adopt pytest-jupyter in test_server_extension

and trade sync requests for async tornado client

.github/workflows/run-tests.yml

@@ -26,16 +26,14 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -e .[testing]
+          pip install -e .[test]
       - name: Install SMART sandbox
         run: |
           git clone https://github.com/smart-on-fhir/smart-launcher-v2.git
           cd smart-launcher-v2
           git switch -c aa0f3b1 # Fix the version we use for the sandbox
           npm ci
           npm run build
-        env:
-          PORT: 5555
       - name: Run tests
         run: |
           pytest tests/

jupyter_smart_on_fhir/server_extension.py

@@ -1,12 +1,14 @@
 import base64
 import hashlib
+import json
 import secrets
 from urllib.parse import urlencode, urljoin
 
-import requests
 import tornado
 from jupyter_server.base.handlers import JupyterHandler
 from jupyter_server.extension.application import ExtensionApp
+from jupyter_server.utils import url_path_join
+from tornado.httpclient import AsyncHTTPClient
 from traitlets import List, Unicode
 
 from jupyter_smart_on_fhir.auth import SMARTConfig, generate_state
@@ -54,7 +56,7 @@ class SMARTAuthHandler(JupyterHandler):
     """Handler for SMART on FHIR authentication"""
 
     @tornado.web.authenticated
-    def get(self):
+    async def get(self):
         fhir_url = self.get_argument("iss")
         smart_config = SMARTConfig.from_url(fhir_url, self.request.full_url())
         self.settings["launch"] = self.get_argument("launch")
@@ -64,11 +66,11 @@ def get(self):
             self.settings["next_url"] = self.request.uri
             self.redirect(login_path)
         else:
-            data = self.get_data(token)
+            data = await self.get_data(token)
             self.write(f"Authorization success: Fetched {str(data)}")
             self.finish()
 
-    def get_data(self, token: str) -> dict:
+    async def get_data(self, token: str) -> dict:
         headers = {
             "Authorization": f"Bearer {token}",
             "Accept": "application/fhir+json",
@@ -77,11 +79,8 @@ def get_data(self, token: str) -> dict:
         url = (
             f"{self.settings['smart_config'].fhir_url}/Condition"  # Endpoint with data
         )
-        f = requests.get(url, headers=headers)
-        try:
-            return f.json()
-        except requests.exceptions.JSONDecodeError:
-            raise RuntimeError(f.text)
+        resp = await AsyncHTTPClient().fetch(url, headers=headers)
+        return json.loads(resp.body.decode("utf8", "replace"))
 
 
 class SMARTLoginHandler(JupyterHandler):
@@ -105,7 +104,9 @@ def get(self):
             "aud": smart_config.fhir_url,
             "state": state["state_id"],
             "launch": self.settings["launch"],
-            "redirect_uri": urljoin(self.request.full_url(), callback_path),
+            "redirect_uri": urljoin(
+                self.request.full_url(), url_path_join(self.base_url, callback_path)
+            ),
             "client_id": self.settings["client_id"],
             "code_challenge": code_challenge,
             "code_challenge_method": "S256",
@@ -118,35 +119,46 @@ def get(self):
 class SMARTCallbackHandler(JupyterHandler):
     """Callback handler for SMART on FHIR"""
 
-    def token_for_code(self, code: str) -> str:
+    async def token_for_code(self, code: str) -> str:
         data = dict(
             client_id=self.settings["client_id"],
             grant_type="authorization_code",
             code=code,
-            code_verifier=self.get_signed_cookie("code_verifier"),
-            redirect_uri=urljoin(self.request.full_url(), callback_path),
+            code_verifier=self.get_signed_cookie("code_verifier").decode("ascii"),
+            redirect_uri=urljoin(
+                self.request.full_url(), url_path_join(self.base_url, callback_path)
+            ),
         )
         headers = {"Content-Type": "application/x-www-form-urlencoded"}
-        token_reply = requests.post(
-            self.settings["smart_config"].token_url, data=data, headers=headers
+        token_reply = await AsyncHTTPClient().fetch(
+            self.settings["smart_config"].token_url,
+            body=urlencode(data),
+            headers=headers,
+            method="POST",
         )
-        return token_reply.json()["access_token"]
+        return json.loads(token_reply.body.decode("utf8", "replace"))["access_token"]
 
     @tornado.web.authenticated
-    def get(self):
+    async def get(self):
         if "error" in self.request.arguments:
             raise tornado.web.HTTPError(400, self.get_argument("error"))
         code = self.get_argument("code")
         if not code:
             raise tornado.web.HTTPError(
                 400, "Error: no code in response from FHIR server"
             )
-        state_id = self.get_signed_cookie("state_id").decode("utf-8")
-        if self.get_argument("state") != state_id:
+        state_id = self.get_signed_cookie("state_id", b"").decode("utf-8")
+        if not state_id:
+            raise tornado.web.HTTPError(400, "Error: missing state cookie")
+        arg_state = self.get_argument("state")
+        if not arg_state:
+            raise tornado.web.HTTPError(400, "Error: missing state argument")
+        if arg_state != state_id:
             raise tornado.web.HTTPError(
                 400, "Error: state received from FHIR server does not match"
             )
-        self.settings["smart_token"] = self.token_for_code(code)
+        self.settings["smart_token"] = await self.token_for_code(code)
+        next_url = self.settings["next_url"]
         self.redirect(self.settings["next_url"])
 
 

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "jupyter_smart_on_fhir"
-version = "0.1.0"
+version = "0.1.0.dev"
 dependencies = [
   "flask",
   "tornado",
@@ -16,7 +16,7 @@ dependencies = [
 ]
 
 [project.optional-dependencies]
-testing = ["pytest"]
+test = ["pytest", "pytest-jupyter[server]"]
 
 
 [tool.setuptools]

tests/conftest.py

@@ -9,14 +9,16 @@
 import pytest
 import requests
 
+pytest_plugins = ["pytest_jupyter.jupyter_server"]
+
 
 @pytest.fixture(scope="function")  # module?
 def sandbox():
     port = 5555
     os.environ["PORT"] = str(port)
     url = f"http://localhost:{port}"
     with subprocess.Popen(
-        ["npm", "run", "start:prod"], cwd=os.environ.get("SANDBOX_DIR", ".")
+        ["npm", "run", "start:prod"], cwd=os.environ["SANDBOX_DIR"]
     ) as sandbox_proc:
         wait_for_server(url)
         yield url

tests/test_server_extension.py

@@ -1,66 +1,40 @@
-import os
-import subprocess
+import json
+from http.cookies import SimpleCookie
+from urllib.parse import parse_qsl, urlparse, urlunparse
 
 import pytest
-import requests
-from conftest import SandboxConfig, wait_for_server
+from conftest import SandboxConfig
+from jupyter_server.utils import url_path_join
+from tornado.httpclient import AsyncHTTPClient, HTTPClientError
+from traitlets.config import Config
 
 from jupyter_smart_on_fhir.server_extension import callback_path, login_path, smart_path
 
-PORT = os.getenv("TEST_PORT", 18888)
-ext_url = f"http://localhost:{PORT}"
-
-
-def request_api(url, session=None, params=None, **kwargs):
-    query_args = {"token": "secret"}
-    query_args.update(params or {})
-    session = session or requests.Session()
-    return session.get(url, params=query_args, **kwargs)
-
 
 @pytest.fixture
-def jupyterdir(tmpdir):
-    path = tmpdir.join("jupyter")
-    path.mkdir()
-    return str(path)
+def client_id():
+    return "client_id"
 
 
 @pytest.fixture
-def jupyter_server(tmpdir, jupyterdir):
-    client_id = os.environ["CLIENT_ID"] = "client_id"
-    env = os.environ.copy()
-    # avoid interacting with user configuration, state
-    env["JUPYTER_CONFIG_DIR"] = str(tmpdir / "dotjupyter")
-    env["JUPYTER_RUNTIME_DIR"] = str(tmpdir / "runjupyter")
-
-    extension_command = ["jupyter", "server", "extension"]
-    command = [
-        "jupyter-server",
-        "--ServerApp.token=secret",
-        f"--SMARTExtensionApp.client_id={client_id}",
-        f"--port={PORT}",
-    ]
-    subprocess.check_call(
-        extension_command + ["enable", "jupyter_smart_on_fhir.server_extension"],
-        env=env,
-    )
+def jp_server_config(client_id):
+    c = Config()
+    c.ServerApp.jpserver_extensions = {"jupyter_smart_on_fhir.server_extension": True}
+    c.SMARTExtensionApp.client_id = client_id
 
-    # launch the server
-    with subprocess.Popen(command, cwd=jupyterdir, env=env) as jupyter_proc:
-        wait_for_server(ext_url)
-        yield jupyter_proc
-        jupyter_proc.terminate()
+    return c
 
 
-def test_uninformed_endpoint(jupyter_server):
-    response = request_api(ext_url + smart_path)
-    assert response.status_code == 400
+async def test_uninformed_endpoint(jp_fetch):
+    with pytest.raises(HTTPClientError) as e:
+        await jp_fetch(smart_path)
+    assert e.value.code == 400
 
 
-@pytest.fixture(scope="function")
-def public_client():
+@pytest.fixture
+def public_client(client_id):
     return SandboxConfig(
-        client_id=os.environ["CLIENT_ID"],
+        client_id=client_id,
         client_type=0,
         pkce_validation=2,
         # setting IDs so we omit login screen in sandbox; unsure I would test that flow
@@ -69,31 +43,75 @@ def public_client():
     )
 
 
-def test_login_handler(jupyter_server, sandbox, public_client):
-    """I think this test can be splitted in three with some engineering. Perhaps useful, not sure"""
-    session = requests.Session()
+async def test_login_handler(
+    http_server_client, jp_base_url, jp_fetch, jp_serverapp, sandbox, public_client
+):
+    """I think this test can be split in three with some engineering. Perhaps useful, not sure"""
     # Try endpoint and get redirected to login
     query = {"iss": f"{sandbox}/v/r4/fhir", "launch": public_client.get_launch_code()}
-    response = request_api(
-        ext_url + smart_path, params=query, allow_redirects=False, session=session
-    )
-    assert response.status_code == 302
+    with pytest.raises(HTTPClientError) as exc_info:
+        response = await jp_fetch(
+            smart_path,
+            params=query,
+            follow_redirects=False,
+        )
+    response = exc_info.value.response
+    assert response.code == 302
     assert response.headers["Location"] == login_path
 
     # Login with headers and get redirected to auth url
-    response = request_api(ext_url + login_path, session=session, allow_redirects=False)
-    assert response.status_code == 302
+    with pytest.raises(HTTPClientError) as exc_info:
+        response = await jp_fetch(login_path, follow_redirects=False)
+    response = exc_info.value.response
+    assert response.code == 302
     auth_url = response.headers["Location"]
     assert auth_url.startswith(sandbox)
+    cookie = SimpleCookie()
+    for c in response.headers.get_list("Set-Cookie"):
+        cookie.load(c)
 
     # Internally, get redirected to provider-auth
-    response = request_api(auth_url, session=session, allow_redirects=False)
-    assert response.status_code == 302
+    with pytest.raises(HTTPClientError) as exc_info:
+        http_client = AsyncHTTPClient()
+        response = await http_client.fetch(auth_url, follow_redirects=False)
+    response = exc_info.value.response
+    assert response.code == 302
     callback_url = response.headers["Location"]
-    assert callback_url.startswith(ext_url + callback_path)
-    assert "code=" in callback_url
-    response = request_api(callback_url, session=session)
-    assert response.status_code == 200
-    assert response.url.startswith(ext_url + smart_path)
-
-    # TODO: Should I test token existence? And how?
+    callback_url_parsed = urlparse(callback_url)
+    # strip proto://host for jp_fetch
+    server_callback_url = urlunparse(callback_url_parsed._replace(netloc="", scheme=""))
+    params = dict(parse_qsl(callback_url_parsed.query))
+    # SMART does different URL escaping
+    # SMART dev server appears to do some weird unescaping with callback URL
+    server_callback_url = server_callback_url.replace("@", "%40")
+    assert server_callback_url.startswith(url_path_join(jp_base_url, callback_path))
+    assert "code" in params
+
+    cookie_header = "; ".join(
+        f"{morsel.key}={morsel.coded_value}" for morsel in cookie.values()
+    )
+    with pytest.raises(HTTPClientError) as exc_info:
+        await jp_fetch(
+            callback_path,
+            params=params,
+            headers={"Cookie": cookie_header},
+            follow_redirects=False,
+        )
+    response = exc_info.value.response
+    assert response.code == 302
+    dest_url = response.headers["Location"]
+
+    # TODO: test dest_url?
+    assert urlparse(dest_url).path.startswith(url_path_join(jp_base_url, smart_path))
+
+    # verify that token was issued and works
+    assert "smart_token" in jp_serverapp.web_app.settings
+    token = jp_serverapp.web_app.settings["smart_token"]
+    smart_config = jp_serverapp.web_app.settings["smart_config"]
+    url = url_path_join(smart_config.fhir_url, "Condition")
+    resp = await http_client.fetch(url, headers={"Authorization": f"Bearer {token}"})
+    data = json.loads(resp.body.decode("utf8"))
+    assert data
+    assert isinstance(data, dict)
+    assert "resourceType" in data
+    assert data["resourceType"] == "Bundle"