From 82ec7c7d093bb834d448c1c447e0dd3762bac94b Mon Sep 17 00:00:00 2001
From: Jon Clucas <jon.clucas@childmind.org>
Date: Tue, 12 Apr 2022 15:20:39 -0400
Subject: [PATCH] :bug: Fix makedirs permission issue

---
 .gitignore                          | 4 +++-
 src/cpac/backends/platform.py       | 2 +-
 src/cpac/helpers/__init__.py        | 5 +----
 src/cpac/helpers/cpac_read_crash.py | 1 -
 src/cpac/utils/utils.py             | 2 ++
 tests/CONSTANTS.py                  | 2 +-
 tests/test_cpac_run.py              | 1 -
 tests/test_cpac_utils.py            | 1 -
 8 files changed, 8 insertions(+), 10 deletions(-)

diff --git a/.gitignore b/.gitignore
index b457ca9f..5a226a96 100644
--- a/.gitignore
+++ b/.gitignore
@@ -12,6 +12,7 @@ __pycache__/*
 .cache/*
 .*.swp
 */.ipynb_checkpoints/*
+tmp
 
 # Project files
 .ropeproject
@@ -49,4 +50,5 @@ MANIFEST
 .venv*/
 
 # Singularity Images
-**/*.simg
\ No newline at end of file
+**/*.simg
+**/*.sif
\ No newline at end of file
diff --git a/src/cpac/backends/platform.py b/src/cpac/backends/platform.py
index 6458099c..a612effc 100644
--- a/src/cpac/backends/platform.py
+++ b/src/cpac/backends/platform.py
@@ -331,7 +331,7 @@ def _prep_binding(self, volume: Volume,
         )
         if not os.path.exists(volume.local):
             try:
-                os.makedirs(volume.local, mode=777)
+                os.makedirs(volume.local, exist_ok=True)
             except PermissionError as perm:
                 if second_try:
                     raise perm
diff --git a/src/cpac/helpers/__init__.py b/src/cpac/helpers/__init__.py
index 3a7f16ef..dce15153 100644
--- a/src/cpac/helpers/__init__.py
+++ b/src/cpac/helpers/__init__.py
@@ -10,10 +10,7 @@
                                   'persists, run\n    '
                                   r'2. `docker attach <container_name>`'
                                   '\n    '
-                                  r'3. `exit`',
-         'permission_denied': 'Pytest is getting "permission denied" errors '
-                              'writing to tmp directories, but running '
-                              'outside of Pytest is working locally'}
+                                  r'3. `exit`'}
 
 
 def get_extra_arg_value(extra_args, argument):
diff --git a/src/cpac/helpers/cpac_read_crash.py b/src/cpac/helpers/cpac_read_crash.py
index 480f9090..000fb784 100755
--- a/src/cpac/helpers/cpac_read_crash.py
+++ b/src/cpac/helpers/cpac_read_crash.py
@@ -7,7 +7,6 @@
 
 import os
 import re
-
 from sys import argv
 
 path_regex = re.compile(
diff --git a/src/cpac/utils/utils.py b/src/cpac/utils/utils.py
index 4091b34b..46303398 100644
--- a/src/cpac/utils/utils.py
+++ b/src/cpac/utils/utils.py
@@ -188,6 +188,8 @@ def __init__(self, local: str, bind: str = None,
     def __init__(self, local, bind=None, mode=None):  # noqa: E301
         self.local = local
         self.bind = bind if bind is not None else local
+        if self.bind is not None and not self.bind.startswith('/'):
+            self.bind = os.path.abspath(self.bind)
         if isinstance(mode, PermissionMode):
             self.mode = mode
         elif mode is not None:
diff --git a/tests/CONSTANTS.py b/tests/CONSTANTS.py
index 0fe90457..9018fa7d 100644
--- a/tests/CONSTANTS.py
+++ b/tests/CONSTANTS.py
@@ -1,6 +1,6 @@
 '''Constants for tests'''
 # pylint: disable=invalid-name
-TAGS = [None, 'latest', 'nightly'
+TAGS = [None, 'latest', 'nightly']
 
 
 def args_before_after(argv, args):
diff --git a/tests/test_cpac_run.py b/tests/test_cpac_run.py
index 8bc577b2..3bc1c229 100644
--- a/tests/test_cpac_run.py
+++ b/tests/test_cpac_run.py
@@ -38,7 +38,6 @@ def run_test(argv):
         run_test(f'cpac {argv}'.split(' '))
 
 
-@pytest.mark.skip(reason=TODOs['permission_denied'])
 @pytest.mark.parametrize('argsep', [' ', '='])
 @pytest.mark.parametrize('pipeline_file', [None, MINIMAL_CONFIG])
 def test_run_test_config(argsep, pipeline_file, tmp_path, platform, tag):
diff --git a/tests/test_cpac_utils.py b/tests/test_cpac_utils.py
index fd9e7eec..ae64d957 100644
--- a/tests/test_cpac_utils.py
+++ b/tests/test_cpac_utils.py
@@ -35,7 +35,6 @@ def run_test(argv, platform):
         run_test(f'cpac {argv}'.split(' '), platform)
 
 
-@pytest.mark.skip(reason=TODOs['permission_denied'])
 @pytest.mark.parametrize('argsep', [' ', '='])
 def test_utils_new_settings_template(argsep, tmp_path, platform, tag):
     """Test 'utils data_config new_settings_template' command"""