From 156cf462c1fc80c1c185c2d15bb70d09d493eb1b Mon Sep 17 00:00:00 2001
From: Chris Filo Gorgolewski <chris.gorgolewski@gmail.com>
Date: Fri, 7 Dec 2012 14:10:39 +0100
Subject: [PATCH 1/6] Respect custom execution parameters in graph based
 models.

---
 nipype/pipeline/plugins/base.py     |  4 ++--
 nipype/pipeline/plugins/dagman.py   | 22 ++++++++++++++++++----
 nipype/pipeline/plugins/pbsgraph.py | 21 ++++++++++++++++++---
 nipype/pipeline/plugins/sgegraph.py | 21 ++++++++++++++++++---
 4 files changed, 56 insertions(+), 12 deletions(-)

diff --git a/nipype/pipeline/plugins/base.py b/nipype/pipeline/plugins/base.py
index 9e34f67295..a21730a578 100644
--- a/nipype/pipeline/plugins/base.py
+++ b/nipype/pipeline/plugins/base.py
@@ -562,9 +562,9 @@ def run(self, graph, config, updatehash=False):
                                            store_exception=False))
             dependencies[idx] = [nodes.index(prevnode) for prevnode in
                                  graph.predecessors(node)]
-        self._submit_graph(pyfiles, dependencies)
+        self._submit_graph(pyfiles, dependencies, nodes)
 
-    def _submit_graph(self, pyfiles, dependencies):
+    def _submit_graph(self, pyfiles, dependencies, nodes):
         """
         pyfiles: list of files corresponding to a topological sort
         dependencies: dictionary of dependencies based on the toplogical sort
diff --git a/nipype/pipeline/plugins/dagman.py b/nipype/pipeline/plugins/dagman.py
index d053b15963..e4e646bc50 100644
--- a/nipype/pipeline/plugins/dagman.py
+++ b/nipype/pipeline/plugins/dagman.py
@@ -49,7 +49,7 @@ def __init__(self, **kwargs):
                 self._dagman_args = plugin_args['dagman_args']
         super(CondorDAGManPlugin, self).__init__(**kwargs)
 
-    def _submit_graph(self, pyfiles, dependencies):
+    def _submit_graph(self, pyfiles, dependencies, nodes):
         # location of all scripts, place dagman output in here too
         batch_dir, _ = os.path.split(pyfiles[0])
         # DAG description filename
@@ -58,12 +58,26 @@ def _submit_graph(self, pyfiles, dependencies):
             # loop over all scripts, create submit files, and define them
             # as jobs in the DAG
             for idx, pyscript in enumerate(pyfiles):
+                node = nodes[idx]
+                template = self._template
+                submit_specs = self._submit_specs
+                if hasattr(node, "plugin_args") and isinstance(node.plugin_args, dict):
+                    if "template" in node.plugin_args:
+                        if 'overwrite' in node.plugin_args and node.plugin_args['overwrite']:
+                            template = node.plugin_args["template"]
+                        else:
+                            template += node.plugin_args["template"]
+                    if "submit_specs" in node.plugin_args:
+                        if 'overwrite' in node.plugin_args and node.plugin_args['overwrite']:
+                            submit_specs = node.plugin_args["submit_specs"]
+                        else:
+                            submit_specs += node.plugin_args['submit_specs']
                 # XXX redundant with previous value? or could it change between
-                # scripts?
+                # scripts?                            
                 batch_dir, name = os.path.split(pyscript)
                 name = '.'.join(name.split('.')[:-1])
                 submitspec = '\n'.join(
-                                (self._template,
+                                (template,
                                  'executable = %s' % sys.executable,
                                  'arguments = %s' % pyscript,
                                  'output = %s' % os.path.join(batch_dir,
@@ -73,7 +87,7 @@ def _submit_graph(self, pyfiles, dependencies):
                                  'log = %s' % os.path.join(batch_dir,
                                                            '%s.log' % name),
                                  'getenv = True',
-                                 self._submit_specs,
+                                 submit_specs,
                                  'queue'
                                  ))
                 # write submit spec for this job
diff --git a/nipype/pipeline/plugins/pbsgraph.py b/nipype/pipeline/plugins/pbsgraph.py
index c177973d91..cdd32f455d 100644
--- a/nipype/pipeline/plugins/pbsgraph.py
+++ b/nipype/pipeline/plugins/pbsgraph.py
@@ -36,15 +36,30 @@ def __init__(self, **kwargs):
                 self._qsub_args = plugin_args['qsub_args']
         super(PBSGraphPlugin, self).__init__(**kwargs)
 
-    def _submit_graph(self, pyfiles, dependencies):
+    def _submit_graph(self, pyfiles, dependencies, nodes):
         batch_dir, _ = os.path.split(pyfiles[0])
         submitjobsfile = os.path.join(batch_dir, 'submit_jobs.sh')
         with open(submitjobsfile, 'wt') as fp:
             fp.writelines('#!/usr/bin/env sh\n')
             for idx, pyscript in enumerate(pyfiles):
+                node = nodes[idx]
+                template = self._template
+                qsub_args = self._qsub_args
+                if hasattr(node, "plugin_args") and isinstance(node.plugin_args, dict):
+                    if "template" in node.plugin_args:
+                        if 'overwrite' in node.plugin_args and node.plugin_args['overwrite']:
+                            template = node.plugin_args["template"]
+                        else:
+                            template += node.plugin_args["template"]
+                    if "qsub_args" in node.plugin_args:
+                        if 'overwrite' in node.plugin_args and node.plugin_args['overwrite']:
+                            qsub_args = node.plugin_args["qsub_args"]
+                        else:
+                            qsub_args += (" " + node.plugin_args['qsub_args'])
+                
                 batch_dir, name = os.path.split(pyscript)
                 name = '.'.join(name.split('.')[:-1])
-                batchscript = '\n'.join((self._template,
+                batchscript = '\n'.join((template,
                                          '%s %s' % (sys.executable, pyscript)))
                 batchscriptfile = os.path.join(batch_dir,
                                                'batchscript_%s.sh' % name)
@@ -57,7 +72,7 @@ def _submit_graph(self, pyfiles, dependencies):
                     if len(values):
                         deps = '-W depend=afterok:%s' % ':'.join(values)
                 fp.writelines('job%05d=`qsub %s %s %s`\n' % (idx, deps,
-                                                             self._qsub_args,
+                                                             qsub_args,
                                                              batchscriptfile))
         cmd = CommandLine('sh', environ=os.environ.data)
         cmd.inputs.args = '%s' % submitjobsfile
diff --git a/nipype/pipeline/plugins/sgegraph.py b/nipype/pipeline/plugins/sgegraph.py
index 64cb49ec08..34df9c5b56 100644
--- a/nipype/pipeline/plugins/sgegraph.py
+++ b/nipype/pipeline/plugins/sgegraph.py
@@ -38,15 +38,30 @@ def __init__(self, **kwargs):
                 self._qsub_args = plugin_args['qsub_args']
         super(SGEGraphPlugin, self).__init__(**kwargs)
 
-    def _submit_graph(self, pyfiles, dependencies):
+    def _submit_graph(self, pyfiles, dependencies, nodes):
         batch_dir, _ = os.path.split(pyfiles[0])
         submitjobsfile = os.path.join(batch_dir, 'submit_jobs.sh')
         with open(submitjobsfile, 'wt') as fp:
             fp.writelines('#!/usr/bin/env bash\n')
             for idx, pyscript in enumerate(pyfiles):
+                node = nodes[idx]
+                template = self._template
+                qsub_args = self._qsub_args
+                if hasattr(node, "plugin_args") and isinstance(node.plugin_args, dict):
+                    if "template" in node.plugin_args:
+                        if 'overwrite' in node.plugin_args and node.plugin_args['overwrite']:
+                            template = node.plugin_args["template"]
+                        else:
+                            template += node.plugin_args["template"]
+                    if "qsub_args" in node.plugin_args:
+                        if 'overwrite' in node.plugin_args and node.plugin_args['overwrite']:
+                            qsub_args = node.plugin_args["qsub_args"]
+                        else:
+                            qsub_args += (" " + node.plugin_args['qsub_args'])
+                        
                 batch_dir, name = os.path.split(pyscript)
                 name = '.'.join(name.split('.')[:-1])
-                batchscript = '\n'.join((self._template,
+                batchscript = '\n'.join((template,
                                          '%s %s' % (sys.executable, pyscript)))
                 batchscriptfile = os.path.join(batch_dir,
                                                'batchscript_%s.sh' % name)
@@ -77,7 +92,7 @@ def _submit_graph(self, pyfiles, dependencies):
                              jobNm=jobname,
                              outFileOption=stdoutFile,
                              errFileOption=stderrFile,
-                             extraQSubArgs=self._qsub_args,
+                             extraQSubArgs=qsub_args,
                              dependantIndex=deps,
                              batchscript=batchscriptfile)
                 fp.writelines( full_line )

From c0195248608c5a18cfabeed20d56843c42729176 Mon Sep 17 00:00:00 2001
From: Chris Filo Gorgolewski <chris.gorgolewski@gmail.com>
Date: Fri, 7 Dec 2012 15:43:50 +0100
Subject: [PATCH 2/6] Reafactoring - less redundant code between SGE and PBS.

---
 nipype/pipeline/plugins/pbsgraph.py | 33 ++++---------------------
 nipype/pipeline/plugins/sgegraph.py | 38 ++++++++++++++++-------------
 2 files changed, 26 insertions(+), 45 deletions(-)

diff --git a/nipype/pipeline/plugins/pbsgraph.py b/nipype/pipeline/plugins/pbsgraph.py
index cdd32f455d..bbf8c5be72 100644
--- a/nipype/pipeline/plugins/pbsgraph.py
+++ b/nipype/pipeline/plugins/pbsgraph.py
@@ -7,9 +7,10 @@
 from .base import (GraphPluginBase, logger)
 
 from ...interfaces.base import CommandLine
+from .sgegraph import SGEGraphPlugin
 
 
-class PBSGraphPlugin(GraphPluginBase):
+class PBSGraphPlugin(SGEGraphPlugin):
     """Execute using PBS/Torque
 
     The plugin_args input to run can be used to control the SGE execution.
@@ -20,21 +21,9 @@ class PBSGraphPlugin(GraphPluginBase):
                   qsub call
 
     """
-
-    def __init__(self, **kwargs):
-        self._template = """
+    _template = """
 #PBS -V
-        """
-        self._qsub_args = None
-        if 'plugin_args' in kwargs:
-            plugin_args = kwargs['plugin_args']
-            if 'template' in plugin_args:
-                self._template = plugin_args['template']
-                if os.path.isfile(self._template):
-                    self._template = open(self._template).read()
-            if 'qsub_args' in plugin_args:
-                self._qsub_args = plugin_args['qsub_args']
-        super(PBSGraphPlugin, self).__init__(**kwargs)
+"""
 
     def _submit_graph(self, pyfiles, dependencies, nodes):
         batch_dir, _ = os.path.split(pyfiles[0])
@@ -43,19 +32,7 @@ def _submit_graph(self, pyfiles, dependencies, nodes):
             fp.writelines('#!/usr/bin/env sh\n')
             for idx, pyscript in enumerate(pyfiles):
                 node = nodes[idx]
-                template = self._template
-                qsub_args = self._qsub_args
-                if hasattr(node, "plugin_args") and isinstance(node.plugin_args, dict):
-                    if "template" in node.plugin_args:
-                        if 'overwrite' in node.plugin_args and node.plugin_args['overwrite']:
-                            template = node.plugin_args["template"]
-                        else:
-                            template += node.plugin_args["template"]
-                    if "qsub_args" in node.plugin_args:
-                        if 'overwrite' in node.plugin_args and node.plugin_args['overwrite']:
-                            qsub_args = node.plugin_args["qsub_args"]
-                        else:
-                            qsub_args += (" " + node.plugin_args['qsub_args'])
+                template, qsub_args = self._get_args(node)
                 
                 batch_dir, name = os.path.split(pyscript)
                 name = '.'.join(name.split('.')[:-1])
diff --git a/nipype/pipeline/plugins/sgegraph.py b/nipype/pipeline/plugins/sgegraph.py
index 34df9c5b56..889a03d42e 100644
--- a/nipype/pipeline/plugins/sgegraph.py
+++ b/nipype/pipeline/plugins/sgegraph.py
@@ -20,13 +20,12 @@ class SGEGraphPlugin(GraphPluginBase):
                   qsub call
 
     """
-
-    def __init__(self, **kwargs):
-        self._template = """
+    _template = """
 #!/bin/bash
 #$ -V
 #$ -S /bin/bash
-        """
+"""
+    def __init__(self, **kwargs):
         self._qsub_args = ''
         if 'plugin_args' in kwargs:
             plugin_args = kwargs['plugin_args']
@@ -38,6 +37,23 @@ def __init__(self, **kwargs):
                 self._qsub_args = plugin_args['qsub_args']
         super(SGEGraphPlugin, self).__init__(**kwargs)
 
+
+    def _get_args(self, node):
+        template = self._template
+        qsub_args = self._qsub_args
+        if hasattr(node, "plugin_args") and isinstance(node.plugin_args, dict):
+            if "template" in node.plugin_args:
+                if 'overwrite' in node.plugin_args and node.plugin_args['overwrite']:
+                    template = node.plugin_args["template"]
+                else:
+                    template += node.plugin_args["template"]
+            if "qsub_args" in node.plugin_args:
+                if 'overwrite' in node.plugin_args and node.plugin_args['overwrite']:
+                    qsub_args = node.plugin_args["qsub_args"]
+                else:
+                    qsub_args += " " + node.plugin_args['qsub_args']
+        return template, qsub_args
+
     def _submit_graph(self, pyfiles, dependencies, nodes):
         batch_dir, _ = os.path.split(pyfiles[0])
         submitjobsfile = os.path.join(batch_dir, 'submit_jobs.sh')
@@ -45,19 +61,7 @@ def _submit_graph(self, pyfiles, dependencies, nodes):
             fp.writelines('#!/usr/bin/env bash\n')
             for idx, pyscript in enumerate(pyfiles):
                 node = nodes[idx]
-                template = self._template
-                qsub_args = self._qsub_args
-                if hasattr(node, "plugin_args") and isinstance(node.plugin_args, dict):
-                    if "template" in node.plugin_args:
-                        if 'overwrite' in node.plugin_args and node.plugin_args['overwrite']:
-                            template = node.plugin_args["template"]
-                        else:
-                            template += node.plugin_args["template"]
-                    if "qsub_args" in node.plugin_args:
-                        if 'overwrite' in node.plugin_args and node.plugin_args['overwrite']:
-                            qsub_args = node.plugin_args["qsub_args"]
-                        else:
-                            qsub_args += (" " + node.plugin_args['qsub_args'])
+                template, qsub_args = self._get_args(node)
                         
                 batch_dir, name = os.path.split(pyscript)
                 name = '.'.join(name.split('.')[:-1])

From 546665cec19e1b3f355d0a0f05b3c651db942ef7 Mon Sep 17 00:00:00 2001
From: Chris Filo Gorgolewski <chris.gorgolewski@gmail.com>
Date: Fri, 7 Dec 2012 16:10:59 +0100
Subject: [PATCH 3/6] Further refactoring

---
 nipype/pipeline/plugins/base.py     | 13 +++++++++++++
 nipype/pipeline/plugins/dagman.py   | 14 +-------------
 nipype/pipeline/plugins/pbsgraph.py |  2 +-
 nipype/pipeline/plugins/sgegraph.py | 19 +------------------
 4 files changed, 16 insertions(+), 32 deletions(-)

diff --git a/nipype/pipeline/plugins/base.py b/nipype/pipeline/plugins/base.py
index a21730a578..99a2c4296c 100644
--- a/nipype/pipeline/plugins/base.py
+++ b/nipype/pipeline/plugins/base.py
@@ -563,6 +563,19 @@ def run(self, graph, config, updatehash=False):
             dependencies[idx] = [nodes.index(prevnode) for prevnode in
                                  graph.predecessors(node)]
         self._submit_graph(pyfiles, dependencies, nodes)
+        
+    def _get_args(self, node, keywords):
+        values = ()
+        for keyword in keywords:
+            value = getattr(self, "_" + keyword)
+            if hasattr(node, "plugin_args") and isinstance(node.plugin_args, dict) and keyword in node.plugin_args:
+                    if 'overwrite' in node.plugin_args and node.plugin_args['overwrite']:
+                        value = node.plugin_args[keyword] 
+                    else:
+                        value += node.plugin_args[keyword]
+            else:
+                values += (value, )
+        return values
 
     def _submit_graph(self, pyfiles, dependencies, nodes):
         """
diff --git a/nipype/pipeline/plugins/dagman.py b/nipype/pipeline/plugins/dagman.py
index e4e646bc50..b72f1c1b4d 100644
--- a/nipype/pipeline/plugins/dagman.py
+++ b/nipype/pipeline/plugins/dagman.py
@@ -59,19 +59,7 @@ def _submit_graph(self, pyfiles, dependencies, nodes):
             # as jobs in the DAG
             for idx, pyscript in enumerate(pyfiles):
                 node = nodes[idx]
-                template = self._template
-                submit_specs = self._submit_specs
-                if hasattr(node, "plugin_args") and isinstance(node.plugin_args, dict):
-                    if "template" in node.plugin_args:
-                        if 'overwrite' in node.plugin_args and node.plugin_args['overwrite']:
-                            template = node.plugin_args["template"]
-                        else:
-                            template += node.plugin_args["template"]
-                    if "submit_specs" in node.plugin_args:
-                        if 'overwrite' in node.plugin_args and node.plugin_args['overwrite']:
-                            submit_specs = node.plugin_args["submit_specs"]
-                        else:
-                            submit_specs += node.plugin_args['submit_specs']
+                template, submit_specs = self._get_args(node, ["template", "submit_specs"])
                 # XXX redundant with previous value? or could it change between
                 # scripts?                            
                 batch_dir, name = os.path.split(pyscript)
diff --git a/nipype/pipeline/plugins/pbsgraph.py b/nipype/pipeline/plugins/pbsgraph.py
index bbf8c5be72..495ce651fb 100644
--- a/nipype/pipeline/plugins/pbsgraph.py
+++ b/nipype/pipeline/plugins/pbsgraph.py
@@ -32,7 +32,7 @@ def _submit_graph(self, pyfiles, dependencies, nodes):
             fp.writelines('#!/usr/bin/env sh\n')
             for idx, pyscript in enumerate(pyfiles):
                 node = nodes[idx]
-                template, qsub_args = self._get_args(node)
+                template, qsub_args = self._get_args(node, ["template", "qsub_args"])
                 
                 batch_dir, name = os.path.split(pyscript)
                 name = '.'.join(name.split('.')[:-1])
diff --git a/nipype/pipeline/plugins/sgegraph.py b/nipype/pipeline/plugins/sgegraph.py
index 889a03d42e..6a547ed923 100644
--- a/nipype/pipeline/plugins/sgegraph.py
+++ b/nipype/pipeline/plugins/sgegraph.py
@@ -37,23 +37,6 @@ def __init__(self, **kwargs):
                 self._qsub_args = plugin_args['qsub_args']
         super(SGEGraphPlugin, self).__init__(**kwargs)
 
-
-    def _get_args(self, node):
-        template = self._template
-        qsub_args = self._qsub_args
-        if hasattr(node, "plugin_args") and isinstance(node.plugin_args, dict):
-            if "template" in node.plugin_args:
-                if 'overwrite' in node.plugin_args and node.plugin_args['overwrite']:
-                    template = node.plugin_args["template"]
-                else:
-                    template += node.plugin_args["template"]
-            if "qsub_args" in node.plugin_args:
-                if 'overwrite' in node.plugin_args and node.plugin_args['overwrite']:
-                    qsub_args = node.plugin_args["qsub_args"]
-                else:
-                    qsub_args += " " + node.plugin_args['qsub_args']
-        return template, qsub_args
-
     def _submit_graph(self, pyfiles, dependencies, nodes):
         batch_dir, _ = os.path.split(pyfiles[0])
         submitjobsfile = os.path.join(batch_dir, 'submit_jobs.sh')
@@ -61,7 +44,7 @@ def _submit_graph(self, pyfiles, dependencies, nodes):
             fp.writelines('#!/usr/bin/env bash\n')
             for idx, pyscript in enumerate(pyfiles):
                 node = nodes[idx]
-                template, qsub_args = self._get_args(node)
+                template, qsub_args = self._get_args(node, ["template", "qsub_args"])
                         
                 batch_dir, name = os.path.split(pyscript)
                 name = '.'.join(name.split('.')[:-1])

From ca8d229126e96f998b6b1b1db63b5fa304eff14b Mon Sep 17 00:00:00 2001
From: Chris Filo Gorgolewski <chris.gorgolewski@gmail.com>
Date: Fri, 7 Dec 2012 16:12:16 +0100
Subject: [PATCH 4/6] PEP8

---
 nipype/pipeline/plugins/base.py     | 32 ++++++++++++++-------------
 nipype/pipeline/plugins/dagman.py   | 34 ++++++++++++++---------------
 nipype/pipeline/plugins/pbsgraph.py |  9 ++++----
 nipype/pipeline/plugins/sgegraph.py | 28 ++++++++++++++----------
 4 files changed, 55 insertions(+), 48 deletions(-)

diff --git a/nipype/pipeline/plugins/base.py b/nipype/pipeline/plugins/base.py
index 99a2c4296c..ce099b994d 100644
--- a/nipype/pipeline/plugins/base.py
+++ b/nipype/pipeline/plugins/base.py
@@ -218,7 +218,7 @@ def run(self, graph, config, updatehash=False):
         # setup polling - TODO: change to threaded model
         notrun = []
         while np.any(self.proc_done == False) | \
-              np.any(self.proc_pending == True):
+                    np.any(self.proc_pending == True):
             toappend = []
             # trigger callbacks for any pending results
             while self.pending_tasks:
@@ -297,11 +297,12 @@ def _submit_mapnode(self, jobid):
         self.procs.extend(mapnodesubids)
         self.depidx = ssp.vstack((self.depidx,
                                   ssp.lil_matrix(np.zeros((numnodes,
-                                                    self.depidx.shape[1])))),
+                                                           self.depidx.shape[1])))),
                                  'lil')
         self.depidx = ssp.hstack((self.depidx,
-                                  ssp.lil_matrix(np.zeros((self.depidx.shape[0],
-                                                           numnodes)))),
+                                  ssp.lil_matrix(
+                                      np.zeros((self.depidx.shape[0],
+                                                numnodes)))),
                                  'lil')
         self.depidx[-numnodes:, jobid] = 1
         self.proc_done = np.concatenate((self.proc_done,
@@ -315,7 +316,7 @@ def _send_procs_to_workers(self, updatehash=False, slots=None, graph=None):
         """
         while np.any(self.proc_done == False):
             # Check to see if a job is available
-            jobids = np.flatnonzero((self.proc_done == False) & \
+            jobids = np.flatnonzero((self.proc_done == False) &
                                     (self.depidx.sum(axis=0) == 0).__array__())
             if len(jobids) > 0:
                 # send all available jobs
@@ -336,20 +337,21 @@ def _send_procs_to_workers(self, updatehash=False, slots=None, 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' % \
-                                    (self.procs[jobid]._id, jobid))
+                    logger.info('Executing: %s ID: %d' %
+                               (self.procs[jobid]._id, jobid))
                     if self._status_callback:
                         self._status_callback(self.procs[jobid], 'start')
                     continue_with_submission = True
                     if str2bool(self.procs[jobid].config['execution']['local_hash_check']):
                         logger.debug('checking hash locally')
                         try:
-                            hash_exists, _, _, _ = self.procs[jobid].hash_exists()
+                            hash_exists, _, _, _ = self.procs[
+                                jobid].hash_exists()
                             logger.debug('Hash exists %s' % str(hash_exists))
                             if (hash_exists and
-                            (self.procs[jobid].overwrite == False or
-                             (self.procs[jobid].overwrite == None and
-                              not self.procs[jobid]._interface.always_run))):
+                               (self.procs[jobid].overwrite == False or
+                               (self.procs[jobid].overwrite == None and
+                                    not self.procs[jobid]._interface.always_run))):
                                 continue_with_submission = False
                                 self._task_finished_cb(jobid)
                                 self._remove_node_dirs()
@@ -385,7 +387,7 @@ def _task_finished_cb(self, jobid):
 
         This is called when a job is completed.
         """
-        logger.info('[Job finished] jobname: %s jobid: %d' % \
+        logger.info('[Job finished] jobname: %s jobid: %d' %
                     (self.procs[jobid]._id, jobid))
         if self._status_callback:
             self._status_callback(self.procs[jobid], 'end')
@@ -431,7 +433,7 @@ def _remove_node_dirs(self):
                     self.refidx[idx, idx] = -1
                     outdir = self.procs[idx]._output_directory()
                     logger.info(('[node dependencies finished] '
-                                 'removing node: %s from directory %s') % \
+                                 'removing node: %s from directory %s') %
                                 (self.procs[idx]._id, outdir))
                     shutil.rmtree(outdir)
 
@@ -563,14 +565,14 @@ def run(self, graph, config, updatehash=False):
             dependencies[idx] = [nodes.index(prevnode) for prevnode in
                                  graph.predecessors(node)]
         self._submit_graph(pyfiles, dependencies, nodes)
-        
+
     def _get_args(self, node, keywords):
         values = ()
         for keyword in keywords:
             value = getattr(self, "_" + keyword)
             if hasattr(node, "plugin_args") and isinstance(node.plugin_args, dict) and keyword in node.plugin_args:
                     if 'overwrite' in node.plugin_args and node.plugin_args['overwrite']:
-                        value = node.plugin_args[keyword] 
+                        value = node.plugin_args[keyword]
                     else:
                         value += node.plugin_args[keyword]
             else:
diff --git a/nipype/pipeline/plugins/dagman.py b/nipype/pipeline/plugins/dagman.py
index b72f1c1b4d..0ee20acf4c 100644
--- a/nipype/pipeline/plugins/dagman.py
+++ b/nipype/pipeline/plugins/dagman.py
@@ -59,28 +59,29 @@ def _submit_graph(self, pyfiles, dependencies, nodes):
             # as jobs in the DAG
             for idx, pyscript in enumerate(pyfiles):
                 node = nodes[idx]
-                template, submit_specs = self._get_args(node, ["template", "submit_specs"])
+                template, submit_specs = self._get_args(
+                    node, ["template", "submit_specs"])
                 # XXX redundant with previous value? or could it change between
-                # scripts?                            
+                # scripts?
                 batch_dir, name = os.path.split(pyscript)
                 name = '.'.join(name.split('.')[:-1])
                 submitspec = '\n'.join(
-                                (template,
-                                 'executable = %s' % sys.executable,
-                                 'arguments = %s' % pyscript,
-                                 'output = %s' % os.path.join(batch_dir,
-                                                             '%s.out' % name),
-                                 'error = %s' % os.path.join(batch_dir,
-                                                             '%s.err' % name),
-                                 'log = %s' % os.path.join(batch_dir,
-                                                           '%s.log' % name),
-                                 'getenv = True',
-                                 submit_specs,
-                                 'queue'
-                                 ))
+                    (template,
+                     'executable = %s' % sys.executable,
+                     'arguments = %s' % pyscript,
+                     'output = %s' % os.path.join(batch_dir,
+                                                  '%s.out' % name),
+                     'error = %s' % os.path.join(batch_dir,
+                                                 '%s.err' % name),
+                     'log = %s' % os.path.join(batch_dir,
+                                               '%s.log' % name),
+                     'getenv = True',
+                     submit_specs,
+                     'queue'
+                     ))
                 # write submit spec for this job
                 submitfile = os.path.join(batch_dir,
-                                               '%s.submit' % name)
+                                          '%s.submit' % name)
                 with open(submitfile, 'wt') as submitfileprt:
                     submitfileprt.writelines(submitspec)
                     submitfileprt.close()
@@ -100,4 +101,3 @@ def _submit_graph(self, pyfiles, dependencies, nodes):
                                                     self._dagman_args)
         cmd.run()
         logger.info('submitted all jobs to Condor DAGMan')
-
diff --git a/nipype/pipeline/plugins/pbsgraph.py b/nipype/pipeline/plugins/pbsgraph.py
index 495ce651fb..710f93a8a1 100644
--- a/nipype/pipeline/plugins/pbsgraph.py
+++ b/nipype/pipeline/plugins/pbsgraph.py
@@ -32,8 +32,9 @@ def _submit_graph(self, pyfiles, dependencies, nodes):
             fp.writelines('#!/usr/bin/env sh\n')
             for idx, pyscript in enumerate(pyfiles):
                 node = nodes[idx]
-                template, qsub_args = self._get_args(node, ["template", "qsub_args"])
-                
+                template, qsub_args = self._get_args(
+                    node, ["template", "qsub_args"])
+
                 batch_dir, name = os.path.split(pyscript)
                 name = '.'.join(name.split('.')[:-1])
                 batchscript = '\n'.join((template,
@@ -45,7 +46,8 @@ def _submit_graph(self, pyfiles, dependencies, nodes):
                     batchfp.close()
                 deps = ''
                 if idx in dependencies:
-                    values = ['$job%05d' % jobid for jobid in dependencies[idx]]
+                    values = ['$job%05d' %
+                              jobid for jobid in dependencies[idx]]
                     if len(values):
                         deps = '-W depend=afterok:%s' % ':'.join(values)
                 fp.writelines('job%05d=`qsub %s %s %s`\n' % (idx, deps,
@@ -55,4 +57,3 @@ def _submit_graph(self, pyfiles, dependencies, nodes):
         cmd.inputs.args = '%s' % submitjobsfile
         cmd.run()
         logger.info('submitted all jobs to queue')
-
diff --git a/nipype/pipeline/plugins/sgegraph.py b/nipype/pipeline/plugins/sgegraph.py
index 6a547ed923..11ac4e4477 100644
--- a/nipype/pipeline/plugins/sgegraph.py
+++ b/nipype/pipeline/plugins/sgegraph.py
@@ -25,6 +25,7 @@ class SGEGraphPlugin(GraphPluginBase):
 #$ -V
 #$ -S /bin/bash
 """
+
     def __init__(self, **kwargs):
         self._qsub_args = ''
         if 'plugin_args' in kwargs:
@@ -44,8 +45,9 @@ def _submit_graph(self, pyfiles, dependencies, nodes):
             fp.writelines('#!/usr/bin/env bash\n')
             for idx, pyscript in enumerate(pyfiles):
                 node = nodes[idx]
-                template, qsub_args = self._get_args(node, ["template", "qsub_args"])
-                        
+                template, qsub_args = self._get_args(
+                    node, ["template", "qsub_args"])
+
                 batch_dir, name = os.path.split(pyscript)
                 name = '.'.join(name.split('.')[:-1])
                 batchscript = '\n'.join((template,
@@ -67,22 +69,24 @@ def _submit_graph(self, pyfiles, dependencies, nodes):
                     if 'job' in values:
                         values = values.rstrip(',')
                         deps = '-hold_jid%s' % values
-                jobname = 'job%05d' % ( idx )
+                jobname = 'job%05d' % (idx)
                 ## Do not use default output locations if they are set in self._qsub_args
                 stderrFile = ''
                 if self._qsub_args.count('-e ') == 0:
-                        stderrFile='-e {errFile}'.format(errFile=batchscripterrfile)
+                        stderrFile = '-e {errFile}'.format(
+                            errFile=batchscripterrfile)
                 stdoutFile = ''
                 if self._qsub_args.count('-o ') == 0:
-                        stdoutFile='-o {outFile}'.format(outFile=batchscriptoutfile)
+                        stdoutFile = '-o {outFile}'.format(
+                            outFile=batchscriptoutfile)
                 full_line = '{jobNm}=$(qsub {outFileOption} {errFileOption} {extraQSubArgs} {dependantIndex} -N {jobNm} {batchscript})\n'.format(
-                             jobNm=jobname,
-                             outFileOption=stdoutFile,
-                             errFileOption=stderrFile,
-                             extraQSubArgs=qsub_args,
-                             dependantIndex=deps,
-                             batchscript=batchscriptfile)
-                fp.writelines( full_line )
+                    jobNm=jobname,
+                    outFileOption=stdoutFile,
+                    errFileOption=stderrFile,
+                    extraQSubArgs=qsub_args,
+                    dependantIndex=deps,
+                    batchscript=batchscriptfile)
+                fp.writelines(full_line)
 
         cmd = CommandLine('bash', environ=os.environ.data)
         cmd.inputs.args = '%s' % submitjobsfile

From 5c3bc19393cd85844b3b131959a06dc49abcff71 Mon Sep 17 00:00:00 2001
From: Chris Filo Gorgolewski <chris.gorgolewski@gmail.com>
Date: Fri, 7 Dec 2012 16:12:40 +0100
Subject: [PATCH 5/6] API fix for somaworkflow

---
 nipype/pipeline/plugins/somaflow.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nipype/pipeline/plugins/somaflow.py b/nipype/pipeline/plugins/somaflow.py
index b9847e4910..b54262d4aa 100644
--- a/nipype/pipeline/plugins/somaflow.py
+++ b/nipype/pipeline/plugins/somaflow.py
@@ -23,7 +23,7 @@ def __init__(self, plugin_args=None):
             raise ImportError('SomaFlow could not be imported')
         super(SomaFlowPlugin, self).__init__(plugin_args=plugin_args)
 
-    def _submit_graph(self, pyfiles, dependencies):
+    def _submit_graph(self, pyfiles, dependencies, nodes):
         jobs = []
         soma_deps = []
         for idx, fname in enumerate(pyfiles):

From b67b1dde9fa6414dfdcb0ac54d6554a48d6036bd Mon Sep 17 00:00:00 2001
From: Chris Filo Gorgolewski <chris.gorgolewski@gmail.com>
Date: Fri, 7 Dec 2012 16:32:06 +0100
Subject: [PATCH 6/6] add support for template files

---
 nipype/pipeline/plugins/base.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/nipype/pipeline/plugins/base.py b/nipype/pipeline/plugins/base.py
index ce099b994d..ff9f428c35 100644
--- a/nipype/pipeline/plugins/base.py
+++ b/nipype/pipeline/plugins/base.py
@@ -570,11 +570,15 @@ def _get_args(self, node, keywords):
         values = ()
         for keyword in keywords:
             value = getattr(self, "_" + keyword)
+            if keyword == "template" and os.path.isfile(value):
+                value = open(value).read()
             if hasattr(node, "plugin_args") and isinstance(node.plugin_args, dict) and keyword in node.plugin_args:
+                    if keyword == "template" and os.path.isfile(node.plugin_args[keyword]):
+                        tmp_value = open(node.plugin_args[keyword]).read()
                     if 'overwrite' in node.plugin_args and node.plugin_args['overwrite']:
-                        value = node.plugin_args[keyword]
+                        value = tmp_value
                     else:
-                        value += node.plugin_args[keyword]
+                        value += tmp_value
             else:
                 values += (value, )
         return values