Merge pull request #2344 from achetverikov/pbs_plugin_fix

FIX: PBS plugin fix

Author: mgxd

.zenodo.json

@@ -568,6 +568,11 @@
       "affiliation": "University College London",
       "name": "Mancini, Matteo",
       "orcid": "0000-0001-7194-4568"
+    },
+    {
+      "affiliation": "Donders Institute for Brain, Cognition and Behavior, Center for Cognitive Neuroimaging",
+      "name": "Chetverikov, Andrey",
+      "orcid": "0000-0003-2767-6310"
     }
   ],
   "keywords": [

nipype/pipeline/plugins/pbs.py

@@ -49,18 +49,20 @@ def __init__(self, **kwargs):
         super(PBSPlugin, self).__init__(template, **kwargs)
 
     def _is_pending(self, taskid):
-        result = CommandLine(
-            'qstat {}'.format(taskid),
-            environ=dict(os.environ),
-            terminal_output='allatonce',
-            resource_monitor=False,
-            ignore_exception=True).run()
-        errmsg = 'Unknown Job Id'  # %s' % taskid
+        result = CommandLine('qstat -f {}'.format(taskid),
+                             environ=dict(os.environ),
+                             terminal_output='file_split',
+                             resource_monitor=False,
+                             ignore_exception=True).run()
+
+        stdout = result.runtime.stdout
+        stderr = result.runtime.stderr
+        errmsg = 'Unknown Job Id' 
         success = 'Job has finished'
-        if success in e:  # Fix for my PBS
+        if (success in stderr) or ('job_state = C' in stdout):  
             return False
         else:
-            return errmsg not in e
+            return errmsg not in stderr
 
     def _submit_batchtask(self, scriptfile, node):
         cmd = CommandLine(