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Add basic authentication in the server (#1670)

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* Add basic authentication in the server

A pattern for creating authentication methods is introduced, with three
authentication types defined:
  none - no authentication
  session - like the current session based auth used for user annotations
  test - used to test the login/logout process end to end

The config endpoint now returns informations about the authentication, like if
the user is authenticated and their username.  The redirect uri's for login and
logout are also returned if the authentication type requires login

This is the first a several PRs for authentication.

*. Update server tests to avoid hardcoded ports

test_api and test_nan_rest now use a common function for starting a test server,
than will initially choose a random port.
This commit is contained in:
bmccandless
2020-07-28 13:28:30 -07:00
committed by GitHub
parent bbef27b8c9
commit 5285556415
14 changed files with 498 additions and 132 deletions
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18
server/app/app.py
View File

@@ -85,6 +85,7 @@ def dataset_index(url_dataroot=None, dataset=None):
try:
cache_manager = current_app.matrix_data_cache_manager
with cache_manager.data_adaptor(url_dataroot, location, app_config) as data_adaptor:
data_adaptor.set_uri_path(f"{url_dataroot}/{dataset}")
dataset_title = app_config.get_title(data_adaptor)
return render_template(
"index.html", datasetTitle=dataset_title, SCRIPTS=scripts, INLINE_SCRIPTS=inline_scripts
@@ -143,6 +144,7 @@ def rest_get_data_adaptor(func):
def wrapped_function(self, dataset=None):
try:
with get_data_adaptor(self.url_dataroot, dataset) as data_adaptor:
data_adaptor.set_uri_path(f"{self.url_dataroot}/{dataset}")
return func(self, data_adaptor)
except DatasetAccessError as e:
return common_rest.abort_and_log(
@@ -160,6 +162,17 @@ def dataroot_test_index():
config = current_app.app_config
server_config = config.server_config
auth = server_config.auth
if auth.is_valid():
if server_config.auth.is_authenticated():
data += f"<p>Logged in as {auth.get_userid()} / {auth.get_username()}</p>"
if auth.requires_client_login():
if server_config.auth.is_authenticated():
data += "<p><a href='/logout'>Logout</a></p>"
else:
data += "<p><a href='/login'>Login</a></p>"
datasets = []
for dataroot_dict in server_config.multi_dataset__dataroot.values():
dataroot = dataroot_dict["dataroot"]
@@ -338,10 +351,15 @@ class Server:
lambda dataset, url_dataroot=url_dataroot: dataset_index(url_dataroot, dataset),
methods=["GET"],
)
else:
bp_api = Blueprint("api", __name__, url_prefix=api_version)
resources = get_api_resources(bp_api)
self.app.register_blueprint(resources.blueprint)
self.app.auth = server_config.auth
if self.app.auth.requires_client_login():
self.app.auth.add_url_rules(self.app)
self.app.matrix_data_cache_manager = server_config.matrix_data_cache_manager
self.app.app_config = app_config

6
server/auth/__init__.py Normal file
View File

@@ -0,0 +1,6 @@
# import the built in auth types so they can be registered
import server.auth.auth_none # noqa: F401
import server.auth.auth_test # noqa: F401
import server.auth.auth_session # noqa: F401

80
server/auth/auth.py Normal file
View File

@@ -0,0 +1,80 @@
from abc import ABC, abstractmethod
class AuthTypeBase(ABC):
"""Base type for all authentication types."""
def __init__(self):
super().__init__()
@abstractmethod
def set_params(self, params):
"""Set the parameters from app config. raise ConfigurationError if any params are invalid"""
pass
@abstractmethod
def is_valid(self):
"""Return True if the auth type can return user info (AuthTypeNone is the only one that cannot)"""
pass
def requires_client_login(self):
"""Return True if the user needs to login from the client (e.g. Login button is shown)"""
return False
@abstractmethod
def is_authenticated(self):
"""Return True if the user is authenticated"""
pass
@abstractmethod
def get_userid(self):
"""Return the id for this user (string)"""
pass
@abstractmethod
def get_username(self):
"""Return the name of the user (string)"""
pass
class AuthTypeClientBase(AuthTypeBase):
"""Base type for all authentication types that require the client to login"""
def __init__(self):
super().__init__()
def requires_client_login(self):
return True
@abstractmethod
def add_url_rules(self, selfapp):
"""Add url rules to the app (like /login, /logout, etc)"""
pass
@abstractmethod
def get_login_url(self, data_adaptor):
"""Return the url for the login route"""
pass
@abstractmethod
def get_logout_url(self, data_adaptor):
"""Return the url for the logout route"""
pass
class AuthTypeFactory:
"""Factory class to create an authentication type"""
auth_types = {}
@staticmethod
def register(name, auth_type):
assert(issubclass(auth_type, AuthTypeBase))
AuthTypeFactory.auth_types[name] = auth_type
@staticmethod
def create(name):
auth_type = AuthTypeFactory.auth_types.get(name)
if auth_type is None:
return None
return auth_type()

27
server/auth/auth_none.py Normal file
View File

@@ -0,0 +1,27 @@
from server.auth.auth import AuthTypeBase, AuthTypeFactory
from server.common.errors import ConfigurationError
class AuthTypeNone(AuthTypeBase):
def __init__(self):
super().__init__()
def is_valid(self):
return False
def set_params(self, params):
if params:
raise ConfigurationError("not expecting authentication parameters")
def is_authenticated(self):
return True
def get_userid(self):
return None
def get_username(self):
return None
AuthTypeFactory.register(None, AuthTypeNone)

36
server/auth/auth_session.py Normal file
View File

@@ -0,0 +1,36 @@
from server.auth.auth import AuthTypeBase, AuthTypeFactory
from flask import session
from uuid import uuid4
class AuthTypeSession(AuthTypeBase):
"""Session based authentication. The user is always logged. The user id is a random number
associated with the session. This is a good choice for desktop servers."""
# key in the session token for userid
CXGUID = "cxguid"
def __init__(self):
super().__init__()
def is_valid(self):
return True
def set_params(self, params):
return
def is_authenticated(self):
# always authenticated
return True
def get_userid(self):
if self.CXGUID not in session:
session[self.CXGUID] = uuid4().hex
session.permanent = True
return session[self.CXGUID]
def get_username(self):
return "anonymous"
AuthTypeFactory.register("session", AuthTypeSession)

69
server/auth/auth_test.py Normal file
View File

@@ -0,0 +1,69 @@
from server.auth.auth import AuthTypeClientBase, AuthTypeFactory
from flask import session, request, redirect, current_app
class AuthTypeTest(AuthTypeClientBase):
"""An authentication type for testing client based logins. When the login route is accessed
the user is automatically logged in with a default or configured username"""
# key in session token with userid and username
CXGUID = "cxguid_test"
CXGUNAME = "cxguname_test"
def __init__(self):
super().__init__()
self.username = "test_account"
self.userid = "id0001"
def is_valid(self):
return True
def requires_client_login(self):
return True
def add_url_rules(self, app):
app.add_url_rule("/login", "login", self.login, methods=["GET"])
app.add_url_rule("/logout", "logout", self.logout, methods=["GET"])
def set_params(self, params):
if params:
self.username = params.get("username", self.username)
self.userid = params.get("userid", self.userid)
def is_authenticated(self):
return self.CXGUID in session
def get_userid(self):
return session.get(self.CXGUID)
def get_username(self):
return session.get(self.CXGUNAME)
def login(self):
args = request.args
return_to = args.get("dataset", "/")
session[self.CXGUID] = args.get("userid", self.userid)
session[self.CXGUNAME] = args.get("username", self.username)
return redirect(return_to)
def logout(self):
session.clear()
return_to = request.args.get("dataset", "/")
return redirect(return_to)
def get_login_url(self, data_adaptor):
"""Return the url for the login route"""
if current_app.app_config.is_multi_dataset():
return f"/login?dataset={data_adaptor.uri_path}"
else:
return "/login"
def get_logout_url(self, data_adaptor):
"""Return the url for the logout route"""
if current_app.app_config.is_multi_dataset():
return f"/logout?dataset={data_adaptor.uri_path}"
else:
return "/logout"
AuthTypeFactory.register("test", AuthTypeTest)

19
server/common/annotations.py
View File

@@ -1,6 +1,5 @@
from datetime import datetime
import re
from uuid import uuid4
import os
import pandas as pd
from hashlib import blake2b
@@ -11,7 +10,7 @@ from server.common.errors import AnnotationsError, OntologyLoadFailure
from server.common.utils import series_to_schema
import fsspec
import fastobo
from flask import session
from flask import session, current_app
from abc import ABCMeta, abstractmethod
@@ -80,7 +79,6 @@ class Annotations(metaclass=ABCMeta):
class AnnotationsLocalFile(Annotations):
CXGUID = "cxguid"
CXG_ANNO_COLLECTION = "cxg_anno_collection"
def __init__(self, output_dir, output_file):
@@ -159,18 +157,12 @@ class AnnotationsLocalFile(Annotations):
self.last_fname = fname
self.last_labels = df
def _get_userid(self):
if self.CXGUID not in session:
session[self.CXGUID] = uuid4().hex
session.permanent = True
return session[self.CXGUID]
def _get_userdata_idhash(self, data_adaptor):
"""
Return a short hash that weakly identifies the user and dataset.
Used to create safe annotations output file names.
"""
uid = self._get_userid()
uid = current_app.auth.get_userid()
id = (uid + data_adaptor.get_location()).encode()
idhash = base64.b32encode(blake2b(id, digest_size=5).digest()).decode("utf-8")
return idhash
@@ -257,8 +249,9 @@ class AnnotationsLocalFile(Annotations):
elif session is not None:
collection = self.get_collection()
params["annotations-user-data-idhash"] = self._get_userdata_idhash(data_adaptor)
params["annotations-data-collection-is-read-only"] = False
params["annotations-data-collection-name"] = collection
if current_app.auth.is_authenticated():
params["annotations-user-data-idhash"] = self._get_userdata_idhash(data_adaptor)
params["annotations-data-collection-is-read-only"] = False
params["annotations-data-collection-name"] = collection
parameters.update(params)

39
server/common/app_config.py
View File

@@ -16,6 +16,7 @@ from server.common.annotations import AnnotationsLocalFile
from server.common.utils import custom_format_warning
import server.compute.diffexp_cxg as diffexp_tiledb
from server.common.data_locator import discover_s3_region_name
from server.auth.auth import AuthTypeFactory
DEFAULT_SERVER_PORT = 5005
# anything bigger than this will generate a special message
@@ -194,6 +195,7 @@ class AppConfig(object):
server_config = self.server_config
dataset_config = data_adaptor.dataset_config
annotation = dataset_config.user_annotations
auth = server_config.auth
# FIXME The current set of config is not consistently presented:
# we have camalCase, hyphen-text, and underscore_text
@@ -257,6 +259,18 @@ class AppConfig(object):
"diffexp_cellcount_max": server_config.limits__diffexp_cellcount_max,
}
if dataset_config.app__authentication_enable and auth.is_valid():
config["authentication"] = {
"is_authenticated": auth.is_authenticated(),
"requires_client_login": auth.requires_client_login(),
"username": auth.get_username(),
}
if auth.requires_client_login():
config["authentication"].update({
"login": auth.get_login_url(data_adaptor),
"logout" : auth.get_logout_url(data_adaptor),
})
return c
@@ -366,6 +380,7 @@ class ServerConfig(BaseConfig):
def __init__(self, app_config, default_config):
dictval_cases = [
("app", "csp_directives"),
("authentication", "params"),
("adaptor", "cxg_adaptor", "tiledb_ctx"),
("multi_dataset", "dataroot"),
]
@@ -384,6 +399,9 @@ class ServerConfig(BaseConfig):
self.app__server_timing_headers = dc["app"]["server_timing_headers"]
self.app__csp_directives = dc["app"]["csp_directives"]
self.authentication__type = dc["authentication"]["type"]
self.authentication__params = dc["authentication"]["params"]
self.multi_dataset__dataroot = dc["multi_dataset"]["dataroot"]
self.multi_dataset__index = dc["multi_dataset"]["index"]
self.multi_dataset__allowed_matrix_types = dc["multi_dataset"]["allowed_matrix_types"]
@@ -414,8 +432,12 @@ class ServerConfig(BaseConfig):
# The matrix data cache manager is created during the complete_config and stored here.
self.matrix_data_cache_manager = None
# The authentication object (BCM -- better name)
self.auth = None
def complete_config(self, context):
self.handle_app(context)
self.handle_authentication(context)
self.handle_data_locator(context)
self.handle_adaptor(context) # may depend on data_locator
self.handle_single_dataset(context) # may depend on adaptor
@@ -484,6 +506,14 @@ class ServerConfig(BaseConfig):
elif not isinstance(v, str):
raise ConfigurationError("CSP directive value must be a string or list of strings.")
def handle_authentication(self, context):
self.check_attr("authentication__type", (type(None), str))
self.check_attr("authentication__params", (type(None), dict))
self.auth = AuthTypeFactory.create(self.authentication__type)
if self.auth is None:
raise ConfigurationError(f"Unknown authentication type: {self.authentication__type}")
self.auth.set_params(self.authentication__params)
def handle_data_locator(self, context):
self.check_attr("data_locator__s3__region_name", (type(None), bool, str))
if self.data_locator__s3__region_name is True:
@@ -660,6 +690,7 @@ class DatasetConfig(BaseConfig):
self.app__inline_scripts = dc["app"]["inline_scripts"]
self.app__about_legal_tos = dc["app"]["about_legal_tos"]
self.app__about_legal_privacy = dc["app"]["about_legal_privacy"]
self.app__authentication_enable = dc["app"]["authentication_enable"]
self.presentation__max_categories = dc["presentation"]["max_categories"]
self.presentation__custom_colors = dc["presentation"]["custom_colors"]
@@ -696,6 +727,7 @@ class DatasetConfig(BaseConfig):
self.check_attr("app__inline_scripts", list)
self.check_attr("app__about_legal_tos", (type(None), str))
self.check_attr("app__about_legal_privacy", (type(None), str))
self.check_attr("app__authentication_enable", bool)
# scripts can be string (filename) or dict (attributes). Convert string to dict.
scripts = []
@@ -721,6 +753,13 @@ class DatasetConfig(BaseConfig):
self.check_attr("user_annotations__ontology__obo_location", (type(None), str))
if self.user_annotations__enable:
server_config = self.app_config.server_config
if not self.app__authentication_enable:
raise ConfigurationError("user annotations requires authentication to be enabled")
if not server_config.auth.is_valid():
auth_type = server_config.authentication__type
raise ConfigurationError(f"authentication method {auth_type} is not compatible with user annotations")
# TODO, replace this with a factory pattern once we have more than one way
# to do annotations. currently only local_file_csv
if self.user_annotations__type != "local_file_csv":

12
server/common/default_config.py
View File

@@ -14,6 +14,15 @@ server:
server_timing_headers: false
csp_directives: null
authentication:
# The authentication types may be "none" or "session"
# none: No authentication support, features like user_annotations must not be enabled.
# session: A session based userid is automatically generated.
type: session
# a dictionary of parameters that may be required for an authentication type
params: null
multi_dataset:
# If dataroot is set, then cellxgene may serve multiple datasets. This parameter is not
# compatible with single_dataset/datapath.
@@ -132,6 +141,9 @@ dataset:
about_legal_tos: null
about_legal_privacy: null
# allow authentication support
authentication_enable: true
presentation:
max_categories: 1000
custom_colors: true

5
server/data_common/data_adaptor.py
View File

@@ -28,6 +28,11 @@ class DataAdaptor(metaclass=ABCMeta):
# parameters set by this data adaptor based on the data.
self.parameters = {}
self.uri_path = None
def set_uri_path(self, path):
# uri path to the dataset, e.g. /d/<datasetname>
self.uri_path = path
@staticmethod
@abstractmethod

29
server/test/__init__.py
View File

@@ -86,15 +86,14 @@ def random_string(n):
return "".join(random.choice(string.ascii_letters) for _ in range(n))
@contextmanager
def test_server(command_line_args=[], app_config=None):
"""A context to run the cellxgene server.
def start_test_server(command_line_args=[], app_config=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
r = requests.get(f"{server}/...")
// check r
where the server can be accessed within the context, and is terminated when
the context is exited.
@@ -104,7 +103,8 @@ def test_server(command_line_args=[], app_config=None):
yaml config file, which this server will read and parse.
"""
port = int(os.environ.get("CXG_SERVER_PORT", DEFAULT_SERVER_PORT))
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 = ["cellxgene", "--no-upgrade-check", "launch", "--verbose", "--port=%d" % port] + command_line_args
@@ -128,10 +128,25 @@ def test_server(command_line_args=[], app_config=None):
if tempdir:
tempdir.cleanup()
return ps, server
def stop_test_server(ps):
try:
ps.terminate()
except ProcessLookupError:
pass
@contextmanager
def test_server(command_line_args=[], app_config=None):
"""A context to run the cellxgene server."""
ps, server = start_test_server(command_line_args, app_config)
try:
yield server
finally:
try:
ps.terminate()
stop_test_server(ps)
except ProcessLookupError:
pass

120
server/test/test_api.py
View File

@@ -2,7 +2,6 @@ import shutil
import time
import unittest
from http import HTTPStatus
from subprocess import Popen
import pandas as pd
import requests
@@ -11,6 +10,7 @@ import server.test.decode_fbs as decode_fbs
from server.data_common.matrix_loader import MatrixDataType
from server.test import data_with_tmp_annotations, make_fbs, PROJECT_ROOT
from server.test.test_datasets.fixtures import pbmc3k_colors
from server.test import start_test_server, stop_test_server
BAD_FILTER = {"filter": {"obs": {"annotation_value": [{"name": "xyz"}]}}}
@@ -21,9 +21,6 @@ BAD_FILTER = {"filter": {"obs": {"annotation_value": [{"name": "xyz"}]}}}
class EndPoints(object):
ANNOTATIONS_ENABLED = True
def setUp(self):
self.session = requests.Session()
def test_initialize(self):
endpoint = "schema"
url = f"{self.URL_BASE}{endpoint}"
@@ -308,13 +305,13 @@ class EndPoints(object):
def test_static(self):
endpoint = "static"
file = "assets/favicon.ico"
url = f"{self.LOCAL_URL}{endpoint}/{file}"
url = f"{self.server}/{endpoint}/{file}"
result = self.session.get(url)
self.assertEqual(result.status_code, HTTPStatus.OK)
@staticmethod
def _setUpClass(child_class, start_command):
child_class.ps = Popen(start_command)
def _setupClass(child_class, command_line):
child_class.ps, child_class.server = start_test_server(command_line)
child_class.URL_BASE = f"{child_class.server}/api/v0.2/"
child_class.session = requests.Session()
for i in range(90):
try:
@@ -323,13 +320,6 @@ class EndPoints(object):
except requests.exceptions.ConnectionError:
time.sleep(1)
@staticmethod
def _tearDownClass(child_class):
try:
child_class.ps.terminate()
except ProcessLookupError:
pass
class EndPointsAnnotations(EndPoints):
def test_get_schema_existing_writable(self):
@@ -385,32 +375,19 @@ class EndPointsAnnotations(EndPoints):
class EndPointsAnndata(unittest.TestCase, EndPoints):
"""Test Case for endpoints"""
PORT = 5010
LOCAL_URL = f"http://127.0.0.1:{PORT}/"
VERSION = "v0.2"
URL_BASE = f"{LOCAL_URL}api/{VERSION}/"
ANNOTATIONS_ENABLED = False
@classmethod
def setUpClass(cls):
cls._setUpClass(
cls,
[
"cellxgene",
"--no-upgrade-check",
"launch",
f"{PROJECT_ROOT}/example-dataset/pbmc3k.h5ad",
"--disable-annotations",
"--verbose",
"--experimental-enable-reembedding",
"--port",
str(cls.PORT),
],
)
cls._setupClass(cls, [
f"{PROJECT_ROOT}/example-dataset/pbmc3k.h5ad",
"--disable-annotations",
"--experimental-enable-reembedding",
])
@classmethod
def tearDownClass(cls):
cls._tearDownClass(cls)
stop_test_server(cls.ps)
@property
def annotations_enabled(self):
@@ -420,98 +397,57 @@ class EndPointsAnndata(unittest.TestCase, EndPoints):
class EndPointsCxg(unittest.TestCase, EndPoints):
"""Test Case for endpoints"""
PORT = 5011
LOCAL_URL = f"http://127.0.0.1:{PORT}/"
VERSION = "v0.2"
URL_BASE = f"{LOCAL_URL}api/{VERSION}/"
ANNOTATIONS_ENABLED = False
@classmethod
def setUpClass(cls):
cls._setUpClass(
cls,
[
"cellxgene",
"--no-upgrade-check",
"launch",
f"{PROJECT_ROOT}/server/test/test_datasets/pbmc3k.cxg",
"--disable-annotations",
"--verbose",
"--port",
str(cls.PORT),
],
)
cls._setupClass(cls, [
f"{PROJECT_ROOT}/server/test/test_datasets/pbmc3k.cxg",
"--disable-annotations",
])
@classmethod
def tearDownClass(cls):
cls._tearDownClass(cls)
stop_test_server(cls.ps)
class EndPointsAnndataAnnotations(unittest.TestCase, EndPointsAnnotations):
"""Test Case for endpoints"""
PORT = 5012
LOCAL_URL = f"http://127.0.0.1:{PORT}/"
VERSION = "v0.2"
URL_BASE = f"{LOCAL_URL}api/{VERSION}/"
ANNOTATIONS_ENABLED = True
MATRIX_DATA_TYPE = MatrixDataType.H5AD
@classmethod
def setUpClass(cls):
cls.data, cls.tmp_dir, cls.annotations = data_with_tmp_annotations(
MatrixDataType.H5AD, annotations_fixture=True
)
cls._setUpClass(
cls,
[
"cellxgene",
"--no-upgrade-check",
"launch",
"--annotations-file",
cls.annotations.output_file,
"--verbose",
"--port",
str(cls.PORT),
cls.data.get_location(),
],
)
cls._setupClass(cls, [
"--annotations-file",
cls.annotations.output_file,
cls.data.get_location(),
])
@classmethod
def tearDownClass(cls):
shutil.rmtree(cls.tmp_dir)
cls._tearDownClass(cls)
stop_test_server(cls.ps)
class EndPointsCxgAnnotations(unittest.TestCase, EndPointsAnnotations):
"""Test Case for endpoints"""
PORT = 5013
LOCAL_URL = f"http://127.0.0.1:{PORT}/"
VERSION = "v0.2"
URL_BASE = f"{LOCAL_URL}api/{VERSION}/"
ANNOTATIONS_ENABLED = True
MATRIX_DATA_TYPE = MatrixDataType.CXG
@classmethod
def setUpClass(cls):
cls.data, cls.tmp_dir, cls.annotations = data_with_tmp_annotations(MatrixDataType.CXG, annotations_fixture=True)
cls._setUpClass(
cls,
[
"cellxgene",
"--no-upgrade-check",
"launch",
"--annotations-file",
cls.annotations.output_file,
"--verbose",
"--port",
str(cls.PORT),
cls.data.get_location(),
],
)
cls._setupClass(cls, [
"--annotations-file",
cls.annotations.output_file,
cls.data.get_location(),
])
@classmethod
def tearDownClass(cls):
shutil.rmtree(cls.tmp_dir)
cls._tearDownClass(cls)
stop_test_server(cls.ps)

142
server/test/test_auth.py Normal file
View File

@@ -0,0 +1,142 @@
import unittest
from server.common.app_config import AppConfig
from server.test import PROJECT_ROOT, test_server
import requests
class AuthTest(unittest.TestCase):
def test_auth_none(self):
c = AppConfig()
c.update_server_config(
authentication__type=None, multi_dataset__dataroot=f"{PROJECT_ROOT}/server/test/test_datasets"
)
c.update_default_dataset_config(user_annotations__enable=False)
c.complete_config()
with test_server(app_config=c) as server:
session = requests.Session()
r = session.get(f"{server}/d/pbmc3k.cxg/api/v0.2/config")
data_config = r.json()
assert "authentication" not in data_config["config"]
def test_auth_session(self):
c = AppConfig()
c.update_server_config(
authentication__type="session", multi_dataset__dataroot=f"{PROJECT_ROOT}/server/test/test_datasets"
)
c.update_default_dataset_config(user_annotations__enable=True)
c.complete_config()
with test_server(app_config=c) as server:
session = requests.Session()
r = session.get(f"{server}/d/pbmc3k.cxg/api/v0.2/config")
data_config = r.json()
assert data_config["config"]["authentication"]["is_authenticated"]
assert not data_config["config"]["authentication"]["requires_client_login"]
assert data_config["config"]["authentication"]["username"] == "anonymous"
def test_auth_test(self):
c = AppConfig()
c.update_server_config(authentication__type="test")
c.update_server_config(
multi_dataset__dataroot=dict(
a1=dict(dataroot=f"{PROJECT_ROOT}/server/test/test_datasets", base_url="auth"),
a2=dict(dataroot=f"{PROJECT_ROOT}/server/test/test_datasets", base_url="no-auth"),
)
)
# specialize the configs
c.add_dataroot_config("a1", app__authentication_enable=True, user_annotations__enable=True)
c.add_dataroot_config("a2", app__authentication_enable=False, user_annotations__enable=False)
c.complete_config()
with test_server(app_config=c) as server:
session = requests.Session()
# auth datasets
r = session.get(f"{server}/auth/pbmc3k.cxg/api/v0.2/config")
data_config = r.json()
assert not data_config["config"]["authentication"]["is_authenticated"]
assert data_config["config"]["authentication"]["requires_client_login"]
assert data_config["config"]["authentication"]["username"] is None
assert data_config["config"]["parameters"]["annotations"]
login_uri = data_config["config"]["authentication"]["login"]
logout_uri = data_config["config"]["authentication"]["logout"]
assert login_uri == "/login?dataset=auth/pbmc3k.cxg"
assert logout_uri == "/logout?dataset=auth/pbmc3k.cxg"
r = session.get(f"{server}/{login_uri}")
# check that the login redirect worked
assert r.history[0].status_code == 302
assert r.url == f"{server}/auth/pbmc3k.cxg/"
r = session.get(f"{server}/auth/pbmc3k.cxg/api/v0.2/config")
data_config = r.json()
assert data_config["config"]["authentication"]["is_authenticated"]
assert data_config["config"]["authentication"]["username"] == "test_account"
assert data_config["config"]["parameters"]["annotations"]
r = session.get(f"{server}/{logout_uri}")
# check that the logout redirect worked
assert r.history[0].status_code == 302
assert r.url == f"{server}/auth/pbmc3k.cxg/"
r = session.get(f"{server}/auth/pbmc3k.cxg/api/v0.2/config")
data_config = r.json()
assert not data_config["config"]["authentication"]["is_authenticated"]
assert data_config["config"]["authentication"]["username"] is None
assert data_config["config"]["parameters"]["annotations"]
# no-auth datasets
r = session.get(f"{server}/no-auth/pbmc3k.cxg/api/v0.2/config")
data_config = r.json()
assert "authentication" not in data_config["config"]
assert not data_config["config"]["parameters"]["annotations"]
def test_auth_test_single(self):
c = AppConfig()
c.update_server_config(
authentication__type="test",
single_dataset__datapath=f"{PROJECT_ROOT}/server/test/test_datasets/pbmc3k.cxg")
c.complete_config()
with test_server(app_config=c) as server:
session = requests.Session()
r = session.get(f"{server}/api/v0.2/config")
data_config = r.json()
assert not data_config["config"]["authentication"]["is_authenticated"]
assert data_config["config"]["authentication"]["requires_client_login"]
assert data_config["config"]["authentication"]["username"] is None
assert data_config["config"]["parameters"]["annotations"]
login_uri = data_config["config"]["authentication"]["login"]
logout_uri = data_config["config"]["authentication"]["logout"]
assert login_uri == "/login"
assert logout_uri == "/logout"
r = session.get(f"{server}/{login_uri}")
# check that the login redirect worked
assert r.history[0].status_code == 302
assert r.url == f"{server}/"
r = session.get(f"{server}/api/v0.2/config")
data_config = r.json()
assert data_config["config"]["authentication"]["is_authenticated"]
assert data_config["config"]["authentication"]["username"] == "test_account"
assert data_config["config"]["parameters"]["annotations"]
r = session.get(f"{server}/{logout_uri}")
# check that the logout redirect worked
assert r.history[0].status_code == 302
assert r.url == f"{server}/"
r = session.get(f"{server}/api/v0.2/config")
data_config = r.json()
assert not data_config["config"]["authentication"]["is_authenticated"]
assert data_config["config"]["authentication"]["username"] is None
assert data_config["config"]["parameters"]["annotations"]

28
server/test/test_nan_rest.py
View File

@@ -1,17 +1,13 @@
from http import HTTPStatus
from subprocess import Popen
import unittest
import time
import math
from server.test import start_test_server, stop_test_server
import server.test.decode_fbs as decode_fbs
import requests
LOCAL_URL = "http://127.0.0.1:5006/"
VERSION = "v0.2"
URL_BASE = f"{LOCAL_URL}api/{VERSION}/"
BAD_FILTER = {"filter": {"obs": {"annotation_value": [{"name": "xyz"}]}}}
@@ -20,33 +16,25 @@ class WithNaNs(unittest.TestCase):
@classmethod
def setUpClass(cls):
cls.ps = Popen(["cellxgene", "launch", "test/test_datasets/nan.h5ad", "--verbose", "--port", "5006"])
session = requests.Session()
for i in range(90):
try:
session.get(f"{URL_BASE}schema")
except requests.exceptions.ConnectionError:
time.sleep(1)
cls.ps, cls.server = start_test_server(["test/test_datasets/nan.h5ad"])
@classmethod
def tearDownClass(cls):
try:
cls.ps.terminate()
except ProcessLookupError:
pass
stop_test_server(cls.ps)
def setUp(self):
self.session = requests.Session()
self.url_base = f"{self.server}/api/{VERSION}/"
def test_initialize(self):
endpoint = "schema"
url = f"{URL_BASE}{endpoint}"
url = f"{self.url_base}{endpoint}"
result = self.session.get(url)
self.assertEqual(result.status_code, HTTPStatus.OK)
def test_data(self):
endpoint = "data/var"
url = f"{URL_BASE}{endpoint}"
url = f"{self.url_base}{endpoint}"
filter = {"filter": {"var": {"index": [[0, 20]]}}}
result = self.session.put(url, json=filter)
self.assertEqual(result.status_code, HTTPStatus.OK)
@@ -56,7 +44,7 @@ class WithNaNs(unittest.TestCase):
def test_annotation_obs(self):
endpoint = "annotations/obs"
url = f"{URL_BASE}{endpoint}"
url = f"{self.url_base}{endpoint}"
result = self.session.get(url)
self.assertEqual(result.status_code, HTTPStatus.OK)
self.assertEqual(result.headers["Content-Type"], "application/octet-stream")
@@ -65,7 +53,7 @@ class WithNaNs(unittest.TestCase):
def test_annotation_var(self):
endpoint = "annotations/var"
url = f"{URL_BASE}{endpoint}"
url = f"{self.url_base}{endpoint}"
result = self.session.get(url)
self.assertEqual(result.status_code, HTTPStatus.OK)
self.assertEqual(result.headers["Content-Type"], "application/octet-stream")