def test_09_array_inputs(instance_path):
"""Test specification of input parameters in arrays."""
argv = [
'echo',
'-A',
'one',
'two',
'three',
'-B=four',
'-B=five',
'-B=six',
'-C=seven,eight,nine',
]
tool = CommandLineToolFactory(argv,
directory=instance_path).generate_tool()
# TODO add grouping for -A and -B
assert tool.inputs[-1].type == 'string[]'
assert tool.inputs[-1].default == ['seven', 'eight', 'nine']
assert tool.inputs[-1].inputBinding.prefix == '-C='
assert tool.inputs[-1].inputBinding.itemSeparator == ','
assert tool.inputs[-1].inputBinding.separate is False
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_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 run(client, no_output, success_codes, command_line):
"""Tracking work on a specific problem."""
working_dir = client.git.working_dir
paths = [x[0] for x in client.git.index.entries]
paths += client.git.untracked_files
candidates = [os.path.join(working_dir, path) for path in paths]
mapped_std = _mapped_std_streams(candidates)
factory = CommandLineToolFactory(command_line=command_line,
directory=os.getcwd(),
working_dir=working_dir,
successCodes=success_codes,
**{
name:
os.path.relpath(path, working_dir)
for name, path in mapped_std.items()
})
with client.with_workflow_storage() as wf:
with factory.watch(client, no_output=no_output) as tool:
returncode = call(
factory.command_line,
cwd=os.getcwd(),
**{key: getattr(sys, key)
for key in mapped_std.keys()},
)
if returncode not in (success_codes or {0}):
raise errors.InvalidSuccessCode(returncode,
success_codes=success_codes)
sys.stdout.flush()
sys.stderr.flush()
wf.add_step(run=tool)
def run(client, no_output, command_line):
"""Tracking work on a specific problem."""
working_dir = client.git.working_dir
candidates = [
os.path.join(working_dir, path)
for path in [x[0] for x in client.git.index.entries] +
client.git.untracked_files
]
mapped_std = _mapped_std_streams(candidates)
factory = CommandLineToolFactory(command_line=command_line,
directory=working_dir,
**{
name:
os.path.relpath(path, working_dir)
for name, path in mapped_std.items()
})
with client.with_workflow_storage() as wf:
with factory.watch(client, no_output=no_output) as tool:
call(
factory.command_line,
cwd=os.getcwd(),
**{key: getattr(sys, key)
for key in mapped_std.keys()},
)
sys.stdout.flush()
sys.stderr.flush()
wf.add_step(run=tool)
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_short_base_command_detection():
"""Test base command detection without arguments."""
tool = CommandLineToolFactory(('echo', 'A')).generate_tool()
assert tool.cwlVersion == 'v1.0'
assert tool.__class__.__name__ == 'CommandLineTool'
assert tool.inputs[0].default == 'A'
assert tool.to_argv() == ['echo', 'A']
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 run(client, outputs, no_output, success_codes, isolation, command_line):
"""Tracking work on a specific problem."""
working_dir = client.repo.working_dir
mapped_std = _mapped_std_streams(client.candidate_paths)
factory = CommandLineToolFactory(
command_line=command_line,
directory=os.getcwd(),
working_dir=working_dir,
successCodes=success_codes,
**{
name: os.path.relpath(path, working_dir)
for name, path in mapped_std.items()
}
)
with client.with_workflow_storage() as wf:
with factory.watch(
client, no_output=no_output, outputs=outputs
) as tool:
# Don't compute paths if storage is disabled.
if client.has_external_storage:
# Make sure all inputs are pulled from a storage.
paths_ = (
path
for _, path in tool.iter_input_files(client.workflow_path)
)
client.pull_paths_from_storage(*paths_)
returncode = call(
factory.command_line,
cwd=os.getcwd(),
**{key: getattr(sys, key)
for key in mapped_std.keys()},
)
if returncode not in (success_codes or {0}):
raise errors.InvalidSuccessCode(
returncode, success_codes=success_codes
)
sys.stdout.flush()
sys.stderr.flush()
wf.add_step(run=tool)
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 run(client, no_output, command_line):
"""Tracking work on a specific problem."""
candidates = [x[0] for x in client.git.index.entries] + \
client.git.untracked_files
mapped_std = _mapped_std_streams(candidates)
factory = CommandLineToolFactory(command_line=command_line, **mapped_std)
with client.with_workflow_storage() as wf:
with factory.watch(client, no_output=no_output) as tool:
call(
factory.command_line,
cwd=os.getcwd(),
**{key: getattr(sys, key)
for key in mapped_std.keys()},
)
sys.stdout.flush()
sys.stderr.flush()
wf.add_step(run=tool)
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 test_exitings_output_directory(client):
"""Test creation of InitialWorkDirRequirement for output directory."""
instance_path = client.path
output = client.path / 'output'
argv = ['script', 'output']
factory = CommandLineToolFactory(
argv,
directory=instance_path,
working_dir=instance_path,
)
with factory.watch(repo=client, no_output=True) as tool:
# Script creates the directory.
output.mkdir(parents=True)
initial_work_dir_requirement = [
r for r in tool.requirements
if r.__class__.__name__ == 'InitialWorkDirRequirement'
]
assert 0 == len(initial_work_dir_requirement)
output.mkdir(parents=True, exist_ok=True)
with factory.watch(repo=client) as tool:
# The directory already exists.
(output / 'result.txt').touch()
initial_work_dir_requirement = [
r for r in tool.requirements
if r.__class__.__name__ == 'InitialWorkDirRequirement'
]
assert 1 == len(initial_work_dir_requirement)
assert initial_work_dir_requirement[0].listing[0].entryname == output.name
assert 1 == len(tool.inputs)
assert 1 == len(tool.outputs)
def test_base_command_as_file_input(instance_path):
"""Test base command detection when it is a script file."""
cwd = Path(instance_path)
script = cwd / 'script.py'
script.touch()
input_file = cwd / 'input.csv'
input_file.touch()
argv = ['script.py', 'input.csv']
tool = CommandLineToolFactory(
argv,
directory=instance_path,
working_dir=instance_path,
).generate_tool()
assert not tool.baseCommand
assert 2 == len(tool.inputs)
def test_1st_tool():
"""Check creation of 1st tool example from args."""
tool = CommandLineToolFactory(('echo', 'Hello world!')).generate_tool()
assert tool.cwlVersion == 'v1.0'
assert tool.__class__.__name__ == 'CommandLineTool'
assert tool.inputs[0].default == 'Hello world!'