Merge pull request #1394 from satra/fix/proc_communicate_py2

fix: unicode characters in stderr on certain systems

Author: satra

CHANGES

@@ -1,6 +1,7 @@
 Next release
 ============
 
+* FIX: Clean up byte/unicode issues using subprocess (https://github.com/nipy/nipype/pull/1394)
 * FIX: Prevent crash when tvtk is loaded - ETS_TOOLKIT=null (https://github.com/nipy/nipype/pull/973)
 * ENH: New interfaces in dipy: RESTORE, EstimateResponseSH, CSD and StreamlineTractography
        (https://github.com/nipy/nipype/pull/1090)

nipype/interfaces/base.py

@@ -19,6 +19,7 @@
 from copy import deepcopy
 import datetime
 import errno
+import locale
 import os
 import re
 import platform
@@ -47,7 +48,7 @@
 from ..utils.provenance import write_provenance
 from .. import config, logging, LooseVersion
 from .. import __version__
-from ..external.six import string_types
+from ..external.six import string_types, text_type
 
 nipype_version = LooseVersion(__version__)
 
@@ -1205,8 +1206,8 @@ def run_command(runtime, output=None, timeout=0.01, redirect_x=False):
     if output == 'file':
         errfile = os.path.join(runtime.cwd, 'stderr.nipype')
         outfile = os.path.join(runtime.cwd, 'stdout.nipype')
-        stderr = open(errfile, 'wt')  # t=='text'===default
-        stdout = open(outfile, 'wt')
+        stderr = open(errfile, 'wb')  # t=='text'===default
+        stdout = open(outfile, 'wb')
 
         proc = subprocess.Popen(cmdline,
                                 stdout=stdout,
@@ -1256,26 +1257,17 @@ def _process(drain=0):
         result['merged'] = [r[1] for r in temp]
     if output == 'allatonce':
         stdout, stderr = proc.communicate()
-        if stdout and isinstance(stdout, bytes):
-            try:
-                stdout = stdout.decode()
-            except UnicodeDecodeError:
-                stdout = stdout.decode("ISO-8859-1")
-        if stderr and isinstance(stderr, bytes):
-            try:
-                stderr = stderr.decode()
-            except UnicodeDecodeError:
-                stderr = stderr.decode("ISO-8859-1")
-
-        result['stdout'] = str(stdout).split('\n')
-        result['stderr'] = str(stderr).split('\n')
+        stdout = stdout.decode(locale.getdefaultlocale()[1])
+        stderr = stderr.decode(locale.getdefaultlocale()[1])
+        result['stdout'] = stdout.split('\n')
+        result['stderr'] = stderr.split('\n')
         result['merged'] = ''
     if output == 'file':
         ret_code = proc.wait()
         stderr.flush()
         stdout.flush()
-        result['stdout'] = [line.strip() for line in open(outfile).readlines()]
-        result['stderr'] = [line.strip() for line in open(errfile).readlines()]
+        result['stdout'] = [line.decode(locale.getdefaultlocale()[1]).strip() for line in open(outfile, 'rb').readlines()]
+        result['stderr'] = [line.decode(locale.getdefaultlocale()[1]).strip() for line in open(errfile, 'rb').readlines()]
         result['merged'] = ''
     if output == 'none':
         proc.communicate()

nipype/interfaces/spm/tests/test_base.py

@@ -12,7 +12,7 @@
 from nipype.interfaces.spm import no_spm
 import nipype.interfaces.matlab as mlab
 from nipype.interfaces.spm.base import SPMCommandInputSpec
-from nipype.interfaces.base import traits
+from nipype.interfaces.base import traits, text_type
 
 try:
     matlab_cmd = os.environ['MATLABCMD']
@@ -57,7 +57,7 @@ def test_scan_for_fnames():
     def test_spm_path():
         spm_path = spm.Info.version()['path']
         if spm_path is not None:
-            yield assert_equal, type(spm_path), type('')
+            yield assert_equal, type(spm_path), text_type
             yield assert_true, 'spm' in spm_path
 
 

nipype/interfaces/tests/test_base.py

@@ -14,7 +14,7 @@
                             skipif)
 import nipype.interfaces.base as nib
 from nipype.utils.filemanip import split_filename
-from nipype.interfaces.base import Undefined, config
+from nipype.interfaces.base import Undefined, config, text_type
 from traits.testing.nose_tools import skip
 import traits.api as traits
 
@@ -661,7 +661,7 @@ def test_CommandLine_output():
     ci.inputs.terminal_output = 'file'
     res = ci.run()
     yield assert_true, 'stdout.nipype' in res.runtime.stdout
-    yield assert_equal, type(res.runtime.stdout), type('hi')
+    yield assert_equal, type(res.runtime.stdout), text_type
     ci = nib.CommandLine(command='ls -l')
     ci.inputs.terminal_output = 'none'
     res = ci.run()