fix: ensure that commandline calls force terminal output if stdout or stderr is required

Author: satra

nipype/interfaces/afni/base.py

@@ -42,7 +42,8 @@ def version():
            Version number as string or None if AFNI not found
 
         """
-        clout = CommandLine(command='afni_vcheck').run()
+        clout = CommandLine(command='afni_vcheck',
+                            terminal_output='allatonce').run()
         out = clout.runtime.stdout
         return out.split('\n')[1]
 
@@ -87,7 +88,8 @@ def standard_image(img_name):
         '''Grab an image from the standard location.
 
         Could be made more fancy to allow for more relocatability'''
-        clout = CommandLine('which afni').run()
+        clout = CommandLine('which afni',
+                            terminal_output='allatonce').run()
         if clout.runtime.returncode is not 0:
             return None
 

nipype/interfaces/base.py

@@ -1164,7 +1164,7 @@ def __init__(self, command=None, **inputs):
         if not isdefined(self.inputs.terminal_output):
             self.inputs.terminal_output = self._terminal_output
         else:
-            self._output_update()
+            self._terminal_output_update()
 
     def _terminal_output_update(self):
         self._terminal_output = self.inputs.terminal_output

nipype/interfaces/diffusion_toolkit/base.py

@@ -42,7 +42,8 @@ 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/fsl/base.py

@@ -73,7 +73,8 @@ def version():
         except KeyError:
             return None
         clout = CommandLine(command='cat',
-                            args='%s/etc/fslversion' % (basedir)).run()
+                            args='%s/etc/fslversion' % (basedir),
+                            terminal_output='allatonce').run()
         out = clout.runtime.stdout
         return out.strip('\n')
 

nipype/interfaces/matlab.py

@@ -17,7 +17,8 @@ def get_matlab_command():
         matlab_cmd = 'matlab'
 
     try:
-        res = CommandLine(command='which', args=matlab_cmd).run()
+        res = CommandLine(command='which', args=matlab_cmd,
+                          terminal_output='allatonce').run()
         matlab_path = res.runtime.stdout.strip()
     except Exception, e:
         return None
@@ -95,6 +96,9 @@ def __init__(self, matlab_cmd = None, **inputs):
                 not isdefined(self.inputs.uses_mcr):
             if config.getboolean('execution','single_thread_matlab'):
                 self.inputs.single_comp_thread = True
+        # For matlab commands force all output to be returned since matlab
+        # does not have a clean way of notifying an error
+        self.inputs.terminal_output = 'allatonce'
 
     @classmethod
     def set_default_matlab_cmd(cls, matlab_cmd):
@@ -130,6 +134,7 @@ def set_default_paths(cls, paths):
         cls._default_paths = paths
 
     def _run_interface(self,runtime):
+        self.inputs.terminal_output = 'allatonce'
         runtime = super(MatlabCommand, self)._run_interface(runtime)
         try:
             # Matlab can leave the terminal in a barbbled state

nipype/pipeline/plugins/condor.py

@@ -45,7 +45,8 @@ def __init__(self, **kwargs):
         super(CondorPlugin, self).__init__(template, **kwargs)
 
     def _is_pending(self, taskid):
-        cmd = CommandLine('condor_q')
+        cmd = CommandLine('condor_q',
+                          terminal_output='allatonce')
         cmd.inputs.args = '%d' % taskid
         # check condor cluster
         oldlevel = iflogger.level
@@ -57,7 +58,8 @@ def _is_pending(self, taskid):
         return False
 
     def _submit_batchtask(self, scriptfile, node):
-        cmd = CommandLine('condor_qsub', environ=os.environ.data)
+        cmd = CommandLine('condor_qsub', environ=os.environ.data,
+                          terminal_output='allatonce')
         path = os.path.dirname(scriptfile)
         qsubargs = ''
         if self._qsub_args:

nipype/pipeline/plugins/dagman.py

@@ -95,7 +95,8 @@ def _submit_graph(self, pyfiles, dependencies, nodes):
                                      % (' '.join([str(i) for i in parents]),
                                         child))
         # hand over DAG to condor_dagman
-        cmd = CommandLine('condor_submit_dag', environ=os.environ.data)
+        cmd = CommandLine('condor_submit_dag', environ=os.environ.data,
+                          terminal_output='allatonce')
         # needs -update_submit or re-running a workflow will fail
         cmd.inputs.args = '-update_submit %s %s' % (dagfilename,
                                                     self._dagman_args)

nipype/pipeline/plugins/lsf.py

@@ -43,7 +43,8 @@ def _is_pending(self, taskid):
         and 'RUN' when it is actively being processed. 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')
+        cmd = CommandLine('bjobs',
+                          terminal_output='allatonce')
         cmd.inputs.args = '%d' % taskid
         # check lsf task
         oldlevel = iflogger.level
@@ -57,7 +58,8 @@ def _is_pending(self, taskid):
             return False
 
     def _submit_batchtask(self, scriptfile, node):
-        cmd = CommandLine('bsub', environ=os.environ.data)
+        cmd = CommandLine('bsub', environ=os.environ.data,
+                          terminal_output='allatonce')
         path = os.path.dirname(scriptfile)
         bsubargs = ''
         if self._bsub_args:

nipype/pipeline/plugins/pbs.py

@@ -45,7 +45,8 @@ def _is_pending(self, taskid):
         return  errmsg not in e
 
     def _submit_batchtask(self, scriptfile, node):
-        cmd = CommandLine('qsub', environ=os.environ.data)
+        cmd = CommandLine('qsub', environ=os.environ.data,
+                          terminal_output='allatonce')
         path = os.path.dirname(scriptfile)
         qsubargs = ''
         if self._qsub_args:

nipype/pipeline/plugins/pbsgraph.py

@@ -53,7 +53,8 @@ def _submit_graph(self, pyfiles, dependencies, nodes):
                 fp.writelines('job%05d=`qsub %s %s %s`\n' % (idx, deps,
                                                              qsub_args,
                                                              batchscriptfile))
-        cmd = CommandLine('sh', environ=os.environ.data)
+        cmd = CommandLine('sh', environ=os.environ.data,
+                          terminal_output='allatonce')
         cmd.inputs.args = '%s' % submitjobsfile
         cmd.run()
         logger.info('submitted all jobs to queue')