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#cython: language_level=3
cdef dict __VIEW_CLASS__= {}
from libc.stdlib cimport malloc
from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
from obitools3.version import version
from ..capi.obiview cimport Alias_column_pair_p, \
obi_new_view, \
obi_open_view, \
obi_clone_view, \
obi_rollback_view, \
obi_save_and_close_view, \
obi_view_get_pointer_on_column_in_view, \
obi_view_delete_column, \
obi_view_create_column_alias, \
obi_view_write_comments, \
obi_delete_view, \
obi_view_formatted_infos, \
obi_view_formatted_infos_one_line
from ..capi.obidmscolumn cimport OBIDMS_column_p
from ..capi.obidms cimport OBIDMS_p
from obitools3.utils cimport tobytes, \
str2bytes, \
bytes2str, \
tostr, \
bytes2str_object, \
str2bytes_object, \
clean_empty_values_from_object, \
get_obitype
from ..object cimport OBIDeactivatedInstanceError
from obitools3.dms.view import typed_view
from ..capi.obitypes cimport is_a_DNA_seq, \
OBI_VOID, \
OBI_BOOL, \
OBI_CHAR, \
OBI_FLOAT, \
OBI_INT, \
OBI_QUAL, \
OBI_SEQ, \
OBI_STR
from ..capi.obidms cimport obi_import_view
from obitools3.format.tab import TabFormat
from cpython.exc cimport PyErr_CheckSignals
import importlib
import inspect
import pkgutil
import json
import sys
from libc.stdlib cimport free
cdef class View(OBIWrapper) :
cdef inline Obiview_p pointer(self) :
return <Obiview_p>(self._pointer)
@staticmethod
# TODO try cdef again
def get_view_class(bytes view_type):
global __VIEW_CLASS__
return __VIEW_CLASS__.get(view_type, View)
@staticmethod
def import_view(object dms_1, object dms_2, object view_name_1, object view_name_2): # TODO argument to import line by line to avoid huge AVL copy
if obi_import_view(tobytes(dms_1), tobytes(dms_2), tobytes(view_name_1), tobytes(view_name_2)) < 0 :
raise Exception("Error importing a view")
@staticmethod
def delete_view(DMS dms, object view_name):
if (obi_delete_view(dms.pointer(), tobytes(view_name)) < 0):
raise Exception("Error deleting a view")
@staticmethod
def new(DMS dms,
object view_name,
object comments={}):
cdef bytes view_name_b = tobytes(view_name)
cdef bytes comments_b
cdef str message
cdef void* pointer
cdef View view # @DuplicatedSignature
comments_b = str2bytes(json.dumps(bytes2str_object(comments)))
pointer = <void*>obi_new_view(<OBIDMS_p>dms._pointer,
view_name_b,
NULL,
NULL,
comments_b)
if pointer == NULL :
message = "Error : Cannot create view %s" % bytes2str(view_name_b)
raise RuntimeError(message)
view = OBIWrapper.new_wrapper(View, pointer)
view._dms = dms
dms.register(view)
return view
def clone(self,
object view_name,
object comments={}):
cdef bytes view_name_b = tobytes(view_name)
cdef bytes comments_b
cdef void* pointer
cdef View view
if not self.active() :
raise OBIDeactivatedInstanceError()
comments_b = str2bytes(json.dumps(bytes2str_object(dict(comments)))) # TODO hmmmmm function in View_comments class probably
pointer = <void*> obi_clone_view(self._dms.pointer(),
self.pointer(),
view_name_b,
NULL,
comments_b)
if pointer == NULL :
raise RuntimeError("Error : Cannot clone view %s into view %s"
% (str(self.name),
bytes2str(view_name_b))
)
view = OBIWrapper.new_wrapper(type(self), pointer)
view._dms = self._dms
self._dms.register(view)
return view
@staticmethod
def open(DMS dms, # @ReservedAssignment
object view_name):
cdef bytes view_name_b = tobytes(view_name)
cdef void* pointer
cdef View view
cdef type view_class
pointer = <void*> obi_open_view(dms.pointer(),
view_name_b)
if pointer == NULL :
raise RuntimeError("Error : Cannot open view %s" % bytes2str(view_name_b))
view_class = View.get_view_class((<Obiview_p>pointer).infos.view_type)
view = OBIWrapper.new_wrapper(view_class, pointer)
view._dms = dms
dms.register(view)
return view
def close(self):
cdef Obiview_p pointer = self.pointer()
if self.active() :
self._dms.unregister(self)
OBIWrapper.close(self)
if obi_save_and_close_view(pointer) < 0 :
raise Exception("Problem closing view %s" %
bytes2str(self.name))
@OBIWrapper.checkIsActive
def __repr__(self) :
cdef str s
cdef char* sc
cdef Obiview_p pointer = self.pointer()
sc = obi_view_formatted_infos(pointer, False)
s = bytes2str(sc)
free(sc)
return s
@OBIWrapper.checkIsActive
def repr_longformat(self) :
cdef str s
cdef char* sc
cdef Obiview_p pointer = self.pointer()
sc = obi_view_formatted_infos(pointer, True)
s = bytes2str(sc)
free(sc)
return s
cpdef print_to_output(self, object output, bint noprogressbar=False):
cdef int i
cdef Line entry
self.checkIsActive(self)
# Initialize the progress bar
if noprogressbar == False:
pb = ProgressBar(len(self))
else:
pb = None
i=0
for entry in self:
PyErr_CheckSignals()
if pb is not None:
pb(i)
output.write(entry.repr_bytes()+b"\n")
i+=1
if pb is not None:
pb(len(self), force=True)
print("", file=sys.stderr)
def keys(self):
cdef bytes col_alias
cdef int i
cdef Obiview_p pointer = self.pointer()
cdef int nb_column = pointer.infos.column_count
cdef Alias_column_pair_p column_p = pointer.infos.column_references
if not self.active() :
raise OBIDeactivatedInstanceError()
for i in range(nb_column) :
col_alias = column_p[i].alias
yield col_alias
def get_column(self,
object column_name):
if not self.active() :
raise OBIDeactivatedInstanceError()
return Column.open(self, tobytes(column_name))
def get_column_with_idx(self,
int column_idx):
cdef Obiview_p pointer = self.pointer()
cdef int nb_column = pointer.infos.column_count
if not self.active() :
raise OBIDeactivatedInstanceError()
if column_idx > nb_column :
raise IndexError(column_idx, "No column with this index")
return Column.open(self, pointer.infos.column_references[column_idx].alias)
cpdef delete_column(self,
object column_name,
bint delete_file=False) :
cdef bytes column_name_b = tobytes(column_name)
if not self.active() :
raise OBIDeactivatedInstanceError()
# Close the cython instance first
col = self[column_name_b]
col.close()
# Remove the column from the view which closes the C structure
if obi_view_delete_column(self.pointer(), column_name_b, delete_file) < 0 :
raise RollbackException("Problem deleting column %s from a view",
bytes2str(column_name_b), self)
cpdef rename_column(self,
object current_name,
object new_name):
cdef Column column
cdef bytes current_name_b = tobytes(current_name)
cdef bytes new_name_b = tobytes(new_name)
if not self.active() :
raise OBIDeactivatedInstanceError()
if (obi_view_create_column_alias(self.pointer(),
tobytes(current_name_b),
tobytes(new_name_b)) < 0) :
raise RollbackException("Problem in renaming column %s to %s" % (
bytes2str(current_name_b),
bytes2str(new_name_b)), self)
# TODO warning, not multithreading compliant
cpdef Column rewrite_column_with_diff_attributes(self,
object column_name,
obitype_t new_data_type=<obitype_t>OBI_VOID,
index_t new_nb_elements_per_line=0,
list new_elements_names=None,
bint rewrite_last_line=False) :
cdef Column old_column
cdef Column new_column
cdef index_t length = len(self)
cdef column_name_b = tobytes(column_name)
if rewrite_last_line is False:
length-=1
if not self.active() :
raise OBIDeactivatedInstanceError()
old_column = self.get_column(column_name_b)
if new_data_type == 0 :
new_data_type = old_column.data_type
if new_nb_elements_per_line == 0 :
new_nb_elements_per_line = old_column.nb_elements_per_line
if new_elements_names is None :
new_elements_names = old_column._elements_names
new_column = Column.new_column(self, old_column.pointer().header.name, new_data_type,
nb_elements_per_line=new_nb_elements_per_line, elements_names=new_elements_names,
dict_column=(new_nb_elements_per_line>1), comments=old_column.comments, alias=column_name_b+tobytes('___new___'))
switch_to_dict = not old_column.dict_column and new_nb_elements_per_line > 1
ori_key = old_column._elements_names[0]
for i in range(length) :
if switch_to_dict :
new_column[i] = {ori_key: old_column[i]}
else:
new_column[i] = old_column[i]
# Remove old column from view
self.delete_column(column_name_b, delete_file=True)
# Rename new
new_column.name = column_name_b
return new_column
cpdef Line_selection new_selection(self, list lines=None):
if not self.active() :
raise OBIDeactivatedInstanceError()
return Line_selection(self, lines)
@OBIWrapper.checkIsActive
def __iter__(self):
# Iteration on each line of all columns
# Declarations
cdef index_t line_nb
# Yield each line
for line_nb in range(self.line_count) :
yield Line(self, line_nb)
# TODO test time gain without
@OBIWrapper.checkIsActive
def __getitem__(self, object ref) :
if type(ref) == int :
return Line(self, ref)
else : # TODO assume str or bytes for optimization (discuss)
return self.get_column(ref) # note: slow, always better to keep column ref in a variable
@OBIWrapper.checkIsActive
def __setitem__(self, index_t idx, object item) :
cdef Column col
line = self[idx]
for k in item :
# If setting from another View Line and the column doesn't exist, create it based on the informations from the other View
# TODO use clone_column
if isinstance(item, Line) and tostr(k) not in self:
col = item.view[k]
Column.new_column(self,
col.original_name,
col.data_type_int,
nb_elements_per_line = col.nb_elements_per_line,
elements_names = col._elements_names,
dict_column = col.dict_column,
tuples = col.tuples,
to_eval = col.to_eval,
comments = col.comments,
alias=k
)
line[k] = item[k]
@OBIWrapper.checkIsActive
def __contains__(self, object column_name):
return (tobytes(column_name) in self.keys())
@OBIWrapper.checkIsActive
def __len__(self):
return(self.line_count)
@OBIWrapper.checkIsActive
def __str__(self) :
cdef Line line
cdef str to_print
to_print = ""
for line in self :
to_print = to_print + str(line) + "\n"
return to_print
@staticmethod
def _config_to_dict(dict config, str command_name, str command_line, list input_str=None, list input_dms_name=None, list input_view_name=None):
INVALID_KEYS = ["__root_config__", "module", "nocreatedms", "logger", "defaultdms", "inputview", "outputview", "log", "loglevel", "progress", "verbose"]
comments = {}
comments["obi"] = {k: config["obi"][k] for k in config["obi"] if k not in INVALID_KEYS}
comments[command_name] = config[command_name] # TODO or discuss update instead of nested dict
comments["command_line"] = command_line
if input_str is None and input_dms_name is None and input_view_name is None:
raise Exception("Can't build view configuration with None input") # TODO discuss
if (input_dms_name is not None and input_view_name is not None and len(input_dms_name) != len(input_view_name)) or \
(input_dms_name is None and input_view_name is not None) or \
(input_dms_name is not None and input_view_name is None):
raise Exception("Error building view configuration: there must be as many input DMS names as input view names") # TODO discuss
comments["input_dms_name"] = input_dms_name
comments["input_view_name"] = input_view_name
if input_str is None:
input_str = []
for i in range(len(input_view_name)):
input_str.append(tostr(input_dms_name[i])+"/"+tostr(input_view_name[i]))
comments["input_str"] = input_str
comments["version"] = version
return bytes2str_object(comments)
@staticmethod
def print_config(dict config, str command_name, str command_line, list input_str=None, list input_dms_name=None, list input_view_name=None):
config_dict = View._config_to_dict(config, command_name, command_line, \
input_str=input_str, input_dms_name=input_dms_name, input_view_name=input_view_name)
# Clean virtually empty values
config_dict = clean_empty_values_from_object(config_dict, exclude=[View_comments.KEEP_KEYS])
# Convert to json string
comments_json = json.dumps(config_dict)
return str2bytes(comments_json)
@staticmethod
def get_config_dict(dict config, str command_name, str command_line, list input_str=None, list input_dms_name=None, list input_view_name=None):
config_dict = View._config_to_dict(config, command_name, command_line, \
input_str=input_str, input_dms_name=input_dms_name, input_view_name=input_view_name)
# Clean virtually empty values
config_dict = clean_empty_values_from_object(config_dict, exclude=[View_comments.KEEP_KEYS])
return config_dict
@OBIWrapper.checkIsActive
def write_config(self, dict config, str command_name, str command_line, list input_str=None, list input_dms_name=None, list input_view_name=None):
self.comments = View._config_to_dict(config, command_name, command_line, \
input_str=input_str, input_dms_name=input_dms_name, input_view_name=input_view_name)
# command and view history DOT graph property getter in the form of a list (to remove duplicate elements afterwards)
@property
def dot_history_graph_list(self):
history = []
view_history = self.view_history
history.append(b"\tnode [shape=record]\n")
history.append(b"\tcompound=true\n")
for i in range(len(view_history)):
level = view_history[i]
for input in level:
# Command node
command = b"\""+level[input][b"command_line"]+b"\""
s = b"\t"
s+=command
s+=b" [style=filled, color=lightblue]\n"
history.append(s)
if len(input) > 1:
# Create invisible node
invi_node_name_no_quotes = b"_".join(input)
invi_node_name_quotes = b"\""+ invi_node_name_no_quotes + b"\""
s = b"\t"
s+=invi_node_name_quotes
s+=b" [width=0, style=invis, shape=point]\n"
history.append(s)
# Connect all inputs to the invisible node
for elt in input:
s = b"\t"
s = s+b"\""+elt+b"\""
s+=b" -> "
s+=invi_node_name_quotes
s+=b" [arrowhead=none]\n"
history.append(s)
to_connect_to_command = invi_node_name_no_quotes
else:
to_connect_to_command = input[0]
# Color node if input element is a taxonomy (to do for output nodes too if taxonomy history is to be recorded)
for elt in input:
if b"taxonomy" in elt:
s = b"\t"
s = s+b"\""+elt+b"\""
s+=b" [style=filled, color=navajowhite]\n"
history.append(s)
# Connect input to command
s = b"\t"
s = s+b"\""+to_connect_to_command+b"\""
s+=b" -> "
s+=command
s+=b"\n"
history.append(s)
# Connect command to output
s = b"\t"
s+=command
s+=b" -> "
s = s+b"\""+level[input][b"output"]+b"\""
s+=b"\n"
history.append(s)
return history
# command history DOT graph property getter in the form of a bytes string
@property
def dot_history_graph(self):
uniq_graph = []
for elt in self.dot_history_graph_list:
if elt not in uniq_graph:
uniq_graph.append(elt)
uniq_graph.insert(0, b"digraph \""+self.name+b"\" {\n")
uniq_graph.append(b"}")
return b"".join(uniq_graph)
# ASCII command history graph property getter
@property
def ascii_history(self):
arrow = b"\t|\n\tV\n"
s = b""
first = True
for level in self.view_history:
command_list = [level[input][b"command_line"] for input in level.keys()]
if not first:
s+=arrow
else:
first=False
for command in command_list:
s+=command
s+=b"\n"
return s
# bash command history property getter
@property
def bash_history(self):
s = b""
first = True
for level in self.view_history:
command_list = [level[input][b"command_line"] for input in level.keys()]
for command in command_list:
s+=b"obi "
s+=command
s+=b"\n"
return s
# View and command history property getter
@property
def view_history(self):
if not self.active() :
raise OBIDeactivatedInstanceError()
current_level = [self]
history = []
while current_level[0] is not None: # TODO not sure about robustness
top_level = []
level_dict = {}
for element in current_level:
if element is not None:
if element.comments[b"input_dms_name"] is not None :
for i in range(len(element.comments[b"input_dms_name"])) :
if b"/" not in element.comments[b"input_view_name"][i] and element.comments[b"input_view_name"][i] in element.dms \
and element.comments[b"input_dms_name"][i] == element.dms.name : # Same DMS and not a special element like a taxonomy and view was not deleted
top_level.append(element.dms[element.comments[b"input_view_name"][i]])
else:
top_level.append(None)
else:
top_level.append(None)
level_dict[tuple(element.comments[b"input_str"])] = {}
level_dict[tuple(element.comments[b"input_str"])][b"output"] = element.dms.name+b"/"+element.name
level_dict[tuple(element.comments[b"input_str"])][b"command_line"] = element.comments[b"command_line"]
history.insert(0, level_dict)
current_level = top_level
return history
# Width (column count) property getter
@property
def width(self):
if not self.active() :
raise OBIDeactivatedInstanceError()
return self.pointer().infos.column_count
# DMS property getter
@property
def dms(self):
if not self.active() :
raise OBIDeactivatedInstanceError()
return self._dms
# line_count property getter
@property
def line_count(self):
if not self.active() :
raise OBIDeactivatedInstanceError()
return self.pointer().infos.line_count
# read_only state property getter
@property
def read_only(self):
if not self.active() :
raise OBIDeactivatedInstanceError()
return self.pointer().read_only
# name property getter
@property
def name(self):
if not self.active() :
raise OBIDeactivatedInstanceError()
return <bytes> self.pointer().infos.name
# view type property getter
@property
def type(self): # @ReservedAssignment
if not self.active() :
raise OBIDeactivatedInstanceError()
return <bytes> self.pointer().infos.view_type
# comments property getter
@property
def comments(self):
return View_comments(self)
@comments.setter
def comments(self, object value):
View_comments(self, value)
cdef class View_comments(dict): # Not thread safe
KEEP_KEYS = [b"input_dms_name", b"input_view_name", b"input_str", "input_dms_name", "input_view_name", "input_str"]
def __init__(self, View view, value=None) :
if not view.active() :
raise OBIDeactivatedInstanceError()
self._view = view
if value is not None:
self.update(value) # TODO test and discuss not overwriting (could use replace bool)
self._update_from_file()
def _update_from_file(self):
cdef bytes comments_json
cdef str comments_json_str
cdef Obiview_p view_p
cdef View view
if not self._view.active() :
raise OBIDeactivatedInstanceError()
view = self._view
view_p = <Obiview_p>(view.pointer())
comments_json = <bytes> view_p.infos.comments
comments_json_str = bytes2str(comments_json)
comments_dict = json.loads(comments_json_str)
comments_dict = str2bytes_object(comments_dict)
super(View_comments, self).update(comments_dict)
def __getitem__(self, object key):
if not self._view.active() :
raise OBIDeactivatedInstanceError()
if type(key) == str:
key = str2bytes(key)
self._update_from_file()
return super(View_comments, self).__getitem__(key)
def __setitem__(self, object key, object value):
cdef Obiview_p view_p
cdef View view
if not self._view.active() :
raise OBIDeactivatedInstanceError()
view = self._view
view_p = <Obiview_p>(view.pointer())
# Remove virtually empty values from the object # TODO discuss
clean_empty_values_from_object(value, exclude=[self.KEEP_KEYS])
# If value is virtually empty, don't add it # TODO discuss
if (key not in self.KEEP_KEYS) and (value is None or len(value) == 0):
return
# Convert to bytes
if type(key) == str:
key = str2bytes(key)
value_bytes = str2bytes_object(value)
# Update dict with comments already written in file
self._update_from_file()
# Add new element # TODO don't overwrite?
super(View_comments, self).__setitem__(key, value_bytes)
# Convert to str because json library doens't like bytes
dict_str = {key:item for key,item in self.items()}
dict_str = bytes2str_object(dict_str)
# Convert to json string
comments_json = json.dumps(dict_str)
# Write new comments
if obi_view_write_comments(view_p, tobytes(comments_json)) < 0:
raise Exception("Could not write view comments, view:", view.name, "comments:", comments_json)
def update(self, value):
for k,v in value.items():
self[k] = v
def __contains__(self, key):
return super(View_comments, self).__contains__(tobytes(key))
def __str__(self):
return bytes2str(self._view.pointer().infos.comments)
cdef class Line :
def __init__(self, View view, index_t line_nb) :
self._index = line_nb
self._view = view
def __getitem__(self, object column_name) :
return (self._view).get_column(tobytes(column_name))[self._index]
def __setitem__(self, object column_name, object value): # TODO discuss
# TODO detect multiple elements (dict type)? put somewhere else? but more risky (in get)
# TODO OBI_QUAL ?
cdef type value_type
cdef obitype_t value_obitype
cdef bytes value_b
cdef bytes column_name_b
column_name_b = tobytes(column_name)
# TODO use functions in utils
#print(column_name, "value:", value, type(value))
if column_name_b not in self._view :
if value is None :
return # TODO discuss. This means that columns aren't created until an identifiable type is found
#raise RollbackException("Trying to create a column from a None value (can't guess type)", self)
value_obitype = get_obitype(value)
if value_obitype == OBI_VOID :
raise CantGuessTypeException(value)
#raise RollbackException("Could not guess the type of a value to create a new column", self._view)
Column.new_column(self._view, column_name_b, value_obitype)
(self._view).get_column(column_name_b).set_line(self._index, value)
def __iter__(self):
cdef bytes column_name
for column_name in (self._view).keys() :
yield column_name
def keys(self):
cdef bytes key
return [key for key in self._view.keys()]
def __contains__(self, object column_name):
return (tobytes(column_name) in self.keys())
def __repr__(self):
return bytes2str(self.repr_bytes())
cpdef repr_bytes(self):
formatter = TabFormat(header=False)
return formatter(self)
# View property getter
@property
def view(self):
return self._view
# index property getter
@property
def index(self):
return self._index
# cpdef dict get_view_infos(self, str view_name) :
#
# cdef Obiview_infos_p view_infos_p
# cdef dict view_infos_d
# cdef Alias_column_pair_p column_refs
# cdef int i, j
# cdef str column_name
#
# view_infos_p = obi_view_map_file(self._pointer,
# tobytes(view_name))
# view_infos_d = {}
# view_infos_d["name"] = bytes2str(view_infos_p.name)
# view_infos_d["comments"] = bytes2str(view_infos_p.comments)
# view_infos_d["view_type"] = bytes2str(view_infos_p.view_type)
# view_infos_d["column_count"] = <int> view_infos_p.column_count
# view_infos_d["line_count"] = <int> view_infos_p.line_count
# view_infos_d["created_from"] = bytes2str(view_infos_p.created_from)
# view_infos_d["creation_date"] = bytes2str(obi_format_date(view_infos_p.creation_date))
# if (view_infos_p.all_lines) :
# view_infos_d["line_selection"] = None
# else :
# view_infos_d["line_selection"] = {}
# view_infos_d["line_selection"]["column_name"] = bytes2str((view_infos_p.line_selection).column_name)
# view_infos_d["line_selection"]["version"] = <int> (view_infos_p.line_selection).version
# view_infos_d["column_references"] = {}
# column_references = view_infos_p.column_references
# for j in range(view_infos_d["column_count"]) :
# column_name = bytes2str((column_references[j]).alias)
# view_infos_d["column_references"][column_name] = {}
# view_infos_d["column_references"][column_name]["original_name"] = bytes2str((column_references[j]).column_refs.column_name)
# view_infos_d["column_references"][column_name]["version"] = (column_references[j]).column_refs.version
#
# obi_view_unmap_file(self._pointer, view_infos_p)
#
# return view_infos_d
cdef class Line_selection(list):
def __init__(self, View view, lines=None) :
if view._pointer == NULL:
raise Exception("Error: trying to create a line selection with an invalidated view")
self._view = view
self._view_name = view.name
if lines is not None:
self.extend(lines)
def extend(self, iterable):
cdef index_t i
cdef index_t max_i = self._view.line_count
for i in iterable: # TODO this is already checked in C
if i > max_i:
raise RuntimeError("Error: trying to select line %d beyond the line count %d of view %s" %
(i,
max_i,
self._view_name)
)
list.append(self,i)
def append(self, index_t idx) :
if idx >= self._view.line_count :
raise IndexError("Error: trying to select line %d beyond the line count %d of view %s" %
(idx,
self._view.line_count,
bytes2str(self.name))
)
list.append(self,idx)
cdef index_t* __build_binary_list__(self):
cdef index_t* line_selection_p = NULL
cdef int i
cdef size_t l_selection = len(self)
line_selection_p = <index_t*> malloc((l_selection + 1) * sizeof(index_t)) # +1 for the -1 flagging the end of the array
for i in range(l_selection) :
line_selection_p[i] = self[i]
line_selection_p[l_selection] = -1 # flagging the end of the array
return line_selection_p
cpdef View materialize(self,
object view_name,
object comments={}):
cdef bytes view_name_b = tobytes(view_name)
cdef bytes comments_b
cdef Obiview_p pointer
cdef View view
if not self._view.active() :
raise OBIDeactivatedInstanceError()
comments_b = str2bytes(json.dumps(bytes2str_object(comments)))
pointer = obi_clone_view(self._view._dms.pointer(),
self._view.pointer(),
view_name_b,
self.__build_binary_list__(),
comments_b)
if pointer == NULL :
raise RuntimeError("Error : Cannot clone view %s into view %s with new line selection"
% (str(self._view.name),
bytes2str(view_name_b))
)
view = OBIWrapper.new_wrapper(type(self._view), pointer)
view._dms = self._view._dms
view._dms.register(view)
return view
#############################################################
class RollbackException(Exception):
def __init__(self, message, *views):
super(RollbackException, self).__init__(message)
for i in range(len(views)):
view = <View>(views[i])
if obi_rollback_view(<Obiview_p>(view.pointer())) < 0 :
raise Exception("Error rollbacking view")
if view.active() :
view._dms.unregister(view)
OBIWrapper.close(view)
class CantGuessTypeException(Exception):
def __init__(self, object value) :
raise Exception("Can't guess type to set value:", value)
#############################################################
cdef register_view_class(bytes view_type_name,
type view_class):
'''
Each subclass of `dms.view` needs to be registered after its declaration
'''
global __VIEW_CLASS__
assert issubclass(view_class, View)
__VIEW_CLASS__[view_type_name] = view_class
cdef register_all_view_classes() :
x = list(pkgutil.walk_packages(typed_view.__path__, prefix="obitools3.dms.view.typed_view."))
all_modules = [importlib.import_module(a[1]) for a in x]
for mod in all_modules :
getattr(mod, 'register_class')()
register_all_view_classes()
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