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FIX/TEST: Gunzip cleanup and test #2564

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merged 1 commit into from
May 1, 2018
Merged

FIX/TEST: Gunzip cleanup and test #2564

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17 changes: 14 additions & 3 deletions nipype/algorithms/misc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -266,21 +266,32 @@ class GunzipOutputSpec(TraitedSpec):

class Gunzip(BaseInterface):
"""Gunzip wrapper

>>> from nipype.algorithms.misc import Gunzip
>>> gunzip = Gunzip(in_file='tpms_msk.nii.gz')
>>> res = gunzip.run()
>>> res.outputs.out_file # doctest: +ELLIPSIS
'.../tpms_msk.nii'

.. testcleanup::

>>> os.unlink('tpms_msk.nii')
"""
input_spec = GunzipInputSpec
output_spec = GunzipOutputSpec

def _gen_output_file_name(self):
_, base, ext = split_filename(self.inputs.in_file)
if ext[-2:].lower() == ".gz":
if ext[-3:].lower() == ".gz":
ext = ext[:-3]
return os.path.abspath(base + ext[:-3])
return os.path.abspath(base + ext)

def _run_interface(self, runtime):
import gzip
import shutil
with gzip.open(self.inputs.in_file, 'rb') as in_file:
with open(self._gen_output_file_name(), 'wb') as out_file:
out_file.write(in_file.read())
shutil.copyfileobj(in_file, out_file)
return runtime

def _list_outputs(self):
Expand Down