Use default mask in os.makedirs() (#1081) (#1082)

* Amends `os.makedirs()` calls to use the default mask value (`0o777`) so that
  temporary directories and files created by `cwltool` would better respect the
  umask settings from the original environment. For example, the parent
  environment might use umask 002 to make sure that all directories and files
  are created with group-write permissions.

Signed-off-by: Tibor Simko <tibor.simko@cern.ch>

Author: tiborsimko

cwltool/docker.py

@@ -259,7 +259,7 @@ def add_writable_directory_volume(self,
                 self.append_volume(runtime, new_dir, volume.target,
                                    writable=True)
             elif not os.path.exists(host_outdir_tgt):
-                os.makedirs(host_outdir_tgt, 0o0755)
+                os.makedirs(host_outdir_tgt)
         else:
             if self.inplace_update:
                 self.append_volume(runtime, volume.resolved, volume.target,

cwltool/job.py

@@ -533,7 +533,7 @@ def create_file_and_add_volume(self,
             contents = volume.resolved
         dirname = os.path.dirname(host_outdir_tgt or new_file)
         if not os.path.exists(dirname):
-            os.makedirs(dirname, 0o0755)
+            os.makedirs(dirname)
         with open(host_outdir_tgt or new_file, "wb") as file_literal:
             file_literal.write(contents.encode("utf-8"))
         if not host_outdir_tgt:

cwltool/process.py

@@ -225,7 +225,7 @@ def stage_files(pathmapper,             # type: PathMapper
         if not entry.staged:
             continue
         if not os.path.exists(os.path.dirname(entry.target)):
-            os.makedirs(os.path.dirname(entry.target), 0o0755)
+            os.makedirs(os.path.dirname(entry.target))
         if entry.type in ("File", "Directory") and os.path.exists(entry.resolved):
             if symlink:  # Use symlink func if allowed
                 if onWindows():
@@ -242,13 +242,13 @@ def stage_files(pathmapper,             # type: PathMapper
                 stage_func(entry.resolved, entry.target)
         elif entry.type == "Directory" and not os.path.exists(entry.target) \
                 and entry.resolved.startswith("_:"):
-            os.makedirs(entry.target, 0o0755)
+            os.makedirs(entry.target)
         elif entry.type == "WritableFile" and not ignore_writable:
             shutil.copy(entry.resolved, entry.target)
             ensure_writable(entry.target)
         elif entry.type == "WritableDirectory" and not ignore_writable:
             if entry.resolved.startswith("_:"):
-                os.makedirs(entry.target, 0o0755)
+                os.makedirs(entry.target)
             else:
                 shutil.copytree(entry.resolved, entry.target)
                 ensure_writable(entry.target)

cwltool/singularity.py

@@ -226,7 +226,7 @@ def add_writable_directory_volume(self,
                 new_dir = os.path.join(
                     tempfile.mkdtemp(prefix=tmp_prefix, dir=tmp_dir),
                     os.path.basename(volume.resolved))
-            os.makedirs(new_dir, 0o0755)
+            os.makedirs(new_dir)
         else:
             if host_outdir_tgt is not None:
                 # workaround for lack of overlapping mounts in Singularity

tests/test_examples.py

@@ -1,6 +1,7 @@
 import json
 import logging
 import os
+import stat
 import sys
 from io import BytesIO, StringIO
 import pytest
@@ -792,10 +793,15 @@ class TestSecondaryFiles():
     def test_secondary_files(self):
         test_file = "secondary-files.cwl"
         test_job_file = "secondary-files-job.yml"
-        error_code, _, stderr = get_main_output(
-            ["--enable-dev",
-             get_data(os.path.join("tests", test_file)),
-             get_data(os.path.join("tests", test_job_file))])
+        try:
+            old_umask = os.umask(stat.S_IWOTH)  # test run with umask 002
+            error_code, _, stderr = get_main_output(
+                ["--enable-dev",
+                get_data(os.path.join("tests", test_file)),
+                get_data(os.path.join("tests", test_job_file))])
+        finally:
+            assert stat.S_IMODE(os.stat('lsout').st_mode) == 436  # 664 in octal, '-rw-rw-r--'
+            os.umask(old_umask)  # revert back to original umask
         assert "completed success" in stderr
         assert error_code == 0