Merge pull request #208 from oesteban/fix/close-fds

[FIX] Close file descriptors
nipreps · Oct 31, 2017 · a1c98e4 · a1c98e4
2 parents 66c0aed + e797409
commit a1c98e4
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Showing 2 changed files with 11 additions and 7 deletions.
diff --git a/nipype b/nipype
diff --git a/niworkflows/viz/utils.py b/niworkflows/viz/utils.py
@@ -46,7 +46,8 @@ def which(cmd):
         """
 
         try:
-            subprocess.run([cmd], stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)
+            subprocess.run([cmd], stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL,
+                           close_fds=True)
         except OSError as e:
             from errno import ENOENT
             if e.errno == ENOENT:
@@ -63,7 +64,8 @@ def which(cmd):
     setattr(subprocess, 'DEVNULL', -3)
 
 if not hasattr(subprocess, 'run'):
-    def _run(args, input=None, stdout=None, stderr=None, shell=False, check=False):
+    def _run(args, input=None, stdout=None, stderr=None, shell=False, check=False,
+             close_fds=False):
         from collections import namedtuple
 
         devnull = open(os.devnull, 'r+')
@@ -75,7 +77,8 @@ def _run(args, input=None, stdout=None, stderr=None, shell=False, check=False):
         if stderr == subprocess.DEVNULL:
             stderr = devnull
 
-        proc = subprocess.Popen(args, stdout=stdout, shell=shell, stdin=stdin)
+        proc = subprocess.Popen(args, stdout=stdout, shell=shell, stdin=stdin,
+                                close_fds=close_fds)
         result = namedtuple('CompletedProcess', 'stdout stderr')
         res = result(*proc.communicate(input=input))
 
@@ -144,7 +147,7 @@ def svg_compress(image, compress='auto'):
         cmd = 'svgo -i - -o - -q -p 3 --pretty --disable=cleanupNumericValues'
         try:
             pout = subprocess.run(cmd, input=image.encode('utf-8'), stdout=subprocess.PIPE,
-                                  shell=True, check=True).stdout
+                                  shell=True, check=True, close_fds=True).stdout
         except OSError as e:
             from errno import ENOENT
             if compress is True and e.errno == ENOENT:
@@ -172,8 +175,9 @@ def svg_compress(image, compress='auto'):
                     right = '"' + '"'.join(right.split('"')[1:])
 
                     cmd = "cwebp -quiet -noalpha -q 80 -o - -- -"
-                    pout = subprocess.run(cmd, input=base64.b64decode(png_b64), shell=True,
-                                          stdout=subprocess.PIPE, check=True).stdout
+                    pout = subprocess.run(
+                        cmd, input=base64.b64decode(png_b64), shell=True,
+                        stdout=subprocess.PIPE, check=True, close_fds=True).stdout
                     webpimg = base64.b64encode(pout).decode('utf-8')
                     new_lines.append(left + webpimg + right)
                 else:
+3 −3		.travis.yml
+1 −1		doc/users/saving_workflows.rst
+1 −1		nipype/interfaces/afni/__init__.py
+33 −1		nipype/interfaces/afni/preprocess.py
+56 −0		nipype/interfaces/afni/tests/test_auto_NwarpCat.py
+5 −0		nipype/interfaces/afni/tests/test_auto_Qwarp.py
+4 −0		nipype/interfaces/afni/tests/test_auto_Warp.py
+117 −0		nipype/interfaces/afni/utils.py
+35 −5		nipype/interfaces/ants/resampling.py
+83 −0		nipype/interfaces/ants/tests/test_resampling.py
+5 −1		nipype/interfaces/base.py
+17 −29		nipype/interfaces/bids_utils.py
+15 −6		nipype/interfaces/io.py
+50 −0		nipype/interfaces/tests/test_bids.py
+1 −0		nipype/interfaces/tests/test_resource_monitor.py
+1 −1		nipype/interfaces/utility/wrappers.py
+3 −2		nipype/pipeline/engine/utils.py
+3 −2		nipype/pipeline/engine/workflows.py
+0 −0		nipype/testing/data/ds005/filler.txt
+17 −0		nipype/utils/filemanip.py
+47 −0		nipype/utils/functions.py
+1 −42		nipype/utils/misc.py
+41 −0		nipype/utils/tests/test_functions.py
+2 −23		nipype/utils/tests/test_misc.py