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,
working_dir=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_04_output(client):
"""Test describtion of outputs from a command."""
hello = Path(client.path) / 'hello.tar'
hello.touch()
client.repo.index.add([str(hello)])
client.repo.index.commit('add hello.tar')
argv = ['tar', 'xf', 'hello.tar']
factory = CommandLineToolFactory(argv,
directory=client.path,
working_dir=client.path)
# simulate run
output = Path(client.path) / 'hello.txt'
output.touch()
parameters = list(factory.guess_outputs([output]))
assert 'File' == parameters[0][0].type
assert 'hello.txt' == parameters[0][0].outputBinding.glob
tool = factory.generate_process_run(client=client,
commit=client.repo.head.commit,
path='dummy.yaml')
tool = tool.association.plan
assert argv == tool.to_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,
working_dir=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_06_params(client):
"""Test referencing input parameters in other fields."""
hello = Path(client.path) / 'hello.tar'
hello.touch()
client.repo.index.add([str(hello)])
client.repo.index.commit('add hello.tar')
argv = ['tar', 'xf', 'hello.tar', 'goodbye.txt']
factory = CommandLineToolFactory(
argv,
directory=client.path,
working_dir=client.path,
)
assert 'goodbye.txt' == factory.inputs[1].default
assert 'string' == factory.inputs[1].type
assert 2 == factory.inputs[1].inputBinding.position
goodbye_id = factory.inputs[1].id
# simulate run
output = Path(client.path) / 'goodbye.txt'
output.touch()
parameters = list(factory.guess_outputs([output]))
assert 'File' == parameters[0][0].type
assert '$(inputs.{0})'.format(goodbye_id) == \
parameters[0][0].outputBinding.glob
tool = factory.generate_process_run(client=client,
commit=client.repo.head.commit,
path='dummy.yaml')
tool = tool.association.plan
assert argv == tool.to_argv()
def test_06_params(client):
"""Test referencing input parameters in other fields."""
hello = Path(client.path) / "hello.tar"
hello.touch()
client.repo.index.add([str(hello)])
client.repo.index.commit("add hello.tar")
argv = ["tar", "xf", "hello.tar", "goodbye.txt"]
factory = CommandLineToolFactory(
argv,
directory=client.path,
working_dir=client.path,
)
assert "goodbye.txt" == factory.inputs[1].default
assert "string" == factory.inputs[1].type
assert 2 == factory.inputs[1].inputBinding.position
goodbye_id = factory.inputs[1].id
# simulate run
output = Path(client.path) / "goodbye.txt"
output.touch()
parameters = list(factory.guess_outputs([output]))
assert "File" == parameters[0][0].type
assert "$(inputs.{0})".format(
goodbye_id) == parameters[0][0].outputBinding.glob
tool = factory.generate_process_run(client=client,
commit=client.repo.head.commit,
path="dummy.yaml")
tool = tool.association.plan
assert argv == tool.to_argv()