From 979d8f02e46492c1c3a9650ca123ebc702800091 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Thu, 19 Apr 2018 15:05:43 +0100
Subject: [PATCH] New/adjusted unit tests for run(submit=True) and
cmd/fslwrapper(submit=True)
---
tests/test_run.py | 52 ++++++++++++++++++-------
tests/test_wrapperutils.py | 77 +++++++++++++++++++++++++++++++++++++-
2 files changed, 114 insertions(+), 15 deletions(-)
diff --git a/tests/test_run.py b/tests/test_run.py
index 849fff60e..b65294ec4 100644
--- a/tests/test_run.py
+++ b/tests/test_run.py
@@ -15,6 +15,7 @@ try: from unittest import mock
# python 2
except ImportError: import mock
+import six
import pytest
import fsl.utils.tempdir as tempdir
@@ -22,7 +23,7 @@ from fsl.utils.platform import platform as fslplatform
import fsl.utils.run as run
import fsl.utils.fslsub as fslsub
-from . import make_random_image, mockFSLDIR
+from . import make_random_image, mockFSLDIR, touch
def test_run():
@@ -142,16 +143,25 @@ def test_runfsl():
fslplatform.fsldir = old_fsldir
-mock_fsl_sub = textwrap.dedent("""
-#!/usr/bin/env bash
-jid=12345
-cmd=$1
-name=`basename $cmd`
-$cmd > "$name".o"$jid"
-touch "$name".e"$jid"
-echo $jid
-exit 0
-""").strip()
+def mock_submit(cmd, **kwargs):
+ if isinstance(cmd, six.string_types):
+ name = cmd.split()[0]
+ else:
+ name = cmd[0]
+
+ name = op.basename(name)
+
+ jid = '12345'
+ output = run.run(cmd)
+
+ with open('{}.o{}'.format(name, jid), 'wt') as f:
+ f.write(output)
+
+ with open('{}.e{}'.format(name, jid), 'wt') as f:
+ for k, v in kwargs.items():
+ f.write('{}: {}\n'.format(k, v))
+
+ return (jid,)
def test_run_submit():
@@ -167,16 +177,30 @@ def test_run_submit():
exit 0
""").strip()
- with tempdir.tempdir(), mockFSLDIR():
+ with tempdir.tempdir(), \
+ mockFSLDIR(), \
+ mock.patch('fsl.utils.fslsub.submit', mock_submit):
mkexec(op.expandvars('$FSLDIR/bin/fsltest'), test_script)
- mkexec(op.expandvars('$FSLDIR/bin/fsl_sub'), mock_fsl_sub)
jid = run.run('fsltest', submit=True)[0]
assert jid == '12345'
- stdout, stderr = fslsub.output(jid, 'fsltest')
+ stdout, stderr = fslsub.output(jid)
assert stdout.strip() == 'test_script running'
assert stderr.strip() == ''
+
+ kwargs = {'name' : 'abcde', 'ram' : '4GB'}
+
+ jid = run.run('fsltest', submit=kwargs)[0]
+
+ assert jid == '12345'
+
+ stdout, stderr = fslsub.output(jid)
+
+ experr = '\n'.join(['{}: {}'.format(k, v) for k, v in kwargs.items()])
+
+ assert stdout.strip() == 'test_script running'
+ assert stderr.strip() == experr
diff --git a/tests/test_wrapperutils.py b/tests/test_wrapperutils.py
index ef5a6fd4f..7d8b84780 100644
--- a/tests/test_wrapperutils.py
+++ b/tests/test_wrapperutils.py
@@ -8,6 +8,10 @@
import os.path as op
import os
import shlex
+import textwrap
+
+try: from unittest import mock
+except ImportError: import mock
import pytest
@@ -16,10 +20,12 @@ import nibabel as nib
import fsl.utils.tempdir as tempdir
import fsl.utils.run as run
+import fsl.utils.fslsub as fslsub
import fsl.wrappers.wrapperutils as wutils
from . import mockFSLDIR
+from .test_run import mock_submit
def test_applyArgStyle():
@@ -310,7 +316,6 @@ def test_cmdwrapper():
assert func(1, 2)[0] == 'func 1 2'
-
def test_fslwrapper():
@wutils.fslwrapper
def func(a, b):
@@ -319,3 +324,73 @@ def test_fslwrapper():
with run.dryrun(), mockFSLDIR() as fsldir:
expected = '{} 1 2'.format(op.join(fsldir, 'bin', 'func'))
assert func(1, 2)[0] == expected
+
+
+_test_script = textwrap.dedent("""
+#!/usr/bin/env bash
+echo "test_script running: $1 $2"
+exit 0
+""").strip()
+
+
+def _test_script_func(a, b):
+ return ['test_script', str(a), str(b)]
+
+
+def test_cmdwrapper_submit():
+
+ test_func = wutils.cmdwrapper(_test_script_func)
+ newpath = op.pathsep.join(('.', os.environ['PATH']))
+
+ with tempdir.tempdir(), \
+ mock.patch('fsl.utils.fslsub.submit', mock_submit), \
+ mock.patch.dict(os.environ, {'PATH' : newpath}):
+
+ with open('test_script', 'wt') as f:
+ f.write(_test_script)
+ os.chmod('test_script', 0o755)
+
+ jid = test_func(1, 2, submit=True)
+
+ assert jid == ('12345',)
+
+ stdout, stderr = fslsub.output('12345')
+
+ assert stdout.strip() == 'test_script running: 1 2'
+ assert stderr.strip() == ''
+
+
+def test_fslwrapper_submit():
+
+ test_func = wutils.fslwrapper(_test_script_func)
+
+ with mockFSLDIR() as fsldir, \
+ mock.patch('fsl.utils.fslsub.submit', mock_submit):
+
+ test_file = op.join(fsldir, 'bin', 'test_script')
+
+ with open(test_file, 'wt') as f:
+ f.write(_test_script)
+ os.chmod(test_file, 0o755)
+
+ jid = test_func(1, 2, submit=True)
+
+ assert jid == ('12345',)
+
+ stdout, stderr = fslsub.output('12345')
+
+ assert stdout.strip() == 'test_script running: 1 2'
+ assert stderr.strip() == ''
+
+ kwargs = {'name' : 'abcde', 'ram' : '4GB'}
+
+ jid = test_func(1, 2, submit=kwargs)
+
+ assert jid == ('12345',)
+
+ stdout, stderr = fslsub.output('12345')
+
+ experr = '\n'.join(['{}: {}'.format(k, v) for k, v in kwargs.items()])
+
+ assert stdout.strip() == 'test_script running: 1 2'
+ assert stderr.strip() == experr
--
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