fix: honor use_relative_paths option

Author: oesteban

nipype/pipeline/engine/nodes.py

@@ -587,7 +587,9 @@ def _load_results(self):
                     runtime=runtime,
                     inputs=self._interface.inputs.get_traitsfree(),
                     outputs=aggouts)
-                _save_resultfile(result, cwd, self.name)
+                _save_resultfile(
+                    result, cwd, self.name,
+                    rebase=str2bool(self.config['execution']['use_relative_paths']))
             else:
                 logger.debug('aggregating mapnode results')
                 result = self._run_interface()
@@ -634,7 +636,9 @@ def _run_command(self, execute, copyfiles=True):
             except Exception as msg:
                 result.runtime.stderr = '{}\n\n{}'.format(
                     getattr(result.runtime, 'stderr', ''), msg)
-                _save_resultfile(result, outdir, self.name)
+                _save_resultfile(
+                    result, outdir, self.name,
+                    rebase=str2bool(self.config['execution']['use_relative_paths']))
                 raise
             cmdfile = op.join(outdir, 'command.txt')
             with open(cmdfile, 'wt') as fd:
@@ -646,7 +650,9 @@ def _run_command(self, execute, copyfiles=True):
         except Exception as msg:
             result.runtime.stderr = '%s\n\n%s'.format(
                 getattr(result.runtime, 'stderr', ''), msg)
-            _save_resultfile(result, outdir, self.name)
+            _save_resultfile(
+                result, outdir, self.name,
+                rebase=str2bool(self.config['execution']['use_relative_paths']))
             raise
 
         dirs2keep = None
@@ -660,7 +666,9 @@ def _run_command(self, execute, copyfiles=True):
             self.needed_outputs,
             self.config,
             dirs2keep=dirs2keep)
-        _save_resultfile(result, outdir, self.name)
+        _save_resultfile(
+            result, outdir, self.name,
+            rebase=str2bool(self.config['execution']['use_relative_paths']))
 
         return result
 

nipype/pipeline/engine/utils.py

@@ -229,8 +229,11 @@ def write_report(node, report_type=None, is_mapnode=False):
     return
 
 
-def save_resultfile(result, cwd, name, rebase=True):
+def save_resultfile(result, cwd, name, rebase=None):
     """Save a result pklz file to ``cwd``."""
+    if rebase is None:
+        rebase = config.getboolean('execution', 'use_relative_paths')
+
     cwd = os.path.abspath(cwd)
     resultsfile = os.path.join(cwd, 'result_%s.pklz' % name)
     logger.debug("Saving results file: '%s'", resultsfile)