def test_get_api_base_url_works(self):
# test the api_base_url feature, and that it can contain a path
config = AppConfig()
backend_port = find_available_port("localhost", 10000)
config.update_server_config(
app__flask_secret_key="secret",
app__api_base_url=
f"http://localhost:{backend_port}/additional/path",
multi_dataset__dataroot=f"{PROJECT_ROOT}/example-dataset",
)
config.complete_config()
with test_server(["-p", str(backend_port)],
app_config=config) as server:
session = requests.Session()
self.assertEqual(server, f"http://localhost:{backend_port}")
response = session.get(
f"{server}/additional/path/d/pbmc3k.h5ad/api/v0.2/config")
self.assertEqual(response.status_code, 200)
data_config = response.json()
self.assertEqual(data_config["config"]["displayNames"]["dataset"],
"pbmc3k")
# test the health check at the correct url
response = session.get(f"{server}/additional/path/health")
assert response.json()["status"] == "pass"
def start_test_server(command_line_args=[], app_config=None, env=None):
"""
Command line arguments can be passed in, as well as an app_config.
This function is meant to be used like this, for example:
with test_server(...) as server:
r = requests.get(f"{server}/...")
// check r
where the server can be accessed within the context, and is terminated when
the context is exited.
The port is automatically set using find_available_port, unless passed in as a command line arg.
The verbose flag is automatically set to True.
If an app_config is provided, then this function writes a temporary
yaml config file, which this server will read and parse.
"""
command = ["cellxgene", "--no-upgrade-check", "launch", "--verbose"]
if "-p" in command_line_args:
port = int(command_line_args[command_line_args.index("-p") + 1])
elif "--port" in command_line_args:
port = int(command_line_args[command_line_args.index("--port") + 1])
else:
start = random.randint(DEFAULT_SERVER_PORT, 2**16 - 1)
port = int(os.environ.get("CXG_SERVER_PORT", start))
port = find_available_port("localhost", port)
command += ["--port=%d" % port]
command += command_line_args
tempdir = None
if app_config:
tempdir = tempfile.TemporaryDirectory()
config_file = os.path.join(tempdir.name, "config.yaml")
app_config.write_config(config_file)
command.extend(["-c", config_file])
server = f"http://localhost:{port}"
ps = Popen(command, env=env)
for _ in range(10):
try:
requests.get(f"{server}/health")
break
except requests.exceptions.ConnectionError:
time.sleep(1)
if tempdir:
tempdir.cleanup()
return ps, server
def handle_app(self, context):
self.validate_correct_type_of_configuration_attribute(
"app__verbose", bool)
self.validate_correct_type_of_configuration_attribute(
"app__debug", bool)
self.validate_correct_type_of_configuration_attribute("app__host", str)
self.validate_correct_type_of_configuration_attribute(
"app__port", (type(None), int))
self.validate_correct_type_of_configuration_attribute(
"app__open_browser", bool)
self.validate_correct_type_of_configuration_attribute(
"app__force_https", bool)
self.validate_correct_type_of_configuration_attribute(
"app__flask_secret_key", str)
self.validate_correct_type_of_configuration_attribute(
"app__generate_cache_control_headers", bool)
if self.app__port:
try:
if not is_port_available(self.app__host, self.app__port):
raise ConfigurationError(
f"The port selected {self.app__port} is in use, please configure an open port."
)
except OverflowError:
raise ConfigurationError(f"Invalid port: {self.app__port}")
else:
try:
default_server_port = int(
os.environ.get("CXG_SERVER_PORT", DEFAULT_SERVER_PORT))
except ValueError:
raise ConfigurationError(
"Invalid port from environment variable CXG_SERVER_PORT: "
+ os.environ.get("CXG_SERVER_PORT"))
try:
self.app__port = find_available_port(self.app__host,
default_server_port)
except OverflowError:
raise ConfigurationError(
f"Invalid port: {default_server_port}")
if self.app__debug:
context["messagefn"](
"in debug mode, setting verbose=True and open_browser=False")
self.app__verbose = True
self.app__open_browser = False
else:
warnings.formatwarning = custom_format_warning
if not self.app__verbose:
sys.tracebacklimit = 0
def handle_app(self, context):
self.validate_correct_type_of_configuration_attribute(
"app__verbose", bool)
self.validate_correct_type_of_configuration_attribute(
"app__debug", bool)
self.validate_correct_type_of_configuration_attribute("app__host", str)
self.validate_correct_type_of_configuration_attribute(
"app__port", (type(None), int))
self.validate_correct_type_of_configuration_attribute(
"app__open_browser", bool)
self.validate_correct_type_of_configuration_attribute(
"app__force_https", bool)
self.validate_correct_type_of_configuration_attribute(
"app__flask_secret_key", str)
self.validate_correct_type_of_configuration_attribute(
"app__generate_cache_control_headers", bool)
self.validate_correct_type_of_configuration_attribute(
"app__server_timing_headers", bool)
self.validate_correct_type_of_configuration_attribute(
"app__csp_directives", (type(None), dict))
self.validate_correct_type_of_configuration_attribute(
"app__api_base_url", (type(None), str))
self.validate_correct_type_of_configuration_attribute(
"app__web_base_url", (type(None), str))
if self.app__port:
try:
if not is_port_available(self.app__host, self.app__port):
raise ConfigurationError(
f"The port selected {self.app__port} is in use, please configure an open port."
)
except OverflowError:
raise ConfigurationError(f"Invalid port: {self.app__port}")
else:
try:
default_server_port = int(
os.environ.get("CXG_SERVER_PORT", DEFAULT_SERVER_PORT))
except ValueError:
raise ConfigurationError(
"Invalid port from environment variable CXG_SERVER_PORT: "
+ os.environ.get("CXG_SERVER_PORT"))
try:
self.app__port = find_available_port(self.app__host,
default_server_port)
except OverflowError:
raise ConfigurationError(
f"Invalid port: {default_server_port}")
if self.app__debug:
context["messagefn"](
"in debug mode, setting verbose=True and open_browser=False")
self.app__verbose = True
self.app__open_browser = False
else:
warnings.formatwarning = custom_format_warning
if not self.app__verbose:
sys.tracebacklimit = 0
# CSP Directives are a dict of string: list(string) or string: string
if self.app__csp_directives is not None:
for k, v in self.app__csp_directives.items():
if not isinstance(k, str):
raise ConfigurationError(
"CSP directive names must be a string.")
if isinstance(v, list):
for policy in v:
if not isinstance(policy, str):
raise ConfigurationError(
"CSP directive value must be a string or list of strings."
)
elif not isinstance(v, str):
raise ConfigurationError(
"CSP directive value must be a string or list of strings."
)
if self.app__web_base_url is None:
self.app__web_base_url = self.app__api_base_url