From 29cbf562fcebb31bfacbd8d47c91728dd42837e8 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Thu, 19 Apr 2018 15:05:24 +0100
Subject: [PATCH] fslsub.output ignores command/name for the time being.
---
fsl/utils/fslsub.py | 21 +++++++++++++--------
1 file changed, 13 insertions(+), 8 deletions(-)
diff --git a/fsl/utils/fslsub.py b/fsl/utils/fslsub.py
index fd7f195b1..81034b1a7 100644
--- a/fsl/utils/fslsub.py
+++ b/fsl/utils/fslsub.py
@@ -42,6 +42,7 @@ Example usage, building a short pipeline::
from six import string_types, BytesIO
import subprocess as sp
import os.path as op
+import glob
import time
import pickle
import sys
@@ -155,22 +156,26 @@ def info(job_id):
return res
-def output(job_id, command, cwd='.', name=None):
+def output(job_id, cwd='.', command=None, name=None):
"""Returns the output of the given job.
- :arg job_id: String with job id
- :arg command: Command that was run
+ :arg job_id: String containing job ID.
:arg cwd: Directory from which command was submitted - defaults to
the current directory.
- :arg name: Job name if it was specified.
+ :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.
"""
- if name is None:
- name = op.basename(command)
+ stdout = list(glob.glob(op.join(cwd, '*.o{}'.format(job_id))))
+ stderr = list(glob.glob(op.join(cwd, '*.e{}'.format(job_id))))
- stdout = op.join(cwd, '{}.o{}'.format(name, job_id))
- stderr = op.join(cwd, '{}.e{}'.format(name, job_id))
+ if len(stdout) != 1 or len(stderr) != 1:
+ raise ValueError('No/too many error/output files for job {}: stdout: '
+ '{}, stderr: {}'.format(job_id, stdout, stderr))
+
+ stdout = stdout[0]
+ stderr = stderr[0]
if op.exists(stdout):
with open(stdout, 'rt') as f:
--
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