def test_05_stdout(client):
"""Test stdout mapping."""
output = Path(client.path) / 'output.txt'
output.touch()
client.repo.index.add([str(output)])
client.repo.index.commit('add output')
argv = ['echo', 'Hello world!']
factory = CommandLineToolFactory(
argv,
directory=client.path,
working_dir=client.path,
stdout='output.txt',
)
assert 'output.txt' == factory.stdout
assert 'stdout' == factory.outputs[0].type
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_stdout_with_conflicting_arg(client):
"""Test stdout with conflicting argument value."""
output = Path(client.path) / 'lalala'
output.touch()
client.repo.index.add([str(output)])
client.repo.index.commit('add lalala')
argv = ['echo', 'lalala']
factory = CommandLineToolFactory(
argv,
directory=client.path,
working_dir=client.path,
stdout='lalala',
)
assert 'lalala' == factory.inputs[0].default
assert 'string' == factory.inputs[0].type
assert 'lalala' == factory.stdout
assert 'stdout' == factory.outputs[0].type
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(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_stdout_with_conflicting_arg(client):
"""Test stdout with conflicting argument value."""
output = Path(client.path) / "lalala"
output.touch()
client.repo.index.add([str(output)])
client.repo.index.commit("add lalala")
argv = ["echo", "lalala"]
factory = CommandLineToolFactory(
argv,
directory=client.path,
working_dir=client.path,
stdout="lalala",
)
assert "lalala" == factory.inputs[0].default
assert "string" == factory.inputs[0].type
assert "lalala" == factory.stdout
assert "stdout" == factory.outputs[0].type
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_05_stdout(client):
"""Test stdout mapping."""
output = Path(client.path) / "output.txt"
output.touch()
client.repo.index.add([str(output)])
client.repo.index.commit("add output")
argv = ["echo", "Hello world!"]
factory = CommandLineToolFactory(
argv,
directory=client.path,
working_dir=client.path,
stdout="output.txt",
)
assert "output.txt" == factory.stdout
assert "stdout" == factory.outputs[0].type
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_existing_output_directory(client, runner, project):
"""Test creation of InitialWorkDirRequirement for output."""
from renku.core.models.workflow.converters.cwl import CWLConverter
client.path = client.path
output = client.path / 'output'
argv = ['script', 'output']
factory = CommandLineToolFactory(
argv,
directory=client.path,
working_dir=client.path,
)
with factory.watch(client, no_output=True) as tool:
# Script creates the directory.
output.mkdir(parents=True)
run = factory.generate_process_run(client=client,
commit=client.repo.head.commit,
path='dummy.yaml')
cwl, _ = CWLConverter.convert(run.association.plan, client)
assert 0 == len([r for r in cwl.requirements if hasattr(r, 'listing')])
output.mkdir(parents=True, exist_ok=True)
with factory.watch(client) as tool:
# The directory already exists.
(output / 'result.txt').touch()
assert 1 == len(tool.inputs)
run = tool.generate_process_run(client=client,
commit=client.repo.head.commit,
path='dummy.yaml')
cwl, _ = CWLConverter.convert(run.association.plan, client)
reqs = [r for r in cwl.requirements if hasattr(r, 'listing')]
assert 1 == len(reqs)
assert output.name == reqs[0].listing[0].entryname
assert 1 == len(tool.outputs)
def test_stdin_and_stdout(argv, client):
"""Test stdout mapping."""
input_ = Path(client.path) / 'input.txt'
input_.touch()
output = Path(client.path) / 'output.txt'
output.touch()
error = Path(client.path) / 'error.log'
error.touch()
client.repo.index.add([str(input_), str(output), str(error)])
client.repo.index.commit('add files')
factory = CommandLineToolFactory(
argv,
directory=client.path,
working_dir=client.path,
stdin='input.txt',
stdout='output.txt',
stderr='error.log',
)
assert factory.stdin
if len(argv) > 1:
assert factory.arguments
assert 'output.txt' == factory.stdout
assert 'stdout' == factory.outputs[0].type
tool = factory.generate_process_run(client=client,
commit=client.repo.head.commit,
path='dummy.yaml')
tool = tool.association.plan
assert argv == tool.to_argv()
assert any(i.mapped_to and i.mapped_to.stream_type == 'stdin'
for i in tool.inputs)
assert any(o.mapped_to and o.mapped_to.stream_type == 'stdout'
for o in tool.outputs)
assert any(o.mapped_to and o.mapped_to.stream_type == 'stderr'
for o in tool.outputs)
def test_stdin_and_stdout(argv, client):
"""Test stdout mapping."""
input_ = Path(client.path) / "input.txt"
input_.touch()
output = Path(client.path) / "output.txt"
output.touch()
error = Path(client.path) / "error.log"
error.touch()
client.repo.index.add([str(input_), str(output), str(error)])
client.repo.index.commit("add files")
factory = CommandLineToolFactory(
argv,
directory=client.path,
working_dir=client.path,
stdin="input.txt",
stdout="output.txt",
stderr="error.log",
)
assert factory.stdin
if len(argv) > 1:
assert factory.arguments
assert "output.txt" == factory.stdout
assert "stdout" == factory.outputs[0].type
tool = factory.generate_process_run(client=client,
commit=client.repo.head.commit,
path="dummy.yaml")
tool = tool.association.plan
assert argv == tool.to_argv()
assert any(i.mapped_to and i.mapped_to.stream_type == "stdin"
for i in tool.inputs)
assert any(o.mapped_to and o.mapped_to.stream_type == "stdout"
for o in tool.outputs)
assert any(o.mapped_to and o.mapped_to.stream_type == "stderr"
for o in tool.outputs)
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()
def test_input_directory(client):
"""Test input directory."""
cwd = Path(client.path)
src = cwd / 'src'
src.mkdir(parents=True)
for i in range(5):
(src / str(i)).touch()
src_tar = cwd / 'src.tar'
src_tar.touch()
client.repo.index.add([str(src), str(src_tar)])
client.repo.index.commit('add file and folder')
argv = ['tar', 'czvf', 'src.tar', 'src']
factory = CommandLineToolFactory(
argv,
directory=client.path,
working_dir=client.path,
)
tool = factory.generate_process_run(client=client,
commit=client.repo.head.commit,
path='dummy.yaml')
tool = tool.association.plan
assert argv == tool.to_argv()
inputs = sorted(tool.inputs, key=lambda x: x.position)
assert src_tar.name == inputs[0].consumes.path
assert isinstance(inputs[0].consumes, Entity)
assert not isinstance(inputs[0].consumes, Collection)
assert inputs[1].consumes.path == src.name
assert isinstance(inputs[1].consumes, Collection)
