async def test_api_post():
cromwell = api.CromwellAPI(server="http://httpbin:80", version="v1")
data = {
"workflowSource": None,
"workflowUrl": "http://my-test-url/hello.wdl",
"workflowInputs": "{'hello.text': 'Hello, world!'}",
"workflowOptions": "{}",
"labels": "{}",
}
# pylint: disable=W0212
(code, response) = await cromwell._api_call("/post", data=data, method="POST")
assert code == 200
assert response.get("files", {}).get("labels") == "{}"
assert (
response.get("files", {}).get("workflowInputs")
== "{'hello.text': 'Hello, world!'}"
)
assert (
response.get("files", {}).get("workflowUrl") == "http://my-test-url/hello.wdl"
)
assert response.get("files", {}).get("workflowOptions") == "{}"
assert "workflowSource" not in response.get("files", {})
await cromwell.close()
async def test_errors_on_post_workflows_no_workflow_source():
cromwell = api.CromwellAPI(server="http://httpbin", version="v1")
with pytest.raises(SystemExit):
await cromwell.post_workflows(workflowUrl=None, workflowSource=None)
await cromwell.close()
async def test_post_workflows_empty_params():
cromwell = api.CromwellAPI(
server="http://httpbin:80", version="v1", route_override="/post"
)
await cromwell.post_workflows(workflowUrl="https://foo/bar")
await cromwell.close()
async def test_errors_on_bad_response():
cromwell = api.CromwellAPI(server="http://httpbin", version="v1")
# pylint: disable=W0212
with pytest.raises(SystemExit):
await cromwell._api_call("/status/404")
await cromwell.close()
async def test_errors_on_unreachable_host():
cromwell = api.CromwellAPI(server="http://foo", version="v1")
# pylint: disable=W0212
with pytest.raises(SystemExit):
await cromwell._api_call("/bar")
await cromwell.close()
async def test_errors_on_unknown_http_method():
cromwell = api.CromwellAPI(server="http://httpbin:80", version="v1")
# pylint: disable=W0212
with pytest.raises(SystemExit):
await cromwell._api_call("/bar", method="BAZ")
await cromwell.close()
async def run() -> None:
parser = argparse.ArgumentParser(
description="An opinionated Cromwell orchestration system.")
# Common arguments
parser.add_argument("--cromwell-server", help="Cromwell host location.")
parser.add_argument("--cromwell-api-version", help="Cromwell API version.")
parser.add_argument(
"-f",
"--force",
default=False,
action="store_true",
help="Force running even with missing parameters.",
)
_args.add_batches_interval_arg(parser)
_args.add_loglevel_group(parser)
# Subparsers
subparsers = parser.add_subparsers(dest="subcommand")
for name, module in SUBCOMMANDS.items():
if not hasattr(module, "register_subparser") or not hasattr(
module, "call"):
errors.report(
f"Subcommand does not have required methods: {name}!",
fatal=True,
exitcode=errors.ERROR_INTERNAL_ERROR,
)
subparser = cast(Any, module).register_subparser(subparsers)
_args.add_loglevel_group(subparser)
args = vars(parser.parse_args())
for k, v in _config.read_config().items():
# if the user has not supplied a parameter on the command line, add the default
# value from the config to `args`.
if not k in args or not args[k]:
args[k] = v
if not args.get("force") and args.get("subcommand") not in [
"configure", "config"
]:
ensure_required_args(args)
if not args.get("subcommand"):
parser.print_help()
sys.exit(1)
logzero.loglevel(logging.WARN)
if args.get("verbose"):
logzero.loglevel(logging.INFO)
elif args.get("debug"):
logzero.loglevel(logging.DEBUG)
cromwell = api.CromwellAPI(server=args["cromwell_server"],
version=args["cromwell_api_version"])
await args["func"](args, cromwell)
await cromwell.close()
async def test_get_workflows():
cromwell = api.CromwellAPI(server="http://cromwell:8000", version="v1")
results = await cromwell.get_workflows_query()
assert len(results) == 5
for result in results:
assert result.get("status") == "Succeeded"
await cromwell.close()
async def test_api_get():
cromwell = api.CromwellAPI(server="http://httpbin:80", version="v1")
# pylint: disable=W0212
(code, response) = await cromwell._api_call(
"/get", params={"includeSubworkflows": "true"}
)
assert code == 200
assert response.get("args", {}).get("includeSubworkflows") == "true"
await cromwell.close()
async def test_post_workflows_with_params():
cromwell = api.CromwellAPI(
server="http://httpbin:80", version="v1", route_override="/post"
)
input_dict = {"input": "foo"}
option_dict = {"option": "bar"}
label_dict = {"label": "baz"}
response = await cromwell.post_workflows(
workflowUrl="https://foo/bar",
workflowInputs=json.dumps(input_dict),
workflowOptions=json.dumps(option_dict),
labels=json.dumps(label_dict),
)
assert json.loads(response.get("files").get("labels")) == label_dict
assert json.loads(response.get("files").get("workflowInputs")) == input_dict
assert json.loads(response.get("files").get("workflowOptions")) == option_dict
await cromwell.close()
async def test_get_workflows_backends_not_implemented():
with pytest.raises(NotImplementedError):
cromwell = api.CromwellAPI(server="http://cromwell:8000", version="v1")
await cromwell.get_workflows_backends()
async def test_post_workflows_query_not_implemented():
with pytest.raises(NotImplementedError):
cromwell = api.CromwellAPI(server="http://cromwell:8000", version="v1")
await cromwell.post_workflows_query()
