Commit 29cbf562 authored by Paul McCarthy's avatar Paul McCarthy 🚵
Browse files

fslsub.output ignores command/name for the time being.

parent bef8751a
......@@ -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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