def test_traverse_workflow_singularity() -> None:
"""Test container extraction tool using Singularity."""
loaded = parser.load_document(str(TEST_CWL.resolve()))
with TemporaryDirectory() as tmpdir:
for req in set(traverse(loaded)):
assert req.dockerPull
image_puller = SingularityImagePuller(req.dockerPull, tmpdir)
image_puller.save_docker_image()
def test_traverse_workflow() -> None:
"""Test container extraction tool using Docker."""
loaded = parser.load_document(str(TEST_CWL.resolve()))
with TemporaryDirectory() as tmpdir:
for req in set(traverse(loaded)):
assert req.dockerPull
image_puller = DockerImagePuller(req.dockerPull, tmpdir)
image_puller.save_docker_image()
_ = image_puller.generate_udocker_loading_command()
def test_v1_0_workflow_top_level_sf_expr_array() -> None:
"""Test for the correct error when converting a secondaryFiles expression (array form) in a workflow level input."""
with raises(WorkflowException, match=r".*secondaryFiles.*"):
result, modified = traverse0(
parser.load_document(
str(HERE / "../testdata/workflow_input_sf_expr_array.cwl")),
False,
False,
False,
False,
)
def test_v1_0_workflow_top_level_format_expr() -> None:
"""Test for the correct error when converting a format expression in a workflow level input."""
with raises(WorkflowException, match=r".*format specification.*"):
result, modified = traverse0(
parser.load_document(
str(HERE / "../testdata/workflow_input_format_expr.cwl")),
False,
False,
False,
False,
)
def main(args: argparse.Namespace) -> None:
"""Extract the docker reqs and download them using Singularity or docker."""
os.makedirs(args.dir, exist_ok=True)
top = cwl.load_document(args.input)
for req in traverse(top):
if not req.dockerPull:
print(
f"Unable to save image from {req} due to lack of 'dockerPull'."
)
continue
if args.singularity:
image_puller: ImagePuller = SingularityImagePuller(
req.dockerPull, args.dir)
else:
image_puller = DockerImagePuller(req.dockerPull, args.dir)
image_puller.save_docker_image()
def get_process_from_step(step: cwl.WorkflowStep) -> ProcessType:
"""Return the process for this step, loading it if necessary."""
if isinstance(step.run, str):
return cast(ProcessType, cwl.load_document(step.run))
return cast(ProcessType, step.run)
def test_traverse_workflow() -> None:
"""Test the citation extraction, simply."""
loaded = parser.load_document(str(TEST_CWL.resolve()))
traverse_workflow(loaded)
def main() -> int:
"""Load the first argument and extract the software requirements."""
top = cwl.load_document(sys.argv[1])
traverse(top)
return 0