From 1a2577d7c12e6d86905635be3686dc7a8a2bd5eb Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Mon, 12 Oct 2020 18:48:39 +0100
Subject: [PATCH] RF: Implement cmdonly in run.run, rather than in wrappers, so
e.g. $FSLDIR is correctly prepended.
---
fsl/utils/run.py | 8 ++++++++
fsl/wrappers/wrapperutils.py | 23 ++++++++++-------------
2 files changed, 18 insertions(+), 13 deletions(-)
diff --git a/fsl/utils/run.py b/fsl/utils/run.py
index 3ed799ca8..cf75fc505 100644
--- a/fsl/utils/run.py
+++ b/fsl/utils/run.py
@@ -151,6 +151,10 @@ def run(*args, **kwargs):
the :func:`.fslsub.submit` function. May also be a
dictionary containing arguments to that function.
+ :arg cmdonly: Defaults to ``False``. If ``True``, the command is not
+ executed, but rather is returned directly, as a list of
+ arguments.
+
:arg log: Must be passed as a keyword argument. An optional ``dict``
which may be used to redirect the command's standard output
and error. The following keys are recognised:
@@ -181,6 +185,7 @@ def run(*args, **kwargs):
returnStderr = kwargs.pop('stderr', False)
returnExitcode = kwargs.pop('exitcode', False)
submit = kwargs.pop('submit', {})
+ cmdonly = kwargs.pop('cmdonly', False)
log = kwargs.pop('log', None)
args = prepareArgs(args)
@@ -207,6 +212,9 @@ def run(*args, **kwargs):
raise ValueError('submit must be a mapping containing '
'options for fsl.utils.fslsub.submit')
+ if cmdonly:
+ return args
+
if DRY_RUN:
return _dryrun(
submit, returnStdout, returnStderr, returnExitcode, *args)
diff --git a/fsl/wrappers/wrapperutils.py b/fsl/wrappers/wrapperutils.py
index 5acaeb454..2bfbf500c 100644
--- a/fsl/wrappers/wrapperutils.py
+++ b/fsl/wrappers/wrapperutils.py
@@ -172,9 +172,7 @@ def genxwrapper(func, runner):
- ``exitcode``: Passed to ``runner``. Defaults to ``False``.
- ``submit``: Passed to ``runner``. Defaults to ``None``.
- ``log``: Passed to ``runner``. Defaults to ``{'tee':True}``.
- - ``cmdonly``: Defaults to ``False``. If ``True``, the return
- value of ``func`` is returned directly, instead of it being passed
- to ``runner``,
+ - ``cmdonly``: Passed to ``runner``. Defaults to ``False``.
:arg func: A function which generates a command line.
:arg runner: Either :func:`.run.run` or :func:`.run.runfsl`.
@@ -184,20 +182,19 @@ def genxwrapper(func, runner):
stdout = kwargs.pop('stdout', True)
stderr = kwargs.pop('stderr', True)
exitcode = kwargs.pop('exitcode', False)
- cmdonly = kwargs.pop('cmdonly', False)
submit = kwargs.pop('submit', None)
+ cmdonly = kwargs.pop('cmdonly', False)
log = kwargs.pop('log', {'tee' : True})
cmd = func(*args, **kwargs)
- if cmdonly:
- return cmd
- else:
- return runner(cmd,
- stderr=stderr,
- log=log,
- submit=submit,
- stdout=stdout,
- exitcode=exitcode)
+ return runner(cmd,
+ stderr=stderr,
+ log=log,
+ submit=submit,
+ cmdonly=cmdonly,
+ stdout=stdout,
+ exitcode=exitcode)
+
return _update_wrapper(wrapper, func)
--
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