def _apply_wildcards(newitems,
olditems,
wildcards,
wildcards_obj,
concretize=apply_wildcards,
ruleio=None):
for name, item in olditems.allitems():
start = len(newitems)
if callable(item):
item = item(wildcards_obj)
if not_iterable(item):
item = [item]
for item_ in item:
if not isinstance(item_, str):
raise RuleException(
"Input function did not return str or list of str.",
rule=self)
concrete = concretize(item_, wildcards)
newitems.append(concrete)
if ruleio is not None:
ruleio[concrete] = item_
else:
if not_iterable(item):
item = [item]
for item_ in item:
concrete = concretize(item_, wildcards)
newitems.append(concrete)
if ruleio is not None:
ruleio[concrete] = item_
if name:
newitems.set_name(name, start, end=len(newitems))
def _apply_wildcards(
newitems,
olditems,
wildcards,
wildcards_obj,
concretize = apply_wildcards,
ruleio = None):
for name, item in olditems.allitems():
start = len(newitems)
if callable(item):
item = item(wildcards_obj)
if not_iterable(item):
item = [item]
for item_ in item:
if not isinstance(item_, str):
raise RuleException("Input function did not return str or list of str.", rule=self)
concrete = concretize(item_, wildcards)
newitems.append(concrete)
if ruleio is not None:
ruleio[concrete] = item_
else:
if not_iterable(item):
item = [item]
for item_ in item:
concrete = concretize(item_, wildcards)
newitems.append(concrete)
if ruleio is not None:
ruleio[concrete] = item_
if name:
newitems.set_name(name, start, end=len(newitems))
def target(self, paths):
if not_iterable(paths):
path = paths
path = path if os.path.isabs(path) else os.path.join(
self.workdir, path)
return flag(path, "subworkflow", self)
return [self.target(path) for path in paths]
def _apply_wildcards(self, newitems, olditems, wildcards,
concretize=apply_wildcards,
check_return_type=True,
mapping=None,
no_flattening=False,
aux_params=None):
if aux_params is None:
aux_params = dict()
for name, item in olditems.allitems():
start = len(newitems)
is_iterable = True
if callable(item):
item = self.apply_input_function(item, wildcards, **aux_params)
if not_iterable(item) or no_flattening:
item = [item]
is_iterable = False
for item_ in item:
if check_return_type and not isinstance(item_, str):
raise WorkflowError("Function did not return str or list "
"of str.", rule=self)
concrete = concretize(item_, wildcards)
newitems.append(concrete)
if mapping is not None:
mapping[concrete] = item_
if name:
newitems.set_name(
name, start,
end=len(newitems) if is_iterable else None)
def _apply_wildcards(newitems,
olditems,
wildcards,
wildcards_obj,
concretize=apply_wildcards,
check_return_type=check_string_type,
ruleio=None,
no_flattening=False):
for name, item in olditems.allitems():
start = len(newitems)
is_iterable = True
if callable(item):
try:
item = item(wildcards_obj)
except (Exception, BaseException) as e:
raise InputFunctionException(e,
rule=self,
wildcards=wildcards)
if not_iterable(item) or no_flattening:
item = [item]
is_iterable = False
for item_ in item:
check_return_type(item_)
concrete = concretize(item_, wildcards)
newitems.append(concrete)
if ruleio is not None:
ruleio[concrete] = item_
if name:
newitems.set_name(
name,
start,
end=len(newitems) if is_iterable else None)
def format_cli_pos_arg(value, quote=True):
if isinstance(value, dict):
return join_cli_args(repr(f"{key}={val}") for key, val in value.items())
elif not_iterable(value):
return repr(value)
else:
return join_cli_args(repr(v) for v in value)
def _apply_wildcards(newitems, olditems, wildcards, wildcards_obj,
concretize=apply_wildcards,
check_return_type=check_string_type,
ruleio=None,
no_flattening=False):
for name, item in olditems.allitems():
start = len(newitems)
is_iterable = True
if callable(item):
try:
item = item(wildcards_obj)
except (Exception, BaseException) as e:
raise InputFunctionException(e, rule=self, wildcards=wildcards)
if not_iterable(item) or no_flattening:
item = [item]
is_iterable = False
for item_ in item:
check_return_type(item_)
concrete = concretize(item_, wildcards)
newitems.append(concrete)
if ruleio is not None:
ruleio[concrete] = item_
if name:
newitems.set_name(
name, start,
end=len(newitems) if is_iterable else None)
def _apply_wildcards(
self,
newitems,
olditems,
wildcards,
concretize=None,
check_return_type=True,
omit_callable=False,
mapping=None,
no_flattening=False,
aux_params=None,
apply_path_modifier=True,
property=None,
incomplete_checkpoint_func=lambda e: None,
allow_unpack=True,
):
if aux_params is None:
aux_params = dict()
for name, item in olditems._allitems():
start = len(newitems)
is_unpack = is_flagged(item, "unpack")
_is_callable = is_callable(item)
if _is_callable:
if omit_callable:
continue
item, incomplete = self.apply_input_function(
item,
wildcards,
incomplete_checkpoint_func=incomplete_checkpoint_func,
is_unpack=is_unpack,
**aux_params)
if apply_path_modifier:
item = self.apply_path_modifier(item, property=property)
if is_unpack and not incomplete:
if not allow_unpack:
raise WorkflowError(
"unpack() is not allowed with params. "
"Simply return a dictionary which can be directly ."
"used, e.g. via {params[mykey]}.")
# Sanity checks before interpreting unpack()
if not isinstance(item, (list, dict)):
raise WorkflowError(
"Can only use unpack() on list and dict", rule=self)
if name:
raise WorkflowError(
"Cannot combine named input file with unpack()",
rule=self)
# Allow streamlined code with/without unpack
if isinstance(item, list):
pairs = zip([None] * len(item), item)
else:
assert isinstance(item, dict)
pairs = item.items()
else:
pairs = [(name, item)]
for name, item in pairs:
is_iterable = True
if not_iterable(item) or no_flattening:
item = [item]
is_iterable = False
for item_ in item:
if (check_return_type and not isinstance(item_, str)
and not isinstance(item_, Path)):
raise WorkflowError(
"Function did not return str or list "
"of str.",
rule=self)
concrete = concretize(item_, wildcards, _is_callable)
newitems.append(concrete)
if mapping is not None:
mapping[concrete] = item_
if name:
newitems._set_name(
name,
start,
end=len(newitems) if is_iterable else None)
start = len(newitems)
def target(self, paths):
if not_iterable(paths):
return flag(os.path.join(self.workdir, paths), "subworkflow", self)
return [self.target(path) for path in paths]
def _apply_wildcards(self,
newitems,
olditems,
wildcards,
concretize=apply_wildcards,
check_return_type=True,
omit_callable=False,
mapping=None,
no_flattening=False,
aux_params=None,
apply_default_remote=True):
if aux_params is None:
aux_params = dict()
for name, item in olditems.allitems():
start = len(newitems)
is_iterable = True
is_unpack = is_flagged(item, "unpack")
if is_callable(item):
if omit_callable:
continue
item = self.apply_input_function(item, wildcards, **aux_params)
if apply_default_remote:
item = self.apply_default_remote(item)
if is_unpack:
# Sanity checks before interpreting unpack()
if not isinstance(item, (list, dict)):
raise WorkflowError(
"Can only use unpack() on list and dict", rule=self)
if name:
raise WorkflowError(
"Cannot combine named input file with unpack()",
rule=self)
# Allow streamlined code with/without unpack
if isinstance(item, list):
pairs = zip([None] * len(item), item)
else:
assert isinstance(item, dict)
pairs = item.items()
else:
pairs = [(name, item)]
for name, item in pairs:
if not_iterable(item) or no_flattening:
item = [item]
is_iterable = False
for item_ in item:
if check_return_type and not isinstance(item_, str):
raise WorkflowError(
"Function did not return str or list "
"of str.",
rule=self)
concrete = concretize(item_, wildcards)
newitems.append(concrete)
if mapping is not None:
mapping[concrete] = item_
if name:
newitems.set_name(
name,
start,
end=len(newitems) if is_iterable else None)
start = len(newitems)
def target(self, paths):
if not_iterable(paths):
return flag(os.path.join(self.workdir, paths), "subworkflow", self)
return [self.target(path) for path in paths]
