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Fix typevar passthrough to argparse with typing.Optional kwargs #83

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Merged
kislyuk merged 1 commit into from
Dec 12, 2017
Merged

Fix typevar passthrough to argparse with typing.Optional kwargs #83

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11 changes: 9 additions & 2 deletions hca/util/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -388,6 +388,13 @@ def _get_command_arg_settings(self, param_data):
else:
return dict(type=type(param_data.default), default=param_data.default)

def _get_param_argparse_type(self, anno):
if anno in {typing.List, typing.Mapping}:
return json.loads
elif isinstance(getattr(anno, "__args__", None), tuple) and anno == typing.Optional[anno.__args__[0]]:
return anno.__args__[0]
return anno

def build_argparse_subparsers(self, subparsers):
for method_name, method_data in self.methods.items():
subcommand_name = method_name.replace("_", "-")
Expand All @@ -398,9 +405,9 @@ def build_argparse_subparsers(self, subparsers):
continue
logger.debug("Registering %s %s %s", method_name, param_name, param.annotation)
nargs = "+" if param.annotation == typing.List else None
argparse_type = json.loads if param.annotation in {typing.List, typing.Mapping} else param.annotation
subparser.add_argument("--" + param_name.replace("_", "-").replace("/", "-"), dest=param_name,
type=argparse_type, nargs=nargs, help=method_data["args"][param_name]["doc"],
type=self._get_param_argparse_type(param.annotation), nargs=nargs,
help=method_data["args"][param_name]["doc"],
choices=method_data["args"][param_name]["choices"],
required=method_data["args"][param_name]["required"])
subparser.set_defaults(entry_point=method_data["entry_point"])
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9 changes: 9 additions & 0 deletions test/test_dss_cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,15 @@


class TestDssCLI(unittest.TestCase):
def test_post_search_cli(self):
query = json.dumps({})
replica = "aws"
args = ["dss", "post-search", "--es-query", query, "--replica", replica, "--output-format", "raw"]
with CapturingIO('stdout') as stdout:
hca.cli.main(args)
result = json.loads(stdout.captured())
self.assertIn("results", result)

def test_get_files_cli(self):
filename = "SRR2967608_1.fastq.gz"
dirpath = os.path.join(os.path.dirname(os.path.realpath(__file__)), "bundle")
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