temporary patches for issue 1396

Author: satra

nipype/interfaces/base.py

@@ -1164,7 +1164,7 @@ def read(self, drain=0):
     def _read(self, drain):
         "Read from the file descriptor"
         fd = self.fileno()
-        buf = os.read(fd, 4096).decode()
+        buf = os.read(fd, 4096).decode(locale.getdefaultlocale()[1])
         if not buf and not self._buf:
             return None
         if '\n' not in buf:

nipype/pipeline/plugins/base.py

@@ -363,7 +363,7 @@ def _send_procs_to_workers(self, updatehash=False, graph=None):
                     self.proc_done[jobid] = True
                     self.proc_pending[jobid] = True
                     # Send job to task manager and add to pending tasks
-                    logger.info('Executing: %s ID: %d' %
+                    logger.info('Submitting: %s ID: %d' %
                                 (self.procs[jobid]._id, jobid))
                     if self._status_callback:
                         self._status_callback(self.procs[jobid], 'start')
@@ -405,7 +405,7 @@ def _send_procs_to_workers(self, updatehash=False, graph=None):
                                 self.proc_pending[jobid] = False
                             else:
                                 self.pending_tasks.insert(0, (tid, jobid))
-                    logger.info('Finished executing: %s ID: %d' %
+                    logger.info('Finished submitting: %s ID: %d' %
                                 (self.procs[jobid]._id, jobid))
             else:
                 break

nipype/pipeline/plugins/pbs.py

@@ -7,7 +7,7 @@
 
 from .base import (SGELikeBatchManagerBase, logger, iflogger, logging)
 
-from nipype.interfaces.base import CommandLine
+from ...interfaces.base import CommandLine, text_type
 
 
 class PBSPlugin(SGELikeBatchManagerBase):
@@ -87,6 +87,8 @@ def _submit_batchtask(self, scriptfile, node):
         iflogger.setLevel(logging.getLevelName('CRITICAL'))
         tries = 0
         while True:
+            result = cmd.run()
+            '''
             try:
                 result = cmd.run()
             except Exception as e:
@@ -97,9 +99,10 @@ def _submit_batchtask(self, scriptfile, node):
                     iflogger.setLevel(oldlevel)
                     raise RuntimeError('\n'.join((('Could not submit pbs task'
                                                    ' for node %s') % node._id,
-                                                  str(e))))
+                                                  text_type(e))))
             else:
                 break
+            '''
         iflogger.setLevel(oldlevel)
         # retrieve pbs taskid
         taskid = result.runtime.stdout.split('.')[0]