def test_from_json(runner, invoke, path_join):
with runner.isolated_filesystem():
result = invoke(
"from",
"-o",
"output.avro",
"json",
path_join("data"),
"-s",
path_join("schema", "kf.avro"),
"--program",
"DEV",
"--project",
"test",
)
assert result.exit_code == 0, result.output
with open("output.avro", "rb") as f:
r = reader(f)
_test_schema(r)
data = list(r)
assert len(data) == 37
for record in data:
if record["name"] == "submitted_aligned_reads":
obj = record["object"]
if "soixantine_counterimpulse" in obj["submitter_id"]:
assert decode_enum(obj["state"]) == "validated"
assert decode_enum(obj["data_type"]) == "Aligned Reads"
assert decode_enum(
obj["data_category"]) == "Sequencing Reads"
assert decode_enum(obj["file_state"]) == "registered"
assert obj["file_format"] == "thumb_cotranspire"
assert obj["file_name"] == "virtuosi_conticent"
def _test_schema(r):
for node in r.writer_schema["fields"][2]["type"]:
if node["name"] == "experiment_metadata":
for field in node["fields"]:
if field["name"] == "state":
assert decode_enum(field["default"]) == "validated"
for type_ in field["type"]:
if isinstance(type_, dict) and type_["type"] == "enum":
for symbol in type_["symbols"]:
decode_enum(symbol)