def test_06_params(instance_path):
"""Test referencing input parameters in other fields."""
hello = Path(instance_path) / 'hello.tar'
hello.touch()
argv = ['tar', 'xf', 'hello.tar', 'goodbye.txt']
factory = CommandLineToolFactory(
argv,
directory=instance_path,
)
assert factory.inputs[1].default == 'goodbye.txt'
assert factory.inputs[1].type == 'string'
assert factory.inputs[1].inputBinding.position == 2
goodbye_id = factory.inputs[1].id
# simulate run
output = Path(instance_path) / 'goodbye.txt'
output.touch()
parameters = list(factory.guess_outputs([output]))
assert parameters[0][0].type == 'File'
assert parameters[0][0].outputBinding.glob == \
'$(inputs.{0})'.format(goodbye_id)
tool = factory.generate_tool()
assert tool.to_argv() == argv
def test_input_directory(instance_path):
"""Test input directory."""
cwd = Path(instance_path)
src = cwd / 'src'
src.mkdir(parents=True)
for i in range(5):
(src / str(i)).touch()
argv = ['tar', 'czvf', 'src.tar', 'src']
factory = CommandLineToolFactory(
argv,
directory=instance_path,
working_dir=instance_path,
)
src_tar = src / 'src.tar'
src_tar.touch()
tool = factory.generate_tool()
assert tool.to_argv() == argv
assert tool.inputs[0].type == 'string'
assert tool.inputs[0].default == src_tar.name
assert tool.inputs[1].type == 'Directory'
assert tool.inputs[1].default.path.samefile(src)
def test_stdin_and_stdout(argv, instance_path):
"""Test stdout mapping."""
input_ = Path(instance_path) / 'input.txt'
input_.touch()
output = Path(instance_path) / 'output.txt'
output.touch()
factory = CommandLineToolFactory(
argv,
directory=instance_path,
working_dir=instance_path,
stdin='input.txt',
stdout='output.txt',
stderr='error.log',
)
assert factory.stdin
if len(argv) > 1:
assert factory.arguments
assert factory.stdout == 'output.txt'
assert factory.outputs[0].type == 'stdout'
tool = factory.generate_tool()
assert tool.to_argv() == argv
std_streams = ' < input.txt > output.txt 2> error.log'
assert str(tool) == ' '.join(argv) + std_streams
def test_05_stdout(instance_path):
"""Test stdout mapping."""
output = Path(instance_path) / 'output.txt'
output.touch()
argv = ['echo', 'Hello world!']
factory = CommandLineToolFactory(
argv,
directory=instance_path,
stdout='output.txt',
)
assert factory.stdout == 'output.txt'
assert factory.outputs[0].type == 'stdout'
tool = factory.generate_tool()
assert tool.to_argv() == argv
def test_stdout_with_conflicting_arg(instance_path):
"""Test stdout with conflicting argument value."""
output = Path(instance_path) / 'lalala'
output.touch()
argv = ['echo', 'lalala']
factory = CommandLineToolFactory(
argv,
directory=instance_path,
stdout='lalala',
)
assert factory.inputs[0].default == 'lalala'
assert factory.inputs[0].type == 'string'
assert factory.stdout == 'lalala'
assert factory.outputs[0].type == 'stdout'
tool = factory.generate_tool()
assert tool.to_argv() == argv
def test_04_output(instance_path):
"""Test describtion of outputs from a command."""
hello = Path(instance_path) / 'hello.tar'
hello.touch()
argv = ['tar', 'xf', 'hello.tar']
factory = CommandLineToolFactory(argv, directory=instance_path)
# simulate run
output = Path(instance_path) / 'hello.txt'
output.touch()
parameters = list(factory.guess_outputs([output]))
assert parameters[0][0].type == 'File'
assert parameters[0][0].outputBinding.glob == 'hello.txt'
tool = factory.generate_tool()
assert tool.to_argv() == argv
def test_stdin_and_stdout(argv, instance_path):
"""Test stdout mapping."""
input_ = Path(instance_path) / 'input.txt'
input_.touch()
output = Path(instance_path) / 'output.txt'
output.touch()
factory = CommandLineToolFactory(
argv,
directory=instance_path,
stdin='input.txt',
stdout='output.txt',
)
assert factory.stdin
if len(argv) > 1:
assert factory.arguments
assert factory.stdout == 'output.txt'
assert factory.outputs[0].type == 'stdout'
tool = factory.generate_tool()
assert tool.to_argv() == argv