Merge pull request #1987 from gjcooper/PBS_Type_fix

FIX: TypeError bug for PBS process communication in python3

Author: satra

nipype/pipeline/plugins/pbs.py

@@ -6,7 +6,6 @@
 
 import os
 from time import sleep
-import subprocess
 
 from ...interfaces.base import CommandLine
 from .base import (SGELikeBatchManagerBase, logger, iflogger, logging)
@@ -46,13 +45,12 @@ def __init__(self, **kwargs):
         super(PBSPlugin, self).__init__(template, **kwargs)
 
     def _is_pending(self, taskid):
-        #  subprocess.Popen requires taskid to be a string
-        proc = subprocess.Popen(["qstat", str(taskid)],
-                                stdout=subprocess.PIPE,
-                                stderr=subprocess.PIPE)
-        _, e = proc.communicate()
+        result = CommandLine('qstat {}'.format(taskid),
+                             environ=dict(os.environ),
+                             terminal_output='allatonce',
+                             ignore_exception=True).run()
         errmsg = 'Unknown Job Id'  # %s' % taskid
-        return errmsg not in e
+        return errmsg not in result.runtime.stderr
 
     def _submit_batchtask(self, scriptfile, node):
         cmd = CommandLine('qsub', environ=dict(os.environ),