def cascade_batchrun_inputs(workflow: Tool, inputs: List[Dict],
options: BatchRunRequirements):
fields_to_group = set(options.fields)
fields_to_group.add(options.groupby)
wfins = workflow.inputs_map()
required_ar_depth_of_groupby_fields = {
f: 1 + count_janisarray_depth(wfins[f].intype)
for f in fields_to_group
}
ins = {}
for inp in inputs:
for k, v in inp.items():
if k in fields_to_group:
if k not in ins:
ins[k] = []
# We'll look at the shape of the data, and decide whether
# we can just use the value, or we need to wrap it in another array
if count_array_depth(
v) < required_ar_depth_of_groupby_fields[k]:
v = [v]
ins[k].extend(v)
else:
# overwrite the previous value
ins[k] = v
# If inputs
return ins
def inputs_modifier(self, tool: Tool, inputs: Dict,
hints: Dict[str, str]) -> Dict:
new_inputs = {}
for inp in tool.inputs_map().values():
if inp.id() not in inputs:
continue
new_inputs[inp.id()] = self.process_single_input(
inp.id(), inp.intype, inputs[inp.id()])
return {**inputs, **new_inputs}
def inputs_modifier(self, wf: Tool, inputs: Dict, hints: Dict[str, str]):
nin = {**inputs}
inmap = wf.inputs_map()
# Change the 'cwd' just for the scope of this block
with Path(self.cwd):
for tag, value in nin.items():
if tag not in inmap:
# Only localise tags within the inputsdict that are in the tool inputs
# This might be a problem later for passthrough inputs (Janis doesn't support yet)
continue
intype = inmap[tag].intype
# If the type of the input is:
# (a) A File / Directory
isfiletype = isinstance(intype.received_type(),
(File, Directory))
# (b) Array with a fundamental type (recursively searches if nested array) of File or Directory
isbasefiletype = isinstance(
intype.received_type(), Array) and isinstance(
intype.fundamental_type(), (File, Directory))
# (Skip if not one of these conditions)
if not (isfiletype or isbasefiletype):
try:
nin[tag] = intype.coerce_value_if_possible(value)
except Exception as e:
raise Exception(
f"Couldn't coerce the input for '{tag}' ({value}) to type '{intype}': {e}"
)
continue
# Qualify the fully qualify the filepath
try:
nin[tag] = self.fully_qualify_filename_array_or_single(
value)
except Exception as e:
raise Exception(
f"Couldn't qualify the filename for the input '{tag}' ({value}) to type '{intype}': {e}"
)
return nin
