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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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server/test/test_api.py
+28 -92
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)