BUG: subprocess.Popen requres list of arguments to be strings

File "/nfsscratch/PREDICT/johnsonhj/src/BRAINSStandAlone-Linux64-gcc44/NIPYPE/nipype/pipeline/plugins/sge.py", line 42, in _is_pending stderr=subprocess.PIPE)
File "/nfsscratch/PREDICT/opt/epd-7.2-1-rh5-x86_64/lib/python2.7/subprocess.py", line 679, in __init__ errread, errwrite)
File "/nfsscratch/PREDICT/opt/epd-7.2-1-rh5-x86_64/lib/python2.7/subprocess.py", line 1228, in _execute_child raise child_exception
TypeError: execv() arg 2 must contain only strings

This was causing nodes to crash when using SGE.

Simply typecast the integer to a string and the nodes pass.

Author: hjmjohnson

nipype/pipeline/plugins/pbs.py

@@ -36,7 +36,8 @@ def __init__(self, **kwargs):
         super(PBSPlugin, self).__init__(template, **kwargs)
 
     def _is_pending(self, taskid):
-        proc = subprocess.Popen(["qstat", taskid],
+        #  subprocess.Popen requires taskid to be a string
+        proc = subprocess.Popen(["qstat", str(taskid)],
                                 stdout=subprocess.PIPE,
                                 stderr=subprocess.PIPE)
         _, e = proc.communicate()

nipype/pipeline/plugins/sge.py

@@ -37,7 +37,8 @@ def __init__(self, **kwargs):
         super(SGEPlugin, self).__init__(template, **kwargs)
 
     def _is_pending(self, taskid):
-        proc = subprocess.Popen(["qstat", '-j', taskid],
+        #  subprocess.Popen requires taskid to be a string
+        proc = subprocess.Popen(["qstat", '-j', str(taskid)],
                                 stdout=subprocess.PIPE,
                                 stderr=subprocess.PIPE)
         o, _ = proc.communicate()