def _run_example(as_dict, out=None):
if not out:
out = _examples_path_for("test.cwl")
abstract_as_dict = from_dict(as_dict)
with open(out, "w") as f:
ordered_dump(abstract_as_dict, f)
check_abstract_def(abstract_as_dict)
# validate format2 workflows
enable_dev = "dev" in CWL_VERSION
loadingContext = LoadingContext()
loadingContext.enable_dev = enable_dev
loadingContext.loader = default_loader(
loadingContext.fetcher_constructor,
enable_dev=enable_dev,
)
loadingContext.resolver = getdefault(loadingContext.resolver, tool_resolver)
loadingContext, workflowobj, uri = fetch_document(out, loadingContext)
loadingContext, uri = resolve_and_validate_document(
loadingContext,
workflowobj,
uri,
)
return abstract_as_dict
def test_string_inputs():
for as_dict in _both_formats(STRING_INPUT):
abstract_as_dict = from_dict(as_dict)
assert abstract_as_dict["inputs"]["seed"]["type"] == "string"
assert abstract_as_dict["inputs"]["seed"]["default"] == "mycooldefault"
def test_float_inputs():
for as_dict in _both_formats(FLOAT_INPUT_DEFAULT):
abstract_as_dict = from_dict(as_dict)
assert abstract_as_dict["inputs"]["num_lines"]["type"] == "float"
assert abstract_as_dict["inputs"]["num_lines"]["default"] == 6.0
def test_int_inputs():
for as_dict in _both_formats(INT_INPUT):
abstract_as_dict = from_dict(as_dict)
assert abstract_as_dict["inputs"]["num_lines"]["type"] == "int"
def test_to_cwl_array():
for as_dict in _both_formats(RULES_TOOL):
abstract_as_dict = from_dict(as_dict)
assert abstract_as_dict["inputs"]["input_c"]["type"] == "File[]"
def test_to_cwl_optional():
for as_dict in _both_formats(OPTIONAL_INPUT):
abstract_as_dict = from_dict(as_dict)
assert abstract_as_dict["inputs"]["the_input"]["type"] == "File?"
def test_basic_workflow():
for as_dict in _both_formats(BASIC_WORKFLOW):
abstract_as_dict = from_dict(as_dict)
assert abstract_as_dict["label"] == "Simple workflow"
assert abstract_as_dict["doc"] == "Simple workflow that no-op cats a file and then selects 10 random lines.\n"
