Revert "removing terminal_output from CommandLine call (ignore_exception is deprecated)"

This reverts commit 708ac1c.

Author: djarecka

nipype/interfaces/afni/base.py

@@ -87,7 +87,8 @@ def standard_image(img_name):
         Could be made more fancy to allow for more relocatability'''
         clout = CommandLine(
             'which afni',
-            resource_monitor=False).run()
+            resource_monitor=False,
+            terminal_output='allatonce').run()
         if clout.runtime.returncode is not 0:
             return None
 

nipype/interfaces/base/core.py

@@ -1314,7 +1314,8 @@ def version(klass):
                 try:
                     clout = CommandLine(
                         command=klass.version_cmd,
-                        resource_monitor=False).run()
+                        resource_monitor=False,
+                        terminal_output='allatonce').run()
                 except IOError:
                     return None
 

nipype/interfaces/diffusion_toolkit/base.py

@@ -48,7 +48,8 @@ def version():
            Version number as string or None if FSL not found
 
         """
-        clout = CommandLine(command='dti_recon').run()
+        clout = CommandLine(
+            command='dti_recon', terminal_output='allatonce').run()
 
         if clout.runtime.returncode is not 0:
             return None

nipype/interfaces/matlab.py

@@ -25,7 +25,8 @@ def get_matlab_command():
         res = CommandLine(
             command='which',
             args=matlab_cmd,
-            resource_monitor=False).run()
+            resource_monitor=False,
+            terminal_output='allatonce').run()
         matlab_path = res.runtime.stdout.strip()
     except Exception:
         return None

nipype/interfaces/minc/base.py

@@ -56,7 +56,8 @@ def version():
         try:
             clout = CommandLine(
                 command='mincinfo',
-                args='-version').run()
+                args='-version',
+                terminal_output='allatonce').run()
         except IOError:
             return None
 

nipype/pipeline/engine/utils.py

@@ -1338,7 +1338,8 @@ def _run_dot(dotfilename, format_ext):
     dot_base =  os.path.splitext(dotfilename)[0]
     formatted_dot = '{}.{}'.format(dot_base, format_ext)
     cmd = 'dot -T{} -o"{}" "{}"'.format(format_ext, formatted_dot, dotfilename)
-    res = CommandLine(cmd, resource_monitor=False).run()
+    res = CommandLine(cmd, terminal_output='allatonce',
+                      resource_monitor=False).run()
     return formatted_dot, res
 
 

nipype/pipeline/plugins/condor.py

@@ -49,7 +49,7 @@ def __init__(self, **kwargs):
 
     def _is_pending(self, taskid):
         cmd = CommandLine(
-            'condor_q', resource_monitor=False)
+            'condor_q', resource_monitor=False, terminal_output='allatonce')
         cmd.inputs.args = '%d' % taskid
         # check condor cluster
         oldlevel = iflogger.level
@@ -64,7 +64,8 @@ def _submit_batchtask(self, scriptfile, node):
         cmd = CommandLine(
             'condor_qsub',
             environ=dict(os.environ),
-            resource_monitor=False)
+            resource_monitor=False,
+            terminal_output='allatonce')
         path = os.path.dirname(scriptfile)
         qsubargs = ''
         if self._qsub_args:

nipype/pipeline/plugins/dagman.py

@@ -158,7 +158,8 @@ def _submit_graph(self, pyfiles, dependencies, nodes):
         cmd = CommandLine(
             'condor_submit_dag',
             environ=dict(os.environ),
-            resource_monitor=False)
+            resource_monitor=False,
+            terminal_output='allatonce')
         # needs -update_submit or re-running a workflow will fail
         cmd.inputs.args = '%s -update_submit %s' % (self._dagman_args,
                                                     dagfilename)

nipype/pipeline/plugins/lsf.py

@@ -48,7 +48,8 @@ def _is_pending(self, taskid):
         But _is_pending should return True until a job has finished and is
         ready to be checked for completeness. So return True if status is
         either 'PEND' or 'RUN'"""
-        cmd = CommandLine('bjobs', resource_monitor=False)
+        cmd = CommandLine(
+            'bjobs', resource_monitor=False, terminal_output='allatonce')
         cmd.inputs.args = '%d' % taskid
         # check lsf task
         oldlevel = iflogger.level
@@ -65,7 +66,8 @@ def _submit_batchtask(self, scriptfile, node):
         cmd = CommandLine(
             'bsub',
             environ=dict(os.environ),
-            resource_monitor=False)
+            resource_monitor=False,
+            terminal_output='allatonce')
         bsubargs = ''
         if self._bsub_args:
             bsubargs = self._bsub_args

nipype/pipeline/plugins/oar.py

@@ -69,7 +69,8 @@ def _submit_batchtask(self, scriptfile, node):
         cmd = CommandLine(
             'oarsub',
             environ=dict(os.environ),
-            resource_monitor=False)
+            resource_monitor=False,
+            terminal_output='allatonce')
         path = os.path.dirname(scriptfile)
         oarsubargs = ''
         if self._oarsub_args:

nipype/pipeline/plugins/pbs.py

@@ -51,6 +51,7 @@ def __init__(self, **kwargs):
     def _is_pending(self, taskid):
         result = CommandLine('qstat -f {}'.format(taskid),
                              environ=dict(os.environ),
+                             terminal_output='file_split',
                              resource_monitor=False).run()
 
         stdout = result.runtime.stdout
@@ -66,7 +67,8 @@ def _submit_batchtask(self, scriptfile, node):
         cmd = CommandLine(
             'qsub',
             environ=dict(os.environ),
-            resource_monitor=False)
+            resource_monitor=False,
+            terminal_output='allatonce')
         path = os.path.dirname(scriptfile)
         qsubargs = ''
         if self._qsub_args:

nipype/pipeline/plugins/pbsgraph.py

@@ -58,7 +58,8 @@ def _submit_graph(self, pyfiles, dependencies, nodes):
         cmd = CommandLine(
             'sh',
             environ=dict(os.environ),
-            resource_monitor=False)
+            resource_monitor=False,
+            terminal_output='allatonce')
         cmd.inputs.args = '%s' % submitjobsfile
         cmd.run()
         logger.info('submitted all jobs to queue')

nipype/pipeline/plugins/sge.py

@@ -392,7 +392,8 @@ def _submit_batchtask(self, scriptfile, node):
         cmd = CommandLine(
             'qsub',
             environ=dict(os.environ),
-            resource_monitor=False)
+            resource_monitor=False,
+            terminal_output='allatonce')
         path = os.path.dirname(scriptfile)
         qsubargs = ''
         if self._qsub_args:

nipype/pipeline/plugins/sgegraph.py

@@ -155,7 +155,8 @@ def make_job_name(jobnumber, nodeslist):
         cmd = CommandLine(
             'bash',
             environ=dict(os.environ),
-            resource_monitor=False)
+            resource_monitor=False,
+            terminal_output='allatonce')
         cmd.inputs.args = '%s' % submitjobsfile
         cmd.run()
         logger.info('submitted all jobs to queue')

nipype/pipeline/plugins/slurm.py

@@ -66,7 +66,8 @@ def _is_pending(self, taskid):
         res = CommandLine(
             'squeue',
             args=' '.join(['-j', '%s' % taskid]),
-            resource_monitor=False).run()
+            resource_monitor=False,
+            terminal_output='allatonce').run()
         return res.runtime.stdout.find(str(taskid)) > -1
 
     def _submit_batchtask(self, scriptfile, node):
@@ -78,7 +79,8 @@ def _submit_batchtask(self, scriptfile, node):
         cmd = CommandLine(
             'sbatch',
             environ=dict(os.environ),
-            resource_monitor=False)
+            resource_monitor=False,
+            terminal_output='allatonce')
         path = os.path.dirname(scriptfile)
 
         sbatch_args = ''

nipype/pipeline/plugins/slurmgraph.py

@@ -155,7 +155,8 @@ def make_job_name(jobnumber, nodeslist):
         cmd = CommandLine(
             'bash',
             environ=dict(os.environ),
-            resource_monitor=False)
+            resource_monitor=False,
+            terminal_output='allatonce')
         cmd.inputs.args = '%s' % submitjobsfile
         cmd.run()
         logger.info('submitted all jobs to queue')

nipype/utils/docparse.py

@@ -254,7 +254,8 @@ def get_doc(cmd, opt_map, help_flag=None, trap_error=True):
     """
     res = CommandLine(
         'which %s' % cmd.split(' ')[0],
-        resource_monitor=False).run()
+        resource_monitor=False,
+        terminal_output='allatonce').run()
     cmd_path = res.runtime.stdout.strip()
     if cmd_path == '':
         raise Exception('Command %s not found' % cmd.split(' ')[0])
@@ -333,7 +334,8 @@ def get_params_from_doc(cmd, style='--', help_flag=None, trap_error=True):
     """
     res = CommandLine(
         'which %s' % cmd.split(' ')[0],
-        resource_monitor=False).run()
+        resource_monitor=False,
+        terminal_output='allatonce').run()
     cmd_path = res.runtime.stdout.strip()
     if cmd_path == '':
         raise Exception('Command %s not found' % cmd.split(' ')[0])