From 218c6a10f22dec7a283e569e7b332dd6e5052bc4 Mon Sep 17 00:00:00 2001
From: Michiel Cottaar <MichielCottaar@gmail.com>
Date: Fri, 27 Apr 2018 15:41:41 +0100
Subject: [PATCH] Clarified that in output the logdir should be provided
If a logdir has been set that directory should be provided rather than the directory from which the job was submitted (which is what the logdir defaults to).
---
fsl/utils/fslsub.py | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/fsl/utils/fslsub.py b/fsl/utils/fslsub.py
index 81034b1a7..4d6bf1a61 100644
--- a/fsl/utils/fslsub.py
+++ b/fsl/utils/fslsub.py
@@ -156,19 +156,19 @@ def info(job_id):
return res
-def output(job_id, cwd='.', command=None, name=None):
+def output(job_id, logdir='.', command=None, name=None):
"""Returns the output of the given job.
:arg job_id: String containing job ID.
- :arg cwd: Directory from which command was submitted - defaults to
+ :arg logdir: Directory containing the log - defaults to
the current directory.
:arg command: Command that was run. Not currently used.
:arg name: Job name if it was specified. Not currently used.
:returns: A tuple containing the standard output and standard error.
"""
- stdout = list(glob.glob(op.join(cwd, '*.o{}'.format(job_id))))
- stderr = list(glob.glob(op.join(cwd, '*.e{}'.format(job_id))))
+ stdout = list(glob.glob(op.join(logdir, '*.o{}'.format(job_id))))
+ stderr = list(glob.glob(op.join(logdir, '*.e{}'.format(job_id))))
if len(stdout) != 1 or len(stderr) != 1:
raise ValueError('No/too many error/output files for job {}: stdout: '
--
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