From 3a874cf2f4048c017cbb5a438474ad382d64eee2 Mon Sep 17 00:00:00 2001
From: Martin Craig <martin.craig@eng.ox.ac.uk>
Date: Tue, 21 Apr 2020 12:30:30 +0100
Subject: [PATCH] Implement revised version of WSL interface using \\wsl$\
mapping This requires WSL 2.0 but enables FSLDIR to be a genuine WIndows
path so that atlases and standard data can be loaded transparently. It also
means we no longer need FSLWSL environment variable, just to be a bit careful
with path mapping
---
fsl/utils/platform.py | 56 ++++++++++++++++++++++++++++++++++++++++--
fsl/utils/run.py | 50 +++++++++++++++++--------------------
tests/test_platform.py | 31 +++++++++++++++++++----
tests/test_run.py | 4 ---
4 files changed, 102 insertions(+), 39 deletions(-)
diff --git a/fsl/utils/platform.py b/fsl/utils/platform.py
index 34f60162c..8599928e1 100644
--- a/fsl/utils/platform.py
+++ b/fsl/utils/platform.py
@@ -17,6 +17,7 @@ import os
import os.path as op
import sys
import importlib
+import re
import fsl.utils.notifier as notifier
@@ -285,7 +286,6 @@ class Platform(notifier.Notifier):
"""
return os.environ.get('FSLDIR', None)
-
@property
def fsldevdir(self):
"""The FSL development directory location. """
@@ -294,7 +294,7 @@ class Platform(notifier.Notifier):
@property
def fslwsl(self):
"""Boolean flag indicating whether FSL is installed in Windows Subsystem for Linux """
- return os.environ.get('FSLWSL', "0") == "1"
+ return self.fsldir is not None and self.fsldir.startswith("\\\\wsl$\\")
@fsldir.setter
def fsldir(self, value):
@@ -405,6 +405,58 @@ 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\$\\([^\\]+).*$", self.fsldir)
+ if match:
+ distro = match.group(1)
+ else:
+ distro = None
+
+ if distro is None:
+ raise RuntimeError("No WSL installations found at \\wsl$\ - a valid WSL 2.0 installation is required")
+ else:
+ return "\\\\wsl$\\" + distro + wslpath.replace("/", "\\")
platform = Platform()
"""An instance of the :class:`Platform` class. Feel free to create your own
diff --git a/fsl/utils/run.py b/fsl/utils/run.py
index abba42f0e..2523f50dc 100644
--- a/fsl/utils/run.py
+++ b/fsl/utils/run.py
@@ -29,7 +29,6 @@ import collections
import subprocess as sp
import os.path as op
import os
-import re
import six
@@ -392,44 +391,39 @@ def wslcmd(cmdpath, *args):
which when executed will run the command in WSL. Windows paths in the argument list will
be converted to WSL paths. If ``cmdpath`` was not executable in WSL, returns None
"""
- # Check if command exists in WSL (translating Windows path separators to Unix as os.path.join
- # may have inserted some backslashes)
- cmdpath = cmdpath.replace("\\", "/")
+ # Check if command exists in WSL (remembering that the command path may include FSLDIR which
+ # is a Windows path)
+ cmdpath = fslplatform.wslpath(cmdpath)
retcode = sp.call(["wsl", "test", "-x", cmdpath])
if retcode == 0:
# Form a new argument list and convert any Windows paths in it into WSL paths
- wslargs = [wslpath(arg) for arg in args]
+ wslargs = [fslplatform.wslpath(arg) for arg in args]
wslargs[0] = cmdpath
+ local_fsldir = fslplatform.wslpath(fslplatform.fsldir)
+ if fslplatform.fsldevdir:
+ local_fsldevdir = fslplatform.wslpath(fslplatform.fsldevdir)
+ else:
+ local_fsldevdir = None
# Prepend important environment variables - note that it seems we cannot
- # use WSLENV for this due to its insistance on path mapping.
- return [
+ # use WSLENV for this due to its insistance on path mapping. FIXME FSLDEVDIR?
+ local_path = "$PATH"
+ if local_fsldevdir:
+ local_path += ":%s/bin" % local_fsldevdir
+ local_path += ":%s/bin" % local_fsldir
+ prepargs = [
"wsl",
- "PATH=$PATH:%s/bin" % fslplatform.fsldir,
- "FSLDIR=%s" % fslplatform.fsldir,
+ "PATH=%s" % local_path,
+ "FSLDIR=%s" % local_fsldir,
"FSLOUTPUTTYPE=%s" % os.environ.get("FSLOUTPUTTYPE", "NIFTI_GZ")
- ] + wslargs
+ ]
+ if local_fsldevdir:
+ prepargs.append("FSLDEVDIR=%s" % local_fsldevdir)
+
+ return prepargs + wslargs
else:
# Command was not found in WSL with this path
return None
-def wslpath(patharg):
- """
- Convert a command line argument containing a Windows path to the equivalent WSL path (e.g. ``c:\\Users`` -> ``/mnt/c/Users``)
-
- :param patharg: Command line argument which may (or may not) contain a Windows path. It is assumed to be
- either of the form <windows path> or --<arg>=<windows path>
- :return: If ``patharg`` matches a Windows path, the converted argument (including the --<arg>= portion). Otherwise
- returns ``patharg`` unchanged.
- """
- match = re.match("^(--[\w-]+=)?([a-zA-z]):(.+)$", patharg)
- if match:
- arg, drive, path = match.group(1, 2, 3)
- if arg is None:
- arg = ""
- return arg + "/mnt/" + drive.lower() + path.replace("\\", "/")
- else:
- return patharg
-
def wait(job_ids):
"""Proxy for :func:`.fslsub.wait`. """
return fslsub.wait(job_ids)
diff --git a/tests/test_platform.py b/tests/test_platform.py
index 9fbb004cb..46dad0ce5 100644
--- a/tests/test_platform.py
+++ b/tests/test_platform.py
@@ -214,11 +214,32 @@ def test_detect_ssh():
assert not p.inVNCSession
def test_fslwsl():
-
- with mock.patch.dict('os.environ', **{ 'FSLWSL' : '1'}):
- p = fslplatform.Platform()
+ """
+ Note that ``Platform.fsldir`` requires the directory in ``FSLDIR`` to exist and
+ sets ``FSLDIR`` to ``None`` if it doesn't. So we create a ``Platform`` first
+ and then overwrite ``FSLDIR``. This is a bit of a hack but the logic we are testing
+ here is whether ``Platform.fslwsl`` recognizes a WSL ``FSLDIR`` string
+ """
+ p = fslplatform.Platform()
+ with mock.patch.dict('os.environ', **{ 'FSLDIR' : '\\\\wsl$\\my cool linux distro v1.0\\usr\\local\\fsl'}):
assert p.fslwsl
- with mock.patch.dict('os.environ', **{ 'FSLWSL' : '0'}):
- p = fslplatform.Platform()
+ with mock.patch.dict('os.environ', **{ 'FSLDIR' : '/usr/local/fsl'}):
assert not p.fslwsl
+
+def test_wslpath():
+ p = fslplatform.Platform()
+ assert p.wslpath('c:\\Users\\Fishcake\\image.nii.gz') == '/mnt/c/Users/Fishcake/image.nii.gz'
+ assert p.wslpath('--input=x:\\transfers\\scratch\\image_2.nii') == '--input=/mnt/x/transfers/scratch/image_2.nii'
+ assert p.wslpath('\\\\wsl$\\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'
diff --git a/tests/test_run.py b/tests/test_run.py
index 39df3603c..363d4489e 100644
--- a/tests/test_run.py
+++ b/tests/test_run.py
@@ -410,7 +410,3 @@ def test_run_logcmd():
assert stdout == expstdout
assert open('my_stdout', 'rt').read() == expcmd + expstdout
-
-def test_wslpath():
- assert run.wslpath('c:\\Users\\Fishcake\\image.nii.gz') == '/mnt/c/Users/Fishcake/image.nii.gz'
- assert run.wslpath('--input=x:\\transfers\\scratch\\image_2.nii') == '--input=/mnt/x/transfers/scratch/image_2.nii'
--
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