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Major changes : new cython subclasses to handle columns with multiple

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elements per line in a more efficient way + now elements_names are
passed as a list + new function to recover only the header of a column
This commit is contained in:
Celine Mercier
2015-10-14 18:05:34 +02:00
parent 21923e213d
commit 0eaa5aa784
22 changed files with 749 additions and 516 deletions
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18
python/obitools3/obidms/_obidms.pxd
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@ -23,22 +23,24 @@ cdef class OBIDMS:
OBIType_t data_type=*,
size_t nb_lines=*,
size_t nb_elements_per_line=*,
str elements_names=*)
list elements_names=*)
cdef class OBIDMS_column:
cdef OBIDMS_column_p pointer
cdef OBIDMS dms
cdef str data_type # TODO keep as OBIType_t? both?
cdef str dms_name
cdef str column_name
cdef OBIDMS_column_p pointer
cdef OBIDMS dms
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 list elements_names
cpdef object get_item(self, size_t line_nb, str element_name)
# 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 str get_creation_date(self)
cpdef close(self)

226
python/obitools3/obidms/_obidms.pyx
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@ -6,37 +6,48 @@ from obitools3.utils cimport bytes2str, str2bytes
from .capi.obidms cimport obi_dms, \
obi_close_dms
from .capi.obidmscolumn cimport obi_column_get_data_type_from_name, \
obi_column_get_latest_version_from_name, \
obi_column_get_line_count_from_name, \
obi_column_get_nb_lines_used, \
from .capi.obidmscolumn cimport obi_column_get_nb_lines_used, \
obi_column_get_elements_names, \
obi_column_get_formatted_creation_date, \
obi_column_get_formatted_creation_date_from_name, \
obi_column_get_header_from_name, \
obi_unmap_header, \
obi_column_get_latest_version_from_name, \
obi_create_column, \
obi_clone_column, \
obi_open_column, \
obi_close_column
from .capi.obitypes cimport const_char_p, name_data_type
obi_close_column, \
OBIDMS_column_header_p
#obi_column_get_formatted_creation_date
from .capi.obitypes cimport const_char_p, \
name_data_type
from ._obidms cimport OBIDMS
from ._obidms cimport OBIDMS_column
from ._obidmscolumn_int cimport OBIDMS_column_int, \
OBIDMS_column_int_writable
OBIDMS_column_int_writable, \
OBIDMS_column_int_multi_elts, \
OBIDMS_column_int_multi_elts_writable
from ._obidmscolumn_float cimport OBIDMS_column_float, \
OBIDMS_column_float_writable
OBIDMS_column_float_writable, \
OBIDMS_column_float_multi_elts, \
OBIDMS_column_float_multi_elts_writable
from ._obidmscolumn_bool cimport OBIDMS_column_bool, \
OBIDMS_column_bool_writable
OBIDMS_column_bool_writable, \
OBIDMS_column_bool_multi_elts, \
OBIDMS_column_bool_multi_elts_writable
from ._obidmscolumn_char cimport OBIDMS_column_char, \
OBIDMS_column_char_writable
OBIDMS_column_char_writable, \
OBIDMS_column_char_multi_elts, \
OBIDMS_column_char_multi_elts_writable
from ._obidmscolumn_idx cimport OBIDMS_column_idx, \
OBIDMS_column_idx_writable
# from ._obidmscolumn_idx cimport OBIDMS_column_idx, \
# OBIDMS_column_idx_writable, \
# OBIDMS_column_idx_multi_elts, \
# OBIDMS_column_idx_multi_elts_writable
cdef class OBIDMS :
@ -72,6 +83,7 @@ cdef class OBIDMS :
cdef str creation_date
cdef obiversion_t latest_version
cdef size_t line_count
cdef OBIDMS_column_header_p header
p = Path(self.dms_name+'.obidms')
@ -85,11 +97,12 @@ cdef class OBIDMS :
column_name = entry.stem
column_name_b = str2bytes(column_name)
dms[column_name] = {}
data_type = bytes2str(name_data_type(obi_column_get_data_type_from_name(self.pointer, column_name_b)))
header = obi_column_get_header_from_name(self.pointer, column_name_b)
data_type = bytes2str(name_data_type(header.data_type))
line_count = header.line_count
latest_version = obi_column_get_latest_version_from_name(self.pointer, column_name_b)
line_count = obi_column_get_line_count_from_name(self.pointer, column_name_b)
# creation_date = bytes2str(obi_column_get_formatted_creation_date_from_name(self.pointer, column_name_b)) #TODO
# creation_date = bytes2str(obi_column_get_formatted_creation_date_from_name(self.pointer, column_name_b)) #TODO (deprecated, use header)
# print(creation_date)
dms[column_name]['data_type'] = data_type
@ -98,6 +111,7 @@ cdef class OBIDMS :
# dms[column_name]['creation_date'] = creation_date
print("{:<25} {:<25} {:<25} {:<25}".format(column_name, data_type, latest_version, line_count))
obi_unmap_header(header) # TODO check if error? but C will already warn and there's nothing to do
return dms
@ -108,97 +122,110 @@ cdef class OBIDMS :
obiversion_t version_number=-1,
OBIType_t data_type= <OBIType_t> 0,
size_t nb_lines=0,
size_t nb_elements_per_line=1,
str elements_names=None):
size_t nb_elements_per_line=0,
list elements_names=None):
# Declarations
cdef OBIDMS_column column
cdef object subclass # TODO object?
cdef bytes column_name_b
cdef OBIDMS_column_header_p header
header = NULL
# Format the character string to send to C function
column_name_b = str2bytes(column_name)
# Get the header of the latest version of the column if
# some needed informations are not provided
if ((not data_type or not nb_elements_per_line) and not create) :
header = obi_column_get_header_from_name(self.pointer, column_name_b)
# Get the data type if not provided
if not data_type :
if create :
raise Exception("A data type must be specified")
else :
data_type = obi_column_get_data_type_from_name(self.pointer, column_name_b)
data_type = header.data_type
# Open the column with the right subclass depending on the data type and the mode (read-only or writable)
# Get the number of elements per line if not provided and needed
if not nb_elements_per_line :
if create : # Set to one if not provided (default value)
nb_elements_per_line = 1
else :
nb_elements_per_line = header.nb_elements_per_line
if nb_elements_per_line > 1 :
elements_names = bytes2str(header.elements_names).split(';')
if header != NULL :
obi_unmap_header(header) # TODO check if error? but C will already warn and there's nothing to do
# Open the column with the right subclass depending on the data type, the mode
# (read-only or writable) and whether there are multiple elements per line or not
if data_type == 1 :
if (create or clone) :
column = OBIDMS_column_int_writable(self, column_name,
create, clone, clone_data,
version_number, data_type,
nb_lines, nb_elements_per_line,
elements_names)
if nb_elements_per_line == 1 :
subclass = OBIDMS_column_int_writable
else :
subclass = OBIDMS_column_int_multi_elts_writable
else :
column = OBIDMS_column_int(self, column_name,
create, clone, clone_data,
version_number, data_type,
nb_lines, nb_elements_per_line,
elements_names)
if nb_elements_per_line == 1 :
subclass = OBIDMS_column_int
else :
subclass = OBIDMS_column_int_multi_elts
elif data_type == 2 :
if (create or clone) :
column = OBIDMS_column_float_writable(self, column_name,
create, clone, clone_data,
version_number, data_type,
nb_lines, nb_elements_per_line,
elements_names)
if nb_elements_per_line == 1 :
subclass = OBIDMS_column_float_writable
else :
subclass = OBIDMS_column_float_multi_elts_writable
else :
column = OBIDMS_column_float(self, column_name,
create, clone, clone_data,
version_number, data_type,
nb_lines, nb_elements_per_line,
elements_names)
if nb_elements_per_line == 1 :
subclass = OBIDMS_column_float
else :
subclass = OBIDMS_column_float_multi_elts
elif data_type == 3 :
if (create or clone) :
column = OBIDMS_column_bool_writable(self, column_name,
create, clone, clone_data,
version_number, data_type,
nb_lines, nb_elements_per_line,
elements_names)
if nb_elements_per_line == 1 :
subclass = OBIDMS_column_bool_writable
else :
subclass = OBIDMS_column_bool_multi_elts_writable
else :
column = OBIDMS_column_bool(self, column_name,
create, clone, clone_data,
version_number, data_type,
nb_lines, nb_elements_per_line,
elements_names)
if nb_elements_per_line == 1 :
subclass = OBIDMS_column_bool
else :
subclass = OBIDMS_column_bool_multi_elts
elif data_type == 4 :
if (create or clone) :
column = OBIDMS_column_char_writable(self, column_name,
create, clone, clone_data,
version_number, data_type,
nb_lines, nb_elements_per_line,
elements_names)
if nb_elements_per_line == 1 :
subclass = OBIDMS_column_char_writable
else :
subclass = OBIDMS_column_char_multi_elts_writable
else :
column = OBIDMS_column_char(self, column_name,
create, clone, clone_data,
version_number, data_type,
nb_lines, nb_elements_per_line,
elements_names)
if nb_elements_per_line == 1 :
subclass = OBIDMS_column_char
else :
subclass = OBIDMS_column_char_multi_elts
# elif data_type == 5 :
# if (create or clone) :
# column = OBIDMS_column_idx_writable(self, column_name,
# create, clone, clone_data,
# version_number, data_type,
# nb_lines, nb_elements_per_line,
# elements_names)
# if nb_elements_per_line == 1 :
# subclass = OBIDMS_column_idx_writable
# else :
# subclass = OBIDMS_column_idx_multi_elts_writable
# else :
# column = OBIDMS_column_idx(self, column_name,
# create, clone, clone_data,
# version_number, data_type,
# nb_lines, nb_elements_per_line,
# elements_names)
# if nb_elements_per_line == 1 :
# subclass = OBIDMS_column_idx
# else :
# subclass = OBIDMS_column_idx_multi_elts
else :
raise Exception("Problem with the data type")
column = subclass(self, column_name,
create, clone, clone_data,
version_number, data_type,
nb_lines, nb_elements_per_line,
elements_names)
return column
@ -215,7 +242,7 @@ cdef class OBIDMS_column :
OBIType_t type,
size_t nb_lines,
size_t nb_elements_per_line,
str elements_names):
list elements_names):
# Declarations
cdef bytes column_name_b
@ -226,6 +253,8 @@ cdef class OBIDMS_column :
self.dms = dms
self.data_type = bytes2str(name_data_type(type))
self.column_name = column_name
self.nb_elements_per_line = nb_elements_per_line
self.elements_names = elements_names
# Format the character strings to send them to C functions
column_name_b = str2bytes(column_name)
@ -236,7 +265,7 @@ cdef class OBIDMS_column :
if elements_names == None :
elements_names_b = column_name_b
else :
elements_names_b = str2bytes(elements_names)
elements_names_b = str2bytes(";".join(elements_names))
self.pointer = obi_create_column(self.dms.pointer, column_name_b, type, nb_lines, nb_elements_per_line, elements_names_b)
else :
if clone :
@ -248,49 +277,28 @@ cdef class OBIDMS_column :
def __iter__(self):
# Declarations
cdef list elements_names
cdef str element_name
cdef bint multiple_elements
cdef object line # TODO
cdef size_t lines_used
cdef size_t line_nb
# Check if there are multiple elements per line anf if yes, get their names
elements_names = self.get_elements_names()
if len(elements_names) > 1 :
multiple_elements = True
else :
element_name = elements_names[0]
# Yield each line
lines_used = obi_column_get_nb_lines_used(self.pointer)
for line_nb in xrange(lines_used):
if multiple_elements :
line = []
for element_name in elements_names :
line.append(self.get_item(line_nb, element_name))
else :
line = self.get_item(line_nb, element_name)
yield line
for line_nb in range(lines_used):
yield self.get_line(line_nb)
def __setitem__(self, size_t line_nb, object value):
self.set_item(line_nb, "", value)
self.set_line(line_nb, value)
def __getitem__(self, size_t line_nb):
return self.get_item(line_nb, "")
return self.get_line(line_nb)
cpdef object get_item(self, size_t line_nb, str element_name):
raise NotImplementedError
# cpdef object get_item(self, size_t line_nb, str element_name): TODO
# raise NotImplementedError
# cpdef set_item(self, size_t line_nb, str element_name, object value): TODO
# raise NotImplementedError
cpdef list get_elements_names(self):
cdef bytes elements_names
elements_names = obi_column_get_elements_names(self.pointer)
return (bytes2str(elements_names)).split(';')
return self.elements_names
cpdef str get_data_type(self):
return self.data_type
@ -298,8 +306,8 @@ cdef class OBIDMS_column :
cpdef size_t get_nb_lines_used(self):
return obi_column_get_nb_lines_used(self.pointer)
cpdef str get_creation_date(self):
return bytes2str(obi_column_get_formatted_creation_date(self.pointer))
# cpdef str get_creation_date(self):
# return bytes2str(obi_column_get_formatted_creation_date(self.pointer))
cpdef close(self):
raise NotImplementedError

20
python/obitools3/obidms/_obidmscolumn_bool.pxd
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@ -1,17 +1,25 @@
#cython: language_level=3
from .capi.obitypes cimport obibool_t
from .capi.obidmscolumn cimport OBIDMS_column_p
from ._obidms cimport OBIDMS_column
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 close(self)
cdef class OBIDMS_column_bool_writable(OBIDMS_column_bool):
cpdef set_line(self, size_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 close(self)
cpdef set_line(self, size_t line_nb, object values)
cdef class OBIDMS_column_bool_writable(OBIDMS_column_bool):
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 close(self)

82
python/obitools3/obidms/_obidmscolumn_bool.pyx
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@ -3,7 +3,9 @@
from .capi.obidmscolumn cimport obi_close_column,\
obi_truncate_and_close_column, \
obi_column_get_obibool_with_elt_name, \
obi_column_set_obibool_with_elt_name
obi_column_get_obibool_with_elt_idx, \
obi_column_set_obibool_with_elt_name, \
obi_column_set_obibool_with_elt_idx
from .capi.obierrno cimport obi_errno
from .capi.obitypes cimport OBIBool_NA
@ -13,7 +15,40 @@ from cpython.bool cimport PyBool_FromLong
cdef class OBIDMS_column_bool(OBIDMS_column):
cpdef object get_line(self, size_t line_nb):
cdef obibool_t value
cdef object result
value = obi_column_get_obibool_with_elt_idx(self.pointer, line_nb, 0)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIBool_NA :
result = None
else :
result = PyBool_FromLong(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_bool_writable(OBIDMS_column_bool):
cpdef set_line(self, size_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")
cpdef close(self):
if obi_truncate_and_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")
cdef class OBIDMS_column_bool_multi_elts(OBIDMS_column_bool):
cpdef object get_item(self, size_t line_nb, str element_name):
cdef obibool_t value
cdef object result
@ -25,22 +60,45 @@ cdef class OBIDMS_column_bool(OBIDMS_column):
else :
result = PyBool_FromLong(value)
return result
cpdef object get_line(self, size_t line_nb) :
cdef obibool_t 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_obibool_with_elt_idx(self.pointer, line_nb, i)
if obi_errno > 0 :
raise IndexError(line_nb)
result[self.elements_names[i]] = PyBool_FromLong(value)
if all_NA and (value != OBIBool_NA) :
all_NA = False
if all_NA :
result = None
return result
cpdef set_item(self, size_t line_nb, str element_name, obibool_t value):
raise Exception("Column is read-only")
cpdef close(self):
if obi_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")
cpdef set_line(self, size_t line_nb, object values):
raise Exception("Column is read-only")
cdef class OBIDMS_column_bool_writable(OBIDMS_column_bool):
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):
if obi_column_set_obibool_with_elt_name(self.pointer, line_nb, str2bytes(element_name), value) < 0 :
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):
cdef obibool_t value
for element_name in values :
value = <obibool_t> 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")

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

@ -1,17 +1,25 @@
#cython: language_level=3
from .capi.obitypes cimport obichar_t
from .capi.obidmscolumn cimport OBIDMS_column_p
from ._obidms cimport OBIDMS_column
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 close(self)
cdef class OBIDMS_column_char_writable(OBIDMS_column_char):
cpdef set_line(self, size_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 close(self)
cpdef set_line(self, size_t line_nb, object values)
cdef class OBIDMS_column_char_writable(OBIDMS_column_char):
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 close(self)

122
python/obitools3/obidms/_obidmscolumn_char.pyx
View File

@ -3,17 +3,52 @@
from .capi.obidmscolumn cimport obi_close_column,\
obi_truncate_and_close_column, \
obi_column_get_obichar_with_elt_name, \
obi_column_set_obichar_with_elt_name
obi_column_get_obichar_with_elt_idx, \
obi_column_set_obichar_with_elt_name, \
obi_column_set_obichar_with_elt_idx
from .capi.obierrno cimport obi_errno
from .capi.obitypes cimport OBIChar_NA
from obitools3.utils cimport str2bytes
cdef class OBIDMS_column_char(OBIDMS_column) :
cdef class OBIDMS_column_char(OBIDMS_column):
cpdef object get_line(self, size_t line_nb):
cdef obichar_t value
cdef object result
value = obi_column_get_obichar_with_elt_idx(self.pointer, line_nb, 0)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIChar_NA :
result = None
else :
result = <bytes> 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_char_writable(OBIDMS_column_char):
cpdef set_line(self, size_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")
cpdef close(self):
if obi_truncate_and_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")
cdef class OBIDMS_column_char_multi_elts(OBIDMS_column_char):
cpdef object get_item(self, size_t line_nb, str element_name):
cdef char value
cdef obichar_t value
cdef object result
value = obi_column_get_obichar_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
if obi_errno > 0 :
@ -23,22 +58,81 @@ cdef class OBIDMS_column_char(OBIDMS_column) :
else :
result = <bytes> value
return result
cpdef object get_line(self, size_t line_nb) :
cdef obichar_t 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_obichar_with_elt_idx(self.pointer, line_nb, i)
if obi_errno > 0 :
raise IndexError(line_nb)
result[self.elements_names[i]] = <bytes> value
if all_NA and (value != OBIChar_NA) :
all_NA = False
if all_NA :
result = None
return result
cpdef set_item(self, size_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_line(self, size_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):
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):
cdef bytes value
for element_name in values :
value = <bytes> 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, size_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, size_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, size_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")
#

21
python/obitools3/obidms/_obidmscolumn_float.pxd
View File

@ -1,16 +1,25 @@
#cython: language_level=3
from .capi.obitypes cimport obifloat_t
from .capi.obidmscolumn cimport OBIDMS_column_p
from ._obidms cimport OBIDMS_column
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 close(self)
cdef class OBIDMS_column_float_writable(OBIDMS_column_float):
cpdef set_line(self, size_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 close(self)
cdef class OBIDMS_column_float_writable(OBIDMS_column_float):
cpdef set_line(self, size_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 close(self)

71
python/obitools3/obidms/_obidmscolumn_float.pyx
View File

@ -3,7 +3,9 @@
from .capi.obidmscolumn cimport obi_close_column,\
obi_truncate_and_close_column, \
obi_column_get_obifloat_with_elt_name, \
obi_column_set_obifloat_with_elt_name
obi_column_get_obifloat_with_elt_idx, \
obi_column_set_obifloat_with_elt_name, \
obi_column_set_obifloat_with_elt_idx
from .capi.obierrno cimport obi_errno
from .capi.obitypes cimport OBIFloat_NA
@ -12,6 +14,39 @@ from obitools3.utils cimport str2bytes
cdef class OBIDMS_column_float(OBIDMS_column):
cpdef object get_line(self, size_t line_nb):
cdef obifloat_t value
cdef object result
value = obi_column_get_obifloat_with_elt_idx(self.pointer, line_nb, 0)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIFloat_NA :
result = None
else :
result = <double> 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_float_writable(OBIDMS_column_float):
cpdef set_line(self, size_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")
cpdef close(self):
if obi_truncate_and_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")
cdef class OBIDMS_column_float_multi_elts(OBIDMS_column_float):
cpdef object get_item(self, size_t line_nb, str element_name):
cdef obifloat_t value
cdef object result
@ -24,21 +59,45 @@ cdef class OBIDMS_column_float(OBIDMS_column):
result = <double> value
return result
cpdef object get_line(self, size_t line_nb) :
cdef obifloat_t 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_obifloat_with_elt_idx(self.pointer, line_nb, i)
if obi_errno > 0 :
raise IndexError(line_nb)
result[self.elements_names[i]] = <double> value
if all_NA and (value != OBIFloat_NA) :
all_NA = False
if all_NA :
result = None
return result
cpdef set_item(self, size_t line_nb, str element_name, obifloat_t value):
raise Exception("Column is read-only")
cpdef close(self):
if obi_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")
cpdef set_line(self, size_t line_nb, object values):
raise Exception("Column is read-only")
cdef class OBIDMS_column_float_writable(OBIDMS_column_float):
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):
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):
cdef obifloat_t value
for element_name in values :
value = <obifloat_t> 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")

21
python/obitools3/obidms/_obidmscolumn_idx.pxd
View File

@ -1,16 +1,25 @@
#cython: language_level=3
from .capi.obitypes cimport obiidx_t
from .capi.obidmscolumn cimport OBIDMS_column_p
from ._obidms cimport OBIDMS_column
from ._obidms cimport OBIDMS_column
cdef class OBIDMS_column_idx(OBIDMS_column):
cpdef object get_line(self, size_t line_nb)
cpdef set_line(self, size_t line_nb, object value)
cpdef close(self)
cdef class OBIDMS_column_idx_writable(OBIDMS_column_idx):
cpdef set_line(self, size_t line_nb, object value)
cpdef close(self)
cdef class OBIDMS_column_idx_multi_elts(OBIDMS_column_idx):
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, obiidx_t value)
cpdef close(self)
cdef class OBIDMS_column_idx_writable(OBIDMS_column_idx):
cpdef set_line(self, size_t line_nb, object values)
cdef class OBIDMS_column_idx_multi_elts_writable(OBIDMS_column_idx_multi_elts):
cpdef set_item(self, size_t line_nb, str element_name, obiidx_t value)
cpdef set_line(self, size_t line_nb, object values)
cpdef close(self)

73
python/obitools3/obidms/_obidmscolumn_idx.pyx
View File

@ -1,9 +1,11 @@
#cython: language_level=3
from .capi.obidmscolumn cimport obi_close_column,\
obi_truncate_and_close_column, \
obi_column_get_obiidx_with_elt_name, \
obi_column_set_obiidx_with_elt_name
obi_column_get_obiidx_with_elt_idx, \
obi_column_set_obiidx_with_elt_name, \
obi_column_set_obiidx_with_elt_idx
from .capi.obierrno cimport obi_errno
from .capi.obitypes cimport OBIIdx_NA
@ -14,6 +16,39 @@ from cpython.int cimport PyInt_FromSsize_t
cdef class OBIDMS_column_idx(OBIDMS_column):
cpdef object get_line(self, size_t line_nb):
cdef obiidx_t value
cdef object result
value = obi_column_get_obiidx_with_elt_idx(self.pointer, line_nb, 0)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIIdx_NA :
result = None
else :
result = PyInt_FromSsize_t(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_idx_writable(OBIDMS_column_idx):
cpdef set_line(self, size_t line_nb, object value):
if obi_column_set_obiidx_with_elt_idx(self.pointer, line_nb, 0, <obiidx_t> 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_idx_multi_elts(OBIDMS_column_idx):
cpdef object get_item(self, size_t line_nb, str element_name):
cdef obiidx_t value
cdef object result
@ -26,21 +61,45 @@ cdef class OBIDMS_column_idx(OBIDMS_column):
result = PyInt_FromSsize_t(value)
return result
cpdef object get_line(self, size_t line_nb) :
cdef obiidx_t 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_obiidx_with_elt_idx(self.pointer, line_nb, i)
if obi_errno > 0 :
raise IndexError(line_nb)
result[self.elements_names[i]] = PyInt_FromSsize_t(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, obiidx_t value):
raise Exception("Column is read-only")
cpdef close(self):
if obi_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")
cpdef set_line(self, size_t line_nb, object values):
raise Exception("Column is read-only")
cdef class OBIDMS_column_idx_writable(OBIDMS_column_idx):
cdef class OBIDMS_column_idx_multi_elts_writable(OBIDMS_column_idx_multi_elts):
cpdef set_item(self, size_t line_nb, str element_name, obiidx_t value):
if obi_column_set_obiidx_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):
cdef obiidx_t value
for element_name in values :
value = <obiidx_t> 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")

21
python/obitools3/obidms/_obidmscolumn_int.pxd
View File

@ -1,16 +1,25 @@
#cython: language_level=3
from .capi.obitypes cimport obiint_t
from .capi.obidmscolumn cimport OBIDMS_column_p
from ._obidms cimport OBIDMS_column
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 close(self)
cdef class OBIDMS_column_int_writable(OBIDMS_column_int):
cpdef set_line(self, size_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 close(self)
cdef class OBIDMS_column_int_writable(OBIDMS_column_int):
cpdef set_line(self, size_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 close(self)

74
python/obitools3/obidms/_obidmscolumn_int.pyx
View File

@ -3,7 +3,9 @@
from .capi.obidmscolumn cimport obi_close_column,\
obi_truncate_and_close_column, \
obi_column_get_obiint_with_elt_name, \
obi_column_set_obiint_with_elt_name
obi_column_get_obiint_with_elt_idx, \
obi_column_set_obiint_with_elt_name, \
obi_column_set_obiint_with_elt_idx
from .capi.obierrno cimport obi_errno
from .capi.obitypes cimport OBIInt_NA
@ -11,11 +13,42 @@ from obitools3.utils cimport str2bytes
from cpython.int cimport PyInt_FromLong
from ._obidms cimport OBIDMS_column
cdef class OBIDMS_column_int(OBIDMS_column):
cpdef object get_line(self, size_t line_nb):
cdef obiint_t value
cdef object result
value = obi_column_get_obiint_with_elt_idx(self.pointer, line_nb, 0)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIInt_NA :
result = None
else :
result = PyInt_FromLong(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_int_writable(OBIDMS_column_int):
cpdef set_line(self, size_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")
cpdef close(self):
if obi_truncate_and_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")
cdef class OBIDMS_column_int_multi_elts(OBIDMS_column_int):
cpdef object get_item(self, size_t line_nb, str element_name):
cdef obiint_t value
cdef object result
@ -28,21 +61,44 @@ cdef class OBIDMS_column_int(OBIDMS_column):
result = PyInt_FromLong(value)
return result
cpdef object get_line(self, size_t line_nb) :
cdef obiint_t 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_obiint_with_elt_idx(self.pointer, line_nb, i)
if obi_errno > 0 :
raise IndexError(line_nb)
result[self.elements_names[i]] = PyInt_FromLong(value)
if all_NA and (value != OBIInt_NA) :
all_NA = False
if all_NA :
result = None
return result
cpdef set_item(self, size_t line_nb, str element_name, obiint_t value):
raise Exception("Column is read-only")
cpdef close(self):
if obi_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")
cpdef set_line(self, size_t line_nb, object values):
raise Exception("Column is read-only")
cdef class OBIDMS_column_int_writable(OBIDMS_column_int):
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):
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):
cdef obiint_t value
for element_name in values :
value = <obiint_t> 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")

87
python/obitools3/obidms/capi/obidmscolumn.pxd
View File

@ -8,13 +8,32 @@ from ..capi.obitypes cimport const_char_p, \
obibool_t, \
obichar_t, \
obifloat_t, \
obiidx_t
obiidx_t, \
time_t
cdef extern from "obidmscolumn.h" nogil:
struct OBIDMS_column_t:
pass
ctypedef OBIDMS_column_t* OBIDMS_column_p
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
const_char_p elements_names
OBIType_t data_type
time_t creation_date
obiversion_t version
obiversion_t cloned_from
const_char_p name
const_char_p comments
ctypedef OBIDMS_column_header_t* OBIDMS_column_header_p
OBIDMS_column_p obi_create_column(OBIDMS_p dms,
const_char_p column_name,
@ -36,10 +55,7 @@ cdef extern from "obidmscolumn.h" nogil:
OBIType_t obi_column_get_type(OBIDMS_column_p column)
int obi_close_column(OBIDMS_column_p column)
OBIType_t obi_column_get_data_type_from_name(OBIDMS_p dms,
const_char_p column_name)
OBIDMS_column_p obi_clone_column(OBIDMS_p dms,
const_char_p column_name,
obiversion_t version_number,
@ -49,17 +65,16 @@ cdef extern from "obidmscolumn.h" nogil:
obiversion_t obi_column_get_latest_version_from_name(OBIDMS_p dms,
const_char_p column_name)
OBIDMS_column_header_p obi_column_get_header_from_name(OBIDMS_p dms,
const_char_p column_name)
OBIType_t obi_column_get_data_type_from_name(OBIDMS_p dms,
const_char_p column_name)
int obi_unmap_header(OBIDMS_column_header_p header)
size_t obi_column_get_line_count_from_name(OBIDMS_p dms,
const_char_p column_name)
# char* obi_column_get_formatted_creation_date(OBIDMS_column_p column)
char* obi_column_get_formatted_creation_date(OBIDMS_column_p column)
char* obi_column_get_formatted_creation_date_from_name(OBIDMS_p dms,
const_char_p column_name)
# char* obi_column_get_formatted_creation_date_from_name(OBIDMS_p dms,
# const_char_p column_name)
cdef extern from "obidmscolumn_int.h" nogil:
@ -67,10 +82,20 @@ cdef extern from "obidmscolumn_int.h" nogil:
size_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,
obiint_t value)
obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column,
size_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)
cdef extern from "obidmscolumn_bool.h" nogil:
@ -79,9 +104,18 @@ cdef extern from "obidmscolumn_bool.h" nogil:
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,
obibool_t value)
obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column,
size_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)
cdef extern from "obidmscolumn_char.h" nogil:
@ -90,9 +124,18 @@ cdef extern from "obidmscolumn_char.h" nogil:
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,
obichar_t value)
obichar_t obi_column_get_obichar_with_elt_name(OBIDMS_column_p column,
size_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)
cdef extern from "obidmscolumn_float.h" nogil:
@ -101,9 +144,18 @@ cdef extern from "obidmscolumn_float.h" nogil:
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,
obifloat_t value)
obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column,
size_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)
cdef extern from "obidmscolumn_idx.h" nogil:
@ -112,7 +164,16 @@ cdef extern from "obidmscolumn_idx.h" nogil:
const_char_p element_name,
obiidx_t value)
int obi_column_set_obiidx_with_elt_idx(OBIDMS_column_p column,
size_t line_nb,
size_t element_idx,
obiidx_t value)
obiidx_t obi_column_get_obiidx_with_elt_name(OBIDMS_column_p column,
size_t line_nb,
const_char_p element_name)
obiidx_t obi_column_get_obiidx_with_elt_idx(OBIDMS_column_p column,
size_t line_nb,
size_t element_idx)

1
python/obitools3/obidms/capi/obitypes.pxd
View File

@ -2,6 +2,7 @@
from libc.stdint cimport int32_t
from posix.types cimport time_t
cdef extern from *:

34
python/obitools3/unit_tests.py
View File

@ -25,15 +25,15 @@ def create_test_column(dms, data_type_code, multiple_elements_per_line=False):
data_types = DATA_TYPES
data_type_code = data_type_code
data_type_str = data_types[data_type_code-1]
col_name = "test_col"+data_type_str
col_name = "test_col_"+data_type_str
if multiple_elements_per_line :
elts_names = elements_names().split(";")
elts_names = elements_names()
col = dms.open_column(col_name,
create=True,
data_type=data_type_code,
nb_elements_per_line=NB_ELEMENTS_PER_LINE,
elements_names=elements_names())
elements_names=elts_names)
return (col, col_name, elts_names, data_type_str)
else :
@ -44,10 +44,8 @@ def create_test_column(dms, data_type_code, multiple_elements_per_line=False):
def elements_names():
names = ""
for i in range(NB_ELEMENTS_PER_LINE):
names = names + str(i) + ";"
return names[:-1]
names = [str(i) for i in range(NB_ELEMENTS_PER_LINE)]
return names
def random_obivalue(data_type):
@ -94,26 +92,36 @@ class OBIDMS_Column_TestCase(unittest.TestCase):
class OBIDMS_Column_multiple_elements_TestCase(OBIDMS_Column_TestCase):
def test_OBIDMS_column_cloning(self):
pass
for i in range(SMALLER_LINE_COUNT_FOR_TEST_COLUMN):
for e in range(NB_ELEMENTS_PER_LINE) :
self.col.set_item(i, self.elts_names[e], random_obivalue(self.data_type_str))
v = {}
for e in self.elts_names :
v[e] = random_obivalue(self.data_type_str)
self.col[i] = v
self.col.close()
clone = self.dms.open_column(self.col_name, clone=True)
self.col = self.dms.open_column(self.col_name)
assert clone.get_nb_lines_used() == self.col.get_nb_lines_used(), "Cloned column doesn't have the same number of lines used"
i=0
for i in range(SMALLER_LINE_COUNT_FOR_TEST_COLUMN):
for e in range(NB_ELEMENTS_PER_LINE) :
assert clone.get_item(i, self.elts_names[e]) == self.col.get_item(i, self.elts_names[e]), "Different value in original column and cloned column"
assert clone.get_item(i, self.elts_names[e]) is not None, "None value"
assert self.col[i] == clone[i], "Different value in original column and cloned column"
assert self.col[i] is not None, "None value"
clone.close()
def test_OBIDMS_column_set_and_get(self):
def test_OBIDMS_column_set_and_get_with_elements_names(self):
for i in range(SMALLER_LINE_COUNT_FOR_TEST_COLUMN):
for e in range(NB_ELEMENTS_PER_LINE) :
v = random_obivalue(self.data_type_str)
self.col.set_item(i, self.elts_names[e], v)
assert self.col.get_item(i, self.elts_names[e]) == v, "Different value than the set value"
assert self.col.get_item(i, self.elts_names[e]) is not None, "None value"
def test_OBIDMS_column_set_and_get(self):
for i in range(SMALLER_LINE_COUNT_FOR_TEST_COLUMN):
v = {}
for e in self.elts_names :
v[e] = random_obivalue(self.data_type_str)
self.col[i] = v
assert self.col[i] == v, "Different value than the set value"
assert self.col[i] is not None, "None value"
class OBIDMS_Column_OBI_INT_TestCase(OBIDMS_Column_TestCase):