From 5c10c92f27734582d41b49bc571266015596f77c Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Fri, 30 Mar 2018 14:32:00 -0400
Subject: [PATCH 1/2] FIX: Build cmdline from working directory

---
 nipype/pipeline/engine/nodes.py      |  5 +++--
 nipype/utils/filemanip.py            |  9 +++++++++
 nipype/utils/tests/test_filemanip.py | 27 ++++++++++++++++++++++++++-
 3 files changed, 38 insertions(+), 3 deletions(-)

diff --git a/nipype/pipeline/engine/nodes.py b/nipype/pipeline/engine/nodes.py
index eb0562ae0e..2d7ea1fbd2 100644
--- a/nipype/pipeline/engine/nodes.py
+++ b/nipype/pipeline/engine/nodes.py
@@ -27,7 +27,7 @@
 from ...utils.filemanip import (md5, FileNotFoundError, filename_to_list,
                                 list_to_filename, copyfiles, fnames_presuffix,
                                 loadpkl, split_filename, load_json, makedirs,
-                                emptydirs, savepkl, to_str)
+                                emptydirs, savepkl, to_str, indirectory)
 
 from ...interfaces.base import (traits, InputMultiPath, CommandLine, Undefined,
                                 DynamicTraitedSpec, Bunch, InterfaceResult,
@@ -627,7 +627,8 @@ def _run_command(self, execute, copyfiles=True):
             self._interface.__class__.__name__)
         if issubclass(self._interface.__class__, CommandLine):
             try:
-                cmd = self._interface.cmdline
+                with indirectory(outdir):
+                    cmd = self._interface.cmdline
             except Exception as msg:
                 result.runtime.stderr = '{}\n\n{}'.format(
                     getattr(result.runtime, 'stderr', ''), msg)
diff --git a/nipype/utils/filemanip.py b/nipype/utils/filemanip.py
index b13e11ae1c..f740a0c3af 100644
--- a/nipype/utils/filemanip.py
+++ b/nipype/utils/filemanip.py
@@ -18,6 +18,7 @@
 import os.path as op
 import re
 import shutil
+import contextlib
 import posixpath
 import simplejson as json
 import numpy as np
@@ -916,3 +917,11 @@ def relpath(path, start=None):
     if not rel_list:
         return os.curdir
     return op.join(*rel_list)
+
+
+@contextlib.contextmanager
+def indirectory(path):
+    cwd = os.getcwd()
+    os.chdir(path)
+    yield
+    os.chdir(cwd)
diff --git a/nipype/utils/tests/test_filemanip.py b/nipype/utils/tests/test_filemanip.py
index b215b15312..4be3124016 100644
--- a/nipype/utils/tests/test_filemanip.py
+++ b/nipype/utils/tests/test_filemanip.py
@@ -14,7 +14,7 @@
     save_json, load_json, fname_presuffix, fnames_presuffix, hash_rename,
     check_forhash, _parse_mount_table, _cifs_table, on_cifs, copyfile,
     copyfiles, filename_to_list, list_to_filename, check_depends,
-    split_filename, get_related_files)
+    split_filename, get_related_files, indirectory)
 
 
 def _ignore_atime(stat):
@@ -490,3 +490,28 @@ def test_cifs_check():
 
     _cifs_table[:] = []
     _cifs_table.extend(orig_table)
+
+
+def test_indirectory(tmpdir):
+    tmpdir.chdir()
+
+    os.makedirs('subdir1/subdir2')
+    sd1 = os.path.abspath('subdir1')
+    sd2 = os.path.abspath('subdir1/subdir2')
+
+    assert os.getcwd() == tmpdir.strpath
+    with indirectory('/'):
+        assert os.getcwd() == '/'
+    assert os.getcwd() == tmpdir.strpath
+    with indirectory('subdir1'):
+        assert os.getcwd() == sd1
+        with indirectory('subdir2'):
+            assert os.getcwd() == sd2
+            with indirectory('..'):
+                assert os.getcwd() == sd1
+                with indirectory('/'):
+                    assert os.getcwd() == '/'
+                assert os.getcwd() == sd1
+            assert os.getcwd() == sd2
+        assert os.getcwd() == sd1
+    assert os.getcwd() == tmpdir.strpath

From 555a905f623be290a16c5fede1ea3a1558ac1f57 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Fri, 30 Mar 2018 15:59:15 -0400
Subject: [PATCH 2/2] FIX: Revert directory when exception raised

---
 nipype/utils/filemanip.py            | 6 ++++--
 nipype/utils/tests/test_filemanip.py | 6 ++++++
 2 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/nipype/utils/filemanip.py b/nipype/utils/filemanip.py
index f740a0c3af..c257476218 100644
--- a/nipype/utils/filemanip.py
+++ b/nipype/utils/filemanip.py
@@ -923,5 +923,7 @@ def relpath(path, start=None):
 def indirectory(path):
     cwd = os.getcwd()
     os.chdir(path)
-    yield
-    os.chdir(cwd)
+    try:
+        yield
+    finally:
+        os.chdir(cwd)
diff --git a/nipype/utils/tests/test_filemanip.py b/nipype/utils/tests/test_filemanip.py
index 4be3124016..fdb4289b36 100644
--- a/nipype/utils/tests/test_filemanip.py
+++ b/nipype/utils/tests/test_filemanip.py
@@ -515,3 +515,9 @@ def test_indirectory(tmpdir):
             assert os.getcwd() == sd2
         assert os.getcwd() == sd1
     assert os.getcwd() == tmpdir.strpath
+    try:
+        with indirectory('subdir1'):
+            raise ValueError("Erroring out of context")
+    except ValueError:
+        pass
+    assert os.getcwd() == tmpdir.strpath