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MAINT: Refactor aggregate_outputs for readability #2969

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merged 4 commits into from
Jul 29, 2019
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MAINT: Refactor aggregate_outputs for readability #2969

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251362e
MAINT: Refactor ``aggregate_outputs`` for readability
oesteban Jul 19, 2019
0c6d121
fix: failing test since raised exception has been changed
oesteban Jul 20, 2019
259e7bc
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oesteban Jul 26, 2019
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oesteban Jul 26, 2019
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60 changes: 31 additions & 29 deletions nipype/interfaces/base/core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -204,10 +204,10 @@ def _check_requires(self, spec, name, value):
]
if any(values) and isdefined(value):
if len(values) > 1:
fmt = ("%s requires values for inputs %s because '%s' is set. "
fmt = ("%s requires values for inputs %s because '%s' is set. "
"For a list of required inputs, see %s.help()")
else:
fmt = ("%s requires a value for input %s because '%s' is set. "
fmt = ("%s requires a value for input %s because '%s' is set. "
"For a list of required inputs, see %s.help()")
msg = fmt % (self.__class__.__name__,
', '.join("'%s'" % req for req in spec.requires),
Expand Down Expand Up @@ -450,34 +450,36 @@ def _list_outputs(self):
return None

def aggregate_outputs(self, runtime=None, needed_outputs=None):
""" Collate expected outputs and check for existence
"""

predicted_outputs = self._list_outputs()
outputs = self._outputs()
if predicted_outputs:
_unavailable_outputs = []
if outputs:
_unavailable_outputs = \
self._check_version_requirements(self._outputs())
for key, val in list(predicted_outputs.items()):
if needed_outputs and key not in needed_outputs:
continue
if key in _unavailable_outputs:
raise KeyError(('Output trait %s not available in version '
'%s of interface %s. Please inform '
'developers.') % (key, self.version,
self.__class__.__name__))
try:
setattr(outputs, key, val)
except TraitError as error:
if getattr(error, 'info',
'default').startswith('an existing'):
msg = ("File/Directory '%s' not found for %s output "
"'%s'." % (val, self.__class__.__name__, key))
raise FileNotFoundError(msg)
raise error
"""Collate expected outputs and apply output traits validation."""
outputs = self._outputs() # Generate an empty output spec object
predicted_outputs = self._list_outputs() # Predictions from _list_outputs
if not predicted_outputs:
return outputs

# Precalculate the list of output trait names that should be aggregated
aggregate_names = set(predicted_outputs)
if needed_outputs is not None:
aggregate_names = set(needed_outputs).intersection(aggregate_names)

if aggregate_names: # Make sure outputs are compatible
_na_outputs = self._check_version_requirements(outputs)
na_names = aggregate_names.intersection(_na_outputs)
if na_names:
# XXX Change to TypeError in Nipype 2.0
raise KeyError("""\
Output trait(s) %s not available in version %s of interface %s.\
""" % (', '.join(na_names), self.version, self.__class__.__name__))

for key in aggregate_names: # Final aggregation
val = predicted_outputs[key]
try:
setattr(outputs, key, val)
except TraitError as error:
if 'an existing' in getattr(error, 'info', 'default'):
msg = "No such file or directory for output '%s' of a %s interface" % \
(key, self.__class__.__name__)
raise FileNotFoundError(val, message=msg)
raise error
return outputs

@property
Expand Down