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Major update: obiarrays with columns containing indices referring to

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character strings.
This commit is contained in:
Celine Mercier
2015-11-06 17:55:15 +01:00
parent 456551ffeb
commit 9b066f4327
35 changed files with 632 additions and 532 deletions
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22
python/obitools3/obidms/_obidms.pxd
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@ -2,7 +2,7 @@
from .capi.obidms cimport OBIDMS_p
from .capi.obidmscolumn cimport OBIDMS_column_p
from .capi.obitypes cimport obiversion_t, OBIType_t
from .capi.obitypes cimport obiversion_t, OBIType_t, index_t
cdef class OBIDMS_column
@ -21,8 +21,8 @@ cdef class OBIDMS:
bint clone=*, bint clone_data=*,
obiversion_t version_number=*,
OBIType_t data_type=*,
size_t nb_lines=*,
size_t nb_elements_per_line=*,
index_t nb_lines=*,
index_t nb_elements_per_line=*,
list elements_names=*,
str array_name=*)
@ -34,14 +34,14 @@ cdef class OBIDMS_column:
cdef str data_type # TODO keep as OBIType_t? both?
cdef str dms_name
cdef str column_name
cdef size_t nb_elements_per_line
cdef index_t nb_elements_per_line
cdef list elements_names
# cpdef object get_item(self, size_t line_nb, str element_name) TODO can't declare because not the same in all subclasses
# cpdef set_item(self, size_t line_nb, str element_name, object value) TODO can't declare because object value
cpdef list get_elements_names(self)
cpdef str get_data_type(self)
cpdef size_t get_nb_lines_used(self)
cpdef str get_creation_date(self)
cpdef close(self)
# cpdef object get_item(self, index_t line_nb, str element_name) TODO can't declare because not the same in all subclasses
# cpdef set_item(self, index_t line_nb, str element_name, object value) TODO can't declare because object value
cpdef list get_elements_names(self)
cpdef str get_data_type(self)
cpdef index_t get_nb_lines_used(self)
cpdef str get_creation_date(self)
cpdef close(self)

26
python/obitools3/obidms/_obidms.pyx
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@ -80,7 +80,7 @@ cdef class OBIDMS :
cdef str data_type
cdef str creation_date
cdef obiversion_t latest_version
cdef size_t line_count
cdef index_t line_count
cdef OBIDMS_column_header_p header
p = Path(self.dms_name+'.obidms')
@ -117,8 +117,8 @@ cdef class OBIDMS :
bint clone=False, bint clone_data=True,
obiversion_t version_number=-1,
OBIType_t data_type= <OBIType_t> 0,
size_t nb_lines=0,
size_t nb_elements_per_line=0,
index_t nb_lines=0,
index_t nb_elements_per_line=0,
list elements_names=None,
str array_name="default_obiarray"):
@ -222,7 +222,7 @@ cdef class OBIDMS :
version_number, data_type,
nb_lines, nb_elements_per_line,
elements_names, array_name)
return column
@ -237,8 +237,8 @@ cdef class OBIDMS_column :
bint clone, bint clone_data,
obiversion_t version_number,
OBIType_t type,
size_t nb_lines,
size_t nb_elements_per_line,
index_t nb_lines,
index_t nb_elements_per_line,
list elements_names,
str array_name):
@ -279,8 +279,8 @@ cdef class OBIDMS_column :
def __iter__(self):
# Declarations
cdef size_t lines_used
cdef size_t line_nb
cdef index_t lines_used
cdef index_t line_nb
# Yield each line
lines_used = self.pointer.header.lines_used
@ -288,19 +288,19 @@ cdef class OBIDMS_column :
yield self.get_line(line_nb)
def __setitem__(self, size_t line_nb, object value):
def __setitem__(self, index_t line_nb, object value):
self.set_line(line_nb, value)
def __getitem__(self, size_t line_nb):
def __getitem__(self, index_t line_nb):
return self.get_line(line_nb)
# cpdef object get_item(self, size_t line_nb, str element_name): TODO
# cpdef object get_item(self, index_t line_nb, str element_name): TODO
# raise NotImplementedError
# cpdef set_item(self, size_t line_nb, str element_name, object value): TODO
# cpdef set_item(self, index_t line_nb, str element_name, object value): TODO
# raise NotImplementedError
@ -312,7 +312,7 @@ cdef class OBIDMS_column :
return self.data_type
cpdef size_t get_nb_lines_used(self):
cpdef index_t get_nb_lines_used(self):
return self.pointer.header.lines_used

20
python/obitools3/obidms/_obidmscolumn_bool.pxd
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@ -1,25 +1,25 @@
#cython: language_level=3
from .capi.obitypes cimport obibool_t
from .capi.obitypes cimport obibool_t, index_t
from ._obidms cimport OBIDMS_column
cdef class OBIDMS_column_bool(OBIDMS_column):
cpdef object get_line(self, size_t line_nb)
cpdef set_line(self, size_t line_nb, object value)
cpdef object get_line(self, index_t line_nb)
cpdef set_line(self, index_t line_nb, object value)
cpdef close(self)
cdef class OBIDMS_column_bool_writable(OBIDMS_column_bool):
cpdef set_line(self, size_t line_nb, object value)
cpdef set_line(self, index_t line_nb, object value)
cpdef close(self)
cdef class OBIDMS_column_bool_multi_elts(OBIDMS_column_bool):
cpdef object get_item(self, size_t line_nb, str element_name)
cpdef object get_line(self, size_t line_nb)
cpdef set_item(self, size_t line_nb, str element_name, obibool_t value)
cpdef set_line(self, size_t line_nb, object values)
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, obibool_t value)
cpdef set_line(self, index_t line_nb, object values)
cdef class OBIDMS_column_bool_multi_elts_writable(OBIDMS_column_bool_multi_elts):
cpdef set_item(self, size_t line_nb, str element_name, obibool_t value)
cpdef set_line(self, size_t line_nb, object values)
cpdef set_item(self, index_t line_nb, str element_name, obibool_t value)
cpdef set_line(self, index_t line_nb, object values)
cpdef close(self)

20
python/obitools3/obidms/_obidmscolumn_bool.pyx
View File

@ -16,7 +16,7 @@ from cpython.bool cimport PyBool_FromLong
cdef class OBIDMS_column_bool(OBIDMS_column):
cpdef object get_line(self, size_t line_nb):
cpdef object get_line(self, index_t line_nb):
cdef obibool_t value
cdef object result
value = obi_column_get_obibool_with_elt_idx(self.pointer, line_nb, 0)
@ -28,7 +28,7 @@ cdef class OBIDMS_column_bool(OBIDMS_column):
result = PyBool_FromLong(value)
return result
cpdef set_line(self, size_t line_nb, object value):
cpdef set_line(self, index_t line_nb, object value):
raise Exception("Column is read-only")
cpdef close(self):
@ -38,7 +38,7 @@ cdef class OBIDMS_column_bool(OBIDMS_column):
cdef class OBIDMS_column_bool_writable(OBIDMS_column_bool):
cpdef set_line(self, size_t line_nb, object value):
cpdef set_line(self, index_t line_nb, object value):
if obi_column_set_obibool_with_elt_idx(self.pointer, line_nb, 0, <obibool_t> value) < 0:
raise Exception("Problem setting a value in a column")
@ -49,7 +49,7 @@ cdef class OBIDMS_column_bool_writable(OBIDMS_column_bool):
cdef class OBIDMS_column_bool_multi_elts(OBIDMS_column_bool):
cpdef object get_item(self, size_t line_nb, str element_name):
cpdef object get_item(self, index_t line_nb, str element_name):
cdef obibool_t value
cdef object result
value = obi_column_get_obibool_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
@ -61,10 +61,10 @@ cdef class OBIDMS_column_bool_multi_elts(OBIDMS_column_bool):
result = PyBool_FromLong(value)
return result
cpdef object get_line(self, size_t line_nb) :
cpdef object get_line(self, index_t line_nb) :
cdef obibool_t value
cdef object result
cdef size_t i
cdef index_t i
cdef bint all_NA
result = {}
all_NA = True
@ -79,20 +79,20 @@ cdef class OBIDMS_column_bool_multi_elts(OBIDMS_column_bool):
result = None
return result
cpdef set_item(self, size_t line_nb, str element_name, obibool_t value):
cpdef set_item(self, index_t line_nb, str element_name, obibool_t value):
raise Exception("Column is read-only")
cpdef set_line(self, size_t line_nb, object values):
cpdef set_line(self, index_t line_nb, object values):
raise Exception("Column is read-only")
cdef class OBIDMS_column_bool_multi_elts_writable(OBIDMS_column_bool_multi_elts):
cpdef set_item(self, size_t line_nb, str element_name, obibool_t value):
cpdef set_item(self, index_t line_nb, str element_name, obibool_t value):
if obi_column_set_obibool_with_elt_name(self.pointer, line_nb, str2bytes(element_name), value) < 0:
raise Exception("Problem setting a value in a column")
cpdef set_line(self, size_t line_nb, object values):
cpdef set_line(self, index_t line_nb, object values):
cdef obibool_t value
for element_name in values :
value = <obibool_t> values[element_name]

20
python/obitools3/obidms/_obidmscolumn_char.pxd
View File

@ -1,25 +1,25 @@
#cython: language_level=3
from .capi.obitypes cimport obichar_t
from .capi.obitypes cimport obichar_t, index_t
from ._obidms cimport OBIDMS_column
cdef class OBIDMS_column_char(OBIDMS_column):
cpdef object get_line(self, size_t line_nb)
cpdef set_line(self, size_t line_nb, object value)
cpdef object get_line(self, index_t line_nb)
cpdef set_line(self, index_t line_nb, object value)
cpdef close(self)
cdef class OBIDMS_column_char_writable(OBIDMS_column_char):
cpdef set_line(self, size_t line_nb, object value)
cpdef set_line(self, index_t line_nb, object value)
cpdef close(self)
cdef class OBIDMS_column_char_multi_elts(OBIDMS_column_char):
cpdef object get_item(self, size_t line_nb, str element_name)
cpdef object get_line(self, size_t line_nb)
cpdef set_item(self, size_t line_nb, str element_name, bytes value)
cpdef set_line(self, size_t line_nb, object values)
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_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, size_t line_nb, str element_name, bytes value)
cpdef set_line(self, size_t line_nb, object values)
cpdef set_item(self, index_t line_nb, str element_name, bytes value)
cpdef set_line(self, index_t line_nb, object values)
cpdef close(self)

26
python/obitools3/obidms/_obidmscolumn_char.pyx
View File

@ -14,7 +14,7 @@ from obitools3.utils cimport str2bytes
cdef class OBIDMS_column_char(OBIDMS_column):
cpdef object get_line(self, size_t line_nb):
cpdef object get_line(self, index_t line_nb):
cdef obichar_t value
cdef object result
value = obi_column_get_obichar_with_elt_idx(self.pointer, line_nb, 0)
@ -26,7 +26,7 @@ cdef class OBIDMS_column_char(OBIDMS_column):
result = <bytes> value
return result
cpdef set_line(self, size_t line_nb, object value):
cpdef set_line(self, index_t line_nb, object value):
raise Exception("Column is read-only")
cpdef close(self):
@ -36,7 +36,7 @@ cdef class OBIDMS_column_char(OBIDMS_column):
cdef class OBIDMS_column_char_writable(OBIDMS_column_char):
cpdef set_line(self, size_t line_nb, object value):
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:
raise Exception("Problem setting a value in a column")
@ -47,7 +47,7 @@ cdef class OBIDMS_column_char_writable(OBIDMS_column_char):
cdef class OBIDMS_column_char_multi_elts(OBIDMS_column_char):
cpdef object get_item(self, size_t line_nb, str element_name):
cpdef object get_item(self, index_t line_nb, str element_name):
cdef obichar_t value
cdef object result
value = obi_column_get_obichar_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
@ -59,10 +59,10 @@ cdef class OBIDMS_column_char_multi_elts(OBIDMS_column_char):
result = <bytes> value
return result
cpdef object get_line(self, size_t line_nb) :
cpdef object get_line(self, index_t line_nb) :
cdef obichar_t value
cdef object result
cdef size_t i
cdef index_t i
cdef bint all_NA
result = {}
all_NA = True
@ -77,20 +77,20 @@ cdef class OBIDMS_column_char_multi_elts(OBIDMS_column_char):
result = None
return result
cpdef set_item(self, size_t line_nb, str element_name, bytes value):
cpdef set_item(self, index_t line_nb, str element_name, bytes value):
raise Exception("Column is read-only")
cpdef set_line(self, size_t line_nb, object values):
cpdef set_line(self, index_t line_nb, object values):
raise Exception("Column is read-only")
cdef class OBIDMS_column_char_multi_elts_writable(OBIDMS_column_char_multi_elts):
cpdef set_item(self, size_t line_nb, str element_name, bytes value):
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 set_line(self, size_t line_nb, object values):
cpdef set_line(self, index_t line_nb, object values):
cdef bytes value
for element_name in values :
value = <bytes> values[element_name]
@ -106,7 +106,7 @@ cdef class OBIDMS_column_char_multi_elts_writable(OBIDMS_column_char_multi_elts)
# cdef class OBIDMS_column_char(OBIDMS_column) :
#
# cpdef object get_item(self, size_t line_nb, str element_name):
# 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))
@ -118,7 +118,7 @@ cdef class OBIDMS_column_char_multi_elts_writable(OBIDMS_column_char_multi_elts)
# result = <bytes> value
# return result
#
# cpdef set_item(self, size_t line_nb, str element_name, bytes value):
# cpdef set_item(self, index_t line_nb, str element_name, bytes value):
# raise Exception("Column is read-only")
#
# cpdef close(self):
@ -128,7 +128,7 @@ cdef class OBIDMS_column_char_multi_elts_writable(OBIDMS_column_char_multi_elts)
#
# cdef class OBIDMS_column_char_writable(OBIDMS_column_char) :
#
# cpdef set_item(self, size_t line_nb, str element_name, bytes value):
# 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")
#

20
python/obitools3/obidms/_obidmscolumn_float.pxd
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@ -1,25 +1,25 @@
#cython: language_level=3
from .capi.obitypes cimport obifloat_t
from .capi.obitypes cimport obifloat_t, index_t
from ._obidms cimport OBIDMS_column
cdef class OBIDMS_column_float(OBIDMS_column):
cpdef object get_line(self, size_t line_nb)
cpdef set_line(self, size_t line_nb, object value)
cpdef object get_line(self, index_t line_nb)
cpdef set_line(self, index_t line_nb, object value)
cpdef close(self)
cdef class OBIDMS_column_float_writable(OBIDMS_column_float):
cpdef set_line(self, size_t line_nb, object value)
cpdef set_line(self, index_t line_nb, object value)
cpdef close(self)
cdef class OBIDMS_column_float_multi_elts(OBIDMS_column_float):
cpdef object get_item(self, size_t line_nb, str element_name)
cpdef object get_line(self, size_t line_nb)
cpdef set_item(self, size_t line_nb, str element_name, obifloat_t value)
cpdef set_line(self, size_t line_nb, object values)
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, obifloat_t value)
cpdef set_line(self, index_t line_nb, object values)
cdef class OBIDMS_column_float_multi_elts_writable(OBIDMS_column_float_multi_elts):
cpdef set_item(self, size_t line_nb, str element_name, obifloat_t value)
cpdef set_line(self, size_t line_nb, object values)
cpdef set_item(self, index_t line_nb, str element_name, obifloat_t value)
cpdef set_line(self, index_t line_nb, object values)
cpdef close(self)

20
python/obitools3/obidms/_obidmscolumn_float.pyx
View File

@ -14,7 +14,7 @@ from obitools3.utils cimport str2bytes
cdef class OBIDMS_column_float(OBIDMS_column):
cpdef object get_line(self, size_t line_nb):
cpdef object get_line(self, index_t line_nb):
cdef obifloat_t value
cdef object result
value = obi_column_get_obifloat_with_elt_idx(self.pointer, line_nb, 0)
@ -26,7 +26,7 @@ cdef class OBIDMS_column_float(OBIDMS_column):
result = <double> value
return result
cpdef set_line(self, size_t line_nb, object value):
cpdef set_line(self, index_t line_nb, object value):
raise Exception("Column is read-only")
cpdef close(self):
@ -36,7 +36,7 @@ cdef class OBIDMS_column_float(OBIDMS_column):
cdef class OBIDMS_column_float_writable(OBIDMS_column_float):
cpdef set_line(self, size_t line_nb, object value):
cpdef set_line(self, index_t line_nb, object value):
if obi_column_set_obifloat_with_elt_idx(self.pointer, line_nb, 0, <obifloat_t> value) < 0:
raise Exception("Problem setting a value in a column")
@ -47,7 +47,7 @@ cdef class OBIDMS_column_float_writable(OBIDMS_column_float):
cdef class OBIDMS_column_float_multi_elts(OBIDMS_column_float):
cpdef object get_item(self, size_t line_nb, str element_name):
cpdef object get_item(self, index_t line_nb, str element_name):
cdef obifloat_t value
cdef object result
value = obi_column_get_obifloat_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
@ -59,10 +59,10 @@ cdef class OBIDMS_column_float_multi_elts(OBIDMS_column_float):
result = <double> value
return result
cpdef object get_line(self, size_t line_nb) :
cpdef object get_line(self, index_t line_nb) :
cdef obifloat_t value
cdef object result
cdef size_t i
cdef index_t i
cdef bint all_NA
result = {}
all_NA = True
@ -77,20 +77,20 @@ cdef class OBIDMS_column_float_multi_elts(OBIDMS_column_float):
result = None
return result
cpdef set_item(self, size_t line_nb, str element_name, obifloat_t value):
cpdef set_item(self, index_t line_nb, str element_name, obifloat_t value):
raise Exception("Column is read-only")
cpdef set_line(self, size_t line_nb, object values):
cpdef set_line(self, index_t line_nb, object values):
raise Exception("Column is read-only")
cdef class OBIDMS_column_float_multi_elts_writable(OBIDMS_column_float_multi_elts):
cpdef set_item(self, size_t line_nb, str element_name, obifloat_t value):
cpdef set_item(self, index_t line_nb, str element_name, obifloat_t value):
if obi_column_set_obifloat_with_elt_name(self.pointer, line_nb, str2bytes(element_name), value) < 0:
raise Exception("Problem setting a value in a column")
cpdef set_line(self, size_t line_nb, object values):
cpdef set_line(self, index_t line_nb, object values):
cdef obifloat_t value
for element_name in values :
value = <obifloat_t> values[element_name]

20
python/obitools3/obidms/_obidmscolumn_int.pxd
View File

@ -1,25 +1,25 @@
#cython: language_level=3
from .capi.obitypes cimport obiint_t
from .capi.obitypes cimport obiint_t, index_t
from ._obidms cimport OBIDMS_column
cdef class OBIDMS_column_int(OBIDMS_column):
cpdef object get_line(self, size_t line_nb)
cpdef set_line(self, size_t line_nb, object value)
cpdef object get_line(self, index_t line_nb)
cpdef set_line(self, index_t line_nb, object value)
cpdef close(self)
cdef class OBIDMS_column_int_writable(OBIDMS_column_int):
cpdef set_line(self, size_t line_nb, object value)
cpdef set_line(self, index_t line_nb, object value)
cpdef close(self)
cdef class OBIDMS_column_int_multi_elts(OBIDMS_column_int):
cpdef object get_item(self, size_t line_nb, str element_name)
cpdef object get_line(self, size_t line_nb)
cpdef set_item(self, size_t line_nb, str element_name, obiint_t value)
cpdef set_line(self, size_t line_nb, object values)
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, obiint_t value)
cpdef set_line(self, index_t line_nb, object values)
cdef class OBIDMS_column_int_multi_elts_writable(OBIDMS_column_int_multi_elts):
cpdef set_item(self, size_t line_nb, str element_name, obiint_t value)
cpdef set_line(self, size_t line_nb, object values)
cpdef set_item(self, index_t line_nb, str element_name, obiint_t value)
cpdef set_line(self, index_t line_nb, object values)
cpdef close(self)

20
python/obitools3/obidms/_obidmscolumn_int.pyx
View File

@ -16,7 +16,7 @@ from cpython.int cimport PyInt_FromLong
cdef class OBIDMS_column_int(OBIDMS_column):
cpdef object get_line(self, size_t line_nb):
cpdef object get_line(self, index_t line_nb):
cdef obiint_t value
cdef object result
value = obi_column_get_obiint_with_elt_idx(self.pointer, line_nb, 0)
@ -28,7 +28,7 @@ cdef class OBIDMS_column_int(OBIDMS_column):
result = PyInt_FromLong(value)
return result
cpdef set_line(self, size_t line_nb, object value):
cpdef set_line(self, index_t line_nb, object value):
raise Exception("Column is read-only")
cpdef close(self):
@ -38,7 +38,7 @@ cdef class OBIDMS_column_int(OBIDMS_column):
cdef class OBIDMS_column_int_writable(OBIDMS_column_int):
cpdef set_line(self, size_t line_nb, object value):
cpdef set_line(self, index_t line_nb, object value):
if obi_column_set_obiint_with_elt_idx(self.pointer, line_nb, 0, <obiint_t> value) < 0:
raise Exception("Problem setting a value in a column")
@ -49,7 +49,7 @@ cdef class OBIDMS_column_int_writable(OBIDMS_column_int):
cdef class OBIDMS_column_int_multi_elts(OBIDMS_column_int):
cpdef object get_item(self, size_t line_nb, str element_name):
cpdef object get_item(self, index_t line_nb, str element_name):
cdef obiint_t value
cdef object result
value = obi_column_get_obiint_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
@ -61,10 +61,10 @@ cdef class OBIDMS_column_int_multi_elts(OBIDMS_column_int):
result = PyInt_FromLong(value)
return result
cpdef object get_line(self, size_t line_nb) :
cpdef object get_line(self, index_t line_nb) :
cdef obiint_t value
cdef object result
cdef size_t i
cdef index_t i
cdef bint all_NA
result = {}
all_NA = True
@ -79,20 +79,20 @@ cdef class OBIDMS_column_int_multi_elts(OBIDMS_column_int):
result = None
return result
cpdef set_item(self, size_t line_nb, str element_name, obiint_t value):
cpdef set_item(self, index_t line_nb, str element_name, obiint_t value):
raise Exception("Column is read-only")
cpdef set_line(self, size_t line_nb, object values):
cpdef set_line(self, index_t line_nb, object values):
raise Exception("Column is read-only")
cdef class OBIDMS_column_int_multi_elts_writable(OBIDMS_column_int_multi_elts):
cpdef set_item(self, size_t line_nb, str element_name, obiint_t value):
cpdef set_item(self, index_t line_nb, str element_name, obiint_t value):
if obi_column_set_obiint_with_elt_name(self.pointer, line_nb, str2bytes(element_name), value) < 0:
raise Exception("Problem setting a value in a column")
cpdef set_line(self, size_t line_nb, object values):
cpdef set_line(self, index_t line_nb, object values):
cdef obiint_t value
for element_name in values :
value = <obiint_t> values[element_name]

19
python/obitools3/obidms/_obidmscolumn_str.pxd
View File

@ -1,24 +1,25 @@
#cython: language_level=3
from .capi.obitypes cimport index_t
from ._obidms cimport OBIDMS_column
cdef class OBIDMS_column_str(OBIDMS_column):
cpdef object get_line(self, size_t line_nb)
cpdef set_line(self, size_t line_nb, object value)
cpdef object get_line(self, index_t line_nb)
cpdef set_line(self, index_t line_nb, object value)
cpdef close(self)
cdef class OBIDMS_column_str_writable(OBIDMS_column_str):
cpdef set_line(self, size_t line_nb, object value)
cpdef set_line(self, index_t line_nb, object value)
cpdef close(self)
cdef class OBIDMS_column_str_multi_elts(OBIDMS_column_str):
cpdef object get_item(self, size_t line_nb, str element_name)
cpdef object get_line(self, size_t line_nb)
cpdef set_item(self, size_t line_nb, str element_name, str value)
cpdef set_line(self, size_t line_nb, object values)
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, str value)
cpdef set_line(self, index_t line_nb, object values)
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)
cpdef set_line(self, size_t line_nb, object values)
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)

44
python/obitools3/obidms/_obidmscolumn_str.pyx
View File

@ -9,42 +9,24 @@ from .capi.obidmscolumn cimport obi_close_column,\
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
cpdef object get_line(self, index_t line_nb):
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)
value = <bytes> obi_column_get_obistr_with_elt_idx(self.pointer, line_nb, 0)
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):
cpdef set_line(self, index_t line_nb, object value):
raise Exception("Column is read-only")
cpdef close(self):
@ -54,7 +36,7 @@ cdef class OBIDMS_column_str(OBIDMS_column):
cdef class OBIDMS_column_str_writable(OBIDMS_column_str):
cpdef set_line(self, size_t line_nb, object value):
cpdef set_line(self, index_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")
@ -65,10 +47,10 @@ cdef class OBIDMS_column_str_writable(OBIDMS_column_str):
cdef class OBIDMS_column_str_multi_elts(OBIDMS_column_str):
cpdef object get_item(self, size_t line_nb, str element_name):
cpdef object get_item(self, index_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))
value = <bytes> 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 :
@ -77,15 +59,15 @@ cdef class OBIDMS_column_str_multi_elts(OBIDMS_column_str):
result = bytes2str(value)
return result
cpdef object get_line(self, size_t line_nb) :
cpdef object get_line(self, index_t line_nb) :
cdef bytes value
cdef object result
cdef size_t i
cdef index_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)
value = <bytes> 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)
@ -95,20 +77,20 @@ cdef class OBIDMS_column_str_multi_elts(OBIDMS_column_str):
result = None
return result
cpdef set_item(self, size_t line_nb, str element_name, str value):
cpdef set_item(self, index_t line_nb, str element_name, str value):
raise Exception("Column is read-only")
cpdef set_line(self, size_t line_nb, object values):
cpdef set_line(self, index_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):
cpdef set_item(self, index_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):
cpdef set_line(self, index_t line_nb, object values):
cdef str value
for element_name in values :
value = values[element_name]

71
python/obitools3/obidms/capi/obidmscolumn.pxd
View File

@ -8,6 +8,7 @@ from ..capi.obitypes cimport const_char_p, \
obibool_t, \
obichar_t, \
obifloat_t, \
index_t, \
time_t
@ -16,9 +17,9 @@ cdef extern from "obidmscolumn.h" nogil:
struct OBIDMS_column_header_t:
bint little_endian
int header_size
size_t line_count
size_t lines_used
size_t nb_elements_per_line
index_t line_count
index_t lines_used
index_t nb_elements_per_line
const_char_p elements_names
OBIType_t data_type
time_t creation_date
@ -38,8 +39,8 @@ cdef extern from "obidmscolumn.h" nogil:
OBIDMS_column_p obi_create_column(OBIDMS_p dms,
const_char_p column_name,
OBIType_t type,
size_t nb_lines,
size_t nb_elements_per_line,
index_t nb_lines,
index_t nb_elements_per_line,
const_char_p elements_names,
const_char_p array_name)
@ -69,101 +70,101 @@ cdef extern from "obidmscolumn.h" nogil:
cdef extern from "obidmscolumn_int.h" nogil:
int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column,
size_t line_nb,
index_t line_nb,
const_char_p element_name,
obiint_t value)
int obi_column_set_obiint_with_elt_idx(OBIDMS_column_p column,
size_t line_nb,
size_t element_idx,
index_t line_nb,
index_t element_idx,
obiint_t value)
obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column,
size_t line_nb,
index_t line_nb,
const_char_p element_name)
obiint_t obi_column_get_obiint_with_elt_idx(OBIDMS_column_p column,
size_t line_nb,
size_t element_idx)
index_t line_nb,
index_t element_idx)
cdef extern from "obidmscolumn_bool.h" nogil:
int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column,
size_t line_nb,
index_t line_nb,
const_char_p element_name,
obibool_t value)
int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column,
size_t line_nb,
size_t element_idx,
index_t line_nb,
index_t element_idx,
obibool_t value)
obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column,
size_t line_nb,
index_t line_nb,
const_char_p element_name)
obibool_t obi_column_get_obibool_with_elt_idx(OBIDMS_column_p column,
size_t line_nb,
size_t element_idx)
index_t line_nb,
index_t element_idx)
cdef extern from "obidmscolumn_char.h" nogil:
int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column,
size_t line_nb,
index_t line_nb,
const_char_p element_name,
obichar_t value)
int obi_column_set_obichar_with_elt_idx(OBIDMS_column_p column,
size_t line_nb,
size_t element_idx,
index_t line_nb,
index_t element_idx,
obichar_t value)
obichar_t obi_column_get_obichar_with_elt_name(OBIDMS_column_p column,
size_t line_nb,
index_t line_nb,
const_char_p element_name)
obichar_t obi_column_get_obichar_with_elt_idx(OBIDMS_column_p column,
size_t line_nb,
size_t element_idx)
index_t line_nb,
index_t element_idx)
cdef extern from "obidmscolumn_float.h" nogil:
int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column,
size_t line_nb,
index_t line_nb,
const_char_p element_name,
obifloat_t value)
int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column,
size_t line_nb,
size_t element_idx,
index_t line_nb,
index_t element_idx,
obifloat_t value)
obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column,
size_t line_nb,
index_t line_nb,
const_char_p element_name)
obifloat_t obi_column_get_obifloat_with_elt_idx(OBIDMS_column_p column,
size_t line_nb,
size_t element_idx)
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,
size_t line_nb,
index_t line_nb,
const_char_p element_name,
char* value)
int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column,
size_t line_nb,
size_t element_idx,
index_t line_nb,
index_t element_idx,
char* value)
const_char_p obi_column_get_obistr_with_elt_name(OBIDMS_column_p column,
size_t line_nb,
index_t line_nb,
const_char_p element_name)
const_char_p obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column,
size_t line_nb,
size_t element_idx)
index_t line_nb,
index_t element_idx)

6
python/obitools3/obidms/capi/obitypes.pxd
View File

@ -1,7 +1,7 @@
#cython: language_level=3
from libc.stdint cimport int32_t
from libc.stdint cimport int32_t, int64_t
from posix.types cimport time_t
@ -33,10 +33,10 @@ cdef extern from "obitypes.h" nogil:
ctypedef int32_t obiint_t
ctypedef double obifloat_t
ctypedef char obichar_t
ctypedef size_t obiidx_t
ctypedef int64_t index_t
extern obiint_t OBIInt_NA
extern obiidx_t OBIIdx_NA
extern index_t OBIIdx_NA
extern obifloat_t OBIFloat_NA
extern obichar_t OBIChar_NA
extern obibool_t OBIBool_NA

64
python/obitools3/unit_tests.py
View File

@ -2,16 +2,17 @@ import os
import sys
import shutil
import unittest
from random import randint, uniform
from random import randint, uniform, choice
import string
from obitools3.obidms._obidms import OBIDMS
LINE_COUNT_FOR_TEST_COLUMN = 100000 # TODO randomize?
SMALLER_LINE_COUNT_FOR_TEST_COLUMN = 10000 # TODO randomize?
NB_ELEMENTS_PER_LINE = 50 # TODO randomize?
LINE_COUNT_FOR_TEST_COLUMN = 10000 # TODO randomize?
SMALLER_LINE_COUNT_FOR_TEST_COLUMN = 1000 # TODO randomize?
NB_ELEMENTS_PER_LINE = 20 # TODO randomize?
DMS_NAME = "unit_test_dms"
DATA_TYPES = ['OBI_INT', 'OBI_FLOAT', 'OBI_BOOL', 'OBI_CHAR']
DATA_TYPES = ['OBI_INT', 'OBI_FLOAT', 'OBI_BOOL', 'OBI_CHAR', 'OBI_IDX']
def create_test_obidms():
@ -26,7 +27,7 @@ def create_test_column(dms, data_type_code, multiple_elements_per_line=False):
data_type_code = data_type_code
data_type_str = data_types[data_type_code-1]
col_name = "unit_test_"+data_type_str
if multiple_elements_per_line :
elts_names = elements_names()
col = dms.open_column(col_name,
@ -41,7 +42,7 @@ def create_test_column(dms, data_type_code, multiple_elements_per_line=False):
create=True,
data_type=data_type_code)
return (col, col_name, data_type_str)
def elements_names():
names = [str(i) for i in range(NB_ELEMENTS_PER_LINE)]
@ -60,8 +61,9 @@ def random_obivalue(data_type):
nucs = 'atgc'
return bytes(nucs[randint(0,3)], 'utf-8')
elif data_type == "OBI_IDX" :
return randint(0,r)
length = randint(1,500)
randoms = ''.join(choice(string.ascii_lowercase) for i in range(length))
return randoms
class OBIDMS_Column_TestCase(unittest.TestCase):
def tearDown(self):
@ -228,14 +230,42 @@ class OBIDMS_Column_OBI_CHAR_multiple_elements_TestCase(OBIDMS_Column_multiple_e
multiple_elements_per_line=True)
class OBIDMS_Column_OBI_STR_TestCase(OBIDMS_Column_TestCase):
def setUp(self):
self.data_type_code = 5
self.dms, \
self.dms_name, \
self.dms_dir_name = create_test_obidms()
self.col, \
self.col_name, \
self.data_type_str = create_test_column(self.dms,
self.data_type_code)
class OBIDMS_Column_OBI_STR_multiple_elements_TestCase(OBIDMS_Column_multiple_elements_TestCase):
def setUp(self):
self.data_type_code = 5
self.dms, \
self.dms_name, \
self.dms_dir_name = create_test_obidms()
self.col, \
self.col_name, \
self.elts_names, \
self.data_type_str = create_test_column(self.dms,
self.data_type_code,
multiple_elements_per_line=True)
if __name__ == '__main__':
unittest.main(verbosity=2, defaultTest=["OBIDMS_Column_OBI_INT_TestCase",
"OBIDMS_Column_OBI_INT_multiple_elements_TestCase",
"OBIDMS_Column_OBI_FLOAT_TestCase",
"OBIDMS_Column_OBI_FLOAT_multiple_elements_TestCase",
"OBIDMS_Column_OBI_BOOL_TestCase",
"OBIDMS_Column_OBI_BOOL_multiple_elements_TestCase",
"OBIDMS_Column_OBI_CHAR_TestCase",
"OBIDMS_Column_OBI_CHAR_multiple_elements_TestCase"])
unittest.main(verbosity=2, defaultTest=["OBIDMS_Column_OBI_INT_TestCase",
"OBIDMS_Column_OBI_INT_multiple_elements_TestCase",
"OBIDMS_Column_OBI_FLOAT_TestCase",
"OBIDMS_Column_OBI_FLOAT_multiple_elements_TestCase",
"OBIDMS_Column_OBI_BOOL_TestCase",
"OBIDMS_Column_OBI_BOOL_multiple_elements_TestCase",
"OBIDMS_Column_OBI_CHAR_TestCase",
"OBIDMS_Column_OBI_CHAR_multiple_elements_TestCase",
"OBIDMS_Column_OBI_STR_TestCase",
"OBIDMS_Column_OBI_STR_multiple_elements_TestCase"])

2
python/obitools3/version.py
View File

@ -2,4 +2,4 @@ major = 1
minor = 1
serial= '16'
version ="%2d.%02d.%s" % (major,minor,serial)
version ="%d.%02d.%s" % (major,minor,serial)