def test_03_input(instance_path):
"""Check the essential input parameters."""
whale = Path(instance_path) / 'whale.txt'
whale.touch()
argv = [
'echo',
'-f',
'-i42',
'--example-string',
'hello',
'--file=whale.txt',
]
tool = CommandLineToolFactory(argv,
directory=instance_path).generate_tool()
assert tool.arguments[0].prefix == '-f'
assert tool.inputs[0].default == 42
assert tool.inputs[0].type == 'int'
assert tool.inputs[0].inputBinding.prefix == '-i'
assert tool.inputs[0].inputBinding.separate is False
assert tool.inputs[1].default == 'hello'
assert tool.inputs[1].type == 'string'
assert tool.inputs[1].inputBinding.prefix == '--example-string'
assert tool.inputs[1].inputBinding.separate is True
assert tool.inputs[2].default.path == Path('whale.txt')
assert tool.inputs[2].type == 'File'
assert tool.inputs[2].inputBinding.prefix == '--file='
assert tool.inputs[2].inputBinding.separate is False
assert tool.to_argv() == argv
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_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_base_command_detection(instance_path):
"""Test base command detection."""
hello = Path(instance_path) / 'hello.tar'
hello.touch()
argv = ['tar', 'xf', 'hello.tar']
tool = CommandLineToolFactory(argv,
directory=instance_path).generate_tool()
assert tool.baseCommand == ['tar', 'xf']
assert tool.inputs[0].default.path == Path('hello.tar')
assert tool.inputs[0].type == 'File'
assert tool.inputs[0].inputBinding.prefix is None
assert tool.inputs[0].inputBinding.separate is True
assert tool.to_argv() == argv
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
def worktree(
self,
path=None,
branch_name=None,
commit=None,
merge_args=('--ff-only', ),
):
"""Create new worktree."""
from git import GitCommandError, NULL_TREE
from renku._contexts import Isolation
delete = path is None
path = path or tempfile.mkdtemp()
branch_name = branch_name or 'renku/run/isolation/' + uuid.uuid4().hex
# TODO sys.argv
if commit is NULL_TREE:
args = ['add', '--detach', path]
self.repo.git.worktree(*args)
client = attr.evolve(self, path=path)
client.repo.git.checkout('--orphan', branch_name)
client.repo.git.rm('-rf', '*')
else:
args = ['add', '-b', branch_name, path]
if commit:
args.append(commit)
self.repo.git.worktree(*args)
client = attr.evolve(self, path=path)
client.repo.config_reader = self.repo.config_reader
# Keep current directory relative to repository root.
relative = Path('.').resolve().relative_to(self.path)
# Reroute standard streams
original_mapped_std = _mapped_std_streams(self.candidate_paths)
mapped_std = {}
for name, stream in original_mapped_std.items():
stream_path = Path(path) / (Path(stream).relative_to(self.path))
stream_path = stream_path.absolute()
if not stream_path.exists():
stream_path.parent.mkdir(parents=True, exist_ok=True)
stream_path.touch()
mapped_std[name] = stream_path
_clean_streams(self.repo, original_mapped_std)
new_cwd = Path(path) / relative
new_cwd.mkdir(parents=True, exist_ok=True)
with Isolation(cwd=str(new_cwd), **mapped_std):
yield client
try:
self.repo.git.merge(branch_name, *merge_args)
except GitCommandError:
raise errors.FailedMerge(self.repo)
if delete:
shutil.rmtree(path)
self.repo.git.worktree('prune')
self.checkout_paths_from_storage()
