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Merge pull request #2260 from oesteban/fix/close_fds
[ENH] Close file descriptors
2 parents fc2c5b4 + bd7f00c commit 557aad3

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nipype/interfaces/base.py

Lines changed: 5 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1373,7 +1373,9 @@ def run_command(runtime, output=None, timeout=0.01):
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stderr=stderr,
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shell=True,
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cwd=runtime.cwd,
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env=env)
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env=env,
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close_fds=True,
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)
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result = {
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'stdout': [],
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'stderr': [],
@@ -1421,12 +1423,14 @@ def _process(drain=0):
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proc.wait()
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if outfile is not None:
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stdout.flush()
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stdout.close()
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with open(outfile, 'rb') as ofh:
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stdoutstr = ofh.read()
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result['stdout'] = read_stream(stdoutstr, logger=iflogger)
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if errfile is not None:
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stderr.flush()
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stderr.close()
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with open(errfile, 'rb') as efh:
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stderrstr = efh.read()
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result['stderr'] = read_stream(stderrstr, logger=iflogger)

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