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Major update : views

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This commit is contained in:
Celine Mercier
2016-02-18 10:38:51 +01:00
parent cfaf069095
commit a8f03248a8
46 changed files with 3207 additions and 1070 deletions
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6
python/obitools3/obidms/_obidms.cfiles
View File

@ -1,5 +1,7 @@
../../../src/obidms.h
../../../src/obidms.c
../../../src/obiview.h
../../../src/obiview.c
../../../src/obidmscolumn.h
../../../src/obidmscolumn.c
../../../src/obidmscolumndir.h
@ -15,4 +17,6 @@
../../../src/obiavl.h
../../../src/obiavl.c
../../../src/encode.h
../../../src/encode.c
../../../src/encode.c
../../../src/obidmscolumn_idx.h
../../../src/obidmscolumn_idx.c

90
python/obitools3/obidms/_obidms.pxd
View File

@ -2,52 +2,80 @@
from .capi.obidms cimport OBIDMS_p
from .capi.obidmscolumn cimport OBIDMS_column_p
from .capi.obiview cimport Obiview_p
from .capi.obitypes cimport obiversion_t, OBIType_t, index_t
cdef class OBIDMS_column
cdef class OBIDMS:
cdef OBIDMS_p pointer
cdef str dms_name
cpdef dict list(self)
cpdef close(self)
cpdef OBIDMS_column open_column(self,
str column_name,
bint create=*,
bint clone=*, bint clone_data=*,
bint referring=*,
obiversion_t version_number=*,
str type=*,
index_t nb_lines=*,
index_t nb_elements_per_line=*,
list elements_names=*,
str avl_name=*,
str comments=*)
cdef class OBIDMS_column:
cdef OBIDMS_column_p pointer
cdef OBIDMS_column_p* pointer
cdef OBIDMS dms
cdef Obiview_p view
cdef str data_type
cdef str dms_name
cdef str column_name
cdef index_t nb_elements_per_line
cdef list elements_names
cpdef OBIDMS_column_p referred_column_pointer
# 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 grep_line(self, index_t line_nb)
cpdef update_pointer(self)
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 str get_comments(self)
cpdef close(self)
@staticmethod
cdef object get_subclass_type(OBIDMS_column_p column_p)
cdef class OBIDMS_column_multi_elts(OBIDMS_column):
cpdef set_line(self, index_t line_nb, dict values)
cdef class OBIDMS_column_line:
cdef OBIDMS_column column
cdef index_t index
cdef class OBIView:
cdef Obiview_p pointer
cdef str name
cdef dict columns
cdef dict columns_pp # TODO this dict might be unnecessary
cdef OBIDMS dms
cpdef delete_column(self, str column_name)
cpdef add_column(self,
str column_name,
obiversion_t version_number=*,
str type=*,
index_t nb_lines=*,
index_t nb_elements_per_line=*,
list elements_names=*,
str avl_name=*,
str comments=*,
bint create=*
)
cpdef select_line(self, index_t line_nb)
cpdef select_lines(self, list line_selection)
cpdef save_and_close(self)
cdef class OBIView_line :
cdef index_t index
cdef OBIView view
cdef class OBIDMS:
cdef OBIDMS_p pointer
cdef str dms_name
cpdef close(self)
cpdef OBIView open_view(self, str view_name)
cpdef OBIView new_view(self, str view_name, object view_to_clone=*, list line_selection=*)

806
python/obitools3/obidms/_obidms.pyx
View File

@ -6,16 +6,12 @@ from obitools3.utils cimport bytes2str, str2bytes
from .capi.obidms cimport obi_dms, \
obi_close_dms
from .capi.obidmscolumn cimport 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.obidmscolumn cimport obi_truncate_and_close_column, \
obi_column_format_date, \
obi_grep_line, \
OBIDMS_column_p, \
OBIDMS_column_header_p
from .capi.obitypes cimport const_char_p, \
OBIType_t, \
OBI_INT, \
@ -24,42 +20,486 @@ from .capi.obitypes cimport const_char_p, \
OBI_CHAR, \
OBI_STR, \
OBI_SEQ, \
name_data_type
name_data_type, \
only_ATGC # discuss
from ._obidms cimport OBIDMS
from ._obidms cimport OBIDMS_column
from ._obidms cimport OBIView_line
from ._obidmscolumn_int cimport OBIDMS_column_int, \
OBIDMS_column_int_writable, \
OBIDMS_column_int_multi_elts, \
OBIDMS_column_int_multi_elts_writable
OBIDMS_column_multi_elts_int
from ._obidmscolumn_float cimport OBIDMS_column_float, \
OBIDMS_column_float_writable, \
OBIDMS_column_float_multi_elts, \
OBIDMS_column_float_multi_elts_writable
OBIDMS_column_multi_elts_float
from ._obidmscolumn_bool cimport OBIDMS_column_bool, \
OBIDMS_column_bool_writable, \
OBIDMS_column_bool_multi_elts, \
OBIDMS_column_bool_multi_elts_writable
OBIDMS_column_multi_elts_bool
from ._obidmscolumn_char cimport OBIDMS_column_char, \
OBIDMS_column_char_writable, \
OBIDMS_column_char_multi_elts, \
OBIDMS_column_char_multi_elts_writable
OBIDMS_column_multi_elts_char
from ._obidmscolumn_str cimport OBIDMS_column_str, \
OBIDMS_column_str_writable, \
OBIDMS_column_str_multi_elts, \
OBIDMS_column_str_multi_elts_writable
OBIDMS_column_multi_elts_str
from ._obidmscolumn_seq cimport OBIDMS_column_seq, \
OBIDMS_column_seq_writable, \
OBIDMS_column_seq_multi_elts, \
OBIDMS_column_seq_multi_elts_writable
OBIDMS_column_multi_elts_seq
from ._obidms cimport OBIView, OBIView_line
from .capi.obiview cimport Obiview_p, \
obi_new_view, \
obi_new_view_cloned_from_name, \
obi_open_view, \
obi_view_delete_column, \
obi_view_add_column, \
obi_view_get_column, \
obi_view_get_pointer_on_column_in_view, \
obi_select_line, \
obi_select_lines, \
obi_save_and_close_view
from libc.stdlib cimport malloc
from cpython.pycapsule cimport PyCapsule_New, PyCapsule_GetPointer
cdef class OBIDMS_column :
# Should only be initialized through a subclass
def __init__(self, OBIView view, str column_name):
cdef OBIDMS_column_p column_p
cdef OBIDMS_column_p* column_pp
column_pp = <OBIDMS_column_p*> PyCapsule_GetPointer(((view.columns_pp)[column_name]), NULL) # or use C function
column_p = column_pp[0] # TODO ugly cython dereferencing but can't find better
# Fill structure
self.pointer = column_pp
self.dms = view.dms
self.view = view.pointer # TODO pointer or instance?
self.data_type = bytes2str(name_data_type((column_p.header).returned_data_type))
self.column_name = bytes2str((column_p.header).name)
self.nb_elements_per_line = (column_p.header).nb_elements_per_line
self.elements_names = (bytes2str((column_p.header).elements_names)).split(';')
def __setitem__(self, index_t line_nb, object value):
self.set_line(line_nb, value)
def __getitem__(self, index_t line_nb):
return self.get_line(line_nb)
def __len__(self):
return (self.pointer)[0].header.lines_used
def __sizeof__(self):
return ((self.pointer)[0].header.header_size + (self.pointer)[0].header.data_size)
def __iter__(self):
# Declarations
cdef index_t lines_used
cdef index_t line_nb
# Yield each line
lines_used = (self.pointer)[0].header.lines_used
for line_nb in range(lines_used):
yield self.get_line(line_nb)
cpdef update_pointer(self):
self.pointer = <OBIDMS_column_p*> obi_view_get_pointer_on_column_in_view(self.view, str2bytes(self.column_name))
cpdef list get_elements_names(self):
return self.elements_names
cpdef str get_data_type(self):
return self.data_type
cpdef index_t get_nb_lines_used(self):
return (self.pointer)[0].header.lines_used
cpdef str get_creation_date(self):
return bytes2str(obi_column_format_date((self.pointer)[0].header.creation_date))
cpdef str get_comments(self):
return bytes2str((self.pointer)[0].header.comments)
def __repr__(self) :
cdef str to_print
to_print = ''
for line in self :
to_print = to_print + str(line) + "\n"
return to_print
cpdef close(self):
if obi_truncate_and_close_column((self.pointer)[0]) < 0 :
raise Exception("Problem closing a column")
@staticmethod
cdef object get_subclass_type(OBIDMS_column_p column_p) :
cdef object subclass
cdef OBIDMS_column_header_p header
cdef OBIType_t col_type
cdef bint col_writable
cdef bint col_one_element_per_line
header = column_p.header
col_type = header.returned_data_type
col_writable = column_p.writable
col_one_element_per_line = ((header.nb_elements_per_line) == 1)
if col_type == OBI_INT :
if col_one_element_per_line :
subclass = OBIDMS_column_int
else :
subclass = OBIDMS_column_multi_elts_int
elif col_type == OBI_FLOAT :
if col_one_element_per_line :
subclass = OBIDMS_column_float
else :
subclass = OBIDMS_column_multi_elts_float
elif col_type == OBI_BOOL :
if col_one_element_per_line :
subclass = OBIDMS_column_bool
else :
subclass = OBIDMS_column_multi_elts_bool
elif col_type == OBI_CHAR :
if col_one_element_per_line :
subclass = OBIDMS_column_char
else :
subclass = OBIDMS_column_multi_elts_char
elif col_type == OBI_STR :
if col_one_element_per_line :
subclass = OBIDMS_column_str
else :
subclass = OBIDMS_column_multi_elts_str
elif col_type == OBI_SEQ :
if col_one_element_per_line :
subclass = OBIDMS_column_seq
else :
subclass = OBIDMS_column_multi_elts_seq
else :
raise Exception("Problem with the data type")
return subclass
######################################################################################################
cdef class OBIDMS_column_multi_elts(OBIDMS_column) :
def __getitem__(self, index_t line_nb):
return OBIDMS_column_line(self, line_nb)
cpdef set_line(self, index_t line_nb, dict values):
for element_name in values :
self.set_item(line_nb, element_name, values[element_name])
######################################################################################################
cdef class OBIDMS_column_line :
def __init__(self, OBIDMS_column column, index_t line_nb) :
self.index = line_nb
self.column = column
def __getitem__(self, str element_name) :
return self.column.get_item(self.index, element_name)
def __setitem__(self, str element_name, object value):
self.column.set_item(self.index, element_name, value)
def __contains__(self, str element_name):
return (element_name in self.column.elements_names)
def __repr__(self) :
return str(self.column.get_line(self.index))
##########################################
cdef class OBIView :
def __init__(self, OBIDMS dms, str view_name, bint new=False, object view_to_clone=None, list line_selection=None):
cdef Obiview_p view = NULL
cdef int i
cdef list col_list
cdef str col_name
cdef OBIDMS_column column
cdef OBIDMS_column_p column_p
cdef OBIDMS_column_p* column_pp
cdef OBIDMS_column_header_p header
cdef index_t* line_selection_p
self.dms = dms
if line_selection is not None :
line_selection_p = <index_t*> malloc((len(line_selection) + 1) * sizeof(index_t))
for i in range(len(line_selection)) :
line_selection_p[i] = line_selection[i] # TODO type problem?
print(line_selection_p[i], line_selection[i])
line_selection_p[len(line_selection)] = -1
else :
line_selection_p = NULL
if new :
if view_to_clone is not None :
if type(view_to_clone) == str :
view = obi_new_view_cloned_from_name(dms.pointer, str2bytes(view_name), str2bytes(view_to_clone), line_selection_p)
else :
view = obi_new_view(dms.pointer, str2bytes(view_name), (<OBIView> view_to_clone).pointer, line_selection_p)
elif view_to_clone is None :
view = obi_new_view(dms.pointer, str2bytes(view_name), NULL, line_selection_p)
elif not new :
if view_name is not None :
view = obi_open_view(dms.pointer, str2bytes(view_name))
elif view_name is None :
view = obi_open_view(dms.pointer, NULL)
if view == NULL :
raise Exception("Error creating/opening view")
self.pointer = view
self.name = bytes2str(view.name)
# go through columns to build list and open python object (TODO make separate function?)
self.columns = {}
self.columns_pp = {}
i = 0
while i < view.column_count :
column_pp = <OBIDMS_column_p*> ((view.columns)+i)
column_p = <OBIDMS_column_p> (view.columns)[i]
header = (column_p).header
col_name = bytes2str(header.name)
col_capsule = PyCapsule_New(column_pp, NULL, NULL) # TODO discuss
(self.columns_pp)[col_name] = col_capsule
subclass = OBIDMS_column.get_subclass_type(column_p)
self.columns[col_name] = subclass(self, col_name)
i+=1
def __repr__(self) :
cdef str s
cdef OBIDMS_column column
cdef OBIDMS_column_p column_p
s = self.name
s = s + ", " + str(self.pointer.line_count) + " lines"
for column_name in self.columns : # TODO make function in OBIDMS_column class
column = self.columns[column_name]
column_p = (column.pointer)[0]
s = s + "\n" + column_name + ", version " + str(column_p.header.version) + ", data type: " + column.data_type
return s
cpdef delete_column(self, str column_name) :
cdef int i
cdef Obiview_p view
cdef OBIDMS_column column
cdef OBIDMS_column_p column_p
cdef OBIDMS_column_p* column_pp
cdef OBIDMS_column_header_p header
cdef str column_n
view = self.pointer
if obi_view_delete_column(view, str2bytes(column_name)) < 0 :
raise Exception("Problem deleting a column from a view")
# Update the dictionaries of column pointers and column objects, and update pointers in column objects (make function?):
(self.columns).pop(column_name)
(self.columns_pp).pop(column_name)
i = 0
while i < view.column_count :
column_pp = <OBIDMS_column_p*> ((view.columns)+i)
column_p = <OBIDMS_column_p> (view.columns)[i]
header = (column_p).header
col_name = bytes2str(header.name)
col_capsule = PyCapsule_New(column_pp, NULL, NULL)
(self.columns_pp)[col_name] = col_capsule
i+=1
for column_n in self.columns :
(self.columns[column_n]).update_pointer()
cpdef add_column(self,
str column_name,
obiversion_t version_number=-1,
str type='',
index_t nb_lines=0,
index_t nb_elements_per_line=1, # TODO 1?
list elements_names=None,
str avl_name="default_AVL_tree",
str comments="",
bint create=True # TODO
) :
cdef bytes column_name_b
cdef bytes elements_names_b
cdef object subclass
cdef OBIDMS_column_p* column_pp
cdef OBIDMS_column_p column_p
column_name_b = str2bytes(column_name)
if nb_elements_per_line > 1 :
elements_names_b = str2bytes(';'.join(elements_names))
elif nb_elements_per_line == 1 :
elements_names_b = column_name_b
if type :
if type == 'OBI_INT' :
data_type = OBI_INT
elif type == 'OBI_FLOAT' :
data_type = OBI_FLOAT
elif type == 'OBI_BOOL' :
data_type = OBI_BOOL
elif type == 'OBI_CHAR' :
data_type = OBI_CHAR
elif type == 'OBI_STR' :
data_type = OBI_STR
elif type == 'OBI_SEQ' :
data_type = OBI_SEQ
else :
raise Exception("Invalid provided data type")
if (obi_view_add_column(self.pointer, column_name_b, version_number, # should return pointer on column?
data_type, nb_lines, nb_elements_per_line,
elements_names_b, str2bytes(avl_name),
str2bytes(comments), create) < 0) :
raise Exception("Problem adding a column in a view")
# Store the column pointer
column_pp = obi_view_get_pointer_on_column_in_view(self.pointer, column_name_b)
if column_pp == NULL :
raise Exception("Problem getting a column in a view")
col_capsule = PyCapsule_New(column_pp, NULL, NULL) # TODO
(self.columns_pp)[column_name] = col_capsule
# Open and store the subclass
column_p = column_pp[0] # TODO ugly cython dereferencing
subclass = OBIDMS_column.get_subclass_type(column_p)
(self.columns)[column_name] = subclass(self, column_name)
cpdef save_and_close(self) :
if (obi_save_and_close_view(self.pointer) < 0) :
raise Exception("Problem closing a view")
def __iter__(self):
# iter on each line of all columns
# Declarations
cdef index_t lines_used
cdef index_t line_nb
cdef OBIView_line line
# Yield each line TODO line class
lines_used = (self.pointer).line_count
for line_nb in range(lines_used) :
line = self[line_nb]
yield line
def __getitem__(self, object item) :
if type(item) == str :
return (self.columns)[item]
elif type(item) == int : # TODO int?
return OBIView_line(self, item)
cpdef select_line(self, index_t line_nb) :
if obi_select_line(self.pointer, line_nb) < 0 :
raise Exception("Problem selecting a line")
cpdef select_lines(self, list line_selection) :
cdef index_t* line_selection_p
line_selection_p = <index_t*> malloc((len(line_selection) + 1) * sizeof(index_t))
for i in range(len(line_selection)) :
line_selection_p[i] = line_selection[i] # TODO type problem?
line_selection_p[len(line_selection)] = -1
if obi_select_lines(self.pointer, line_selection_p) < 0 :
raise Exception("Problem selecting a list of lines")
def __contains__(self, str column_name):
return (column_name in self.columns)
def __str__(self) :
cdef OBIView_line line
cdef str to_print
to_print = ""
for line in self.__iter__() :
to_print = to_print + str(line) + "\n"
return to_print
#############################################
cdef class OBIView_line :
def __init__(self, OBIView view, index_t line_nb) :
self.index = line_nb
self.view = view
def __getitem__(self, str column_name) :
return ((self.view).columns)[column_name][self.index]
def __setitem__(self, str column_name, object value):
# TODO detect multiple elements (dict type)? put somewhere else? but more risky (in get)
cdef type value_type
cdef str value_obitype
if column_name not in self.view :
if value == None :
raise Exception("Trying to create a column from a None value (can't guess type)")
value_type = type(value)
if value_type == int :
value_obitype = 'OBI_INT'
elif value_type == float :
value_obitype = 'OBI_FLOAT'
elif value_type == bool :
value_obitype = 'OBI_BOOL'
elif value_type == str :
if only_ATGC(str2bytes(value)) : # TODO
value_obitype = 'OBI_SEQ'
elif len(value) == 1 :
value_obitype = 'OBI_CHAR'
elif (len(value) > 1) :
value_obitype = 'OBI_STR'
else :
raise Exception("Could not guess the type of a value to create a new column")
self.view.add_column(column_name, type=value_obitype)
(((self.view).columns)[column_name]).set_line(self.index, value)
def __contains__(self, str column_name):
return (column_name in self.view)
def __repr__(self):
cdef dict line
cdef str column_name
line = {}
for column_name in self.view.columns :
line[column_name] = self[column_name]
return str(line)
##########################################
cdef class OBIDMS :
@ -81,310 +521,12 @@ cdef class OBIDMS :
cpdef close(self) :
if (obi_close_dms(self.pointer)) < 0 :
raise Exception("Problem closing an OBIDMS")
cpdef dict list(self): # TDODO This is a temporary function that will be rewritten
# Declarations
cdef object p
cdef dict dms = {}
cdef str column_name
cdef bytes column_name_b
cdef str data_type
cdef str creation_date
cdef obiversion_t latest_version
cdef index_t line_count
cdef OBIDMS_column_header_p header
p = Path(self.dms_name+'.obidms')
print("{:<30} {:<12} {:<25} {:<30} {:<40}".format('-Column name-',
'-Data type-',
'-Latest version number-',
'-Line count of latest version-',
'-Creation date of latest version-'))
for entry in p.iterdir():
if entry.suffix == ".obicol":
column_name = entry.stem
column_name_b = str2bytes(column_name)
dms[column_name] = {}
header = obi_column_get_header_from_name(self.pointer, column_name_b, -1)
data_type = bytes2str(name_data_type(header.returned_data_type))
line_count = header.line_count
creation_date = bytes2str(obi_column_format_date(header.creation_date))
obi_unmap_header(header)
latest_version = obi_column_get_latest_version_from_name(self.pointer, column_name_b)
dms[column_name]['data_type'] = data_type
dms[column_name]['latest_version'] = latest_version
dms[column_name]['line_count'] = line_count
dms[column_name]['creation_date'] = creation_date
print("{:<30} {:<12} {:<25} {:<30} {:<40}".format(column_name, data_type, latest_version, line_count, creation_date))
return dms
cpdef OBIDMS_column open_column(self,
str column_name,
bint create=False,
bint clone=False, bint clone_data=True,
bint referring=False,
obiversion_t version_number=-1,
str type='',
index_t nb_lines=0,
index_t nb_elements_per_line=0,
list elements_names=None,
str avl_name="default_AVL_tree",
str comments=""):
# Declarations
cdef OBIDMS_column column
cdef object subclass # TODO object?
cdef bytes column_name_b
cdef OBIDMS_column_header_p header
cdef OBIType_t data_type
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 type or not nb_elements_per_line) and not create) :
header = obi_column_get_header_from_name(self.pointer, column_name_b, version_number)
# Get the data type if not provided
if not type :
if create :
raise Exception("A data type must be specified")
else :
data_type = header.returned_data_type
else :
if type == 'OBI_INT' :
data_type = OBI_INT
elif type == 'OBI_FLOAT' :
data_type = OBI_FLOAT
elif type == 'OBI_BOOL' :
data_type = OBI_BOOL
elif type == 'OBI_CHAR' :
data_type = OBI_CHAR
elif type == 'OBI_STR' :
data_type = OBI_STR
elif type == 'OBI_SEQ' :
data_type = OBI_SEQ
else :
raise Exception("Invalid provided data type")
# 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.returned_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 == OBI_INT :
if (create or clone) :
if nb_elements_per_line == 1 :
subclass = OBIDMS_column_int_writable
else :
subclass = OBIDMS_column_int_multi_elts_writable
else :
if nb_elements_per_line == 1 :
subclass = OBIDMS_column_int
else :
subclass = OBIDMS_column_int_multi_elts
elif data_type == OBI_FLOAT :
if (create or clone) :
if nb_elements_per_line == 1 :
subclass = OBIDMS_column_float_writable
else :
subclass = OBIDMS_column_float_multi_elts_writable
else :
if nb_elements_per_line == 1 :
subclass = OBIDMS_column_float
else :
subclass = OBIDMS_column_float_multi_elts
elif data_type == OBI_BOOL :
if (create or clone) :
if nb_elements_per_line == 1 :
subclass = OBIDMS_column_bool_writable
else :
subclass = OBIDMS_column_bool_multi_elts_writable
else :
if nb_elements_per_line == 1 :
subclass = OBIDMS_column_bool
else :
subclass = OBIDMS_column_bool_multi_elts
elif data_type == OBI_CHAR :
if (create or clone) :
if nb_elements_per_line == 1 :
subclass = OBIDMS_column_char_writable
else :
subclass = OBIDMS_column_char_multi_elts_writable
else :
if nb_elements_per_line == 1 :
subclass = OBIDMS_column_char
else :
subclass = OBIDMS_column_char_multi_elts
elif data_type == OBI_STR :
if (create or clone) :
if nb_elements_per_line == 1 :
subclass = OBIDMS_column_str_writable
else :
subclass = OBIDMS_column_str_multi_elts_writable
else :
if nb_elements_per_line == 1 :
subclass = OBIDMS_column_str
else :
subclass = OBIDMS_column_str_multi_elts
elif data_type == OBI_SEQ :
if (create or clone) :
if nb_elements_per_line == 1 :
subclass = OBIDMS_column_seq_writable
else :
subclass = OBIDMS_column_seq_multi_elts_writable
else :
if nb_elements_per_line == 1 :
subclass = OBIDMS_column_seq
else :
subclass = OBIDMS_column_seq_multi_elts
else :
raise Exception("Problem with the data type")
column = subclass(self, column_name,
create, clone, clone_data,
referring,
version_number, data_type,
nb_lines, nb_elements_per_line,
elements_names, avl_name,
comments)
return column
cdef class OBIDMS_column :
# Should only be initialized through a subclass
def __init__(self,
OBIDMS dms,
str column_name,
bint create,
bint clone, bint clone_data,
bint referring,
obiversion_t version_number,
OBIType_t type,
index_t nb_lines,
index_t nb_elements_per_line,
list elements_names,
str avl_name,
str comments):
# Declarations
cdef bytes column_name_b
cdef bytes dms_name_b
cdef bytes avl_name_b
cdef bytes elements_names_b
cdef bytes comments_b
# Fill structure
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)
dms_name_b = str2bytes(self.dms.dms_name)
avl_name_b = str2bytes(avl_name)
comments_b = str2bytes(comments)
# Create, clone or open column
if create :
if elements_names == None :
elements_names_b = column_name_b
else :
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, avl_name_b, comments_b,
referring)
else :
if clone :
self.pointer = obi_clone_column(self.dms.pointer, column_name_b, version_number, referring, clone_data)
elif referring :
self.pointer = obi_clone_column(self.dms.pointer, column_name_b, version_number, referring, False)
referred_column_pointer = self.pointer.referred_column
else :
self.pointer = obi_open_column(self.dms.pointer, column_name_b, version_number)
def __len__(self):
return self.pointer.header.lines_used
def __sizeof__(self):
return (self.pointer.header.header_size + self.pointer.header.data_size)
def __iter__(self):
# Declarations
cdef index_t lines_used
cdef index_t line_nb
# Yield each line
lines_used = self.pointer.header.lines_used
for line_nb in range(lines_used):
yield self.get_line(line_nb)
cpdef OBIView open_view(self, str view_name) :
return OBIView(self, view_name)
cpdef OBIView new_view(self, str view_name, object view_to_clone=None, list line_selection=None) :
return OBIView(self, view_name, new=True, view_to_clone=view_to_clone, line_selection=line_selection)
def __setitem__(self, index_t line_nb, object value):
self.set_line(line_nb, value)
def __getitem__(self, index_t line_nb):
return self.get_line(line_nb)
# cpdef object get_item(self, index_t line_nb, str element_name): TODO
# raise NotImplementedError
# cpdef set_item(self, index_t line_nb, str element_name, object value): TODO
# raise NotImplementedError
cpdef grep_line(self, index_t line_nb):
if obi_grep_line(self.pointer, line_nb) < 0 :
raise Exception("Error grepping line")
cpdef list get_elements_names(self):
return self.elements_names
cpdef str get_data_type(self):
return self.data_type
cpdef index_t get_nb_lines_used(self):
return self.pointer.header.lines_used
cpdef str get_creation_date(self):
return bytes2str(obi_column_format_date(self.pointer.header.creation_date))
cpdef str get_comments(self):
return bytes2str(self.pointer.header.comments)
cpdef close(self):
raise NotImplementedError

2
python/obitools3/obidms/_obidmscolumn_bool.cfiles
View File

@ -1,5 +1,7 @@
../../../src/obidmscolumn_bool.c
../../../src/obidmscolumn_bool.h
../../../src/obiview.h
../../../src/obiview.c
../../../src/obidmscolumn.h
../../../src/obidmscolumn.c
../../../src/obidmscolumndir.h

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

@ -1,25 +1,14 @@
#cython: language_level=3
from .capi.obitypes cimport obibool_t, index_t
from ._obidms cimport OBIDMS_column
from .capi.obitypes cimport index_t
from ._obidms cimport OBIDMS_column, OBIDMS_column_multi_elts
cdef class OBIDMS_column_bool(OBIDMS_column):
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, index_t line_nb, object value)
cpdef close(self)
cdef class OBIDMS_column_bool_multi_elts(OBIDMS_column_bool):
cdef class OBIDMS_column_multi_elts_bool(OBIDMS_column_multi_elts):
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, index_t line_nb, str element_name, obibool_t value)
cpdef set_line(self, index_t line_nb, object values)
cpdef close(self)
cpdef set_item(self, index_t line_nb, str element_name, object value)

78
python/obitools3/obidms/_obidmscolumn_bool.pyx
View File

@ -1,13 +1,12 @@
#cython: language_level=3
from .capi.obidmscolumn cimport obi_close_column,\
obi_truncate_and_close_column, \
obi_column_get_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.obidmscolumn cimport obi_truncate_and_close_column, \
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
from .capi.obierrno cimport obi_errno
from .capi.obitypes cimport OBIBool_NA
from .capi.obitypes cimport OBIBool_NA, obibool_t
from obitools3.utils cimport str2bytes
@ -19,7 +18,7 @@ cdef class OBIDMS_column_bool(OBIDMS_column):
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)
value = obi_column_get_obibool_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIBool_NA :
@ -27,32 +26,20 @@ cdef class OBIDMS_column_bool(OBIDMS_column):
else :
result = PyBool_FromLong(value)
return result
cpdef set_line(self, index_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, index_t line_nb, object value):
if obi_column_set_obibool_with_elt_idx(self.pointer, line_nb, 0, <obibool_t> value) < 0:
if value is None :
value = OBIBool_NA
if obi_column_set_obibool_with_elt_idx_in_view(self.view, (self.pointer)[0], 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):
cdef class OBIDMS_column_multi_elts_bool(OBIDMS_column_multi_elts):
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))
value = obi_column_get_obibool_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name))
if obi_errno > 0 :
raise IndexError(line_nb, element_name)
if value == OBIBool_NA :
@ -63,42 +50,29 @@ cdef class OBIDMS_column_bool_multi_elts(OBIDMS_column_bool):
cpdef object get_line(self, index_t line_nb) :
cdef obibool_t value
cdef object result
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) :
value = obi_column_get_obibool_with_elt_idx(self.pointer, line_nb, i)
value = obi_column_get_obibool_with_elt_idx_in_view(self.view, (self.pointer)[0], 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) :
raise IndexError(line_nb)
if value == OBIBool_NA :
value_in_result = None
else :
value_in_result = PyBool_FromLong(value)
result[self.elements_names[i]] = value_in_result
if all_NA and (value_in_result is not None) :
all_NA = False
if all_NA :
result = None
return result
cpdef set_item(self, index_t line_nb, str element_name, obibool_t value):
raise Exception("Column is read-only")
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, 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:
cpdef set_item(self, index_t line_nb, str element_name, object value):
if value is None :
value = OBIBool_NA
if obi_column_set_obibool_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name), <obibool_t> value) < 0:
raise Exception("Problem setting a value in a column")
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]
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")

2
python/obitools3/obidms/_obidmscolumn_char.cfiles
View File

@ -1,5 +1,7 @@
../../../src/obidmscolumn_char.c
../../../src/obidmscolumn_char.h
../../../src/obiview.h
../../../src/obiview.c
../../../src/obidmscolumn.h
../../../src/obidmscolumn.c
../../../src/obidmscolumndir.h

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

@ -1,25 +1,14 @@
#cython: language_level=3
from .capi.obitypes cimport obichar_t, index_t
from ._obidms cimport OBIDMS_column
from .capi.obitypes cimport index_t
from ._obidms cimport OBIDMS_column, OBIDMS_column_multi_elts
cdef class OBIDMS_column_char(OBIDMS_column):
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, index_t line_nb, object value)
cpdef close(self)
cdef class OBIDMS_column_char_multi_elts(OBIDMS_column_char):
cdef class OBIDMS_column_multi_elts_char(OBIDMS_column_multi_elts):
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_char_multi_elts_writable(OBIDMS_column_char_multi_elts):
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)
cpdef set_item(self, index_t line_nb, str element_name, object value)

79
python/obitools3/obidms/_obidmscolumn_char.pyx
View File

@ -1,13 +1,12 @@
#cython: language_level=3
from .capi.obidmscolumn cimport obi_close_column,\
obi_truncate_and_close_column, \
obi_column_get_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.obidmscolumn cimport obi_truncate_and_close_column, \
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
from .capi.obierrno cimport obi_errno
from .capi.obitypes cimport OBIChar_NA
from .capi.obitypes cimport OBIChar_NA, obichar_t
from obitools3.utils cimport str2bytes, bytes2str
@ -17,7 +16,7 @@ cdef class OBIDMS_column_char(OBIDMS_column):
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)
value = obi_column_get_obichar_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIChar_NA :
@ -27,30 +26,18 @@ cdef class OBIDMS_column_char(OBIDMS_column):
return result
cpdef set_line(self, index_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, index_t line_nb, object value):
if obi_column_set_obichar_with_elt_idx(self.pointer, line_nb, 0, str2bytes(value)[0]) < 0:
if value is None :
value = OBIChar_NA
if obi_column_set_obichar_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0, str2bytes(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):
cdef class OBIDMS_column_multi_elts_char(OBIDMS_column_multi_elts):
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))
value = obi_column_get_obichar_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name))
if obi_errno > 0 :
raise IndexError(line_nb, element_name)
if value == OBIChar_NA :
@ -58,45 +45,33 @@ cdef class OBIDMS_column_char_multi_elts(OBIDMS_column_char):
else :
result = bytes2str(value)
return result
cpdef object get_line(self, index_t line_nb) :
cdef obichar_t value
cdef object result
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) :
value = obi_column_get_obichar_with_elt_idx(self.pointer, line_nb, i)
value = obi_column_get_obichar_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, i)
if obi_errno > 0 :
raise IndexError(line_nb)
result[self.elements_names[i]] = bytes2str(value)
if all_NA and (value != OBIChar_NA) :
raise IndexError(line_nb)
if value == OBIChar_NA :
value_in_result = None
else :
value_in_result = bytes2str(value)
result[self.elements_names[i]] = value_in_result
if all_NA and (value_in_result is not None) :
all_NA = False
if all_NA :
result = None
return result
cpdef set_item(self, index_t line_nb, str element_name, str value):
raise Exception("Column is read-only")
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, index_t line_nb, str element_name, str value):
if obi_column_set_obichar_with_elt_name(self.pointer, line_nb, str2bytes(element_name), str2bytes(value)[0]) < 0:
cpdef set_item(self, index_t line_nb, str element_name, object value):
if value is None :
value = OBIChar_NA
if obi_column_set_obichar_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name), str2bytes(value)[0]) < 0:
raise Exception("Problem setting a value in a column")
cpdef set_line(self, index_t line_nb, object values):
cdef str value
for element_name in values :
value = values[element_name]
self.set_item(line_nb, element_name, value)
cpdef close(self):
if obi_truncate_and_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")

2
python/obitools3/obidms/_obidmscolumn_float.cfiles
View File

@ -1,5 +1,7 @@
../../../src/obidmscolumn_float.c
../../../src/obidmscolumn_float.h
../../../src/obiview.h
../../../src/obiview.c
../../../src/obidmscolumn.h
../../../src/obidmscolumn.c
../../../src/obidmscolumndir.h

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

@ -1,25 +1,14 @@
#cython: language_level=3
from .capi.obitypes cimport obifloat_t, index_t
from ._obidms cimport OBIDMS_column
from .capi.obitypes cimport index_t
from ._obidms cimport OBIDMS_column, OBIDMS_column_multi_elts
cdef class OBIDMS_column_float(OBIDMS_column):
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, index_t line_nb, object value)
cpdef close(self)
cdef class OBIDMS_column_float_multi_elts(OBIDMS_column_float):
cdef class OBIDMS_column_multi_elts_float(OBIDMS_column_multi_elts):
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, index_t line_nb, str element_name, obifloat_t value)
cpdef set_line(self, index_t line_nb, object values)
cpdef close(self)
cpdef set_item(self, index_t line_nb, str element_name, object value)

82
python/obitools3/obidms/_obidmscolumn_float.pyx
View File

@ -1,13 +1,12 @@
#cython: language_level=3
from .capi.obidmscolumn cimport obi_close_column,\
obi_truncate_and_close_column, \
obi_column_get_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.obidmscolumn cimport obi_truncate_and_close_column,\
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
from .capi.obierrno cimport obi_errno
from .capi.obitypes cimport OBIFloat_NA
from .capi.obitypes cimport OBIFloat_NA, obifloat_t
from obitools3.utils cimport str2bytes
@ -17,7 +16,7 @@ cdef class OBIDMS_column_float(OBIDMS_column):
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)
value = obi_column_get_obifloat_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIFloat_NA :
@ -27,30 +26,18 @@ cdef class OBIDMS_column_float(OBIDMS_column):
return result
cpdef set_line(self, index_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, index_t line_nb, object value):
if obi_column_set_obifloat_with_elt_idx(self.pointer, line_nb, 0, <obifloat_t> value) < 0:
if value is None :
value = OBIFloat_NA
if obi_column_set_obifloat_with_elt_idx_in_view(self.view, (self.pointer)[0], 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):
cdef class OBIDMS_column_multi_elts_float(OBIDMS_column_multi_elts):
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))
value = obi_column_get_obifloat_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name))
if obi_errno > 0 :
raise IndexError(line_nb, element_name)
if value == OBIFloat_NA :
@ -58,46 +45,33 @@ cdef class OBIDMS_column_float_multi_elts(OBIDMS_column_float):
else :
result = <double> value
return result
cpdef object get_line(self, index_t line_nb) :
cdef obifloat_t value
cdef object result
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) :
value = obi_column_get_obifloat_with_elt_idx(self.pointer, line_nb, i)
value = obi_column_get_obifloat_with_elt_idx_in_view(self.view, (self.pointer)[0], 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) :
raise IndexError(line_nb)
if value == OBIFloat_NA :
value_in_result = None
else :
value_in_result = <double> value
result[self.elements_names[i]] = value_in_result
if all_NA and (value_in_result is not None) :
all_NA = False
if all_NA :
result = None
return result
cpdef set_item(self, index_t line_nb, str element_name, obifloat_t value):
raise Exception("Column is read-only")
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, 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:
cpdef set_item(self, index_t line_nb, str element_name, object value):
if value is None :
value = OBIFloat_NA
if obi_column_set_obifloat_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name), <obifloat_t> value) < 0:
raise Exception("Problem setting a value in a column")
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]
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")

2
python/obitools3/obidms/_obidmscolumn_int.cfiles
View File

@ -1,5 +1,7 @@
../../../src/obidmscolumn_int.c
../../../src/obidmscolumn_int.h
../../../src/obiview.h
../../../src/obiview.c
../../../src/obidmscolumn.h
../../../src/obidmscolumn.c
../../../src/obidmscolumndir.h

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

@ -1,25 +1,14 @@
#cython: language_level=3
from .capi.obitypes cimport obiint_t, index_t
from ._obidms cimport OBIDMS_column
from .capi.obitypes cimport index_t
from ._obidms cimport OBIDMS_column, OBIDMS_column_multi_elts
cdef class OBIDMS_column_int(OBIDMS_column):
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, index_t line_nb, object value)
cpdef close(self)
cdef class OBIDMS_column_int_multi_elts(OBIDMS_column_int):
cdef class OBIDMS_column_multi_elts_int(OBIDMS_column_multi_elts):
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, index_t line_nb, str element_name, obiint_t value)
cpdef set_line(self, index_t line_nb, object values)
cpdef close(self)
cpdef set_item(self, index_t line_nb, str element_name, object value)

81
python/obitools3/obidms/_obidmscolumn_int.pyx
View File

@ -1,13 +1,12 @@
#cython: language_level=3
from .capi.obidmscolumn cimport obi_close_column,\
obi_truncate_and_close_column, \
obi_column_get_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.obidmscolumn cimport obi_truncate_and_close_column, \
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
from .capi.obierrno cimport obi_errno
from .capi.obitypes cimport OBIInt_NA
from .capi.obitypes cimport OBIInt_NA, obiint_t
from obitools3.utils cimport str2bytes
@ -19,7 +18,7 @@ cdef class OBIDMS_column_int(OBIDMS_column):
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)
value = obi_column_get_obiint_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIInt_NA :
@ -27,32 +26,20 @@ cdef class OBIDMS_column_int(OBIDMS_column):
else :
result = PyInt_FromLong(value)
return result
cpdef set_line(self, index_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, index_t line_nb, object value):
if obi_column_set_obiint_with_elt_idx(self.pointer, line_nb, 0, <obiint_t> value) < 0:
if value is None :
value = OBIInt_NA
if obi_column_set_obiint_with_elt_idx_in_view(self.view, (self.pointer)[0], 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):
cdef class OBIDMS_column_multi_elts_int(OBIDMS_column_multi_elts):
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))
value = obi_column_get_obiint_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name))
if obi_errno > 0 :
raise IndexError(line_nb, element_name)
if value == OBIInt_NA :
@ -63,42 +50,30 @@ cdef class OBIDMS_column_int_multi_elts(OBIDMS_column_int):
cpdef object get_line(self, index_t line_nb) :
cdef obiint_t value
cdef object result
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) :
value = obi_column_get_obiint_with_elt_idx(self.pointer, line_nb, i)
value = obi_column_get_obiint_with_elt_idx_in_view(self.view, (self.pointer)[0], 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) :
raise IndexError(line_nb)
if value == OBIInt_NA :
value_in_result = None
else :
value_in_result = PyInt_FromLong(value)
result[self.elements_names[i]] = value_in_result
if all_NA and (value_in_result is not None) :
all_NA = False
if all_NA :
result = None
result = None # TODO discuss
return result
cpdef set_item(self, index_t line_nb, str element_name, obiint_t value):
raise Exception("Column is read-only")
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, 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:
cpdef set_item(self, index_t line_nb, str element_name, object value):
if value is None :
value = OBIInt_NA
if obi_column_set_obiint_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name), <obiint_t> value) < 0:
raise Exception("Problem setting a value in a column")
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]
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")

2
python/obitools3/obidms/_obidmscolumn_seq.cfiles
View File

@ -1,5 +1,7 @@
../../../src/obidmscolumn_seq.c
../../../src/obidmscolumn_seq.h
../../../src/obiview.h
../../../src/obiview.c
../../../src/obidmscolumn.h
../../../src/obidmscolumn.c
../../../src/obidmscolumndir.h

17
python/obitools3/obidms/_obidmscolumn_seq.pxd
View File

@ -1,25 +1,14 @@
#cython: language_level=3
from .capi.obitypes cimport index_t
from ._obidms cimport OBIDMS_column
from ._obidms cimport OBIDMS_column, OBIDMS_column_multi_elts
cdef class OBIDMS_column_seq(OBIDMS_column):
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_seq_writable(OBIDMS_column_seq):
cpdef set_line(self, index_t line_nb, object value)
cpdef close(self)
cdef class OBIDMS_column_seq_multi_elts(OBIDMS_column_seq):
cdef class OBIDMS_column_multi_elts_seq(OBIDMS_column_multi_elts):
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_seq_multi_elts_writable(OBIDMS_column_seq_multi_elts):
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)
cpdef set_item(self, index_t line_nb, str element_name, object value)

90
python/obitools3/obidms/_obidmscolumn_seq.pyx
View File

@ -1,13 +1,12 @@
#cython: language_level=3
from .capi.obidmscolumn cimport obi_close_column,\
obi_truncate_and_close_column, \
obi_column_get_obiseq_with_elt_name, \
obi_column_get_obiseq_with_elt_idx, \
obi_column_set_obiseq_with_elt_name, \
obi_column_set_obiseq_with_elt_idx
from .capi.obidmscolumn cimport obi_truncate_and_close_column, \
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
from .capi.obierrno cimport obi_errno
from .capi.obitypes cimport OBIIdx_NA, const_char_p
from .capi.obitypes cimport OBISeq_NA, const_char_p
from obitools3.utils cimport str2bytes, bytes2str
@ -17,87 +16,68 @@ cdef class OBIDMS_column_seq(OBIDMS_column):
cpdef object get_line(self, index_t line_nb):
cdef bytes value
cdef object result
value = <bytes> obi_column_get_obiseq_with_elt_idx(self.pointer, line_nb, 0)
value = <bytes> obi_column_get_obiseq_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIIdx_NA :
if value == OBISeq_NA : # TODO
result = None
else :
result = bytes2str(value)
return result
cpdef set_line(self, index_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_seq_writable(OBIDMS_column_seq):
cpdef set_line(self, index_t line_nb, object value):
if obi_column_set_obiseq_with_elt_idx(self.pointer, line_nb, 0, str2bytes(value)) < 0:
cdef bytes value_b
if value is None :
value_b = OBISeq_NA
else :
value_b = str2bytes(value)
if obi_column_set_obiseq_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0, value_b) < 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_seq_multi_elts(OBIDMS_column_seq):
cdef class OBIDMS_column_multi_elts_seq(OBIDMS_column_multi_elts):
cpdef object get_item(self, index_t line_nb, str element_name):
cdef bytes value
cdef object result
value = <bytes> obi_column_get_obiseq_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
value = <bytes> obi_column_get_obiseq_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name))
if obi_errno > 0 :
raise IndexError(line_nb, element_name)
if value == OBIIdx_NA :
if value == OBISeq_NA :
result = None
else :
result = bytes2str(value)
return result
cpdef object get_line(self, index_t line_nb) :
cdef bytes value
cdef object result
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) :
value = <bytes> obi_column_get_obiseq_with_elt_idx(self.pointer, line_nb, i)
value = <bytes> obi_column_get_obiseq_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, i)
if obi_errno > 0 :
raise IndexError(line_nb)
result[self.elements_names[i]] = bytes2str(value)
if all_NA and (value != OBIIdx_NA) :
raise IndexError(line_nb)
if value == OBISeq_NA :
value_in_result = None
else :
value_in_result = bytes2str(value)
result[self.elements_names[i]] = value_in_result
if all_NA and (value_in_result is not None) :
all_NA = False
if all_NA :
result = None
return result
cpdef set_item(self, index_t line_nb, str element_name, str value):
raise Exception("Column is read-only")
cpdef set_line(self, index_t line_nb, object values):
raise Exception("Column is read-only")
cdef class OBIDMS_column_seq_multi_elts_writable(OBIDMS_column_seq_multi_elts):
cpdef set_item(self, index_t line_nb, str element_name, str value):
if obi_column_set_obiseq_with_elt_name(self.pointer, line_nb, str2bytes(element_name), str2bytes(value)) < 0:
cpdef set_item(self, index_t line_nb, str element_name, object value):
cdef bytes value_b
if value is None :
value_b = OBISeq_NA
else :
value_b = str2bytes(value)
if obi_column_set_obiseq_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name), value_b) < 0:
raise Exception("Problem setting a value in a column")
cpdef set_line(self, index_t line_nb, object values):
cdef str value
for element_name in values :
value = values[element_name]
self.set_item(line_nb, element_name, value)
cpdef close(self):
if obi_truncate_and_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")

2
python/obitools3/obidms/_obidmscolumn_str.cfiles
View File

@ -1,5 +1,7 @@
../../../src/obidmscolumn_str.c
../../../src/obidmscolumn_str.h
../../../src/obiview.h
../../../src/obiview.c
../../../src/obidmscolumn.h
../../../src/obidmscolumn.c
../../../src/obidmscolumndir.h

17
python/obitools3/obidms/_obidmscolumn_str.pxd
View File

@ -1,25 +1,14 @@
#cython: language_level=3
from .capi.obitypes cimport index_t
from ._obidms cimport OBIDMS_column
from ._obidms cimport OBIDMS_column, OBIDMS_column_multi_elts
cdef class OBIDMS_column_str(OBIDMS_column):
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, index_t line_nb, object value)
cpdef close(self)
cdef class OBIDMS_column_str_multi_elts(OBIDMS_column_str):
cdef class OBIDMS_column_multi_elts_str(OBIDMS_column_multi_elts):
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, index_t line_nb, str element_name, str value)
cpdef set_line(self, index_t line_nb, object values)
cpdef close(self)
cpdef set_item(self, index_t line_nb, str element_name, object value)

90
python/obitools3/obidms/_obidmscolumn_str.pyx
View File

@ -1,13 +1,12 @@
#cython: language_level=3
from .capi.obidmscolumn cimport obi_close_column,\
obi_truncate_and_close_column, \
obi_column_get_obistr_with_elt_name, \
obi_column_get_obistr_with_elt_idx, \
obi_column_set_obistr_with_elt_name, \
obi_column_set_obistr_with_elt_idx
from .capi.obidmscolumn cimport obi_truncate_and_close_column, \
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
from .capi.obierrno cimport obi_errno
from .capi.obitypes cimport OBIIdx_NA, const_char_p
from .capi.obitypes cimport OBIStr_NA, const_char_p
from obitools3.utils cimport str2bytes, bytes2str
@ -17,87 +16,68 @@ cdef class OBIDMS_column_str(OBIDMS_column):
cpdef object get_line(self, index_t line_nb):
cdef bytes value
cdef object result
value = <bytes> obi_column_get_obistr_with_elt_idx(self.pointer, line_nb, 0)
value = <bytes> obi_column_get_obistr_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIIdx_NA :
if value == OBIStr_NA : # TODO
result = None
else :
result = bytes2str(value)
return result
cpdef set_line(self, index_t line_nb, object value):
raise Exception("Column is read-only")
cpdef close(self):
if obi_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")
cdef class OBIDMS_column_str_writable(OBIDMS_column_str):
cpdef set_line(self, index_t line_nb, object value):
if obi_column_set_obistr_with_elt_idx(self.pointer, line_nb, 0, str2bytes(value)) < 0:
cdef bytes value_b
if value is None :
value_b = OBIStr_NA
else :
value_b = str2bytes(value)
if obi_column_set_obistr_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0, value_b) < 0:
raise Exception("Problem setting a value in a column")
cpdef close(self):
if obi_truncate_and_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")
cdef class OBIDMS_column_str_multi_elts(OBIDMS_column_str):
cdef class OBIDMS_column_multi_elts_str(OBIDMS_column_multi_elts):
cpdef object get_item(self, index_t line_nb, str element_name):
cdef bytes value
cdef object result
value = <bytes> obi_column_get_obistr_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
value = <bytes> obi_column_get_obistr_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name))
if obi_errno > 0 :
raise IndexError(line_nb, element_name)
if value == OBIIdx_NA :
if value == OBIStr_NA :
result = None
else :
result = bytes2str(value)
return result
cpdef object get_line(self, index_t line_nb) :
cdef bytes value
cdef object result
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) :
value = <bytes> obi_column_get_obistr_with_elt_idx(self.pointer, line_nb, i)
value = <bytes> obi_column_get_obistr_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, i)
if obi_errno > 0 :
raise IndexError(line_nb)
result[self.elements_names[i]] = bytes2str(value)
if all_NA and (value != OBIIdx_NA) :
raise IndexError(line_nb)
if value == OBIStr_NA :
value_in_result = None
else :
value_in_result = bytes2str(value)
result[self.elements_names[i]] = value_in_result
if all_NA and (value_in_result is not None) :
all_NA = False
if all_NA :
result = None
return result
cpdef set_item(self, index_t line_nb, str element_name, str value):
raise Exception("Column is read-only")
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, 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:
cpdef set_item(self, index_t line_nb, str element_name, object value):
cdef bytes value_b
if value is None :
value_b = OBIStr_NA
else :
value_b = str2bytes(value)
if obi_column_set_obistr_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name), value_b) < 0:
raise Exception("Problem setting a value in a column")
cpdef set_line(self, index_t line_nb, object values):
cdef str value
for element_name in values :
value = values[element_name]
self.set_item(line_nb, element_name, value)
cpdef close(self):
if obi_truncate_and_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")

192
python/obitools3/obidms/capi/obidmscolumn.pxd
View File

@ -19,16 +19,13 @@ cdef extern from "obidmscolumn.h" nogil:
size_t data_size
index_t line_count
index_t lines_used
index_t returned_nb_elements_per_line
index_t stored_nb_elements_per_line
index_t nb_elements_per_line
const_char_p elements_names
OBIType_t returned_data_type
OBIType_t stored_data_type
time_t creation_date
obiversion_t version
obiversion_t cloned_from
bint referring
obiversion_t referred_column_version
const_char_p name
const_char_p avl_name
const_char_p comments
@ -36,9 +33,10 @@ cdef extern from "obidmscolumn.h" nogil:
ctypedef OBIDMS_column_header_t* OBIDMS_column_header_p
struct OBIDMS_column_t:
OBIDMS_p dms
OBIDMS_column_header_p header
OBIDMS_column_t* referred_column
bint writable
ctypedef OBIDMS_column_t* OBIDMS_column_p
OBIDMS_column_p obi_create_column(OBIDMS_p dms,
@ -48,8 +46,7 @@ cdef extern from "obidmscolumn.h" nogil:
index_t nb_elements_per_line,
const_char_p elements_names,
const_char_p avl_name,
const_char_p comments,
bint referring)
const_char_p comments)
OBIDMS_column_p obi_open_column(OBIDMS_p dms,
const_char_p column_name,
@ -58,9 +55,9 @@ cdef extern from "obidmscolumn.h" nogil:
int obi_close_column(OBIDMS_column_p column)
OBIDMS_column_p obi_clone_column(OBIDMS_p dms,
OBIDMS_column_p line_selection,
const_char_p column_name,
obiversion_t version_number,
bint referring,
bint clone_data)
int obi_truncate_and_close_column(OBIDMS_column_p column)
@ -76,10 +73,34 @@ cdef extern from "obidmscolumn.h" nogil:
char* obi_column_format_date(time_t date)
int obi_grep_line(OBIDMS_column_p referring_column, index_t line_to_grep)
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,
const_char_p element_name,
@ -88,7 +109,7 @@ cdef extern from "obidmscolumn_int.h" nogil:
int obi_column_set_obiint_with_elt_idx(OBIDMS_column_p column,
index_t line_nb,
index_t element_idx,
obiint_t value)
obiint_t value)
obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column,
index_t line_nb,
@ -98,14 +119,35 @@ cdef extern from "obidmscolumn_int.h" nogil:
index_t line_nb,
index_t element_idx)
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,
obibool_t value)
int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column,
index_t line_nb,
index_t element_idx,
@ -121,11 +163,33 @@ 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,
obichar_t value)
int obi_column_set_obichar_with_elt_idx(OBIDMS_column_p column,
index_t line_nb,
index_t element_idx,
@ -141,39 +205,83 @@ cdef extern from "obidmscolumn_char.h" nogil:
cdef extern from "obidmscolumn_float.h" nogil:
int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name,
obifloat_t value)
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)
int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column,
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,
index_t element_idx,
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)
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)
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)
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)
int obi_column_set_obistr_with_elt_name(OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name,
char* 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 obi_column_get_obistr_with_elt_name(OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name)
index_t line_nb,
char* element_name)
const_char_p obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column,
index_t line_nb,
@ -181,19 +289,41 @@ 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)
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 obi_column_get_obiseq_with_elt_name(OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name)
index_t line_nb,
char* element_name)
const_char_p obi_column_get_obiseq_with_elt_idx(OBIDMS_column_p column,
index_t line_nb,

17
python/obitools3/obidms/capi/obitypes.pxd
View File

@ -8,6 +8,9 @@ from posix.types cimport time_t
cdef extern from *:
ctypedef char* const_char_p "const char*"
cdef extern from "encode.h" nogil:
bint only_ATGC(const_char_p seq)
cdef extern from "obidmscolumn.h" nogil:
@ -38,10 +41,12 @@ cdef extern from "obitypes.h" nogil:
ctypedef char obichar_t
ctypedef int64_t index_t
extern obiint_t OBIInt_NA
extern index_t OBIIdx_NA
extern obifloat_t OBIFloat_NA
extern obichar_t OBIChar_NA
extern obibool_t OBIBool_NA
extern obiint_t OBIInt_NA
extern index_t OBIIdx_NA
extern obifloat_t OBIFloat_NA
extern obichar_t OBIChar_NA
extern obibool_t OBIBool_NA
extern const_char_p OBISeq_NA
extern const_char_p OBIStr_NA
char* name_data_type(int data_type)
const_char_p name_data_type(int data_type)

68
python/obitools3/obidms/capi/obiview.pxd Normal file
View File

@ -0,0 +1,68 @@
#cython: language_level=3
from .obitypes cimport const_char_p, \
OBIType_t, \
obiversion_t, \
index_t
from ..capi.obidms cimport OBIDMS_p
from ..capi.obidmscolumn cimport OBIDMS_column_p
cdef extern from "obiview.h" nogil:
struct Column_reference_t :
char column_name
obiversion_t version
ctypedef Column_reference_t* Column_reference_p
struct Obiview_t :
OBIDMS_p dms
const_char_p name
OBIDMS_column_p line_selection
OBIDMS_column_p new_line_selection
OBIDMS_column_p columns
bint read_only
Column_reference_t line_selection_reference
index_t line_count
int column_count
ctypedef Obiview_t* Obiview_p
Obiview_p obi_new_view(OBIDMS_p dms, const_char_p view_name, Obiview_p view_to_clone, index_t* line_selection)
Obiview_p obi_new_view_cloned_from_name(OBIDMS_p dms, const char* view_name, const char* view_to_clone_name, index_t* line_selection)
Obiview_p obi_open_view(OBIDMS_p dms, const_char_p view_name)
int obi_view_add_column(Obiview_p view,
const_char_p column_name,
obiversion_t version_number,
OBIType_t data_type,
index_t nb_lines,
index_t nb_elements_per_line,
const_char_p elements_names,
const_char_p avl_name,
const_char_p comments,
bint create)
int obi_view_delete_column(Obiview_p view, const_char_p column_name)
int obi_select_line(Obiview_p view, index_t line_nb)
int obi_select_lines(Obiview_p view, index_t* line_nbs)
OBIDMS_column_p obi_view_clone_column(Obiview_p view, const_char_p column_name)
OBIDMS_column_p obi_view_get_column(Obiview_p view, const_char_p column_name)
OBIDMS_column_p* obi_view_get_pointer_on_column_in_view(Obiview_p view, const_char_p column_name)
int obi_save_view(Obiview_p view)
int obi_close_view(Obiview_p view)
int obi_save_and_close_view(Obiview_p view)