fix:plugins: os.environ.data to dict(os.environ)

Author: alexsavio

nipype/pipeline/plugins/condor.py

@@ -58,7 +58,7 @@ 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=dict(os.environ),
                           terminal_output='allatonce')
         path = os.path.dirname(scriptfile)
         qsubargs = ''
@@ -77,11 +77,11 @@ def _submit_batchtask(self, scriptfile, node):
         if '-e' not in qsubargs:
             qsubargs = '%s -e %s' % (qsubargs, path)
         if node._hierarchy:
-            jobname = '.'.join((os.environ.data['LOGNAME'],
+            jobname = '.'.join((dict(os.environ)['LOGNAME'],
                                 node._hierarchy,
                                 node._id))
         else:
-            jobname = '.'.join((os.environ.data['LOGNAME'],
+            jobname = '.'.join((dict(os.environ)['LOGNAME'],
                                 node._id))
         jobnameitems = jobname.split('.')
         jobnameitems.reverse()

nipype/pipeline/plugins/dagman.py

@@ -150,7 +150,7 @@ 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=dict(os.environ),
                           terminal_output='allatonce')
         # needs -update_submit or re-running a workflow will fail
         cmd.inputs.args = '%s -update_submit %s' % (self._dagman_args,

nipype/pipeline/plugins/lsf.py

@@ -60,7 +60,7 @@ def _is_pending(self, taskid):
             return True
 
     def _submit_batchtask(self, scriptfile, node):
-        cmd = CommandLine('bsub', environ=os.environ.data,
+        cmd = CommandLine('bsub', environ=dict(os.environ),
                           terminal_output='allatonce')
         path = os.path.dirname(scriptfile)
         bsubargs = ''
@@ -77,11 +77,11 @@ def _submit_batchtask(self, scriptfile, node):
         if '-e' not in bsubargs:
             bsubargs = '%s -e %s' % (bsubargs, scriptfile + ".log")  # -e error file
         if node._hierarchy:
-            jobname = '.'.join((os.environ.data['LOGNAME'],
+            jobname = '.'.join((dict(os.environ)['LOGNAME'],
                                 node._hierarchy,
                                 node._id))
         else:
-            jobname = '.'.join((os.environ.data['LOGNAME'],
+            jobname = '.'.join((dict(os.environ)['LOGNAME'],
                                 node._id))
         jobnameitems = jobname.split('.')
         jobnameitems.reverse()

nipype/pipeline/plugins/oar.py

@@ -63,7 +63,7 @@ def _is_pending(self, taskid):
         return is_pending
 
     def _submit_batchtask(self, scriptfile, node):
-        cmd = CommandLine('oarsub', environ=os.environ.data,
+        cmd = CommandLine('oarsub', environ=dict(os.environ),
                           terminal_output='allatonce')
         path = os.path.dirname(scriptfile)
         oarsubargs = ''
@@ -79,11 +79,11 @@ def _submit_batchtask(self, scriptfile, node):
                 oarsubargs += (" " + node.plugin_args['oarsub_args'])
 
         if node._hierarchy:
-            jobname = '.'.join((os.environ.data['LOGNAME'],
+            jobname = '.'.join((dict(os.environ)['LOGNAME'],
                                 node._hierarchy,
                                 node._id))
         else:
-            jobname = '.'.join((os.environ.data['LOGNAME'],
+            jobname = '.'.join((dict(os.environ)['LOGNAME'],
                                 node._id))
         jobnameitems = jobname.split('.')
         jobnameitems.reverse()

nipype/pipeline/plugins/pbs.py

@@ -52,7 +52,7 @@ 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=dict(os.environ),
                           terminal_output='allatonce')
         path = os.path.dirname(scriptfile)
         qsubargs = ''
@@ -69,11 +69,11 @@ def _submit_batchtask(self, scriptfile, node):
         if '-e' not in qsubargs:
             qsubargs = '%s -e %s' % (qsubargs, path)
         if node._hierarchy:
-            jobname = '.'.join((os.environ.data['LOGNAME'],
+            jobname = '.'.join((dict(os.environ)['LOGNAME'],
                                 node._hierarchy,
                                 node._id))
         else:
-            jobname = '.'.join((os.environ.data['LOGNAME'],
+            jobname = '.'.join((dict(os.environ)['LOGNAME'],
                                 node._id))
         jobnameitems = jobname.split('.')
         jobnameitems.reverse()

nipype/pipeline/plugins/pbsgraph.py

@@ -53,7 +53,7 @@ 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=dict(os.environ),
                           terminal_output='allatonce')
         cmd.inputs.args = '%s' % submitjobsfile
         cmd.run()

nipype/pipeline/plugins/sge.py

@@ -363,7 +363,7 @@ def _is_pending(self, taskid):
         return self._refQstatSubstitute.is_job_pending(int(taskid))
 
     def _submit_batchtask(self, scriptfile, node):
-        cmd = CommandLine('qsub', environ=os.environ.data,
+        cmd = CommandLine('qsub', environ=dict(os.environ),
                           terminal_output='allatonce')
         path = os.path.dirname(scriptfile)
         qsubargs = ''
@@ -380,11 +380,11 @@ def _submit_batchtask(self, scriptfile, node):
         if '-e' not in qsubargs:
             qsubargs = '%s -e %s' % (qsubargs, path)
         if node._hierarchy:
-            jobname = '.'.join((os.environ.data['LOGNAME'],
+            jobname = '.'.join((dict(os.environ)['LOGNAME'],
                                 node._hierarchy,
                                 node._id))
         else:
-            jobname = '.'.join((os.environ.data['LOGNAME'],
+            jobname = '.'.join((dict(os.environ)['LOGNAME'],
                                 node._id))
         jobnameitems = jobname.split('.')
         jobnameitems.reverse()

nipype/pipeline/plugins/sgegraph.py

@@ -144,7 +144,7 @@ def make_job_name(jobnumber, nodeslist):
                         dependantIndex=deps,
                         batchscript=batchscriptfile)
                     fp.writelines(full_line)
-        cmd = CommandLine('bash', environ=os.environ.data,
+        cmd = CommandLine('bash', environ=dict(os.environ),
                           terminal_output='allatonce')
         cmd.inputs.args = '%s' % submitjobsfile
         cmd.run()

nipype/pipeline/plugins/slurm.py

@@ -67,7 +67,7 @@ def _submit_batchtask(self, scriptfile, node):
         This is more or less the _submit_batchtask from sge.py with flipped variable
         names, different command line switches, and different output formatting/processing
         """
-        cmd = CommandLine('sbatch', environ=os.environ.data,
+        cmd = CommandLine('sbatch', environ=dict(os.environ),
                           terminal_output='allatonce')
         path = os.path.dirname(scriptfile)
 
@@ -85,11 +85,11 @@ def _submit_batchtask(self, scriptfile, node):
         if '-e' not in sbatch_args:
             sbatch_args = '%s -e %s' % (sbatch_args, os.path.join(path, 'slurm-%j.out'))
         if node._hierarchy:
-            jobname = '.'.join((os.environ.data['LOGNAME'],
+            jobname = '.'.join((dict(os.environ)['LOGNAME'],
                                 node._hierarchy,
                                 node._id))
         else:
-            jobname = '.'.join((os.environ.data['LOGNAME'],
+            jobname = '.'.join((dict(os.environ)['LOGNAME'],
                                 node._id))
         jobnameitems = jobname.split('.')
         jobnameitems.reverse()

nipype/pipeline/plugins/slurmgraph.py

@@ -143,7 +143,7 @@ def make_job_name(jobnumber, nodeslist):
                         dependantIndex=deps,
                         batchscript=batchscriptfile)
                     fp.writelines(full_line)
-        cmd = CommandLine('bash', environ=os.environ.data,
+        cmd = CommandLine('bash', environ=dict(os.environ),
                           terminal_output='allatonce')
         cmd.inputs.args = '%s' % submitjobsfile
         cmd.run()