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def _capture_snapshot(a_snapshot: Snapshot, resolved_kwargs: Mapping[str, Any]) -> Any:
"""
Capture the snapshot from the keyword arguments resolved before the function call (including the default values).
:param a_snapshot: snapshot to be captured
:param resolved_kwargs: resolved keyword arguments (including the default values)
:return: captured value
"""
if a_snapshot.arg is not None:
if a_snapshot.arg not in resolved_kwargs:
raise TypeError(("The argument of the snapshot has not been set: {}. "
"Does the original function define it? Did you supply it in the call?").format(
a_snapshot.arg))
value = a_snapshot.capture(**{a_snapshot.arg: resolved_kwargs[a_snapshot.arg]})
else:
value = a_snapshot.capture()
return value | Capture the snapshot from the keyword arguments resolved before the function call (including the default values).
:param a_snapshot: snapshot to be captured
:param resolved_kwargs: resolved keyword arguments (including the default values)
:return: captured value | entailment |
def decorate_with_checker(func: CallableT) -> CallableT:
"""Decorate the function with a checker that verifies the preconditions and postconditions."""
assert not hasattr(func, "__preconditions__"), \
"Expected func to have no list of preconditions (there should be only a single contract checker per function)."
assert not hasattr(func, "__postconditions__"), \
"Expected func to have no list of postconditions (there should be only a single contract checker per function)."
assert not hasattr(func, "__postcondition_snapshots__"), \
"Expected func to have no list of postcondition snapshots (there should be only a single contract checker " \
"per function)."
sign = inspect.signature(func)
param_names = list(sign.parameters.keys())
# Determine the default argument values.
kwdefaults = dict() # type: Dict[str, Any]
# Add to the defaults all the values that are needed by the contracts.
for param in sign.parameters.values():
if param.default != inspect.Parameter.empty:
kwdefaults[param.name] = param.default
def wrapper(*args, **kwargs):
"""Wrap func by checking the preconditions and postconditions."""
preconditions = getattr(wrapper, "__preconditions__") # type: List[List[Contract]]
snapshots = getattr(wrapper, "__postcondition_snapshots__") # type: List[Snapshot]
postconditions = getattr(wrapper, "__postconditions__") # type: List[Contract]
resolved_kwargs = _kwargs_from_call(param_names=param_names, kwdefaults=kwdefaults, args=args, kwargs=kwargs)
if postconditions:
if 'result' in resolved_kwargs:
raise TypeError("Unexpected argument 'result' in a function decorated with postconditions.")
if 'OLD' in resolved_kwargs:
raise TypeError("Unexpected argument 'OLD' in a function decorated with postconditions.")
# Assert the preconditions in groups. This is necessary to implement "require else" logic when a class
# weakens the preconditions of its base class.
violation_err = None # type: Optional[ViolationError]
for group in preconditions:
violation_err = None
try:
for contract in group:
_assert_precondition(contract=contract, resolved_kwargs=resolved_kwargs)
break
except ViolationError as err:
violation_err = err
if violation_err is not None:
raise violation_err # pylint: disable=raising-bad-type
# Capture the snapshots
if postconditions:
old_as_mapping = dict() # type: MutableMapping[str, Any]
for snap in snapshots:
# This assert is just a last defense.
# Conflicting snapshot names should have been caught before, either during the decoration or
# in the meta-class.
assert snap.name not in old_as_mapping, "Snapshots with the conflicting name: {}"
old_as_mapping[snap.name] = _capture_snapshot(a_snapshot=snap, resolved_kwargs=resolved_kwargs)
resolved_kwargs['OLD'] = _Old(mapping=old_as_mapping)
# Execute the wrapped function
result = func(*args, **kwargs)
if postconditions:
resolved_kwargs['result'] = result
# Assert the postconditions as a conjunction
for contract in postconditions:
_assert_postcondition(contract=contract, resolved_kwargs=resolved_kwargs)
return result # type: ignore
# Copy __doc__ and other properties so that doctests can run
functools.update_wrapper(wrapper=wrapper, wrapped=func)
assert not hasattr(wrapper, "__preconditions__"), "Expected no preconditions set on a pristine contract checker."
assert not hasattr(wrapper, "__postcondition_snapshots__"), \
"Expected no postcondition snapshots set on a pristine contract checker."
assert not hasattr(wrapper, "__postconditions__"), "Expected no postconditions set on a pristine contract checker."
# Precondition is a list of condition groups (i.e. disjunctive normal form):
# each group consists of AND'ed preconditions, while the groups are OR'ed.
#
# This is necessary in order to implement "require else" logic when a class weakens the preconditions of
# its base class.
setattr(wrapper, "__preconditions__", [])
setattr(wrapper, "__postcondition_snapshots__", [])
setattr(wrapper, "__postconditions__", [])
return wrapper | Decorate the function with a checker that verifies the preconditions and postconditions. | entailment |
def _find_self(param_names: List[str], args: Tuple[Any, ...], kwargs: Dict[str, Any]) -> Any:
"""Find the instance of ``self`` in the arguments."""
instance_i = param_names.index("self")
if instance_i < len(args):
instance = args[instance_i]
else:
instance = kwargs["self"]
return instance | Find the instance of ``self`` in the arguments. | entailment |
def _decorate_with_invariants(func: CallableT, is_init: bool) -> CallableT:
"""
Decorate the function ``func`` of the class ``cls`` with invariant checks.
If the function has been already decorated with invariant checks, the function returns immediately.
:param func: function to be wrapped
:param is_init: True if the ``func`` is __init__
:return: function wrapped with invariant checks
"""
if _already_decorated_with_invariants(func=func):
return func
sign = inspect.signature(func)
param_names = list(sign.parameters.keys())
if is_init:
def wrapper(*args, **kwargs):
"""Wrap __init__ method of a class by checking the invariants *after* the invocation."""
result = func(*args, **kwargs)
instance = _find_self(param_names=param_names, args=args, kwargs=kwargs)
for contract in instance.__class__.__invariants__:
_assert_invariant(contract=contract, instance=instance)
return result
else:
def wrapper(*args, **kwargs):
"""Wrap a function of a class by checking the invariants *before* and *after* the invocation."""
instance = _find_self(param_names=param_names, args=args, kwargs=kwargs)
for contract in instance.__class__.__invariants__:
_assert_invariant(contract=contract, instance=instance)
result = func(*args, **kwargs)
for contract in instance.__class__.__invariants__:
_assert_invariant(contract=contract, instance=instance)
return result
functools.update_wrapper(wrapper=wrapper, wrapped=func)
setattr(wrapper, "__is_invariant_check__", True)
return wrapper | Decorate the function ``func`` of the class ``cls`` with invariant checks.
If the function has been already decorated with invariant checks, the function returns immediately.
:param func: function to be wrapped
:param is_init: True if the ``func`` is __init__
:return: function wrapped with invariant checks | entailment |
def _already_decorated_with_invariants(func: CallableT) -> bool:
"""Check if the function has been already decorated with an invariant check by going through its decorator stack."""
already_decorated = False
for a_decorator in _walk_decorator_stack(func=func):
if getattr(a_decorator, "__is_invariant_check__", False):
already_decorated = True
break
return already_decorated | Check if the function has been already decorated with an invariant check by going through its decorator stack. | entailment |
def add_invariant_checks(cls: type) -> None:
"""Decorate each of the class functions with invariant checks if not already decorated."""
# Candidates for the decoration as list of (name, dir() value)
init_name_func = None # type: Optional[Tuple[str, Callable[..., None]]]
names_funcs = [] # type: List[Tuple[str, Callable[..., None]]]
names_properties = [] # type: List[Tuple[str, property]]
# Filter out entries in the directory which are certainly not candidates for decoration.
for name, value in [(name, getattr(cls, name)) for name in dir(cls)]:
# We need to ignore __repr__ to prevent endless loops when generating error messages.
# __getattribute__, __setattr__ and __delattr__ are too invasive and alter the state of the instance.
# Hence we don't consider them "public".
if name in ["__repr__", "__getattribute__", "__setattr__", "__delattr__"]:
continue
if name == "__init__":
assert inspect.isfunction(value) or isinstance(value, _SLOT_WRAPPER_TYPE), \
"Expected __init__ to be either a function or a slot wrapper, but got: {}".format(type(value))
init_name_func = (name, value)
continue
if not inspect.isfunction(value) and not isinstance(value, _SLOT_WRAPPER_TYPE) and \
not isinstance(value, property):
continue
# Ignore class methods
if getattr(value, "__self__", None) is cls:
continue
# Ignore "protected"/"private" methods
if name.startswith("_") and not (name.startswith("__") and name.endswith("__")):
continue
if inspect.isfunction(value) or isinstance(value, _SLOT_WRAPPER_TYPE):
names_funcs.append((name, value))
elif isinstance(value, property):
names_properties.append((name, value))
else:
raise NotImplementedError("Unhandled directory entry of class {} for {}: {}".format(cls, name, value))
if init_name_func:
name, func = init_name_func
wrapper = _decorate_with_invariants(func=func, is_init=True)
setattr(cls, name, wrapper)
for name, func in names_funcs:
wrapper = _decorate_with_invariants(func=func, is_init=False)
setattr(cls, name, wrapper)
for name, prop in names_properties:
new_prop = property( # type: ignore
fget=_decorate_with_invariants(func=prop.fget, is_init=False) if prop.fget else None,
fset=_decorate_with_invariants(func=prop.fset, is_init=False) if prop.fset else None,
fdel=_decorate_with_invariants(func=prop.fdel, is_init=False) if prop.fdel else None,
doc=prop.__doc__)
setattr(cls, name, new_prop) | Decorate each of the class functions with invariant checks if not already decorated. | entailment |
def main() -> None:
""""Execute the main routine."""
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument("--module", help="name of the module to import",
choices=[
"functions_100_with_no_contract",
"functions_100_with_1_contract",
"functions_100_with_5_contracts",
"functions_100_with_10_contracts",
"functions_100_with_1_disabled_contract",
"functions_100_with_5_disabled_contracts",
"functions_100_with_10_disabled_contracts",
"classes_100_with_no_invariant",
"classes_100_with_1_invariant",
"classes_100_with_5_invariants",
"classes_100_with_10_invariants",
"classes_100_with_1_disabled_invariant",
"classes_100_with_5_disabled_invariants",
"classes_100_with_10_disabled_invariants",
],
required=True)
args = parser.parse_args()
a_module = str(args.module)
if a_module == "functions_100_with_no_contract":
start = time.time()
import functions_100_with_no_contract
print(time.time() - start)
elif a_module == "functions_100_with_1_contract":
start = time.time()
import functions_100_with_1_contract
print(time.time() - start)
elif a_module == "functions_100_with_5_contracts":
start = time.time()
import functions_100_with_5_contracts
print(time.time() - start)
elif a_module == "functions_100_with_10_contracts":
start = time.time()
import functions_100_with_10_contracts
print(time.time() - start)
elif a_module == "functions_100_with_1_disabled_contract":
start = time.time()
import functions_100_with_1_disabled_contract
print(time.time() - start)
elif a_module == "functions_100_with_5_disabled_contracts":
start = time.time()
import functions_100_with_5_disabled_contracts
print(time.time() - start)
elif a_module == "functions_100_with_10_disabled_contracts":
start = time.time()
import functions_100_with_10_disabled_contracts
print(time.time() - start)
elif a_module == "classes_100_with_no_invariant":
start = time.time()
import classes_100_with_no_invariant
print(time.time() - start)
elif a_module == "classes_100_with_1_invariant":
start = time.time()
import classes_100_with_1_invariant
print(time.time() - start)
elif a_module == "classes_100_with_5_invariants":
start = time.time()
import classes_100_with_5_invariants
print(time.time() - start)
elif a_module == "classes_100_with_10_invariants":
start = time.time()
import classes_100_with_10_invariants
print(time.time() - start)
elif a_module == "classes_100_with_1_disabled_invariant":
start = time.time()
import classes_100_with_1_disabled_invariant
print(time.time() - start)
elif a_module == "classes_100_with_5_disabled_invariants":
start = time.time()
import classes_100_with_5_disabled_invariants
print(time.time() - start)
elif a_module == "classes_100_with_10_disabled_invariants":
start = time.time()
import classes_100_with_10_disabled_invariants
print(time.time() - start)
else:
raise NotImplementedError("Unhandled module: {}".format(a_module)) | Execute the main routine. | entailment |
def main() -> None:
""""Execute the main routine."""
modules = [
"functions_100_with_no_contract",
"functions_100_with_1_contract",
"functions_100_with_5_contracts",
"functions_100_with_10_contracts",
"functions_100_with_1_disabled_contract",
"functions_100_with_5_disabled_contracts",
"functions_100_with_10_disabled_contracts",
"classes_100_with_no_invariant",
"classes_100_with_1_invariant",
"classes_100_with_5_invariants",
"classes_100_with_10_invariants",
"classes_100_with_1_disabled_invariant",
"classes_100_with_5_disabled_invariants",
"classes_100_with_10_disabled_invariants",
]
for a_module in modules:
durations = [] # type: List[float]
for i in range(0, 10):
duration = float(
subprocess.check_output(["./measure.py", "--module", a_module], cwd=os.path.dirname(__file__)).strip())
durations.append(duration)
print("Duration to import the module {} (in milliseconds): {:.2f} ± {:.2f}".format(
a_module, statistics.mean(durations) * 10e3, statistics.stdev(durations) * 10e3)) | Execute the main routine. | entailment |
def main() -> None:
""""Execute the main routine."""
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument("--outdir", help="output directory", default=os.path.dirname(__file__))
args = parser.parse_args()
outdir = pathlib.Path(args.outdir)
if not outdir.exists():
raise FileNotFoundError("Output directory is missing: {}".format(outdir))
for contracts in [0, 1, 5, 10]:
if contracts == 0:
pth = outdir / "functions_100_with_no_contract.py"
elif contracts == 1:
pth = outdir / "functions_100_with_1_contract.py"
else:
pth = outdir / "functions_100_with_{}_contracts.py".format(contracts)
text = generate_functions(functions=100, contracts=contracts, disabled=False)
pth.write_text(text)
for contracts in [1, 5, 10]:
if contracts == 1:
pth = outdir / "functions_100_with_1_disabled_contract.py"
else:
pth = outdir / "functions_100_with_{}_disabled_contracts.py".format(contracts)
text = generate_functions(functions=100, contracts=contracts, disabled=True)
pth.write_text(text)
for invariants in [0, 1, 5, 10]:
if invariants == 0:
pth = outdir / "classes_100_with_no_invariant.py"
elif invariants == 1:
pth = outdir / "classes_100_with_1_invariant.py"
else:
pth = outdir / "classes_100_with_{}_invariants.py".format(invariants)
text = generate_classes(classes=100, invariants=invariants, disabled=False)
pth.write_text(text)
for invariants in [1, 5, 10]:
if invariants == 1:
pth = outdir / "classes_100_with_1_disabled_invariant.py"
else:
pth = outdir / "classes_100_with_{}_disabled_invariants.py".format(invariants)
text = generate_classes(classes=100, invariants=invariants, disabled=True)
pth.write_text(text) | Execute the main routine. | entailment |
def visit_Num(self, node: ast.Num) -> Union[int, float]:
"""Recompute the value as the number at the node."""
result = node.n
self.recomputed_values[node] = result
return result | Recompute the value as the number at the node. | entailment |
def visit_Str(self, node: ast.Str) -> str:
"""Recompute the value as the string at the node."""
result = node.s
self.recomputed_values[node] = result
return result | Recompute the value as the string at the node. | entailment |
def visit_Bytes(self, node: ast.Bytes) -> bytes:
"""Recompute the value as the bytes at the node."""
result = node.s
self.recomputed_values[node] = result
return node.s | Recompute the value as the bytes at the node. | entailment |
def visit_List(self, node: ast.List) -> List[Any]:
"""Visit the elements and assemble the results into a list."""
if isinstance(node.ctx, ast.Store):
raise NotImplementedError("Can not compute the value of a Store on a list")
result = [self.visit(node=elt) for elt in node.elts]
self.recomputed_values[node] = result
return result | Visit the elements and assemble the results into a list. | entailment |
def visit_Tuple(self, node: ast.Tuple) -> Tuple[Any, ...]:
"""Visit the elements and assemble the results into a tuple."""
if isinstance(node.ctx, ast.Store):
raise NotImplementedError("Can not compute the value of a Store on a tuple")
result = tuple(self.visit(node=elt) for elt in node.elts)
self.recomputed_values[node] = result
return result | Visit the elements and assemble the results into a tuple. | entailment |
def visit_Set(self, node: ast.Set) -> Set[Any]:
"""Visit the elements and assemble the results into a set."""
result = set(self.visit(node=elt) for elt in node.elts)
self.recomputed_values[node] = result
return result | Visit the elements and assemble the results into a set. | entailment |
def visit_Dict(self, node: ast.Dict) -> Dict[Any, Any]:
"""Visit keys and values and assemble a dictionary with the results."""
recomputed_dict = dict() # type: Dict[Any, Any]
for key, val in zip(node.keys, node.values):
recomputed_dict[self.visit(node=key)] = self.visit(node=val)
self.recomputed_values[node] = recomputed_dict
return recomputed_dict | Visit keys and values and assemble a dictionary with the results. | entailment |
def visit_NameConstant(self, node: ast.NameConstant) -> Any:
"""Forward the node value as a result."""
self.recomputed_values[node] = node.value
return node.value | Forward the node value as a result. | entailment |
def visit_Name(self, node: ast.Name) -> Any:
"""Load the variable by looking it up in the variable look-up and in the built-ins."""
if not isinstance(node.ctx, ast.Load):
raise NotImplementedError("Can only compute a value of Load on a name {}, but got context: {}".format(
node.id, node.ctx))
result = None # type: Optional[Any]
if node.id in self._name_to_value:
result = self._name_to_value[node.id]
if result is None and hasattr(builtins, node.id):
result = getattr(builtins, node.id)
if result is None and node.id != "None":
# The variable refers to a name local of the lambda (e.g., a target in the generator expression).
# Since we evaluate generator expressions with runtime compilation, None is returned here as a placeholder.
return PLACEHOLDER
self.recomputed_values[node] = result
return result | Load the variable by looking it up in the variable look-up and in the built-ins. | entailment |
def visit_Expr(self, node: ast.Expr) -> Any:
"""Visit the node's ``value``."""
result = self.visit(node=node.value)
self.recomputed_values[node] = result
return result | Visit the node's ``value``. | entailment |
def visit_UnaryOp(self, node: ast.UnaryOp) -> Any:
"""Visit the node operand and apply the operation on the result."""
if isinstance(node.op, ast.UAdd):
result = +self.visit(node=node.operand)
elif isinstance(node.op, ast.USub):
result = -self.visit(node=node.operand)
elif isinstance(node.op, ast.Not):
result = not self.visit(node=node.operand)
elif isinstance(node.op, ast.Invert):
result = ~self.visit(node=node.operand)
else:
raise NotImplementedError("Unhandled op of {}: {}".format(node, node.op))
self.recomputed_values[node] = result
return result | Visit the node operand and apply the operation on the result. | entailment |
def visit_BinOp(self, node: ast.BinOp) -> Any:
"""Recursively visit the left and right operand, respectively, and apply the operation on the results."""
# pylint: disable=too-many-branches
left = self.visit(node=node.left)
right = self.visit(node=node.right)
if isinstance(node.op, ast.Add):
result = left + right
elif isinstance(node.op, ast.Sub):
result = left - right
elif isinstance(node.op, ast.Mult):
result = left * right
elif isinstance(node.op, ast.Div):
result = left / right
elif isinstance(node.op, ast.FloorDiv):
result = left // right
elif isinstance(node.op, ast.Mod):
result = left % right
elif isinstance(node.op, ast.Pow):
result = left**right
elif isinstance(node.op, ast.LShift):
result = left << right
elif isinstance(node.op, ast.RShift):
result = left >> right
elif isinstance(node.op, ast.BitOr):
result = left | right
elif isinstance(node.op, ast.BitXor):
result = left ^ right
elif isinstance(node.op, ast.BitAnd):
result = left & right
elif isinstance(node.op, ast.MatMult):
result = left @ right
else:
raise NotImplementedError("Unhandled op of {}: {}".format(node, node.op))
self.recomputed_values[node] = result
return result | Recursively visit the left and right operand, respectively, and apply the operation on the results. | entailment |
def visit_BoolOp(self, node: ast.BoolOp) -> Any:
"""Recursively visit the operands and apply the operation on them."""
values = [self.visit(value_node) for value_node in node.values]
if isinstance(node.op, ast.And):
result = functools.reduce(lambda left, right: left and right, values, True)
elif isinstance(node.op, ast.Or):
result = functools.reduce(lambda left, right: left or right, values, True)
else:
raise NotImplementedError("Unhandled op of {}: {}".format(node, node.op))
self.recomputed_values[node] = result
return result | Recursively visit the operands and apply the operation on them. | entailment |
def visit_Compare(self, node: ast.Compare) -> Any:
"""Recursively visit the comparators and apply the operations on them."""
# pylint: disable=too-many-branches
left = self.visit(node=node.left)
comparators = [self.visit(node=comparator) for comparator in node.comparators]
result = None # type: Optional[Any]
for comparator, op in zip(comparators, node.ops):
if isinstance(op, ast.Eq):
comparison = left == comparator
elif isinstance(op, ast.NotEq):
comparison = left != comparator
elif isinstance(op, ast.Lt):
comparison = left < comparator
elif isinstance(op, ast.LtE):
comparison = left <= comparator
elif isinstance(op, ast.Gt):
comparison = left > comparator
elif isinstance(op, ast.GtE):
comparison = left >= comparator
elif isinstance(op, ast.Is):
comparison = left is comparator
elif isinstance(op, ast.IsNot):
comparison = left is not comparator
elif isinstance(op, ast.In):
comparison = left in comparator
elif isinstance(op, ast.NotIn):
comparison = left not in comparator
else:
raise NotImplementedError("Unhandled op of {}: {}".format(node, op))
if result is None:
result = comparison
else:
result = result and comparison
left = comparator
self.recomputed_values[node] = result
return result | Recursively visit the comparators and apply the operations on them. | entailment |
def visit_Call(self, node: ast.Call) -> Any:
"""Visit the function and the arguments and finally make the function call with them."""
func = self.visit(node=node.func)
args = [] # type: List[Any]
for arg_node in node.args:
if isinstance(arg_node, ast.Starred):
args.extend(self.visit(node=arg_node))
else:
args.append(self.visit(node=arg_node))
kwargs = dict() # type: Dict[str, Any]
for keyword in node.keywords:
if keyword.arg is None:
kw = self.visit(node=keyword.value)
for key, val in kw.items():
kwargs[key] = val
else:
kwargs[keyword.arg] = self.visit(node=keyword.value)
result = func(*args, **kwargs)
self.recomputed_values[node] = result
return result | Visit the function and the arguments and finally make the function call with them. | entailment |
def visit_IfExp(self, node: ast.IfExp) -> Any:
"""Visit the ``test``, and depending on its outcome, the ``body`` or ``orelse``."""
test = self.visit(node=node.test)
if test:
result = self.visit(node=node.body)
else:
result = self.visit(node=node.orelse)
self.recomputed_values[node] = result
return result | Visit the ``test``, and depending on its outcome, the ``body`` or ``orelse``. | entailment |
def visit_Attribute(self, node: ast.Attribute) -> Any:
"""Visit the node's ``value`` and get the attribute from the result."""
value = self.visit(node=node.value)
if not isinstance(node.ctx, ast.Load):
raise NotImplementedError(
"Can only compute a value of Load on the attribute {}, but got context: {}".format(node.attr, node.ctx))
result = getattr(value, node.attr)
self.recomputed_values[node] = result
return result | Visit the node's ``value`` and get the attribute from the result. | entailment |
def visit_Index(self, node: ast.Index) -> Any:
"""Visit the node's ``value``."""
result = self.visit(node=node.value)
self.recomputed_values[node] = result
return result | Visit the node's ``value``. | entailment |
def visit_Slice(self, node: ast.Slice) -> slice:
"""Visit ``lower``, ``upper`` and ``step`` and recompute the node as a ``slice``."""
lower = None # type: Optional[int]
if node.lower is not None:
lower = self.visit(node=node.lower)
upper = None # type: Optional[int]
if node.upper is not None:
upper = self.visit(node=node.upper)
step = None # type: Optional[int]
if node.step is not None:
step = self.visit(node=node.step)
result = slice(lower, upper, step)
self.recomputed_values[node] = result
return result | Visit ``lower``, ``upper`` and ``step`` and recompute the node as a ``slice``. | entailment |
def visit_ExtSlice(self, node: ast.ExtSlice) -> Tuple[Any, ...]:
"""Visit each dimension of the advanced slicing and assemble the dimensions in a tuple."""
result = tuple(self.visit(node=dim) for dim in node.dims)
self.recomputed_values[node] = result
return result | Visit each dimension of the advanced slicing and assemble the dimensions in a tuple. | entailment |
def visit_Subscript(self, node: ast.Subscript) -> Any:
"""Visit the ``slice`` and a ``value`` and get the element."""
value = self.visit(node=node.value)
a_slice = self.visit(node=node.slice)
result = value[a_slice]
self.recomputed_values[node] = result
return result | Visit the ``slice`` and a ``value`` and get the element. | entailment |
def _execute_comprehension(self, node: Union[ast.ListComp, ast.SetComp, ast.GeneratorExp, ast.DictComp]) -> Any:
"""Compile the generator or comprehension from the node and execute the compiled code."""
args = [ast.arg(arg=name) for name in sorted(self._name_to_value.keys())]
func_def_node = ast.FunctionDef(
name="generator_expr",
args=ast.arguments(args=args, kwonlyargs=[], kw_defaults=[], defaults=[]),
decorator_list=[],
body=[ast.Return(node)])
module_node = ast.Module(body=[func_def_node])
ast.fix_missing_locations(module_node)
code = compile(source=module_node, filename='<ast>', mode='exec')
module_locals = {} # type: Dict[str, Any]
module_globals = {} # type: Dict[str, Any]
exec(code, module_globals, module_locals) # pylint: disable=exec-used
generator_expr_func = module_locals["generator_expr"]
return generator_expr_func(**self._name_to_value) | Compile the generator or comprehension from the node and execute the compiled code. | entailment |
def visit_GeneratorExp(self, node: ast.GeneratorExp) -> Any:
"""Compile the generator expression as a function and call it."""
result = self._execute_comprehension(node=node)
for generator in node.generators:
self.visit(generator.iter)
# Do not set the computed value of the node since its representation would be non-informative.
return result | Compile the generator expression as a function and call it. | entailment |
def visit_ListComp(self, node: ast.ListComp) -> Any:
"""Compile the list comprehension as a function and call it."""
result = self._execute_comprehension(node=node)
for generator in node.generators:
self.visit(generator.iter)
self.recomputed_values[node] = result
return result | Compile the list comprehension as a function and call it. | entailment |
def visit_SetComp(self, node: ast.SetComp) -> Any:
"""Compile the set comprehension as a function and call it."""
result = self._execute_comprehension(node=node)
for generator in node.generators:
self.visit(generator.iter)
self.recomputed_values[node] = result
return result | Compile the set comprehension as a function and call it. | entailment |
def visit_DictComp(self, node: ast.DictComp) -> Any:
"""Compile the dictionary comprehension as a function and call it."""
result = self._execute_comprehension(node=node)
for generator in node.generators:
self.visit(generator.iter)
self.recomputed_values[node] = result
return result | Compile the dictionary comprehension as a function and call it. | entailment |
def visit_Return(self, node: ast.Return) -> Any: # pylint: disable=no-self-use
"""Raise an exception that this node is unexpected."""
raise AssertionError("Unexpected return node during the re-computation: {}".format(ast.dump(node))) | Raise an exception that this node is unexpected. | entailment |
def generic_visit(self, node: ast.AST) -> None:
"""Raise an exception that this node has not been handled."""
raise NotImplementedError("Unhandled recomputation of the node: {} {}".format(type(node), node)) | Raise an exception that this node has not been handled. | entailment |
def tokenize_words(string):
"""
Tokenize input text to words.
:param string: Text to tokenize
:type string: str or unicode
:return: words
:rtype: list of strings
"""
string = six.text_type(string)
return re.findall(WORD_TOKENIZATION_RULES, string) | Tokenize input text to words.
:param string: Text to tokenize
:type string: str or unicode
:return: words
:rtype: list of strings | entailment |
def tokenize_sents(string):
"""
Tokenize input text to sentences.
:param string: Text to tokenize
:type string: str or unicode
:return: sentences
:rtype: list of strings
"""
string = six.text_type(string)
spans = []
for match in re.finditer('[^\s]+', string):
spans.append(match)
spans_count = len(spans)
rez = []
off = 0
for i in range(spans_count):
tok = string[spans[i].start():spans[i].end()]
if i == spans_count - 1:
rez.append(string[off:spans[i].end()])
elif tok[-1] in ['.', '!', '?', '…', '»']:
tok1 = tok[re.search('[.!?…»]', tok).start()-1]
next_tok = string[spans[i + 1].start():spans[i + 1].end()]
if (next_tok[0].isupper()
and not tok1.isupper()
and not (tok[-1] != '.'
or tok1[0] == '('
or tok in ABBRS)):
rez.append(string[off:spans[i].end()])
off = spans[i + 1].start()
return rez | Tokenize input text to sentences.
:param string: Text to tokenize
:type string: str or unicode
:return: sentences
:rtype: list of strings | entailment |
def tokenize_text(string):
"""
Tokenize input text to paragraphs, sentences and words.
Tokenization to paragraphs is done using simple Newline algorithm
For sentences and words tokenizers above are used
:param string: Text to tokenize
:type string: str or unicode
:return: text, tokenized into paragraphs, sentences and words
:rtype: list of list of list of words
"""
string = six.text_type(string)
rez = []
for part in string.split('\n'):
par = []
for sent in tokenize_sents(part):
par.append(tokenize_words(sent))
if par:
rez.append(par)
return rez | Tokenize input text to paragraphs, sentences and words.
Tokenization to paragraphs is done using simple Newline algorithm
For sentences and words tokenizers above are used
:param string: Text to tokenize
:type string: str or unicode
:return: text, tokenized into paragraphs, sentences and words
:rtype: list of list of list of words | entailment |
def collate(self, graph, collation):
'''
:type graph: VariantGraph
:type collation: Collation
'''
# Build the variant graph for the first witness
# this is easy: generate a vertex for every token
first_witness = collation.witnesses[0]
tokens = first_witness.tokens()
token_to_vertex = self.merge(graph, first_witness.sigil, tokens)
# let the scorer prepare the first witness
self.scorer.prepare_witness(first_witness)
# construct superbase
superbase = tokens
# align witness 2 - n
for x in range(1, len(collation.witnesses)):
next_witness = collation.witnesses[x]
# let the scorer prepare the next witness
self.scorer.prepare_witness(next_witness)
# # VOOR CONTROLE!
# alignment = self._align_table(superbase, next_witness, token_to_vertex)
# self.table2 = self.table
# alignment = token -> vertex
alignment = self.align_function(superbase, next_witness, token_to_vertex)
# merge
token_to_vertex.update(self.merge(graph, next_witness.sigil, next_witness.tokens(), alignment))
# print("actual")
# self._debug_edit_graph_table(self.table)
# print("expected")
# self._debug_edit_graph_table(self.table2)
# change superbase
superbase = self.new_superbase
if self.debug_scores:
self._debug_edit_graph_table(self.table) | :type graph: VariantGraph
:type collation: Collation | entailment |
def align(self):
'''
Every step we have 3 choices:
1) Move pointer witness a --> omission
2) Move pointer witness b --> addition
3) Move pointer of both witness a/b --> match
Note: a replacement is omission followed by an addition or the other way around
Choice 1 and 2 are only possible if token a and b are not a match OR when tokens are repeated.
For now I ignore token repetition..
'''
# extract tokens from witness (note that this can be done in a streaming manner if desired)
tokens_a = self.witness_a.tokens()
tokens_b = self.witness_b.tokens()
# create virtual decision tree (nodes are created on demand)
# see above
# create start node
start = DecisionTreeNode(self)
# search the decision tree
result = self.tree.search(start)
print(result)
pass | Every step we have 3 choices:
1) Move pointer witness a --> omission
2) Move pointer witness b --> addition
3) Move pointer of both witness a/b --> match
Note: a replacement is omission followed by an addition or the other way around
Choice 1 and 2 are only possible if token a and b are not a match OR when tokens are repeated.
For now I ignore token repetition.. | entailment |
def connect(self, source, target, witnesses):
"""
:type source: integer
:type target: integer
"""
# print("Adding Edge: "+source+":"+target)
if self.graph.has_edge(source, target):
self.graph[source][target]["label"] += ", " + str(witnesses)
else:
self.graph.add_edge(source, target, label=witnesses) | :type source: integer
:type target: integer | entailment |
def connect_near(self, source, target, weight):
# Near edges are added to self.near_graph, not self.graph, to avoid cycles
"""
:type source: integer
:type target: integer
"""
self.near_graph.add_edge(source, target, weight = weight, type='near') | :type source: integer
:type target: integer | entailment |
def merge(self, graph, witness_sigil, witness_tokens, alignments={}):
"""
:type graph: VariantGraph
"""
# NOTE: token_to_vertex only contains newly generated vertices
token_to_vertex = {}
last = graph.start
for token in witness_tokens:
vertex = alignments.get(token, None)
if not vertex:
vertex = graph.add_vertex(token, witness_sigil)
token_to_vertex[token] = vertex
else:
vertex.add_token(witness_sigil, token)
# graph.add_token_to_vertex(vertex, token, witness_sigil)
graph.connect(last, vertex, witness_sigil)
last = vertex
graph.connect(last, graph.end, witness_sigil)
return token_to_vertex | :type graph: VariantGraph | entailment |
def collate(self, graph):
"""
:type graph: VariantGraph
"""
# prepare the token index
self.token_index.prepare()
self.vertex_array = [None] * len(self.token_index.token_array)
# Build the variant graph for the first witness
# this is easy: generate a vertex for every token
first_witness = self.collation.witnesses[0]
tokens = first_witness.tokens()
token_to_vertex = self.merge(graph, first_witness.sigil, tokens)
# print("> token_to_vertex=", token_to_vertex)
self.update_token_position_to_vertex(token_to_vertex)
self.update_token_to_vertex_array(tokens, first_witness, self.token_position_to_vertex)
# align witness 2 - n
for x in range(1, len(self.collation.witnesses)):
witness = self.collation.witnesses[x]
tokens = witness.tokens()
# print("\nwitness", witness.sigil)
variant_graph_ranking = VariantGraphRanking.of(graph)
# print("> x =", x, ", variant_graph_ranking =", variant_graph_ranking.byRank)
variant_graph_ranks = list(set(map(lambda v: variant_graph_ranking.byVertex.get(v), graph.vertices())))
# we leave in the rank of the start vertex, but remove the rank of the end vertex
variant_graph_ranks.pop()
# now the vertical stuff
tokens_as_index_list = self.as_index_list(tokens)
match_cube = MatchCube(self.token_index, witness, self.vertex_array, variant_graph_ranking,
self.properties_filter)
# print("> match_cube.matches=", match_cube.matches)
self.fill_needleman_wunsch_table(variant_graph_ranks, tokens_as_index_list, match_cube)
aligned = self.align_matching_tokens(match_cube)
# print("> aligned=", aligned)
# print("self.token_index.token_array=", self.token_index.token_array)
# alignment = self.align_function(superbase, next_witness, token_to_vertex, match_cube)
# merge
witness_token_to_generated_vertex = self.merge(graph, witness.sigil, witness.tokens(), aligned)
# print("> witness_token_to_generated_vertex =", witness_token_to_generated_vertex)
token_to_vertex.update(witness_token_to_generated_vertex)
# print("> token_to_vertex =", token_to_vertex)
self.update_token_position_to_vertex(token_to_vertex, aligned)
witness_token_position_to_vertex = {}
for p in self.token_index.get_range_for_witness(witness.sigil):
# print("> p= ", p)
witness_token_position_to_vertex[p] = self.token_position_to_vertex[p]
self.update_token_to_vertex_array(tokens, witness, witness_token_position_to_vertex)
# print("> vertex_array =", self.vertex_array)
# print("actual")
# self._debug_edit_graph_table(self.table)
# print("expected")
# self._debug_edit_graph_table(self.table2)
# change superbase
# superbase = self.new_superbase
if self.detect_transpositions:
detector = TranspositionDetection(self)
detector.detect() | :type graph: VariantGraph | entailment |
def _parse(self, pattern):
"""Parse string of comma-separated x-y/step -like ranges"""
# Comma separated ranges
if pattern.find(',') < 0:
subranges = [pattern]
else:
subranges = pattern.split(',')
for subrange in subranges:
if subrange.find('/') < 0:
step = 1
baserange = subrange
else:
baserange, step = subrange.split('/', 1)
try:
step = int(step)
except ValueError:
raise RangeSetParseError(subrange,
"cannot convert string to integer")
if baserange.find('-') < 0:
if step != 1:
raise RangeSetParseError(subrange,
"invalid step usage")
begin = end = baserange
else:
begin, end = baserange.split('-', 1)
# compute padding and return node range info tuple
try:
pad = 0
if int(begin) != 0:
begins = begin.lstrip("0")
if len(begin) - len(begins) > 0:
pad = len(begin)
start = int(begins)
else:
if len(begin) > 1:
pad = len(begin)
start = 0
if int(end) != 0:
ends = end.lstrip("0")
else:
ends = end
stop = int(ends)
except ValueError:
raise RangeSetParseError(subrange,
"cannot convert string to integer")
# check preconditions
if stop > 1e100 or start > stop or step < 1:
raise RangeSetParseError(subrange,
"invalid values in range")
self.add_range(start, stop + 1, step, pad) | Parse string of comma-separated x-y/step -like ranges | entailment |
def fromlist(cls, rnglist, autostep=None):
"""Class method that returns a new RangeSet with ranges from provided
list."""
inst = RangeSet(autostep=autostep)
inst.updaten(rnglist)
return inst | Class method that returns a new RangeSet with ranges from provided
list. | entailment |
def fromone(cls, index, pad=0, autostep=None):
"""Class method that returns a new RangeSet of one single item or
a single range (from integer or slice object)."""
inst = RangeSet(autostep=autostep)
# support slice object with duck-typing
try:
inst.add(index, pad)
except TypeError:
if not index.stop:
raise ValueError("Invalid range upper limit (%s)" % index.stop)
inst.add_range(index.start or 0, index.stop, index.step or 1, pad)
return inst | Class method that returns a new RangeSet of one single item or
a single range (from integer or slice object). | entailment |
def set_autostep(self, val):
"""Set autostep value (property)"""
if val is None:
# disabled by default for pdsh compat (+inf is 1E400, but a bug in
# python 2.4 makes it impossible to be pickled, so we use less)
# NOTE: Later, we could consider sys.maxint here
self._autostep = 1E100
else:
# - 1 because user means node count, but we means real steps
self._autostep = int(val) - 1 | Set autostep value (property) | entailment |
def striter(self):
"""Iterate over each (optionally padded) string element in RangeSet."""
pad = self.padding or 0
for i in self._sorted():
yield "%0*d" % (pad, i) | Iterate over each (optionally padded) string element in RangeSet. | entailment |
def contiguous(self):
"""Object-based iterator over contiguous range sets."""
pad = self.padding or 0
for sli in self._contiguous_slices():
yield RangeSet.fromone(slice(sli.start, sli.stop, sli.step), pad) | Object-based iterator over contiguous range sets. | entailment |
def _strslices(self):
"""Stringify slices list (x-y/step format)"""
pad = self.padding or 0
for sli in self.slices():
if sli.start + 1 == sli.stop:
yield "%0*d" % (pad, sli.start)
else:
assert sli.step >= 0, "Internal error: sli.step < 0"
if sli.step == 1:
yield "%0*d-%0*d" % (pad, sli.start, pad, sli.stop - 1)
else:
yield "%0*d-%0*d/%d" % (pad, sli.start, pad, sli.stop - 1, \
sli.step) | Stringify slices list (x-y/step format) | entailment |
def _contiguous_slices(self):
"""Internal iterator over contiguous slices in RangeSet."""
k = j = None
for i in self._sorted():
if k is None:
k = j = i
if i - j > 1:
yield slice(k, j + 1, 1)
k = i
j = i
if k is not None:
yield slice(k, j + 1, 1) | Internal iterator over contiguous slices in RangeSet. | entailment |
def _folded_slices(self):
"""Internal generator that is able to retrieve ranges organized by step.
Complexity: O(n) with n = number of ranges in tree."""
if len(self) == 0:
return
prng = None # pending range
istart = None # processing starting indice
m = 0 # processing step
for sli in self._contiguous_slices():
start = sli.start
stop = sli.stop
unitary = (start + 1 == stop) # one indice?
if istart is None: # first loop
if unitary:
istart = start
else:
prng = [start, stop, 1]
istart = stop - 1
i = k = istart
elif m == 0: # istart is set but step is unknown
if not unitary:
if prng is not None:
# yield and replace pending range
yield slice(*prng)
else:
yield slice(istart, istart + 1, 1)
prng = [start, stop, 1]
istart = k = stop - 1
continue
i = start
else: # step m > 0
assert m > 0
i = start
# does current range lead to broken step?
if m != i - k or not unitary:
#j = i if m == i - k else k
if m == i - k: j = i
else: j = k
# stepped is True when autostep setting does apply
stepped = (j - istart >= self._autostep * m)
if prng: # yield pending range?
if stepped:
prng[1] -= 1
else:
istart += m
yield slice(*prng)
prng = None
if m != i - k:
# case: step value has changed
if stepped:
yield slice(istart, k + 1, m)
else:
for j in range(istart, k - m + 1, m):
yield slice(j, j + 1, 1)
if not unitary:
yield slice(k, k + 1, 1)
if unitary:
if stepped:
istart = i = k = start
else:
istart = k
else:
prng = [start, stop, 1]
istart = i = k = stop - 1
elif not unitary:
# case: broken step by contiguous range
if stepped:
# yield 'range/m' by taking first indice of new range
yield slice(istart, i + 1, m)
i += 1
else:
# autostep setting does not apply in that case
for j in range(istart, i - m + 1, m):
yield slice(j, j + 1, 1)
if stop > i + 1: # current->pending only if not unitary
prng = [i, stop, 1]
istart = i = k = stop - 1
m = i - k # compute step
k = i
# exited loop, process pending range or indice...
if m == 0:
if prng:
yield slice(*prng)
else:
yield slice(istart, istart + 1, 1)
else:
assert m > 0
stepped = (k - istart >= self._autostep * m)
if prng:
if stepped:
prng[1] -= 1
else:
istart += m
yield slice(*prng)
prng = None
if stepped:
yield slice(istart, i + 1, m)
else:
for j in range(istart, i + 1, m):
yield slice(j, j + 1, 1) | Internal generator that is able to retrieve ranges organized by step.
Complexity: O(n) with n = number of ranges in tree. | entailment |
def split(self, nbr):
"""
Split the rangeset into nbr sub-rangesets (at most). Each
sub-rangeset will have the same number of elements more or
less 1. Current rangeset remains unmodified. Returns an
iterator.
>>> RangeSet("1-5").split(3)
RangeSet("1-2")
RangeSet("3-4")
RangeSet("foo5")
"""
assert(nbr > 0)
# We put the same number of element in each sub-nodeset.
slice_size = len(self) / nbr
left = len(self) % nbr
begin = 0
for i in range(0, min(nbr, len(self))):
length = slice_size + int(i < left)
yield self[begin:begin + length]
begin += length | Split the rangeset into nbr sub-rangesets (at most). Each
sub-rangeset will have the same number of elements more or
less 1. Current rangeset remains unmodified. Returns an
iterator.
>>> RangeSet("1-5").split(3)
RangeSet("1-2")
RangeSet("3-4")
RangeSet("foo5") | entailment |
def add_range(self, start, stop, step=1, pad=0):
"""
Add a range (start, stop, step and padding length) to RangeSet.
Like the Python built-in function range(), the last element is
the largest start + i * step less than stop.
"""
assert start < stop, "please provide ordered node index ranges"
assert step > 0
assert pad >= 0
assert stop - start < 1e9, "range too large"
if pad > 0 and self.padding is None:
self.padding = pad
set.update(self, range(start, stop, step)) | Add a range (start, stop, step and padding length) to RangeSet.
Like the Python built-in function range(), the last element is
the largest start + i * step less than stop. | entailment |
def copy(self):
"""Return a shallow copy of a RangeSet."""
cpy = self.__class__()
cpy._autostep = self._autostep
cpy.padding = self.padding
cpy.update(self)
return cpy | Return a shallow copy of a RangeSet. | entailment |
def _wrap_set_op(self, fun, arg):
"""Wrap built-in set operations for RangeSet to workaround built-in set
base class issues (RangeSet.__new/init__ not called)"""
result = fun(self, arg)
result._autostep = self._autostep
result.padding = self.padding
return result | Wrap built-in set operations for RangeSet to workaround built-in set
base class issues (RangeSet.__new/init__ not called) | entailment |
def intersection(self, other):
"""Return the intersection of two RangeSets as a new RangeSet.
(I.e. all elements that are in both sets.)
"""
#NOTE: This is a work around
# Python 3 return as the result of set.intersection a new set instance.
# Python 2 however returns as a the result a ClusterShell.RangeSet.RangeSet instance.
# ORIGINAL CODE: return self._wrap_set_op(set.intersection, other)
copy = self.copy()
copy.intersection_update(other)
return copy | Return the intersection of two RangeSets as a new RangeSet.
(I.e. all elements that are in both sets.) | entailment |
def difference(self, other):
"""Return the difference of two RangeSets as a new RangeSet.
(I.e. all elements that are in this set and not in the other.)
"""
#NOTE: This is a work around
# Python 3 return as the result of set.intersection a new set instance.
# Python 2 however returns as a the result a ClusterShell.RangeSet.RangeSet instance.
# ORIGINAL CODE: return self._wrap_set_op(set.difference, other)
copy = self.copy()
copy.difference_update(other)
return copy | Return the difference of two RangeSets as a new RangeSet.
(I.e. all elements that are in this set and not in the other.) | entailment |
def issubset(self, other):
"""Report whether another set contains this RangeSet."""
self._binary_sanity_check(other)
return set.issubset(self, other) | Report whether another set contains this RangeSet. | entailment |
def issuperset(self, other):
"""Report whether this RangeSet contains another set."""
self._binary_sanity_check(other)
return set.issuperset(self, other) | Report whether this RangeSet contains another set. | entailment |
def difference_update(self, other, strict=False):
"""Remove all elements of another set from this RangeSet.
If strict is True, raise KeyError if an element cannot be removed.
(strict is a RangeSet addition)"""
if strict and other not in self:
raise KeyError(other.difference(self)[0])
set.difference_update(self, other) | Remove all elements of another set from this RangeSet.
If strict is True, raise KeyError if an element cannot be removed.
(strict is a RangeSet addition) | entailment |
def update(self, iterable):
"""Add all integers from an iterable (such as a list)."""
if isinstance(iterable, RangeSet):
# keep padding unless is has not been defined yet
if self.padding is None and iterable.padding is not None:
self.padding = iterable.padding
assert type(iterable) is not str
set.update(self, iterable) | Add all integers from an iterable (such as a list). | entailment |
def updaten(self, rangesets):
"""
Update a rangeset with the union of itself and several others.
"""
for rng in rangesets:
if isinstance(rng, set):
self.update(rng)
else:
self.update(RangeSet(rng)) | Update a rangeset with the union of itself and several others. | entailment |
def add(self, element, pad=0):
"""Add an element to a RangeSet.
This has no effect if the element is already present.
"""
set.add(self, int(element))
if pad > 0 and self.padding is None:
self.padding = pad | Add an element to a RangeSet.
This has no effect if the element is already present. | entailment |
def discard(self, element):
"""Remove element from the RangeSet if it is a member.
If the element is not a member, do nothing.
"""
try:
i = int(element)
set.discard(self, i)
except ValueError:
pass | Remove element from the RangeSet if it is a member.
If the element is not a member, do nothing. | entailment |
def _open(filename, mode="r"):
"""
Universal open file facility.
With normal files, this function behaves as the open builtin.
With gzip-ed files, it decompress or compress according to the specified mode.
In addition, when filename is '-', it opens the standard input or output according to
the specified mode.
Mode are expected to be either 'r' or 'w'.
"""
if filename.endswith(".gz"):
return GzipFile(filename, mode, COMPRESSION_LEVEL)
elif filename == "-":
if mode == "r":
return _stdin
elif mode == "w":
return _stdout
else:
# TODO: set encoding to UTF-8?
return open(filename, mode=mode) | Universal open file facility.
With normal files, this function behaves as the open builtin.
With gzip-ed files, it decompress or compress according to the specified mode.
In addition, when filename is '-', it opens the standard input or output according to
the specified mode.
Mode are expected to be either 'r' or 'w'. | entailment |
def _radixPass(a, b, r, n, K):
"""
Stable sort of the sequence a according to the keys given in r.
>>> a=range(5)
>>> b=[0]*5
>>> r=[2,1,3,0,4]
>>> _radixPass(a, b, r, 5, 5)
>>> b
[3, 1, 0, 2, 4]
When n is less than the length of a, the end of b must be left unaltered.
>>> b=[5]*5
>>> _radixPass(a, b, r, 2, 2)
>>> b
[1, 0, 5, 5, 5]
>>> _a=a=[1, 0]
>>> b= [0]*2
>>> r=[0, 1]
>>> _radixPass(a, b, r, 2, 2)
>>> a=_a
>>> b
[0, 1]
>>> a=[1, 1]
>>> _radixPass(a, b, r, 2, 2)
>>> b
[1, 1]
>>> a=[0, 1, 1, 0]
>>> b= [0]*4
>>> r=[0, 1]
>>> _radixPass(a, b, r, 4, 2)
>>> a=_a
>>> b
[0, 0, 1, 1]
"""
c = _array("i", [0] * (K + 1)) # counter array
for i in range(n): # count occurrences
c[r[a[i]]] += 1
sum = 0
for i in range(K + 1): # exclusive prefix sums
t = c[i]
c[i] = sum
sum += t
for a_i in a[:n]: # sort
b[c[r[a_i]]] = a_i
c[r[a_i]] += 1 | Stable sort of the sequence a according to the keys given in r.
>>> a=range(5)
>>> b=[0]*5
>>> r=[2,1,3,0,4]
>>> _radixPass(a, b, r, 5, 5)
>>> b
[3, 1, 0, 2, 4]
When n is less than the length of a, the end of b must be left unaltered.
>>> b=[5]*5
>>> _radixPass(a, b, r, 2, 2)
>>> b
[1, 0, 5, 5, 5]
>>> _a=a=[1, 0]
>>> b= [0]*2
>>> r=[0, 1]
>>> _radixPass(a, b, r, 2, 2)
>>> a=_a
>>> b
[0, 1]
>>> a=[1, 1]
>>> _radixPass(a, b, r, 2, 2)
>>> b
[1, 1]
>>> a=[0, 1, 1, 0]
>>> b= [0]*4
>>> r=[0, 1]
>>> _radixPass(a, b, r, 4, 2)
>>> a=_a
>>> b
[0, 0, 1, 1] | entailment |
def _nbOperations(n):
"""
Exact number of atomic operations in _radixPass.
"""
if n < 2:
return 0
else:
n0 = (n + 2) // 3
n02 = n0 + n // 3
return 3 * (n02) + n0 + _nbOperations(n02) | Exact number of atomic operations in _radixPass. | entailment |
def _suffixArrayWithTrace(s, SA, n, K, operations, totalOperations):
"""
This function is a rewrite in Python of the C implementation proposed in Kärkkäinen and Sanders paper.
Find the suffix array SA of s[0..n-1] in {1..K}^n
Require s[n]=s[n+1]=s[n+2]=0, n>=2
"""
if _trace:
_traceSuffixArray(operations, totalOperations)
n0 = (n + 2) // 3
n1 = (n + 1) // 3
n2 = n // 3
n02 = n0 + n2
SA12 = _array("i", [0] * (n02 + 3))
SA0 = _array("i", [0] * n0)
s0 = _array("i", [0] * n0)
# s12 : positions of mod 1 and mod 2 suffixes
s12 = _array("i", [i for i in range(n + (n0 - n1)) if i % 3]) # <- writing i%3 is more efficient than i%3!=0
s12.extend([0] * 3)
# lsb radix sort the mod 1 and mod 2 triples
_radixPass(s12, SA12, s[2:], n02, K)
if _trace:
operations += n02
_traceSuffixArray(operations, totalOperations)
_radixPass(SA12, s12, s[1:], n02, K)
if _trace:
operations += n02
_traceSuffixArray(operations, totalOperations)
_radixPass(s12, SA12, s, n02, K)
if _trace:
operations += n02
_traceSuffixArray(operations, totalOperations)
# find lexicographic names of triples
name = 0
c = _array("i", [-1] * 3)
for i in range(n02):
cSA12 = s[SA12[i]:SA12[i] + 3]
if cSA12 != c:
name += 1
c = cSA12
if SA12[i] % 3 == 1:
s12[SA12[i] // 3] = name # left half
else:
s12[(SA12[i] // 3) + n0] = name # right half
if name < n02: # recurse if names are not yet unique
operations = _suffixArrayWithTrace(s12, SA12, n02, name + 1, operations, totalOperations)
if _trace:
_traceSuffixArray(operations, totalOperations)
# store unique names in s12 using the suffix array
for i, SA12_i in enumerate(SA12[:n02]):
s12[SA12_i] = i + 1
else: # generate the suffix array of s12 directly
if _trace:
operations += _nbOperations(n02)
_traceSuffixArray(operations, totalOperations)
for i, s12_i in enumerate(s12[:n02]):
SA12[s12_i - 1] = i
# stably sort the mod 0 suffixes from SA12 by their first character
j = 0
for SA12_i in SA12[:n02]:
if (SA12_i < n0):
s0[j] = 3 * SA12_i
j += 1
_radixPass(s0, SA0, s, n0, K)
if _trace:
operations += n0
_traceSuffixArray(operations, totalOperations)
# merge sorted SA0 suffixes and sorted SA12 suffixes
p = j = k = 0
t = n0 - n1
while k < n:
if SA12[t] < n0: # pos of current offset 12 suffix
i = SA12[t] * 3 + 1
else:
i = (SA12[t] - n0) * 3 + 2
j = SA0[p] # pos of current offset 0 suffix
if SA12[t] < n0:
bool = (s[i], s12[SA12[t] + n0]) <= (s[j], s12[int(j / 3)])
else:
bool = (s[i], s[i + 1], s12[SA12[t] - n0 + 1]) <= (s[j], s[j + 1], s12[int(j / 3) + n0])
if (bool):
SA[k] = i
t += 1
if t == n02: # done --- only SA0 suffixes left
k += 1
while p < n0:
SA[k] = SA0[p]
p += 1
k += 1
else:
SA[k] = j
p += 1
if p == n0: # done --- only SA12 suffixes left
k += 1
while t < n02:
if SA12[t] < n0: # pos of current offset 12 suffix
SA[k] = (SA12[t] * 3) + 1
else:
SA[k] = ((SA12[t] - n0) * 3) + 2
t += 1
k += 1
k += 1
return operations | This function is a rewrite in Python of the C implementation proposed in Kärkkäinen and Sanders paper.
Find the suffix array SA of s[0..n-1] in {1..K}^n
Require s[n]=s[n+1]=s[n+2]=0, n>=2 | entailment |
def _longestCommonPrefix(seq1, seq2, start1=0, start2=0):
"""
Returns the length of the longest common prefix of seq1
starting at offset start1 and seq2 starting at offset start2.
>>> _longestCommonPrefix("abcdef", "abcghj")
3
>>> _longestCommonPrefix("abcghj", "abcdef")
3
>>> _longestCommonPrefix("miss", "")
0
>>> _longestCommonPrefix("", "mr")
0
>>> _longestCommonPrefix(range(128), range(128))
128
>>> _longestCommonPrefix("abcabcabc", "abcdefabcdef", 0, 6)
3
>>> _longestCommonPrefix("abcdefabcdef", "abcabcabc", 6, 0)
3
>>> _longestCommonPrefix("abc", "abcabc", 1, 4)
2
>>> _longestCommonPrefix("abcabc", "abc", 4, 1)
2
"""
len1 = len(seq1) - start1
len2 = len(seq2) - start2
# We set seq2 as the shortest sequence
if len1 < len2:
seq1, seq2 = seq2, seq1
start1, start2 = start2, start1
len1, len2 = len2, len1
# if seq2 is empty returns 0
if len2 == 0:
return 0
i = 0
pos2 = start2
for i in range(min(len1, len2)):
# print seq1, seq2, start1, start2
if seq1[start1 + i] != seq2[start2 + i]:
return i
# we have reached the end of seq2 (need to increment i)
return i + 1 | Returns the length of the longest common prefix of seq1
starting at offset start1 and seq2 starting at offset start2.
>>> _longestCommonPrefix("abcdef", "abcghj")
3
>>> _longestCommonPrefix("abcghj", "abcdef")
3
>>> _longestCommonPrefix("miss", "")
0
>>> _longestCommonPrefix("", "mr")
0
>>> _longestCommonPrefix(range(128), range(128))
128
>>> _longestCommonPrefix("abcabcabc", "abcdefabcdef", 0, 6)
3
>>> _longestCommonPrefix("abcdefabcdef", "abcabcabc", 6, 0)
3
>>> _longestCommonPrefix("abc", "abcabc", 1, 4)
2
>>> _longestCommonPrefix("abcabc", "abc", 4, 1)
2 | entailment |
def LCP(SA):
"""
Compute the longest common prefix for every adjacent suffixes.
The result is a list of same size as SA.
Given two suffixes at positions i and i+1,
their LCP is stored at position i+1.
A zero is stored at position 0 of the output.
>>> SA=SuffixArray("abba", unit=UNIT_BYTE)
>>> SA._LCP_values
array('i', [0, 1, 0, 1])
>>> SA=SuffixArray("", unit=UNIT_BYTE)
>>> SA._LCP_values
array('i')
>>> SA=SuffixArray("", unit=UNIT_CHARACTER)
>>> SA._LCP_values
array('i')
>>> SA=SuffixArray("", unit=UNIT_WORD)
>>> SA._LCP_values
array('i')
>>> SA=SuffixArray("abab", unit=UNIT_BYTE)
>>> SA._LCP_values
array('i', [0, 2, 0, 1])
"""
string = SA.string
length = SA.length
lcps = _array("i", [0] * length)
SA = SA.SA
if _trace:
delta = max(length // 100, 1)
for i, pos in enumerate(SA):
if i % delta == 0:
percent = float((i + 1) * 100) / length
print >> _stderr, "Compute_LCP %.2f%% (%i/%i)\r" % (percent, i + 1, length),
lcps[i] = _longestCommonPrefix(string, string, SA[i - 1], pos)
else:
for i, pos in enumerate(SA):
lcps[i] = _longestCommonPrefix(string, string, SA[i - 1], pos)
if _trace:
print >> _stderr, "Compute_LCP %.2f%% (%i/%i)\r" % (100.0, length, length)
if lcps: # Correct the case where string[0] == string[-1]
lcps[0] = 0
return lcps | Compute the longest common prefix for every adjacent suffixes.
The result is a list of same size as SA.
Given two suffixes at positions i and i+1,
their LCP is stored at position i+1.
A zero is stored at position 0 of the output.
>>> SA=SuffixArray("abba", unit=UNIT_BYTE)
>>> SA._LCP_values
array('i', [0, 1, 0, 1])
>>> SA=SuffixArray("", unit=UNIT_BYTE)
>>> SA._LCP_values
array('i')
>>> SA=SuffixArray("", unit=UNIT_CHARACTER)
>>> SA._LCP_values
array('i')
>>> SA=SuffixArray("", unit=UNIT_WORD)
>>> SA._LCP_values
array('i')
>>> SA=SuffixArray("abab", unit=UNIT_BYTE)
>>> SA._LCP_values
array('i', [0, 2, 0, 1]) | entailment |
def parseArgv():
"""
Command line option parser.
"""
parser = OptionParser()
parser.usage = r""" cat <TEXT> | %prog [--unit <UNIT>] [--output <SA_FILE>]
Create the suffix array of TEXT with the processing UNIT and optionally store it in SA_FILE for subsequent use.
UNIT may be set to 'byte', 'character' (given an encoding with the --encoding option) or 'word', which is the default.
"""
parser.add_option("-i", "--input",
action="store", type="string", dest="input",
default=False,
help="Path of the file containing the input text. When '-' is given, read the standard input (default). If the path ends with '.gz', reads the decompressed file.")
parser.add_option("-o", "--output",
action="store", type="string", dest="output",
default=False,
help="Store the suffix array of the input to the file OUTPUT. When '-' is given, writes to the standard output. If the filename ends with '.gz', the suffix array will be stored compressed.")
parser.add_option("", "--load",
action="store", type="string", dest="SAFile",
default=False,
help="Load a suffix array from SAFILE, this option and --input are mutually exclusive.")
parser.add_option("-u", "--unit",
action="store", type="string", dest="unit",
default=DEFAULT_UNIT_STR,
help="Processing unit used for the creation of the suffix array." + \
'Possible values are "byte", "character" and "word". Default is "%s".' % DEFAULT_UNIT_STR + \
"This option is ignored when the suffix array is loaded from SAFILE." + \
'For characters, the input is decoded according to the encoding set via the option --encoding.')
parser.add_option("-e", "--encoding",
action="store", type="string", dest="encoding",
default=DEFAULT_ENCODING,
help="Encoding of the input. This information is required only when processing characters. Default is '%s'." % DEFAULT_ENCODING)
parser.add_option("-p", "--print",
action="store_true", dest="printSA",
default=False,
help="Prints the suffix array in a human readable format to the standard error output.")
parser.add_option("", "--verbose",
action="store_true", dest="verbose",
default=False,
help="Prints more information.")
parser.add_option("", "--no-lcps",
action="store_true", dest="noLCPs",
default=False,
help="Switch off the computation of LCPs. By doing so, the find functions are unusable.")
(options, args) = parser.parse_args(_argv)
strings = args[1:]
return (options, strings) | Command line option parser. | entailment |
def main():
"""
Entry point for the standalone script.
"""
(options, strings) = parseArgv()
global _suffixArray, _trace
#############
# Verbosity #
#############
_trace = options.verbose
###################
# Processing unit #
###################
if options.unit == "byte":
options.unit = UNIT_BYTE
elif options.unit == "character":
options.unit = UNIT_CHARACTER
elif options.unit == "word":
options.unit = UNIT_WORD
else:
print >> _stderr, "Please specify a valid unit type."
exit(EXIT_BAD_OPTION)
######################
# Build suffix array #
######################
if not options.SAFile: # Build the suffix array from INPUT
if not options.input: # default is standard input
options.input = "-"
try:
string = _open(options.input, "r").read()
except IOError:
print >> _stderr, "File %s does not exist." % options.input
exit(EXIT_ERROR_FILE)
SA = SuffixArray(string, options.unit, options.encoding, options.noLCPs)
########################
# Or load suffix array #
########################
elif not options.input and options.SAFile: # Load suffix array from SA_FILE
try:
SA = SuffixArray.fromFile(options.SAFile)
except IOError:
print >> _stderr, "SA_FILE %s does not exist." % options.SAFile
exit(EXIT_ERROR_FILE)
else:
print >> _stderr, "Please set only one option amongst --input and --load.\n" + \
"Type %s --help for more details." % _argv[0]
exit(EXIT_BAD_OPTION)
######################
# Print suffix array #
######################
if options.printSA:
# Buffered ouptut
deltaLength = 1000
start = 0
while start < SA.length:
print >> _stderr, SA.__str__(start, start + deltaLength)
start += deltaLength
####################################
# Look for every string in strings #
####################################
for string in strings:
print >> _stderr, ""
print >> _stderr, "Positions of %s:" % string
print >> _stderr, " %s" % list(SA.find(string))
#########################
# Save SAFILE if needed #
#########################
if options.output:
SA.toFile(options.output)
if _trace: print >> _stderr, "Done\r\n" | Entry point for the standalone script. | entailment |
def addFeatureSA(self, callback, default=None, name=None):
"""
Add a feature to the suffix array.
The callback must return a sequence such that
the feature at position i is attached to the suffix referenced by
self.SA[i].
It is called with one argument: the instance of SuffixArray self.
The callback may traverse self.SA in any fashion.
The default behavior is to name the new feature after the callback name.
To give another name, set the argument name accordingly.
When the feature of an unknown substring of the text is requested,
the value of the default argument is used.
If the feature attached to a suffix is independent of the other suffix
features, then the method addFeature gives a better alternative.
You may use addFeatureSA as a decorator as in the following example.
Example: feature named bigram which attach the frequencies of the
leading bigram to each suffix.
>>> SA=SuffixArray("mississippi", unit=UNIT_BYTE)
>>> def bigram(SA):
... res=[0]*SA.length
... end=0
... while end <= SA.length:
...
... begin=end-1
... while end < SA.length and SA._LCP_values[end]>=2:
... if SA.SA[end]+2<=SA.length: #end of string
... end+=1
...
... nbBigram=end-begin
... for i in xrange(begin, end):
... if SA.SA[i]+2<=SA.length:
... res[i]=nbBigram
...
... end+=1
... return res
>>> SA.addFeatureSA(bigram, 0)
>>> SA._bigram_values
[0, 1, 2, 2, 1, 1, 1, 2, 2, 2, 2]
>>> print str(SA).expandtabs(14) #doctest: +SKIP
... 10 'i' LCP=0 , bigram=0
... 7 'ippi' LCP=1 , bigram=1
... 4 'issippi' LCP=1 , bigram=2
... 1 'ississippi' LCP=4 , bigram=2
... 0 'mississipp' LCP=0 , bigram=1
... 9 'pi' LCP=0 , bigram=1
... 8 'ppi' LCP=1 , bigram=1
... 6 'sippi' LCP=0 , bigram=2
... 3 'sissippi' LCP=2 , bigram=2
... 5 'ssippi' LCP=1 , bigram=2
... 2 'ssissippi' LCP=3 , bigram=2
>>> SA.bigram('ip')
1
>>> SA.bigram('si')
2
>>> SA.bigram('zw')
0
"""
if name is None:
featureName = callback.__name__
else:
featureName = name
featureValues = callback(self)
setattr(self, "_%s_values" % featureName, featureValues)
setattr(self, "%s_default" % featureName, default)
self.features.append(featureName)
def findFeature(substring):
res = self._findOne(substring, )
if res is not False:
return featureValues[res]
else:
return default
setattr(self, featureName, findFeature) | Add a feature to the suffix array.
The callback must return a sequence such that
the feature at position i is attached to the suffix referenced by
self.SA[i].
It is called with one argument: the instance of SuffixArray self.
The callback may traverse self.SA in any fashion.
The default behavior is to name the new feature after the callback name.
To give another name, set the argument name accordingly.
When the feature of an unknown substring of the text is requested,
the value of the default argument is used.
If the feature attached to a suffix is independent of the other suffix
features, then the method addFeature gives a better alternative.
You may use addFeatureSA as a decorator as in the following example.
Example: feature named bigram which attach the frequencies of the
leading bigram to each suffix.
>>> SA=SuffixArray("mississippi", unit=UNIT_BYTE)
>>> def bigram(SA):
... res=[0]*SA.length
... end=0
... while end <= SA.length:
...
... begin=end-1
... while end < SA.length and SA._LCP_values[end]>=2:
... if SA.SA[end]+2<=SA.length: #end of string
... end+=1
...
... nbBigram=end-begin
... for i in xrange(begin, end):
... if SA.SA[i]+2<=SA.length:
... res[i]=nbBigram
...
... end+=1
... return res
>>> SA.addFeatureSA(bigram, 0)
>>> SA._bigram_values
[0, 1, 2, 2, 1, 1, 1, 2, 2, 2, 2]
>>> print str(SA).expandtabs(14) #doctest: +SKIP
... 10 'i' LCP=0 , bigram=0
... 7 'ippi' LCP=1 , bigram=1
... 4 'issippi' LCP=1 , bigram=2
... 1 'ississippi' LCP=4 , bigram=2
... 0 'mississipp' LCP=0 , bigram=1
... 9 'pi' LCP=0 , bigram=1
... 8 'ppi' LCP=1 , bigram=1
... 6 'sippi' LCP=0 , bigram=2
... 3 'sissippi' LCP=2 , bigram=2
... 5 'ssippi' LCP=1 , bigram=2
... 2 'ssissippi' LCP=3 , bigram=2
>>> SA.bigram('ip')
1
>>> SA.bigram('si')
2
>>> SA.bigram('zw')
0 | entailment |
def addFeature(self, callback, default=None, name=None, arguments=None):
"""
Add a feature to the suffix array.
The callback must return the feature corresponding to the suffix at
position self.SA[i].
The callback must be callable (a function or lambda).
The argument names of the callback are used to determine the data
needed. If an argument is the name of feature already defined, then
this argument will be the value of that feature for the current suffix.
In addition the argument pos is the position of the current suffix
and iSA is the index of pos in SA.
Other attributes of the SuffixArray instance may be use as argument
names.
If the feature attached to a suffix depends on other suffix features,
then the method addFeatureSA is the only choice.
"""
if name is None:
featureName = callback.__name__
else:
featureName = name
if arguments is None:
signature = getargspec(callback)[0]
else:
signature = arguments
featureValues = [default] * (self.length)
args = [getattr(self, "_%s_values" % featName) for featName in signature]
# print args
for i, pos in enumerate(self.SA):
arg = [j[i] for j in args]
# print arg
featureValues[i] = callback(*arg)
# end alternative
setattr(self, "_%s_values" % featureName, featureValues)
setattr(self, "%s_default" % featureName, default)
self.features.append(featureName)
def findFeature(substring):
res = self._findOne(substring)
if res:
return featureValues[res]
else:
return default
setattr(self, featureName, findFeature) | Add a feature to the suffix array.
The callback must return the feature corresponding to the suffix at
position self.SA[i].
The callback must be callable (a function or lambda).
The argument names of the callback are used to determine the data
needed. If an argument is the name of feature already defined, then
this argument will be the value of that feature for the current suffix.
In addition the argument pos is the position of the current suffix
and iSA is the index of pos in SA.
Other attributes of the SuffixArray instance may be use as argument
names.
If the feature attached to a suffix depends on other suffix features,
then the method addFeatureSA is the only choice. | entailment |
def tokenize(self, string):
"""
Tokenizer utility.
When processing byte, outputs the string unaltered.
The character unit type is used for unicode data, the string is
decoded according to the encoding provided.
In the case of word unit, EOL characters are detached from the
preceding word, and outputs the list of words, i.e. the list of non-space strings
separated by space strings.
>>> SA=SuffixArray('abecedaire', UNIT_BYTE)
>>> SA.tokenize('abecedaire')=='abecedaire'
True
>>> len(SA.tokenize('abecedaire'))
10
>>> SA=SuffixArray('abecedaire', UNIT_BYTE, "utf-8")
>>> SA.tokenize('abecedaire')==u'abecedaire'
True
>>> len(SA.tokenize('abecedaire'))
10
>>> SA=SuffixArray('mississippi', UNIT_WORD)
>>> SA.tokenize('miss issi ppi')
['miss', 'issi', 'ppi']
>>> SA.tokenize('miss issi\\nppi')
['miss', 'issi', '\\n', 'ppi']
"""
if self.unit == UNIT_WORD:
# the EOL character is treated as a word, hence a substitution
# before split
return [token for token in string.replace("\n", " \n ").split(self.tokSep) if token != ""]
elif self.unit == UNIT_CHARACTER:
return string.decode(self.encoding)
else:
return string | Tokenizer utility.
When processing byte, outputs the string unaltered.
The character unit type is used for unicode data, the string is
decoded according to the encoding provided.
In the case of word unit, EOL characters are detached from the
preceding word, and outputs the list of words, i.e. the list of non-space strings
separated by space strings.
>>> SA=SuffixArray('abecedaire', UNIT_BYTE)
>>> SA.tokenize('abecedaire')=='abecedaire'
True
>>> len(SA.tokenize('abecedaire'))
10
>>> SA=SuffixArray('abecedaire', UNIT_BYTE, "utf-8")
>>> SA.tokenize('abecedaire')==u'abecedaire'
True
>>> len(SA.tokenize('abecedaire'))
10
>>> SA=SuffixArray('mississippi', UNIT_WORD)
>>> SA.tokenize('miss issi ppi')
['miss', 'issi', 'ppi']
>>> SA.tokenize('miss issi\\nppi')
['miss', 'issi', '\\n', 'ppi'] | entailment |
def reprString(self, string, length):
"""
Output a string of length tokens in the original form.
If string is an integer, it is considered as an offset in the text.
Otherwise string is considered as a sequence of ids (see voc and
tokId).
>>> SA=SuffixArray('mississippi', UNIT_BYTE)
>>> SA.reprString(0, 3)
'mis'
>>> SA=SuffixArray('mississippi', UNIT_BYTE)
>>> SA.reprString([1, 4, 1, 3, 3, 2], 5)
'isipp'
>>> SA=SuffixArray('missi ssi ppi', UNIT_WORD)
>>> SA.reprString(0, 3)
'missi ssi ppi'
>>> SA=SuffixArray('missi ssi ppi', UNIT_WORD)
>>> SA.reprString([1, 3, 2], 3)
'missi ssi ppi'
"""
if isinstance(string, int):
length = min(length, self.length - string)
string = self.string[string:string + length]
voc = self.voc
res = self.tokSep.join((voc[id] for id in string[:length]))
if self.unit == UNIT_WORD:
res = res.replace(" \n", "\n")
res = res.replace("\n ", "\n")
if self.unit == UNIT_CHARACTER:
res = res.encode(self.encoding)
return res | Output a string of length tokens in the original form.
If string is an integer, it is considered as an offset in the text.
Otherwise string is considered as a sequence of ids (see voc and
tokId).
>>> SA=SuffixArray('mississippi', UNIT_BYTE)
>>> SA.reprString(0, 3)
'mis'
>>> SA=SuffixArray('mississippi', UNIT_BYTE)
>>> SA.reprString([1, 4, 1, 3, 3, 2], 5)
'isipp'
>>> SA=SuffixArray('missi ssi ppi', UNIT_WORD)
>>> SA.reprString(0, 3)
'missi ssi ppi'
>>> SA=SuffixArray('missi ssi ppi', UNIT_WORD)
>>> SA.reprString([1, 3, 2], 3)
'missi ssi ppi' | entailment |
def toFile(self, filename):
"""
Save the suffix array instance including all features attached in
filename. Accept any filename following the _open conventions,
for example if it ends with .gz the file created will be a compressed
GZip file.
"""
start = _time()
fd = _open(filename, "w")
savedData = [self.string, self.unit, self.voc, self.vocSize, self.SA, self.features]
for featureName in self.features:
featureValues = getattr(self, "_%s_values" % featureName)
featureDefault = getattr(self, "%s_default" % featureName)
savedData.append((featureValues, featureDefault))
fd.write(_dumps(savedData, _HIGHEST_PROTOCOL))
fd.flush()
try:
self.sizeOfSavedFile = getsize(fd.name)
except OSError: # if stdout is used
self.sizeOfSavedFile = "-1"
self.toFileTime = _time() - start
if _trace: print >> _stderr, "toFileTime %.2fs" % self.toFileTime
if _trace: print >> _stderr, "sizeOfSavedFile %sb" % self.sizeOfSavedFile
fd.close() | Save the suffix array instance including all features attached in
filename. Accept any filename following the _open conventions,
for example if it ends with .gz the file created will be a compressed
GZip file. | entailment |
def fromFile(cls, filename):
"""
Load a suffix array instance from filename, a file created by
toFile.
Accept any filename following the _open conventions.
"""
self = cls.__new__(cls) # new instance which does not call __init__
start = _time()
savedData = _loads(_open(filename, "r").read())
# load common attributes
self.string, self.unit, self.voc, self.vocSize, self.SA, features = savedData[:6]
self.length = len(self.SA)
# determine token delimiter
if self.unit == UNIT_WORD:
self.tokSep = " "
elif self.unit in (UNIT_CHARACTER, UNIT_BYTE):
self.tokSep = ""
else:
raise Exception("Unknown unit type identifier:", self.unit)
# recompute tokId based on voc
self.tokId = dict((char, iChar) for iChar, char in enumerate(self.voc))
self.nbSentences = self.string.count(self.tokId.get("\n", 0))
# Load features
self.features = []
for featureName, (featureValues, featureDefault) in zip(features, savedData[6:]):
self.addFeatureSA((lambda _: featureValues), name=featureName, default=featureDefault)
self.fromFileTime = _time() - start
if _trace: print >> _stderr, "fromFileTime %.2fs" % self.fromFileTime
return self | Load a suffix array instance from filename, a file created by
toFile.
Accept any filename following the _open conventions. | entailment |
def _findOne(self, subString):
"""
>>> SA=SuffixArray("mississippi", unit=UNIT_BYTE)
>>> SA._findOne("ippi")
1
>>> SA._findOne("missi")
4
"""
SA = self.SA
LCPs = self._LCP_values
string = self.string
try:
subString = _array("i", [self.tokId[c] for c in self.tokenize(subString)])
except KeyError:
# if a token of the subString is not in the vocabulary
# the substring can't be in the string
return False
lenSubString = len(subString)
#################################
# Dichotomy search of subString #
#################################
lower = 0
upper = self.length
success = False
while upper - lower > 0:
middle = (lower + upper) // 2
middleSubString = string[SA[middle]:min(SA[middle] + lenSubString, self.length)]
# NOTE: the cmp function is removed in Python 3
# Strictly speaking we are doing one comparison more now
if subString < middleSubString:
upper = middle
elif subString > middleSubString:
lower = middle + 1
else:
success = True
break
if not success:
return False
else:
return middle | >>> SA=SuffixArray("mississippi", unit=UNIT_BYTE)
>>> SA._findOne("ippi")
1
>>> SA._findOne("missi")
4 | entailment |
def find(self, subString, features=[]):
"""
Dichotomy search of subString in the suffix array.
As soon as a suffix which starts with subString is found,
it uses the LCPs in order to find the other matching suffixes.
The outputs consists in a list of tuple (pos, feature0, feature1, ...)
where feature0, feature1, ... are the features attached to the suffix
at position pos.
Features are listed in the same order as requested in the input list of
features [featureName0, featureName1, ...]
>>> SA=SuffixArray('mississippi', UNIT_BYTE)
>>> SA.find("ssi")
array('i', [5, 2])
>>> SA.find("mi")
array('i', [0])
>>> SA=SuffixArray('miss A and miss B', UNIT_WORD)
>>> SA.find("miss")
array('i', [0, 3])
>>> SA=SuffixArray('mississippi', UNIT_BYTE)
>>> SA.find("iss", ['LCP'])
[(4, 1), (1, 4)]
>>> SA=SuffixArray('mississippi', UNIT_BYTE)
>>> SA.find("A")
array('i')
>>> SA=SuffixArray('mississippi', UNIT_BYTE)
>>> SA.find("pp")
array('i', [8])
>>> SA=SuffixArray('mississippi', UNIT_BYTE)
>>> SA.find("ppp")
array('i')
>>> SA=SuffixArray('mississippi', UNIT_BYTE)
>>> SA.find("im")
array('i')
"""
SA = self.SA
LCPs = self._LCP_values
string = self.string
middle = self._findOne(subString)
if middle is False:
return _array('i')
subString = _array("i", [self.tokId[c] for c in self.tokenize(subString)])
lenSubString = len(subString)
###########################################
# Use LCPS to retrieve the other suffixes #
###########################################
lower = middle
upper = middle + 1
middleLCP = LCPs[middle]
while lower > 0 and LCPs[lower] >= lenSubString:
lower -= 1
while upper < self.length and LCPs[upper] >= lenSubString:
upper += 1
###############################################
# When features is empty, outputs a flat list #
###############################################
res = SA[lower:upper]
if len(features) == 0:
return res
##############################################
# When features is non empty, outputs a list #
# of tuples (pos, feature_1, feature_2, ...) #
##############################################
else:
features = [getattr(self, "_%s_values" % featureName) for featureName in features]
features = [featureValues[lower:upper] for featureValues in features]
return zip(res, *features) | Dichotomy search of subString in the suffix array.
As soon as a suffix which starts with subString is found,
it uses the LCPs in order to find the other matching suffixes.
The outputs consists in a list of tuple (pos, feature0, feature1, ...)
where feature0, feature1, ... are the features attached to the suffix
at position pos.
Features are listed in the same order as requested in the input list of
features [featureName0, featureName1, ...]
>>> SA=SuffixArray('mississippi', UNIT_BYTE)
>>> SA.find("ssi")
array('i', [5, 2])
>>> SA.find("mi")
array('i', [0])
>>> SA=SuffixArray('miss A and miss B', UNIT_WORD)
>>> SA.find("miss")
array('i', [0, 3])
>>> SA=SuffixArray('mississippi', UNIT_BYTE)
>>> SA.find("iss", ['LCP'])
[(4, 1), (1, 4)]
>>> SA=SuffixArray('mississippi', UNIT_BYTE)
>>> SA.find("A")
array('i')
>>> SA=SuffixArray('mississippi', UNIT_BYTE)
>>> SA.find("pp")
array('i', [8])
>>> SA=SuffixArray('mississippi', UNIT_BYTE)
>>> SA.find("ppp")
array('i')
>>> SA=SuffixArray('mississippi', UNIT_BYTE)
>>> SA.find("im")
array('i') | entailment |
def escape(s, quote=False):
"""Replace special characters "&", "<" and ">" to HTML-safe sequences. If
the optional flag `quote` is `True`, the quotation mark character (") is
also translated.
There is a special handling for `None` which escapes to an empty string.
:param s: the string to escape.
:param quote: set to true to also escape double quotes.
"""
if s is None:
return ''
elif hasattr(s, '__html__'):
return s.__html__()
elif not isinstance(s, basestring):
s = unicode(s)
s = s.replace('&', '&').replace('<', '<').replace('>', '>')
if quote:
s = s.replace('"', """)
return s | Replace special characters "&", "<" and ">" to HTML-safe sequences. If
the optional flag `quote` is `True`, the quotation mark character (") is
also translated.
There is a special handling for `None` which escapes to an empty string.
:param s: the string to escape.
:param quote: set to true to also escape double quotes. | entailment |
def add(self, *args, **kwargs):
"""Add a new entry to the feed. This function can either be called
with a :class:`FeedEntry` or some keyword and positional arguments
that are forwarded to the :class:`FeedEntry` constructor.
"""
if len(args) == 1 and not kwargs and isinstance(args[0], FeedEntry):
self.entries.append(args[0])
else:
kwargs['feed_url'] = self.feed_url
kwargs['timezone'] = self.timezone
self.entries.append(FeedEntry(*args, **kwargs)) | Add a new entry to the feed. This function can either be called
with a :class:`FeedEntry` or some keyword and positional arguments
that are forwarded to the :class:`FeedEntry` constructor. | entailment |
def generate(self):
"""Return a generator that yields pieces of XML."""
# atom demands either an author element in every entry or a global one
if not self.author:
if False in map(lambda e: bool(e.author), self.entries):
self.author = ({'name': u'unbekannter Autor'},)
if not self.updated:
dates = sorted([entry.updated for entry in self.entries])
self.updated = dates and dates[-1] or datetime.utcnow()
yield u'<?xml version="1.0" encoding="utf-8"?>\n'
yield u'<feed xmlns="http://www.w3.org/2005/Atom">\n'
yield ' ' + _make_text_block('title', self.title, self.title_type)
yield u' <id>%s</id>\n' % escape(self.id)
yield u' <updated>%s</updated>\n' % format_iso8601(self.updated, self.timezone)
if self.url:
yield u' <link href="%s" />\n' % escape(self.url, True)
if self.feed_url:
yield u' <link href="%s" rel="self" />\n' % \
escape(self.feed_url, True)
for link in self.links:
yield u' <link %s/>\n' % ''.join('%s="%s" ' % \
(k, escape(link[k], True)) for k in link)
for author in self.author:
yield u' <author>\n'
yield u' <name>%s</name>\n' % escape(author['name'])
if 'uri' in author:
yield u' <uri>%s</uri>\n' % escape(author['uri'])
if 'email' in author:
yield ' <email>%s</email>\n' % escape(author['email'])
yield ' </author>\n'
if self.subtitle:
yield ' ' + _make_text_block('subtitle', self.subtitle,
self.subtitle_type)
if self.icon:
yield u' <icon>%s</icon>\n' % escape(self.icon)
if self.logo:
yield u' <logo>%s</logo>\n' % escape(self.logo)
if self.rights:
yield ' ' + _make_text_block('rights', self.rights,
self.rights_type)
generator_name, generator_url, generator_version = self.generator
if generator_name or generator_url or generator_version:
tmp = [u' <generator']
if generator_url:
tmp.append(u' uri="%s"' % escape(generator_url, True))
if generator_version:
tmp.append(u' version="%s"' % escape(generator_version, True))
tmp.append(u'>%s</generator>\n' % escape(generator_name))
yield u''.join(tmp)
for entry in self.entries:
for line in entry.generate():
yield u' ' + line
yield u'</feed>\n' | Return a generator that yields pieces of XML. | entailment |
def generate(self):
"""Yields pieces of ATOM XML."""
base = ''
if self.xml_base:
base = ' xml:base="%s"' % escape(self.xml_base, True)
yield u'<entry%s>\n' % base
yield u' ' + _make_text_block('title', self.title, self.title_type)
yield u' <id>%s</id>\n' % escape(self.id)
yield u' <updated>%s</updated>\n' % format_iso8601(self.updated, self.timezone)
if self.published:
yield u' <published>%s</published>\n' % \
format_iso8601(self.published, self.timezone)
if self.url:
yield u' <link href="%s" />\n' % escape(self.url)
for author in self.author:
yield u' <author>\n'
yield u' <name>%s</name>\n' % escape(author['name'])
if 'uri' in author:
yield u' <uri>%s</uri>\n' % escape(author['uri'])
if 'email' in author:
yield u' <email>%s</email>\n' % escape(author['email'])
yield u' </author>\n'
for link in self.links:
yield u' <link %s/>\n' % ''.join('%s="%s" ' % \
(k, escape(link[k], True)) for k in link)
if self.summary:
yield u' ' + _make_text_block('summary', self.summary,
self.summary_type)
if self.content:
if issubclass(self.content.__class__, dict):
if "content" in self.content:
yield u' <content %s>%s</content>\n' % (' '.join('%s="%s"' % \
(k, escape(self.content[k], True)) for k in self.content if k != "content"), escape(self.content["content"]))
else:
yield u' <content %s/>\n' % ' '.join('%s="%s" ' % \
(k, escape(self.content[k], True)) for k in self.content)
else:
yield u' ' + _make_text_block('content', self.content,
self.content_type)
yield u'</entry>\n' | Yields pieces of ATOM XML. | entailment |
def override_djconfig(**new_cache_values):
"""
Temporarily override config values.
This is similar to :py:func:`django.test.override_settings`,\
use it in testing.
:param new_cache_values: Keyword arguments,\
the key should match one in the config,\
a new one is created otherwise,\
the value is overridden within\
the decorated function
"""
def decorator(func):
@wraps(func)
def func_wrapper(*args, **kw):
old_cache_values = {
key: getattr(conf.config, key)
for key in new_cache_values}
conf.config._set_many(new_cache_values)
try:
# todo: make a note about this in the docs:
# don't populate the config within migrations
# This works coz the config table is empty,
# so even if the middleware gets called,
# it won't update the config (_updated_at
# will be None), this is assuming the table
# is not populated by the user (ie: within
# a migration), in which case it will load
# all the default values
return func(*args, **kw)
finally:
conf.config._set_many(old_cache_values)
return func_wrapper
return decorator | Temporarily override config values.
This is similar to :py:func:`django.test.override_settings`,\
use it in testing.
:param new_cache_values: Keyword arguments,\
the key should match one in the config,\
a new one is created otherwise,\
the value is overridden within\
the decorated function | entailment |
def serialize(value, field):
"""
Form values serialization
:param object value: A value to be serialized\
for saving it into the database and later\
loading it into the form as initial value
"""
assert isinstance(field, forms.Field)
if isinstance(field, forms.ModelMultipleChoiceField):
return json.dumps([v.pk for v in value])
# todo: remove
if isinstance(value, models.Model):
return value.pk
return value | Form values serialization
:param object value: A value to be serialized\
for saving it into the database and later\
loading it into the form as initial value | entailment |
def get_version(package):
"""Get version without importing the lib"""
with io.open(os.path.join(BASE_DIR, package, '__init__.py'), encoding='utf-8') as fh:
return [
l.split('=', 1)[1].strip().strip("'").strip('"')
for l in fh.readlines()
if '__version__' in l][0] | Get version without importing the lib | entailment |
def _check_backend():
"""
Check :py:class:`djconfig.middleware.DjConfigMiddleware`\
is registered into ``settings.MIDDLEWARE_CLASSES``
"""
# Django 1.10 does not allow
# both settings to be set
middleware = set(
getattr(settings, 'MIDDLEWARE', None) or
getattr(settings, 'MIDDLEWARE_CLASSES', None) or
[])
# Deprecated alias
if "djconfig.middleware.DjConfigLocMemMiddleware" in middleware:
return
if "djconfig.middleware.DjConfigMiddleware" in middleware:
return
raise ValueError(
"djconfig.middleware.DjConfigMiddleware "
"is required but it was not found in "
"MIDDLEWARE_CLASSES nor in MIDDLEWARE") | Check :py:class:`djconfig.middleware.DjConfigMiddleware`\
is registered into ``settings.MIDDLEWARE_CLASSES`` | entailment |
def _register(self, form_class, check_middleware=True):
"""
Register a config form into the registry
:param object form_class: The form class to register.\
Must be an instance of :py:class:`djconfig.forms.ConfigForm`
:param bool check_middleware: Check\
:py:class:`djconfig.middleware.DjConfigMiddleware`\
is registered into ``settings.MIDDLEWARE_CLASSES``. Default True
"""
if not issubclass(form_class, _ConfigFormBase):
raise ValueError(
"The form does not inherit from `forms.ConfigForm`")
self._registry.add(form_class)
if check_middleware:
_check_backend() | Register a config form into the registry
:param object form_class: The form class to register.\
Must be an instance of :py:class:`djconfig.forms.ConfigForm`
:param bool check_middleware: Check\
:py:class:`djconfig.middleware.DjConfigMiddleware`\
is registered into ``settings.MIDDLEWARE_CLASSES``. Default True | entailment |
def _reload(self):
"""
Gets every registered form's field value.\
If a field name is found in the db, it will load it from there.\
Otherwise, the initial value from the field form is used
"""
ConfigModel = apps.get_model('djconfig.Config')
cache = {}
data = dict(
ConfigModel.objects
.all()
.values_list('key', 'value'))
# populate cache with initial form values,
# then with cleaned database values,
# then with raw database file/image paths
for form_class in self._registry:
empty_form = form_class()
cache.update({
name: field.initial
for name, field in empty_form.fields.items()})
form = form_class(data={
name: _deserialize(data[name], field)
for name, field in empty_form.fields.items()
if name in data and not isinstance(field, forms.FileField)})
form.is_valid()
cache.update({
name: _unlazify(value)
for name, value in form.cleaned_data.items()
if name in data})
# files are special because they don't have an initial value
# and the POSTED data must contain the file. So, we keep
# the stored path as is
# TODO: see if serialize/deserialize/unlazify can be used for this instead
cache.update({
name: data[name]
for name, field in empty_form.fields.items()
if name in data and isinstance(field, forms.FileField)})
cache['_updated_at'] = data.get('_updated_at')
self._cache = cache | Gets every registered form's field value.\
If a field name is found in the db, it will load it from there.\
Otherwise, the initial value from the field form is used | entailment |
def _reload_maybe(self):
"""
Reload the config if the config\
model has been updated. This is called\
once on every request by the middleware.\
Should not be called directly.
"""
ConfigModel = apps.get_model('djconfig.Config')
data = dict(
ConfigModel.objects
.filter(key='_updated_at')
.values_list('key', 'value'))
if (not hasattr(self, '_updated_at') or
self._updated_at != data.get('_updated_at')):
self._reload() | Reload the config if the config\
model has been updated. This is called\
once on every request by the middleware.\
Should not be called directly. | entailment |
def save(self):
"""
Save the config with the cleaned data,\
update the last modified date so\
the config is reloaded on other process/nodes.\
Reload the config so it can be called right away.
"""
assert self.__class__ in conf.config._registry,\
'%(class_name)s is not registered' % {
'class_name': self.__class__.__name__
}
ConfigModel = apps.get_model('djconfig.Config')
for field_name, value in self.cleaned_data.items():
value = utils.serialize(
value=value,
field=self.fields.get(field_name, None))
# TODO: use update_or_create
count = (ConfigModel.objects
.filter(key=field_name)
.update(value=value))
if not count:
ConfigModel.objects.create(
key=field_name,
value=value)
count = (ConfigModel.objects
.filter(key='_updated_at')
.update(value=str(timezone.now())))
if not count:
ConfigModel.objects.create(
key='_updated_at',
value=str(timezone.now()))
conf.config._reload() | Save the config with the cleaned data,\
update the last modified date so\
the config is reloaded on other process/nodes.\
Reload the config so it can be called right away. | entailment |
def register(conf, conf_admin, **options):
"""
Register a new admin section.
:param conf: A subclass of ``djconfig.admin.Config``
:param conf_admin: A subclass of ``djconfig.admin.ConfigAdmin``
:param options: Extra options passed to ``django.contrib.admin.site.register``
"""
assert issubclass(conf_admin, ConfigAdmin), (
'conf_admin is not a ConfigAdmin subclass')
assert issubclass(
getattr(conf_admin, 'change_list_form', None),
ConfigForm), 'No change_list_form set'
assert issubclass(conf, Config), (
'conf is not a Config subclass')
assert conf.app_label, 'No app_label set'
assert conf.verbose_name_plural, 'No verbose_name_plural set'
assert not conf.name or re.match(r"^[a-zA-Z_]+$", conf.name), (
'Not a valid name. Valid chars are [a-zA-Z_]')
config_class = type("Config", (), {})
config_class._meta = type("Meta", (_ConfigMeta,), {
'app_label': conf.app_label,
'verbose_name_plural': conf.verbose_name_plural,
'object_name': 'Config',
'model_name': conf.name,
'module_name': conf.name})
admin.site.register([config_class], conf_admin, **options) | Register a new admin section.
:param conf: A subclass of ``djconfig.admin.Config``
:param conf_admin: A subclass of ``djconfig.admin.ConfigAdmin``
:param options: Extra options passed to ``django.contrib.admin.site.register`` | entailment |
def Mixed(*types):
"""Mixed type, used to indicate a field in a schema can be
one of many types. Use as a last resort only.
The Mixed type can be used directly as a class to indicate
any type is permitted for a given field:
`"my_field": {"type": Mixed}`
It can also be instantiated with list of specific types the
field may is allowed to be for more control:
`"my_field": {"type": Mixed(ObjectId, int)}`
"""
if len(types) < 2:
raise ValueError("Mixed type requires at least 2 specific types")
types = set(types) # dedupe
class MixedType(type):
def __instancecheck__(cls, instance):
"""Returns true if the given value is an instance of
one of the types enclosed by this mixed type."""
for mtype in types:
if isinstance(instance, mtype):
return True
return False
class Mixed(object):
__metaclass__ = MixedType
return Mixed | Mixed type, used to indicate a field in a schema can be
one of many types. Use as a last resort only.
The Mixed type can be used directly as a class to indicate
any type is permitted for a given field:
`"my_field": {"type": Mixed}`
It can also be instantiated with list of specific types the
field may is allowed to be for more control:
`"my_field": {"type": Mixed(ObjectId, int)}` | entailment |
def one_of(*args):
"""
Validates that a field value matches one of the values
given to this validator.
"""
if len(args) == 1 and isinstance(args[0], list):
items = args[0]
else:
items = list(args)
def validate(value):
if not value in items:
return e("{} is not in the list {}", value, items)
return validate | Validates that a field value matches one of the values
given to this validator. | entailment |
def gte(min_value):
"""
Validates that a field value is greater than or equal to the
value given to this validator.
"""
def validate(value):
if value < min_value:
return e("{} is not greater than or equal to {}", value, min_value)
return validate | Validates that a field value is greater than or equal to the
value given to this validator. | entailment |
Subsets and Splits