def validate_wdl(wdl: str, cmd: Command = None, explore=True):
"""
:param explore: If true, we're in explore mode, and we should ignore subcommands
"""
try:
doc = parse_document(wdl)
except Error.SyntaxError as e:
print(wdl)
raise e
task = doc.tasks[0]
# task.inputs might be None
cmd_input_names = {inp.name for inp in task.inputs or []}
# Verify that every parameter has been documented
wdl_input_names = {meta for meta in task.parameter_meta.keys()}
assert cmd_input_names == wdl_input_names
# wdl_input_descriptions = {meta for meta in doc.tasks[0].parameter_meta.values()}
# cmd_input_descriptions = {arg.description for arg in [*cmd.subcommands, *cmd.named, *cmd.positional]}
# assert wdl_input_descriptions == cmd_input_descriptions, wdl_input_descriptions ^ cmd_input_descriptions
# Check that the generated WDL has the correct parameter meta fields
if cmd:
cmd_names = [arg.full_name() for arg in [*cmd.named, *cmd.positional]]
target = len(cmd.named) + len(cmd.positional)
# If we're not in explore mode, subcommands will be parsed as inputs
if not explore:
target += len(cmd.subcommands)
assert len(task.parameter_meta) == target, "{} vs {}".format(
task.parameter_meta.keys(), cmd_names)
# We should have all the official outputs, plus stdout
assert len(task.outputs) == len(cmd.outputs) + 1
def __find_workflow_meta(self, key):
"""Find value for a key in workflow's meta section
Returns:
None if key not found or any error occurs.
"""
try:
wdl = parse_document(self._wdl_str)
if key in wdl.workflow.meta:
return wdl.workflow.meta[key]
except:
pass
return None
def __init__(self, wdl):
"""Wraps miniwdl's parse_document().
"""
u = AutoURI(wdl)
if not u.exists:
raise FileNotFoundError(
'WDL does not exist: wdl={wdl}'.format(wdl=wdl))
self._wdl = wdl
self._wdl_contents = AutoURI(wdl).read()
try:
self._wdl_doc = parse_document(self._wdl_contents)
except Exception:
logger.error('Failed to parse WDL with miniwdl.')
self._wdl_doc = None
def test_docker_conversion(bedtools_cmd):
intersect = bedtools_cmd["intersect"]
container = "quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0"
intersect.docker_image = container
with tempfile.NamedTemporaryFile() as cwl_file:
CwlGenerator().save_to_file(intersect, path=Path(cwl_file.name))
cwl_file.seek(0)
parsed_cwl = yaml.load(cwl_file)
assert any([
hint["class"] == "DockerRequirement"
and hint["dockerPull"] == container for hint in parsed_cwl["hints"]
])
wdl = WdlGenerator().save_to_string(intersect)
parsed_wdl = parse_document(wdl).tasks[0]
assert parsed_wdl.runtime["docker"].literal.value == container