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fix: logging error if % in node cmd #2364

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Merged
merged 2 commits into from
Jan 19, 2018
Merged

fix: logging error if % in node cmd #2364

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6dcb3c8
fix: logging error if % in node cmd
mgxd Jan 10, 2018
df80e44
fix: substitute first
mgxd Jan 10, 2018
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12 changes: 6 additions & 6 deletions nipype/pipeline/engine/nodes.py
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Original file line number Diff line number Diff line change
Expand Up @@ -577,25 +577,25 @@ def _run_command(self, execute, copyfiles=True):
self._originputs = deepcopy(self._interface.inputs)
self._copyfiles_to_wd(execute=execute)

message = '[Node] Running "%s" ("%s.%s")'
message = '[Node] Running "{}" ("{}.{}")'
if issubclass(self._interface.__class__, CommandLine):
try:
cmd = self._interface.cmdline
except Exception as msg:
result.runtime.stderr = '%s\n\n%s' % (
result.runtime.stderr = '{}\n\n{}'.format(
getattr(result.runtime, 'stderr', ''), msg)
_save_resultfile(result, outdir, self.name)
raise
cmdfile = op.join(outdir, 'command.txt')
with open(cmdfile, 'wt') as fd:
print(cmd + "\n", file=fd)
message += ', a CommandLine Interface with command:\n%s' % cmd
logger.info(message, self.name, self._interface.__module__,
self._interface.__class__.__name__)
message += ', a CommandLine Interface with command:\n{}'.format(cmd)
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why not cmd.replace('%', '%%')?

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Actually, this problem now will happen the same if the command has braces...

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good call - I would prefer to not alter the cmd if possible, what about substitution first?

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cmd.replace('%', '%%') is not an in-place operation, why not just do it here?

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sure, we can replace to cover against substitution (%%) / escape characters (\", \\, etc), but isn't .format cleaner?

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It is just to use python's logging standards, but I'm not particularly attached to one solution or another 👍

logger.info(message.format(self.name, self._interface.__module__,
self._interface.__class__.__name__))
try:
result = self._interface.run()
except Exception as msg:
result.runtime.stderr = '%s\n\n%s' % (
result.runtime.stderr = '%s\n\n%s'.format(
getattr(result.runtime, 'stderr', ''), msg)
_save_resultfile(result, outdir, self.name)
raise
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