def test_auth_invalid_key_format():
parser = OneCodexArgParser()
input_args = ["upload", "my_file.fasta",
"--api-key",
"my_api_key_is_too_short"]
args = parser.parse_args(input_args)
OneCodexAuth(args, check_for_update=False, creds_file=TEST_CREDS)
def test_cli_upload():
parser = OneCodexArgParser()
input_args = ["upload", "my_file.fasta", "--no-threads"]
args = parser.parse_args(input_args)
assert isinstance(args.file, list)
assert args.file[0] == "my_file.fasta"
assert args.threads is False
assert args.max_threads == onecodex.api_v0.DEFAULT_THREADS
def test_auth_login():
parser = OneCodexArgParser()
API_KEY = "12345678123456781234567812345678"
input_args = ["login"]
with mock.patch("getpass.getpass", return_value=API_KEY):
args = parser.parse_args(input_args)
assert not hasattr(args, "credentials")
OneCodexAuth(args, check_for_update=False, creds_file=TEST_CREDS)
assert hasattr(args, "credentials")
assert args.credentials["api_key"] == API_KEY
assert args.credentials["saved_at"] == datetime.datetime.now().strftime("%Y-%m-%d %H:%M")
assert args.credentials["updated_at"] is None # We disable checking in the test
def test_auth_w_32_len_cli_api_key():
parser = OneCodexArgParser()
API_KEY = "12345678123456781234567812345678"
input_args = ["upload", "my_file.fasta",
"--api-key", API_KEY]
args = parser.parse_args(input_args)
assert not hasattr(args, "credentials")
OneCodexAuth(args, check_for_update=False, creds_file=TEST_CREDS)
assert hasattr(args, "credentials")
assert args.credentials["api_key"] == API_KEY
assert args.credentials["saved_at"] is None
assert args.credentials["updated_at"] is None
def test_bad_aws_creds():
# we modify the env here so we have to clean up
replace_env = False
aws_access = None
aws_secret = None
if os.environ.get("AWS_ACCESS_KEY_ID"):
aws_access = os.environ["AWS_ACCESS_KEY_ID"]
replace_env = True
if os.environ.get("AWS_SECRET_ACCESS_KEY"):
aws_secret = os.environ["AWS_SECRET_ACCESS_KEY"]
replace_env = True
# set bad credentials in ENV
# then send the upload request
try:
os.environ["AWS_ACCESS_KEY_ID"] = "CRAPPYKEY"
os.environ["AWS_SECRET_ACCESS_KEY"] = "CRAPPYKEY"
API_KEY = "12345678123456781234567812345678"
parser = OneCodexArgParser()
input_args = ["--api-key", API_KEY, "upload", "big1.fastq"]
args = parser.parse_args(input_args)
OneCodexAuth(args, check_for_update=False, creds_file=TEST_CREDS)
assert hasattr(args, "credentials")
assert args.credentials["api_key"] == API_KEY
args.run(args)
# catch the expected exit
except SystemExit:
# clean up the crappy env vars
if replace_env:
os.environ["AWS_ACCESS_KEY_ID"] = aws_access
os.environ["AWS_SECRET_ACCESS_KEY"] = aws_secret
else:
del os.environ["AWS_ACCESS_KEY_ID"]
del os.environ["AWS_SECRET_ACCESS_KEY"]
# try and find the pidof aws
# aws should have been killed so this raises CalledProcessError
check_output(["pidof", "aws"])
except OSError:
raise SkipTest("Skipping test - no large fastq file present to test with")
def test_cli_help_exit_0():
parser = OneCodexArgParser()
input_args = ["--help"]
parser.parse_args(input_args)
def test_cli_references():
parser = OneCodexArgParser()
input_args = ["references"]
args = parser.parse_args(input_args)
assert isinstance(args.references, list)
assert len(args.references) == 0
def test_cli_analyses_table_error():
parser = OneCodexArgParser()
input_args = ["analyses", "uuid1", "uuid2", "--table"]
args = parser.parse_args(input_args)
args.run(args)
def test_cli_analyses():
parser = OneCodexArgParser()
input_args = ["analyses", "uuid1", "uuid2", "uuid3"]
args = parser.parse_args(input_args)
assert isinstance(args.analyses, list)
assert len(args.analyses) == 3
def test_cli_upload_req():
# Check for required args
parser = OneCodexArgParser()
input_args = ["upload"]
parser.parse_args(input_args)
def test_auth_logout():
parser = OneCodexArgParser()
input_args = ["logout"]
args = parser.parse_args(input_args)
OneCodexAuth(args, check_for_update=False, creds_file=TEST_CREDS)
assert not os.path.exists(TEST_CREDS)
def test_auth_login_file_already_exists():
parser = OneCodexArgParser()
input_args = ["login"]
args = parser.parse_args(input_args)
OneCodexAuth(args, check_for_update=False, creds_file=TEST_CREDS)
