From 114783ae44181e800ba4d7740d954091a98f387b Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Tue, 13 Oct 2020 20:01:45 +0100
Subject: [PATCH] RF: FileOrThing passes through if cmdonly=True
---
fsl/wrappers/wrapperutils.py | 35 ++++++++++++++++++++---------------
1 file changed, 20 insertions(+), 15 deletions(-)
diff --git a/fsl/wrappers/wrapperutils.py b/fsl/wrappers/wrapperutils.py
index 2bfbf500c..51f269bcb 100644
--- a/fsl/wrappers/wrapperutils.py
+++ b/fsl/wrappers/wrapperutils.py
@@ -482,25 +482,27 @@ class FileOrThing(object):
the dictionary.
- **Cluster submission**
+ **Exceptions**
- The above description holds in all situations, except when an argument
- called ``submit`` is passed, and is set to a value which evaluates to
- ``True``. In this case, the ``FileOrThing`` decorator will pass all
- arguments straight through to the decorated function, and will return its
- return value unchanged.
-
+ The above description holds in all situations, except when arguments called
+ ``submit`` and/or ``cmdonly`` are passed, and are set to values which
+ evaluate to ``True``. In this case, the ``FileOrThing`` decorator will pass
+ all arguments straight through to the decorated function, and will return
+ its return value unchanged.
This is because most functions that are decorated with the
:func:`fileOrImage` or :func:`fileOrArray` decorators will invoke a call
- to :func:`.run.run` or :func:`.runfsl`, where a value of ``submit=True``
- will cause the command to be executed asynchronously on a cluster
- platform.
+ to :func:`.run.run` or :func:`.runfsl`, where:
+ - a value of ``submit=True`` will cause the command to be executed
+ asynchronously on a cluster platform.
+ - a value of ``cmdonly=True`` will cause the command to *not* be executed,
+ but instead the command that would have been executed is returned.
A :exc:`ValueError` will be raised if the decorated function is called
- with ``submit=True``, and with any in-memory objects or ``LOAD`` symbols.
+ with ``submit=True`` and/or ``cmdonly=True``, and with any in-memory
+ objects or ``LOAD`` symbols.
**Example**
@@ -684,9 +686,11 @@ class FileOrThing(object):
# Special case - if fsl.utils.run[fsl] is
# being decorated (e.g. via cmdwrapper/
- # fslwrapper), and submit=True, this call
- # will ultimately submit the job to the
- # cluster, and will return immediately.
+ # fslwrapper), and submit=True or
+ # cmdonly=True, this call will ultimately
+ # submit the job to the cluster, or will
+ # return the command that would have been
+ # executed, and will return immediately.
#
# We error if we are given any in-memory
# things, or LOAD symbols.
@@ -694,7 +698,8 @@ class FileOrThing(object):
# n.b. testing values to be strings could
# interfere with the fileOrText decorator.
# Possible solution is to use pathlib?
- if kwargs.get('submit', False):
+ if kwargs.get('submit', False) or \
+ kwargs.get('cmdonly', False):
allargs = {**dict(zip(argnames, args)), **kwargs}
for name, val in allargs.items():
if (name in self.__things) and \
--
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