def test_CommandLine_output():
tmp_infile = setup_file()
tmpd, name = os.path.split(tmp_infile)
pwd = os.getcwd()
os.chdir(tmpd)
yield assert_true, os.path.exists(tmp_infile)
ci = nib.CommandLine(command='ls -l')
ci.inputs.terminal_output = 'allatonce'
res = ci.run()
yield assert_equal, res.runtime.merged, ''
yield assert_true, name in res.runtime.stdout
ci = nib.CommandLine(command='ls -l')
ci.inputs.terminal_output = 'file'
res = ci.run()
yield assert_true, 'stdout.nipype' in res.runtime.stdout
yield assert_true, isinstance(res.runtime.stdout, (str, bytes))
ci = nib.CommandLine(command='ls -l')
ci.inputs.terminal_output = 'none'
res = ci.run()
yield assert_equal, res.runtime.stdout, ''
ci = nib.CommandLine(command='ls -l')
res = ci.run()
yield assert_true, 'stdout.nipype' in res.runtime.stdout
os.chdir(pwd)
teardown_file(tmpd)
def test_Commandline():
yield assert_raises, Exception, nib.CommandLine
ci = nib.CommandLine(command='which')
yield assert_equal, ci.cmd, 'which'
yield assert_equal, ci.inputs.args, Undefined
ci2 = nib.CommandLine(command='which', args='ls')
yield assert_equal, ci2.cmdline, 'which ls'
ci3 = nib.CommandLine(command='echo')
ci3.inputs.environ = {'MYENV': 'foo'}
res = ci3.run()
yield assert_equal, res.runtime.environ['MYENV'], 'foo'
yield assert_equal, res.outputs, None
class CommandLineInputSpec1(nib.CommandLineInputSpec):
foo = nib.traits.Str(argstr='%s', desc='a str')
goo = nib.traits.Bool(argstr='-g', desc='a bool', position=0)
hoo = nib.traits.List(argstr='-l %s', desc='a list')
moo = nib.traits.List(argstr='-i %d...',
desc='a repeated list',
position=-1)
noo = nib.traits.Int(argstr='-x %d', desc='an int')
roo = nib.traits.Str(desc='not on command line')
soo = nib.traits.Bool(argstr="-soo")
nib.CommandLine.input_spec = CommandLineInputSpec1
ci4 = nib.CommandLine(command='cmd')
ci4.inputs.foo = 'foo'
ci4.inputs.goo = True
ci4.inputs.hoo = ['a', 'b']
ci4.inputs.moo = [1, 2, 3]
ci4.inputs.noo = 0
ci4.inputs.roo = 'hello'
ci4.inputs.soo = False
cmd = ci4._parse_inputs()
yield assert_equal, cmd[0], '-g'
yield assert_equal, cmd[-1], '-i 1 -i 2 -i 3'
yield assert_true, 'hello' not in ' '.join(cmd)
yield assert_true, '-soo' not in ' '.join(cmd)
ci4.inputs.soo = True
cmd = ci4._parse_inputs()
yield assert_true, '-soo' in ' '.join(cmd)
class CommandLineInputSpec2(nib.CommandLineInputSpec):
foo = nib.File(argstr='%s', desc='a str', genfile=True)
nib.CommandLine.input_spec = CommandLineInputSpec2
ci5 = nib.CommandLine(command='cmd')
yield assert_raises, NotImplementedError, ci5._parse_inputs
class DerivedClass(nib.CommandLine):
input_spec = CommandLineInputSpec2
def _gen_filename(self, name):
return 'filename'
ci6 = DerivedClass(command='cmd')
yield assert_equal, ci6._parse_inputs()[0], 'filename'
nib.CommandLine.input_spec = nib.CommandLineInputSpec
def test_Commandline_environ(monkeypatch, tmpdir):
from nipype import config
config.set_default_config()
tmpdir.chdir()
monkeypatch.setitem(os.environ, 'DISPLAY', ':1')
# Test environment
ci3 = nib.CommandLine(command='echo')
res = ci3.run()
assert res.runtime.environ['DISPLAY'] == ':1'
# Test display_variable option
monkeypatch.delitem(os.environ, 'DISPLAY', raising=False)
config.set('execution', 'display_variable', ':3')
res = ci3.run()
assert not 'DISPLAY' in ci3.inputs.environ
assert not 'DISPLAY' in res.runtime.environ
# If the interface has _redirect_x then yes, it should be set
ci3._redirect_x = True
res = ci3.run()
assert res.runtime.environ['DISPLAY'] == ':3'
# Test overwrite
monkeypatch.setitem(os.environ, 'DISPLAY', ':1')
ci3.inputs.environ = {'DISPLAY': ':2'}
res = ci3.run()
assert res.runtime.environ['DISPLAY'] == ':2'
def test_CommandLine_output(tmpdir):
# Create one file
tmpdir.chdir()
file = tmpdir.join('foo.txt')
file.write('123456\n')
name = os.path.basename(file.strpath)
ci = nib.CommandLine(command='ls -l')
ci.terminal_output = 'allatonce'
res = ci.run()
assert res.runtime.merged == ''
assert name in res.runtime.stdout
# Check stdout is written
ci = nib.CommandLine(command='ls -l')
ci.terminal_output = 'file_stdout'
res = ci.run()
assert os.path.isfile('stdout.nipype')
assert name in res.runtime.stdout
tmpdir.join('stdout.nipype').remove(ignore_errors=True)
# Check stderr is written
ci = nib.CommandLine(command='ls -l')
ci.terminal_output = 'file_stderr'
res = ci.run()
assert os.path.isfile('stderr.nipype')
tmpdir.join('stderr.nipype').remove(ignore_errors=True)
# Check outputs are thrown away
ci = nib.CommandLine(command='ls -l')
ci.terminal_output = 'none'
res = ci.run()
assert res.runtime.stdout == '' and \
res.runtime.stderr == '' and \
res.runtime.merged == ''
# Check that new interfaces are set to default 'stream'
ci = nib.CommandLine(command='ls -l')
res = ci.run()
assert ci.terminal_output == 'stream'
assert name in res.runtime.stdout and \
res.runtime.stderr == ''
# Check only one file is generated
ci = nib.CommandLine(command='ls -l')
ci.terminal_output = 'file'
res = ci.run()
assert os.path.isfile('output.nipype')
assert name in res.runtime.merged and \
res.runtime.stdout == '' and \
res.runtime.stderr == ''
tmpdir.join('output.nipype').remove(ignore_errors=True)
# Check split files are generated
ci = nib.CommandLine(command='ls -l')
ci.terminal_output = 'file_split'
res = ci.run()
assert os.path.isfile('stdout.nipype')
assert os.path.isfile('stderr.nipype')
assert name in res.runtime.stdout
def test_global_CommandLine_output(setup_file):
tmp_infile = setup_file
tmpd, name = os.path.split(tmp_infile)
ci = nib.CommandLine(command='ls -l')
res = ci.run()
assert name in res.runtime.stdout
assert os.path.exists(tmp_infile)
nib.CommandLine.set_default_terminal_output('allatonce')
ci = nib.CommandLine(command='ls -l')
res = ci.run()
assert res.runtime.merged == ''
assert name in res.runtime.stdout
nib.CommandLine.set_default_terminal_output('file')
ci = nib.CommandLine(command='ls -l')
res = ci.run()
assert 'stdout.nipype' in res.runtime.stdout
nib.CommandLine.set_default_terminal_output('none')
ci = nib.CommandLine(command='ls -l')
res = ci.run()
assert res.runtime.stdout == ''
def test_global_CommandLine_output(tmpdir):
"""Ensures CommandLine.set_default_terminal_output works"""
from nipype.interfaces.fsl import BET
ci = nib.CommandLine(command='ls -l')
assert ci.terminal_output == 'stream' # default case
ci = BET()
assert ci.terminal_output == 'stream' # default case
nib.CommandLine.set_default_terminal_output('allatonce')
ci = nib.CommandLine(command='ls -l')
assert ci.terminal_output == 'allatonce'
nib.CommandLine.set_default_terminal_output('file')
ci = nib.CommandLine(command='ls -l')
assert ci.terminal_output == 'file'
# Check default affects derived interfaces
ci = BET()
assert ci.terminal_output == 'file'
def test_CommandLine_output(setup_file):
tmp_infile = setup_file
tmpd, name = os.path.split(tmp_infile)
assert os.path.exists(tmp_infile)
ci = nib.CommandLine(command='ls -l')
ci.inputs.terminal_output = 'allatonce'
res = ci.run()
assert res.runtime.merged == ''
assert name in res.runtime.stdout
ci = nib.CommandLine(command='ls -l')
ci.inputs.terminal_output = 'file'
res = ci.run()
assert 'stdout.nipype' in res.runtime.stdout
assert isinstance(res.runtime.stdout, (str, bytes))
ci = nib.CommandLine(command='ls -l')
ci.inputs.terminal_output = 'none'
res = ci.run()
assert res.runtime.stdout == ''
ci = nib.CommandLine(command='ls -l')
res = ci.run()
assert 'stdout.nipype' in res.runtime.stdout
def test_Commandline_environ():
from nipype import config
config.set_default_config()
ci3 = nib.CommandLine(command='echo')
res = ci3.run()
yield assert_equal, res.runtime.environ['DISPLAY'], ':1'
config.set('execution', 'display_variable', ':3')
res = ci3.run()
yield assert_false, 'DISPLAY' in ci3.inputs.environ
yield assert_equal, res.runtime.environ['DISPLAY'], ':3'
ci3.inputs.environ = {'DISPLAY': ':2'}
res = ci3.run()
yield assert_equal, res.runtime.environ['DISPLAY'], ':2'
def test_global_CommandLine_output():
tmp_infile = setup_file()
tmpd, name = os.path.split(tmp_infile)
pwd = os.getcwd()
os.chdir(tmpd)
ci = nib.CommandLine(command='ls -l')
res = ci.run()
yield assert_true, name in res.runtime.stdout
yield assert_true, os.path.exists(tmp_infile)
nib.CommandLine.set_default_terminal_output('allatonce')
ci = nib.CommandLine(command='ls -l')
res = ci.run()
yield assert_equal, res.runtime.merged, ''
yield assert_true, name in res.runtime.stdout
nib.CommandLine.set_default_terminal_output('file')
ci = nib.CommandLine(command='ls -l')
res = ci.run()
yield assert_true, 'stdout.nipype' in res.runtime.stdout
nib.CommandLine.set_default_terminal_output('none')
ci = nib.CommandLine(command='ls -l')
res = ci.run()
yield assert_equal, res.runtime.stdout, ''
os.chdir(pwd)
teardown_file(tmpd)
