From 49c91d74aea5326a70fdebbac6f9d2c88a4abb63 Mon Sep 17 00:00:00 2001
From: Martin Craig <martin.craig@eng.ox.ac.uk>
Date: Wed, 22 Apr 2020 13:53:28 +0100
Subject: [PATCH] Moved fslpath and winpath from fsl.utils.platform to
fsl.utils.path Also minor bugfix - allow forward or backslash after \\wsl$
when specifying FSLDIR as a WSL network share
---
fsl/utils/path.py | 55 +++++++++++++++++++++++++++++++++++
fsl/utils/platform.py | 56 +-----------------------------------
fsl/utils/run.py | 11 ++++---
tests/test_fsl_utils_path.py | 17 +++++++++++
tests/test_platform.py | 17 -----------
5 files changed, 78 insertions(+), 78 deletions(-)
diff --git a/fsl/utils/path.py b/fsl/utils/path.py
index 8d312bef5..7f7f80cf0 100644
--- a/fsl/utils/path.py
+++ b/fsl/utils/path.py
@@ -30,7 +30,9 @@ import os.path as op
import os
import glob
import operator
+import re
+from fsl.utils.platform import platform
class PathError(Exception):
"""``Exception`` class raised by the functions defined in this module
@@ -524,3 +526,56 @@ def commonBase(paths):
return base
raise PathError('No common base')
+
+def wslpath(winpath):
+ """
+ Convert Windows path (or a command line argument containing a Windows path)
+ to the equivalent WSL path (e.g. ``c:\\Users`` -> ``/mnt/c/Users``). Also supports
+ paths in the form ``\\wsl$\\(distro)\\users\\...``
+
+ :param winpath: Command line argument which may (or may not) contain a Windows path. It is assumed to be
+ either of the form <windows path> or --<arg>=<windows path>. Note that we don't need to
+ handle --arg <windows path> or -a <windows path> since in these cases the argument
+ and the path will be parsed as separate entities.
+ :return: If ``winpath`` matches a Windows path, the converted argument (including the --<arg>= portion).
+ Otherwise returns ``winpath`` unchanged.
+ """
+ match = re.match(r"^(--[\w-]+=)?\\\\wsl\$[\\\/][^\\^\/]+(.*)$", winpath)
+ if match:
+ arg, path = match.group(1, 2)
+ if arg is None:
+ arg = ""
+ return arg + path.replace("\\", "/")
+
+ match = re.match(r"^(--[\w-]+=)?([a-zA-z]):(.+)$", winpath)
+ if match:
+ arg, drive, path = match.group(1, 2, 3)
+ if arg is None:
+ arg = ""
+ return arg + "/mnt/" + drive.lower() + path.replace("\\", "/")
+
+ return winpath
+
+def winpath(wslpath):
+ """
+ Convert a WSL-local filepath (for example ``/usr/local/fsl/``) into a path that can be used from
+ Windows.
+
+ If ``self.fslwsl`` is ``False``, simply returns ``wslpath`` unmodified
+ Otherwise, uses ``FSLDIR`` to deduce the WSL distro in use for FSL.
+ This requires WSL2 which supports the ``\\wsl$\`` network path.
+ wslpath is assumed to be an absolute path.
+ """
+ if not platform.fslwsl:
+ return wslpath
+ else:
+ match = re.match(r"^\\\\wsl\$\\([^\\]+).*$", platform.fsldir)
+ if match:
+ distro = match.group(1)
+ else:
+ distro = None
+
+ if not distro:
+ raise RuntimeError("Could not identify WSL installation from FSLDIR (%s)" % platform.fsldir)
+
+ return "\\\\wsl$\\" + distro + wslpath.replace("/", "\\")
diff --git a/fsl/utils/platform.py b/fsl/utils/platform.py
index 173b031cb..73d0937d2 100644
--- a/fsl/utils/platform.py
+++ b/fsl/utils/platform.py
@@ -17,7 +17,6 @@ import os
import os.path as op
import sys
import importlib
-import re
import fsl.utils.notifier as notifier
@@ -294,7 +293,7 @@ class Platform(notifier.Notifier):
@property
def fslwsl(self):
"""Boolean flag indicating whether FSL is installed in Windows Subsystem for Linux """
- return self.fsldir is not None and self.fsldir.startswith("\\\\wsl$\\")
+ return self.fsldir is not None and self.fsldir.startswith("\\\\wsl$")
@fsldir.setter
def fsldir(self, value):
@@ -405,59 +404,6 @@ class Platform(notifier.Notifier):
"""
return self.__glIsSoftware
- def wslpath(self, winpath):
- """
- Convert Windows path (or a command line argument containing a Windows path)
- to the equivalent WSL path (e.g. ``c:\\Users`` -> ``/mnt/c/Users``). Also supports
- paths in the form ``\\wsl$\\(distro)\\users\\...``
-
- :param winpath: Command line argument which may (or may not) contain a Windows path. It is assumed to be
- either of the form <windows path> or --<arg>=<windows path>. Note that we don't need to
- handle --arg <windows path> or -a <windows path> since in these cases the argument
- and the path will be parsed as separate entities.
- :return: If ``winpath`` matches a Windows path, the converted argument (including the --<arg>= portion).
- Otherwise returns ``winpath`` unchanged.
- """
- match = re.match(r"^(--[\w-]+=)?\\\\wsl\$\\[^\\]+(\\.*)$", winpath)
- if match:
- arg, path = match.group(1, 2)
- if arg is None:
- arg = ""
- return arg + path.replace("\\", "/")
-
- match = re.match(r"^(--[\w-]+=)?([a-zA-z]):(.+)$", winpath)
- if match:
- arg, drive, path = match.group(1, 2, 3)
- if arg is None:
- arg = ""
- return arg + "/mnt/" + drive.lower() + path.replace("\\", "/")
-
- return winpath
-
- def winpath(self, wslpath):
- """
- Convert a WSL-local filepath (for example ``/usr/local/fsl/``) into a path that can be used from
- Windows.
-
- If ``self.fslwsl`` is ``False``, simply returns ``wslpath`` unmodified
- Otherwise, uses ``FSLDIR`` to deduce the WSL distro in use for FSL.
- This requires WSL2 which supports the ``\\wsl$\`` network path.
- wslpath is assumed to be an absolute path.
- """
- if not self.fslwsl:
- return wslpath
- else:
- match = re.match(r"^\\\\wsl\$\\([^\\]+).*$", self.fsldir)
- if match:
- distro = match.group(1)
- else:
- distro = None
-
- if not distro:
- raise RuntimeError("Could not identify WSL installation from FSLDIR (%s)" % self.fsldir)
-
- return "\\\\wsl$\\" + distro + wslpath.replace("/", "\\")
-
platform = Platform()
"""An instance of the :class:`Platform` class. Feel free to create your own
instance, but be aware that if you do so you will not be updated of changes
diff --git a/fsl/utils/run.py b/fsl/utils/run.py
index 2523f50dc..acb77c741 100644
--- a/fsl/utils/run.py
+++ b/fsl/utils/run.py
@@ -35,7 +35,7 @@ import six
from fsl.utils.platform import platform as fslplatform
import fsl.utils.fslsub as fslsub
import fsl.utils.tempdir as tempdir
-
+import fsl.utils.path as fslpath
log = logging.getLogger(__name__)
@@ -393,15 +393,15 @@ def wslcmd(cmdpath, *args):
"""
# Check if command exists in WSL (remembering that the command path may include FSLDIR which
# is a Windows path)
- cmdpath = fslplatform.wslpath(cmdpath)
+ cmdpath = fslpath.wslpath(cmdpath)
retcode = sp.call(["wsl", "test", "-x", cmdpath])
if retcode == 0:
# Form a new argument list and convert any Windows paths in it into WSL paths
- wslargs = [fslplatform.wslpath(arg) for arg in args]
+ wslargs = [fslpath.wslpath(arg) for arg in args]
wslargs[0] = cmdpath
- local_fsldir = fslplatform.wslpath(fslplatform.fsldir)
+ local_fsldir = fslpath.wslpath(fslplatform.fsldir)
if fslplatform.fsldevdir:
- local_fsldevdir = fslplatform.wslpath(fslplatform.fsldevdir)
+ local_fsldevdir = fslpath.wslpath(fslplatform.fsldevdir)
else:
local_fsldevdir = None
# Prepend important environment variables - note that it seems we cannot
@@ -418,7 +418,6 @@ def wslcmd(cmdpath, *args):
]
if local_fsldevdir:
prepargs.append("FSLDEVDIR=%s" % local_fsldevdir)
-
return prepargs + wslargs
else:
# Command was not found in WSL with this path
diff --git a/tests/test_fsl_utils_path.py b/tests/test_fsl_utils_path.py
index d4cc1bec5..0361ced5e 100644
--- a/tests/test_fsl_utils_path.py
+++ b/tests/test_fsl_utils_path.py
@@ -13,6 +13,7 @@ import shutil
import tempfile
import pytest
+import mock
import fsl.utils.path as fslpath
import fsl.data.image as fslimage
@@ -1395,3 +1396,19 @@ def test_commonBase():
for ft in failtests:
with pytest.raises(fslpath.PathError):
fslpath.commonBase(ft)
+
+def test_wslpath():
+ assert fslpath.wslpath('c:\\Users\\Fishcake\\image.nii.gz') == '/mnt/c/Users/Fishcake/image.nii.gz'
+ assert fslpath.wslpath('--input=x:\\transfers\\scratch\\image_2.nii') == '--input=/mnt/x/transfers/scratch/image_2.nii'
+ assert fslpath.wslpath('\\\\wsl$\\centos 7\\users\\fsl\\file.nii') == '/users/fsl/file.nii'
+ assert fslpath.wslpath('--file=\\\\wsl$\\centos 7\\home\\fsl\\img.nii.gz') == '--file=/home/fsl/img.nii.gz'
+ assert fslpath.wslpath('\\\\wsl$/centos 7/users\\fsl\\file.nii') == '/users/fsl/file.nii'
+
+def test_winpath():
+ """
+ See comment for ``test_fslwsl`` for why we are overwriting FSLDIR
+ """
+ with mock.patch.dict('os.environ', **{ 'FSLDIR' : '\\\\wsl$\\my cool linux distro v2.0\\usr\\local\\fsl'}):
+ assert fslpath.winpath("/home/fsl/myfile.dat") == '\\\\wsl$\\my cool linux distro v2.0\\home\\fsl\\myfile.dat'
+ with mock.patch.dict('os.environ', **{ 'FSLDIR' : '/opt/fsl'}):
+ assert fslpath.winpath("/home/fsl/myfile.dat") == '/home/fsl/myfile.dat'
diff --git a/tests/test_platform.py b/tests/test_platform.py
index 46dad0ce5..9024bec82 100644
--- a/tests/test_platform.py
+++ b/tests/test_platform.py
@@ -226,20 +226,3 @@ def test_fslwsl():
with mock.patch.dict('os.environ', **{ 'FSLDIR' : '/usr/local/fsl'}):
assert not p.fslwsl
-
-def test_wslpath():
- p = fslplatform.Platform()
- assert p.wslpath('c:\\Users\\Fishcake\\image.nii.gz') == '/mnt/c/Users/Fishcake/image.nii.gz'
- assert p.wslpath('--input=x:\\transfers\\scratch\\image_2.nii') == '--input=/mnt/x/transfers/scratch/image_2.nii'
- assert p.wslpath('\\\\wsl$\\centos 7\\users\\fsl\\file.nii') == '/users/fsl/file.nii'
- assert p.wslpath('--file=\\\\wsl$\\centos 7\\home\\fsl\\img.nii.gz') == '--file=/home/fsl/img.nii.gz'
-
-def test_winpath():
- """
- See comment for ``test_fslwsl``
- """
- p = fslplatform.Platform()
- with mock.patch.dict('os.environ', **{ 'FSLDIR' : '\\\\wsl$\\my cool linux distro v2.0\\usr\\local\\fsl'}):
- assert p.winpath("/home/fsl/myfile.dat") == '\\\\wsl$\\my cool linux distro v2.0\\home\\fsl\\myfile.dat'
- with mock.patch.dict('os.environ', **{ 'FSLDIR' : '/opt/fsl'}):
- assert p.winpath("/home/fsl/myfile.dat") == '/home/fsl/myfile.dat'
--
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