Fixed PBS plugin to work with the Donders Torque cluster

Author: achetverikov

nipype/pipeline/plugins/pbs.py

@@ -47,18 +47,20 @@ def __init__(self, **kwargs):
         super(PBSPlugin, self).__init__(template, **kwargs)
 
     def _is_pending(self, taskid):
-        result = CommandLine('qstat {}'.format(taskid),
+        result = CommandLine('qstat -f {}'.format(taskid),
                              environ=dict(os.environ),
                              terminal_output='allatonce',
                              resource_monitor=False,
                              ignore_exception=True).run()
+
+        stdout = result.runtime.stdout
         stderr = result.runtime.stderr
-        errmsg = 'Unknown Job Id'  # %s' % taskid
+        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('qsub', environ=dict(os.environ),