From 6f8ebf44a84dbb5a0e20897bc6ae493cdf4b03cb Mon Sep 17 00:00:00 2001
From: Martin Craig <martin.craig@eng.ox.ac.uk>
Date: Tue, 10 Jul 2018 13:24:07 +0100
Subject: [PATCH] Make log key 'cmd' into a stream rather than a boolean This
enables a common use case - logging the command but not the standard output
---
fsl/utils/run.py | 25 ++++++++++++-------------
1 file changed, 12 insertions(+), 13 deletions(-)
diff --git a/fsl/utils/run.py b/fsl/utils/run.py
index bf63d578d..a08d05cef 100644
--- a/fsl/utils/run.py
+++ b/fsl/utils/run.py
@@ -163,8 +163,8 @@ def run(*args, **kwargs):
- stderr: Optional file-like object to which the command's
standard error stream can be forwarded.
- - cmd: If ``True``, the command itself is logged to the
- standard output stream(s).
+ - cmd: Optional file-like object to which the command itself
+ is logged.
:returns: If ``submit`` is provided, the return value of
:func:`.fslsub` is returned. Otherwise returns a single
@@ -191,7 +191,7 @@ def run(*args, **kwargs):
tee = log .get('tee', False)
logStdout = log .get('stdout', None)
logStderr = log .get('stderr', None)
- logCmd = log .get('cmd', False)
+ logCmd = log .get('cmd', None)
args = _prepareArgs(args)
if not bool(submit):
@@ -269,8 +269,8 @@ def _realrun(tee, logStdout, logStderr, logCmd, *args):
:arg logStderr: Optional file-like object to which the command's standard
error stream can be forwarded.
- :arg logCmd: If ``True``, the command itself is logged to the standard
- output stream(s).
+ :arg logCmd: Optional file-like object to which the command itself is
+ logged.
:arg args: Command to run
@@ -305,15 +305,13 @@ def _realrun(tee, logStdout, logStderr, logCmd, *args):
if logStdout is not None: outstreams.append(logStdout)
if logStderr is not None: errstreams.append(logStderr)
- # log the command to
- # stdout if requested
- if logCmd:
+ # log the command if requested
+ if logCmd is not None:
cmd = ' '.join(args) + '\n'
- for o in outstreams:
- if 'b' in getattr(o, 'mode', 'w'):
- o.write(cmd.encode('utf-8'))
- else:
- o.write(cmd)
+ if 'b' in getattr(logCmd, 'mode', 'w'):
+ logCmd.write(cmd.encode('utf-8'))
+ else:
+ logCmd.write(cmd)
stdoutt = _forwardStream(proc.stdout, *outstreams)
stderrt = _forwardStream(proc.stderr, *errstreams)
@@ -369,6 +367,7 @@ def runfsl(*args, **kwargs):
return run(*args, **kwargs)
+
def wait(job_ids):
"""Proxy for :func:`.fslsub.wait`. """
return fslsub.wait(job_ids)
--
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