def apply_input_function(self,
func,
wildcards,
incomplete_checkpoint_func=lambda e: None,
raw_exceptions=False,
**aux_params):
incomplete = False
if isinstance(func, _IOFile):
func = func._file.callable
elif isinstance(func, AnnotatedString):
func = func.callable
sig = inspect.signature(func)
_aux_params = {
k: v
for k, v in aux_params.items() if k in sig.parameters
}
try:
value = func(Wildcards(fromdict=wildcards), **_aux_params)
except IncompleteCheckpointException as e:
value = incomplete_checkpoint_func(e)
incomplete = True
except FileNotFoundError as e:
# Function evaluation can depend on input files. Since expansion can happen during dryrun,
# where input files are not yet present, we need to skip such cases and
# mark them as <TBD>.
if e.filename in aux_params["input"]:
value = TBDString()
else:
raise e
except (Exception, BaseException) as e:
if raw_exceptions:
raise e
else:
raise InputFunctionException(e, rule=self, wildcards=wildcards)
return value, incomplete
def handle_incomplete_checkpoint(exception):
"""If checkpoint is incomplete, target it such that it is completed
before this rule gets executed."""
if exception.targetfile in input:
return TBDString()
else:
raise WorkflowError(
"Rule parameter depends on checkpoint but checkpoint output is not defined as input file for the rule. "
"Please add the output of the respective checkpoint to the rule inputs."
)
def format_files(job, io, dynamicio):
for f in io:
if f in dynamicio:
yield "{} (dynamic)".format(f.format_dynamic())
elif is_flagged(f, "pipe"):
yield "{} (pipe)".format(f)
elif is_flagged(f, "checkpoint_target"):
yield TBDString()
else:
yield f
def apply_input_function(
self,
func,
wildcards,
incomplete_checkpoint_func=lambda e: None,
raw_exceptions=False,
groupid=None,
**aux_params,
):
incomplete = False
if isinstance(func, _IOFile):
func = func._file.callable
elif isinstance(func, AnnotatedString):
func = func.callable
if "groupid" in get_function_params(func):
if groupid is not None:
aux_params["groupid"] = groupid
else:
# Return empty list of files and incomplete marker
# the job will be reevaluated once groupids have been determined
return [], True
_aux_params = get_input_function_aux_params(func, aux_params)
try:
value = func(Wildcards(fromdict=wildcards), **_aux_params)
if isinstance(value, types.GeneratorType):
# generators should be immediately collected here,
# otherwise we would miss any exceptions and
# would have to capture them again later.
value = list(value)
except IncompleteCheckpointException as e:
value = incomplete_checkpoint_func(e)
incomplete = True
except FileNotFoundError as e:
# Function evaluation can depend on input files. Since expansion can happen during dryrun,
# where input files are not yet present, we need to skip such cases and
# mark them as <TBD>.
if "input" in aux_params and e.filename in aux_params["input"]:
value = TBDString()
else:
raise e
except (Exception, BaseException) as e:
if raw_exceptions:
raise e
else:
raise InputFunctionException(e, rule=self, wildcards=wildcards)
return value, incomplete