def prov(self):
"""
Extracts provenance information from the study for storage alongside
generated derivatives. Typically for reference purposes only as only
the pipeline workflow, inputs and outputs are checked by default when
determining which sessions require reprocessing.
Returns
-------
prov : dict[str, *]
A dictionary containing the provenance information to record
for the study
"""
# Get list of repositories where inputs to the study are stored
input_repos = list(set((i.repository for i in self.inputs)))
inputs = {}
for input in self.inputs:
inputs[input.name] = {
'repository_index': input_repos.index(input.repository)
}
if input.frequency == 'per_study':
inputs[input.name]['names'] = next(input.collection).name
elif input.frequency == 'per_subject':
inputs[input.name]['names'] = {
i.subject_id: i.name
for i in input.collection
}
elif input.frequency == 'per_visit':
inputs[input.name]['names'] = {
i.visit_id: i.name
for i in input.collection
}
elif input.frequency == 'per_session':
names = defaultdict(dict)
for item in input.collection:
names[item.subject_id][item.visit_id] = item.name
# Convert from defaultdict to dict
inputs[input.name]['names'] = dict(names.items())
return {
'name': self.name,
'type': get_class_info(type(self)),
'parameters': {p.name: p.value
for p in self.parameters},
'inputs': inputs,
'environment': self.environment.prov,
'repositories': [r.prov for r in input_repos],
'processor': self.processor.prov,
'subject_ids': tuple(self.subject_ids),
'visit_ids': tuple(self.visit_ids)
}
def prov(self):
prov = {
'interface': get_class_info(type(self.interface)),
'requirements': {v.name: v.prov for v in self.versions},
'parameters': {}}
for trait_name in self.inputs.visible_traits():
val = getattr(self.inputs, trait_name)
try:
val_prov = val.prov
except AttributeError:
val_prov = val
if isdefined(val):
prov['parameters'][trait_name] = val_prov
return prov
def prov(self):
return {'type': get_class_info(type(self)), 'host': HOSTNAME}
def prov(self):
return {'type': get_class_info(type(self)), 'echo': self._echo}
def prov(self):
return {'type': get_class_info(type(self))}
def prov(self):
return {
'type': get_class_info(type(self)),
'server': self.server}