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, kwargs[k]) for k in sorted(kwargs.keys())])
assert stdout.strip() == 'test_script running: 1 2'
assert stderr.strip() == experr
def test_run_submit():
def mkexec(path, contents):
with open(path, 'wt') as f:
f.write(contents)
os.chmod(path, 0o755)
test_script = textwrap.dedent("""
#!/usr/bin/env bash
echo test_script running
exit 0
""").strip()
with tempdir.tempdir(), \
mockFSLDIR(), \
mock.patch('fsl.utils.fslsub.submit', mock_submit):
mkexec(op.expandvars('$FSLDIR/bin/fsltest'), test_script)
jid = run.run('fsltest', submit=True)
assert jid == '12345'
stdout, stderr = fslsub.output(jid)
assert stdout == 'test_script running\n'
assert stderr == ''
# or can pass submit opts as a dict
kwargs = {'name': 'abcde', 'ram': '4GB'}
jid = run.run('fsltest', submit=kwargs)
assert jid == '12345'
stdout, stderr = fslsub.output(jid)
experr = '\n'.join(
['{}: {}'.format(k, kwargs[k])
for k in sorted(kwargs.keys())]) + '\n'
assert stdout == 'test_script running\n'
assert stderr == experr
# or can pass submit opts as kwargs
kwargs = {'name': 'abcde', 'ram': '4GB'}
jid = run.run('fsltest', submit=True, **kwargs)
assert jid == '12345'
stdout, stderr = fslsub.output(jid)
experr = '\n'.join(
['{}: {}'.format(k, kwargs[k])
for k in sorted(kwargs.keys())]) + '\n'
assert stdout == 'test_script running\n'
assert stderr == experr
def test_func_to_cmd():
with fslsub_mockFSLDIR(), tempdir():
cmd = fslsub.func_to_cmd(myfunc, (), {})
jid = fslsub.submit(cmd)
stdout, stderr = fslsub.output(jid)
assert stdout.strip() == 'standard output'
assert stderr.strip() == 'standard error'
def test_submit():
script = tw.dedent("""#!/usr/bin/env bash
echo "standard output"
echo "standard error" >&2
exit 0
""").strip()
with fslsub_mockFSLDIR(), tempdir():
cmd = op.join('.', 'myscript')
with open(cmd, 'wt') as f:
f.write(script)
os.chmod(cmd, 0o755)
jid = fslsub.submit(cmd)
stdout, stderr = fslsub.output(jid)
assert stdout.strip() == 'standard output'
assert stderr.strip() == 'standard error'
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() == ''