def validate_cwl(cwl: str, cmd: Command = None, explore: bool = True):
parsed = yaml.load(cwl)
with tempfile.TemporaryDirectory() as tmpdir:
tmpdir = Path(tmpdir)
tmpfile = tmpdir / parsed["id"]
tmpfile.write_text(cwl)
loading_context, workflowobj, uri = fetch_document(str(tmpfile))
resolve_and_validate_document(loading_context, workflowobj, uri)
if cmd:
assert len(
workflowobj["inputs"]) == len(cmd.positional) + len(cmd.named)
def test_round_trip(bwamem_help):
command = parse_help(["bwa", "mem"], bwamem_help)
# Dump
buffer = StringIO()
yaml.dump(command, buffer)
# Load
buffer.seek(0)
output = yaml.load(buffer)
# Assert the round trip worked
assert command == output
def samtools_cmd():
with open(resource_filename(__name__,
"test_data/samtools/samtools.yml")) as fp:
return yaml.load(fp)
def validate_yml(yml: str, cmd: Command = None, explore=True):
stream = StringIO(yml)
yaml.load(stream)