_t element_idx,
char* value)
const_char_p obi_column_get_obistr_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name)
const_char_p obi_column_get_obistr_with_elt_idx_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
index_t element_idx)
cdef extern from "obidmscolumn_str.h" nogil:
int obi_column_set_obistr_with_elt_name(OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name,
char* value)
const_char_p value)
int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column,
index_t line_nb,
index_t element_idx,
char* value)
const_char_p value)
const_char_p obi_column_get_obistr_with_elt_name(OBIDMS_column_p column,
index_t line_nb,
char* element_name)
index_t line_nb,
const_char_p element_name)
const_char_p obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column,
index_t line_nb,
......@@ -289,43 +178,21 @@ cdef extern from "obidmscolumn_str.h" nogil:
cdef extern from "obidmscolumn_seq.h" nogil:
int obi_column_set_obiseq_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name,
char* value)
int obi_column_set_obiseq_with_elt_idx_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
index_t element_idx,
char* value)
const_char_p obi_column_get_obiseq_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name)
const_char_p obi_column_get_obiseq_with_elt_idx_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
index_t element_idx)
int obi_column_set_obiseq_with_elt_name(OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name,
char* value)
const_char_p value)
int obi_column_set_obiseq_with_elt_idx(OBIDMS_column_p column,
index_t line_nb,
index_t element_idx,
char* value)
const_char_p value)
const_char_p obi_column_get_obiseq_with_elt_name(OBIDMS_column_p column,
index_t line_nb,
char* element_name)
char* obi_column_get_obiseq_with_elt_name(OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name)
const_char_p obi_column_get_obiseq_with_elt_idx(OBIDMS_column_p column,
index_t line_nb,
index_t element_idx)
char* obi_column_get_obiseq_with_elt_idx(OBIDMS_column_p column,
index_t line_nb,
index_t element_idx)
python/obitools3/obidms/capi/obiview.pxd
View file @ 9d042f7b
......@@ -3,6 +3,10 @@
from .obitypes cimport const_char_p, \
OBIType_t, \
obiversion_t, \
obiint_t, \
obibool_t, \
obichar_t, \
obifloat_t, \
index_t, \
time_t
from ..capi.obidms cimport OBIDMS_p
......@@ -111,4 +115,136 @@ cdef extern from "obiview.h" nogil:
int obi_close_view(Obiview_p view)
int obi_save_and_close_view(Obiview_p view)
int obi_column_set_obiint_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name,
obiint_t value)
int obi_column_set_obiint_with_elt_idx_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
index_t element_idx,
obiint_t value)
obiint_t obi_column_get_obiint_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name)
obiint_t obi_column_get_obiint_with_elt_idx_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
index_t element_idx)
int obi_column_set_obibool_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name,
obibool_t value)
int obi_column_set_obibool_with_elt_idx_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
index_t element_idx,
obibool_t value)
obibool_t obi_column_get_obibool_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name)
obibool_t obi_column_get_obibool_with_elt_idx_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
index_t element_idx)
int obi_column_set_obichar_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name,
obichar_t value)
int obi_column_set_obichar_with_elt_idx_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
index_t element_idx,
obichar_t value)
obichar_t obi_column_get_obichar_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name)
obichar_t obi_column_get_obichar_with_elt_idx_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
index_t element_idx)
int obi_column_set_obifloat_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name,
obifloat_t value)
int obi_column_set_obifloat_with_elt_idx_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
index_t element_idx,
obifloat_t value)
obifloat_t obi_column_get_obifloat_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name)
obifloat_t obi_column_get_obifloat_with_elt_idx_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
index_t element_idx)
int obi_column_set_obistr_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name,
const_char_p value)
int obi_column_set_obistr_with_elt_idx_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
index_t element_idx,
const_char_p value)
const_char_p obi_column_get_obistr_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name)
const_char_p obi_column_get_obistr_with_elt_idx_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
index_t element_idx)
int obi_column_set_obiseq_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name,
const_char_p value)
int obi_column_set_obiseq_with_elt_idx_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
index_t element_idx,
const_char_p value)
char* obi_column_get_obiseq_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name)
char* obi_column_get_obiseq_with_elt_idx_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
index_t element_idx)
python/obitools3/obiimport.py
View file @ 9d042f7b
......@@ -26,16 +26,16 @@ if __name__ == '__main__':
view = d.new_view('uniq view', view_type="NUC_SEQS_VIEW")
for i in range(35000000) :
if (not (i%500000)) :
print(str(time.time())+'\t'+str(i))
id = "@HWI-D00405:142:C71BAANXX:4:1101:1234:2234_CONS_SUB_SUB_"+str(i)
view[i].set_id(id)
if id != view[i]["ID"] :
print("nope", id, view[i]["ID"])
# for i in range(35000000) :
# if (not (i%500000)) :
# print(str(time.time())+'\t'+str(i))
# id = "@HWI-D00405:142:C71BAANXX:4:1101:1234:2234_CONS_SUB_SUB_"+str(i)
# view[i].set_id(id)
# if id != view[i]["ID"] :
# print("nope", id, view[i]["ID"])
# input_file = open(args.input_file, 'r')
# input_file_buffered = bufferedRead(input_file)
input_file = open(args.input_file, 'r')
input_file_buffered = bufferedRead(input_file)
#
# if args.input_file[-1:] == "a" :
......@@ -113,32 +113,32 @@ if __name__ == '__main__':
# l = 0
# next = False
#
# l=0
# i=0
l=0
i=0
# while (True):
# l+=1
# line = input_file.readline()
# if line=="":
# break
# for line in input_file_buffered :
for line in input_file_buffered :
#
# #if i > 1E7 :
#if i > 1E7 :
# # print('hmm?')
#
# if i == 6000000 :
# break
#
# if l%4 == 0 :
if l%4 == 0 :
#
# if (not (i%500000)) :
# print(str(time.time())+'\t'+str(i))
if (not (i%500000)) :
print(str(time.time())+'\t'+str(i))
# #
# # #print("header", line)
# #
# id = line.split(" ", 1)[0][1:]
id = line.split(" ", 1)[0][1:]
# print(id)
# # #rest = (line[:-1].split(" ", 1)[1]).split(";")
# view[i].set_id(id)
view[i].set_id(id)
# print(view[i]["ID"])
#
# i+=1
......@@ -178,17 +178,17 @@ if __name__ == '__main__':
# # description = description.strip()
# # view[i].set_description(description)
#
# # elif l%4 == 1 :
elif l%4 == 1 :
# #
# # seq = line[:-1]
seq = line[:-1]
# #print("seq", seq)
# # view[i].set_sequence(seq)
# # i+=1
view[i].set_sequence(seq)
i+=1
#
# l+=1
l+=1
#
#
# input_file.close()
input_file.close()
#print(view)
print(view.__repr__())
......
src/obidmscolumn.c
View file @ 9d042f7b
......@@ -1418,7 +1418,53 @@ index_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const cha
}
char* obi_column_format_date(time_t date