Add some UI tests

.github/workflows/server-pr.yaml

@@ -55,7 +55,7 @@ jobs:
       working-directory: ${{ github.workspace }}/server
       CLIENT_ID: ""
       CLIENT_SECRET: ""
-      DATABASE_URI: ""
+      DATABASE_URI: "sqlite:///test.db"
     steps:
       - uses: actions/checkout@v4
 

server/pyproject.toml

@@ -35,6 +35,7 @@ ruff = "^0.11.0"
 bandit = "^1.8.3"
 testcontainers = {extras = ["postgres"], version = "^4.10.0"}
 coverage = "^7.10.2"
+pyquery = "^2.0.1"
 
 [tool.poetry.scripts]
 start = "ttfd.main:main"

server/test/conftest.py

@@ -5,11 +5,14 @@
 from pathlib import Path
 
 import pytest
+from fastapi.testclient import TestClient
 from sqlalchemy import create_engine
-from sqlalchemy.orm import sessionmaker
+from sqlalchemy.orm import Session, sessionmaker
 from testcontainers.postgres import PostgresContainer
 
 from ttfd import abomination, crud
+from ttfd.deps import get_db
+from ttfd.main import app
 from ttfd.models import Base
 
 
@@ -25,7 +28,7 @@ def setup_postgres(request):
 @pytest.fixture(scope="session")
 def database(setup_postgres):
     """Populate the database with random data."""
-    engine = create_engine(os.environ["DATABASE_URI"], echo=True, future=True)
+    engine = create_engine(os.environ["DATABASE_URI"], echo=False, future=True)
     Base.metadata.create_all(engine)
     # Add data here
     # 1. Sample 1000 entries from TTFD data
@@ -46,9 +49,14 @@ def database(setup_postgres):
                 database=session,
                 name=metabolite,
                 common_name=metabolite,
-                size=0,
+                size=1,
                 human=False,
-                mol={},
+                mol={
+                    "atoms": [{"x": 0.0, "y": 0.0, "element": "N"}],
+                    "bonds": [],
+                    "width": 0.0,
+                    "height": 0.0,
+                },
                 categories=[],
             )
 
@@ -112,3 +120,16 @@ def regression_database(setup_postgres):
         yield session
 
     engine.dispose()
+
+
+@pytest.fixture
+def test_client(database: Session):
+    """Provide a http client to access the app in a test environment."""
+    def get_db_override():
+        return database
+
+    app.app.dependency_overrides[get_db] = get_db_override
+    client = TestClient(app)
+
+    yield client
+    app.app.dependency_overrides.clear()

server/test/test_ui.py

@@ -0,0 +1,66 @@
+"""Test the UI as the browser would see it."""
+
+from fastapi import status
+from pyquery import PyQuery as pq
+
+
+def test_ui_index_login_button(test_client):
+    response = test_client.get("/")
+    assert response.status_code == status.HTTP_200_OK
+    assert response.headers["content-type"] == "text/html; charset=utf-8"
+    doc = pq(response.text)
+    assert doc(".vib-auth-button").text() == "Login"
+
+    # Ensure the rest of the document is displayed too
+    assert "Theoretical Tracer Fate Detection" in doc.text()
+
+
+def test_ui_404_page(test_client):
+    response = test_client.get("/does-not-exist")
+    assert response.status_code == status.HTTP_404_NOT_FOUND
+    assert response.headers["content-type"] == "text/html; charset=utf-8"
+    doc = pq(response.text)
+    assert "Oops!" in doc.text()
+
+    # Ensure the rest of the document is displayed too
+    assert "Theoretical Tracer Fate Detection" in doc.text()
+
+
+def test_ui_existing_metabolite(test_client):
+    response = test_client.get("/atoms/L-LACTATE")
+    assert response.status_code == status.HTTP_200_OK
+    assert response.headers["content-type"] == "text/html; charset=utf-8"
+    doc = pq(response.text)
+    assert doc(".ttfd-button").text() == "Back"
+    assert len(doc(".ttfd-metabolite-container > svg")) == 1
+
+    # Ensure the rest of the document is displayed too
+    assert "Theoretical Tracer Fate Detection" in doc.text()
+
+
+def test_ui_nonexisting_metabolite(test_client):
+    response = test_client.get("/atoms/NOEXIST")
+    assert response.status_code == status.HTTP_404_NOT_FOUND
+    assert response.headers["content-type"] == "text/html; charset=utf-8"
+    doc = pq(response.text)
+    assert "Oops!" in doc.text()
+    assert "NOEXIST" in doc.text()
+
+    # Ensure the rest of the document is displayed too
+    assert "Theoretical Tracer Fate Detection" in doc.text()
+
+
+def test_ui_select_gauge(test_client):
+    response = test_client.get("/gauge/ALPHA-GLUCOSE/3,4")
+    assert response.status_code == status.HTTP_200_OK
+    assert response.headers["content-type"] == "text/html; charset=utf-8"
+    doc = pq(response.text)
+
+    assert {title.text for title in doc(".ttfd-metabolite-title")} == {
+        "GLT",
+        "UMP",
+        "L-LACTATE",
+    }
+
+    # Ensure the rest of the document is displayed too
+    assert "Theoretical Tracer Fate Detection" in doc.text()

server/ttfd/auth.py

@@ -172,13 +172,13 @@ def logout(
     if user is None:
         return response
 
-    if (session := request.session.get("token")) is None:
+    if (token := request.session.get("token")) is None:
         return response
-    if (login_session := crud.get_session(database, session)) is None:
+    if (session := crud.get_session_by_token(database, token)) is None:
         return response
 
     del request.session["token"]
-    database.delete(login_session)
+    database.delete(session)
     database.commit()
     return response
 

server/ttfd/auth_html_controllers.py

@@ -8,59 +8,57 @@
 from starlette.templating import _TemplateResponse
 
 from ttfd import crud
-from ttfd.auth import current_user
-from ttfd.context import user_context
+from ttfd.context import Context, user_context
 from ttfd.deps import get_db
-from ttfd.html_controllers import templates
-from ttfd.models import User
+from ttfd.templates import templates
 
 router = APIRouter()
 
 
 @router.get("/me", response_model=None)
 def me(
     request: Request,
-    user: Annotated[User | None, Depends(current_user)],
+    context: Annotated[Context, Depends(user_context)],
 ) -> _TemplateResponse | RedirectResponse:
     """Display the user info page for a logged in user."""
-    if user is None:
+    if "user" not in context:
         return RedirectResponse("/")
     return templates.TemplateResponse(
-        request=request, name="me.html", context=user_context(user)
+        request=request, name="me.html", context=dict(context)
     )
 
 
 @router.get("/me/apikey", response_model=None)
 def make_api_key_arguments(
     request: Request,
-    user: Annotated[User | None, Depends(current_user)],
+    context: Annotated[Context, Depends(user_context)],
 ) -> _TemplateResponse | RedirectResponse:
     """Display the API key creation form to the user."""
-    if user is None:
+    if "user" not in context:
         return RedirectResponse("/")
 
     return templates.TemplateResponse(
         request=request,
         name="create_api_key.html",
-        context=user_context(user),
+        context=dict(context),
     )
 
 
 @router.post("/me/apikey", response_model=None)
 def make_api_key(
     request: Request,
-    user: Annotated[User | None, Depends(current_user)],
+    context: Annotated[Context, Depends(user_context)],
     session: Annotated[Session, Depends(get_db)],
     keyname: Annotated[str, Form()],
 ) -> _TemplateResponse | RedirectResponse:
     """Create an API key."""
-    if user is None:
+    if (user := context.get("user")) is None:
         return RedirectResponse("/")
 
     api_key = crud.create_api_key(session, name=keyname, user=user)
 
     return templates.TemplateResponse(
         request=request,
         name="new_api_key.html",
-        context={"api_key": api_key} | user_context(user),
+        context={"api_key": api_key} | context,
     )

server/ttfd/context.py

@@ -4,11 +4,16 @@
 
 from dataclasses import dataclass
 from itertools import islice
-from typing import TYPE_CHECKING, Self, TypedDict, Unpack
+from typing import TYPE_CHECKING, Annotated, Self, TypedDict, Unpack
 
-from pydantic.tools import parse_obj_as
+from fastapi import Depends, Request
 
-from ttfd import molecule, schemas
+# This import is needed at _runtime_ by pydantic/fastapi
+from sqlalchemy.orm import Session  # noqa: TC002
+
+from ttfd import crud, deps, molecule, schemas
+from ttfd.auth import current_user
+from ttfd.config import settings
 
 if TYPE_CHECKING:
     from collections.abc import Callable, Iterable
@@ -29,6 +34,20 @@
 ]
 
 
+class AppContext(TypedDict, total=True):
+    """Context that all templates require."""
+
+    version: str
+    maintenance_mode: bool
+
+
+class Context(TypedDict, total=False):
+    """TTFD template context."""
+
+    ttfd: AppContext
+    user: User | None
+
+
 class HistoryData(TypedDict, total=False):
     """The data required to build a history context."""
 
@@ -297,7 +316,7 @@ def metabolite_image(
         "name": metabolite.name,
         "common_name": metabolite.common_name,
         "image": molecule.render(
-            parse_obj_as(schemas.Molecule, metabolite.mol),
+            schemas.Molecule.model_validate(metabolite.mol),
             selected=selected,
             labels=None,
             width=200,
@@ -328,9 +347,25 @@ def _selected_atoms_query(atoms: list[int]) -> Iterable[tuple[str, str]]:
     return (("selected", str(atom)) for atom in atoms)
 
 
-def user_context(user: User | None) -> dict[str, User]:
-    """Put the user into the context dictionary."""
-    if not user:
-        return {}
+def app_context(
+    session: Annotated[Session, Depends(deps.get_db)],
+) -> Context:
+    """Create the app context."""
+    return {
+        "ttfd": {
+            "version": settings.server_version,
+            "maintenance_mode": crud.in_maintenance_mode(session),
+        }
+    }
+
+
+def user_context(
+    request: Request,
+    app: Annotated[Context, Depends(app_context)],
+    session: Annotated[Session, Depends(deps.get_db)],
+) -> Context:
+    """Create the user context."""
+    if (user := current_user(request, session)) is None:
+        return app
 
-    return {"user": user}
+    return app | {"user": user}

server/ttfd/crud.py

@@ -9,7 +9,6 @@
 from operator import itemgetter
 from typing import TYPE_CHECKING
 
-from pydantic.tools import parse_obj_as
 from sqlalchemy import delete, select, text, update
 from sqlalchemy.dialects.postgresql import aggregate_order_by, insert
 from sqlalchemy.exc import SQLAlchemyError
@@ -577,7 +576,7 @@ def metabolites_for_path(
                 name=metabolite.name,
                 common_name=metabolite.common_name,
                 input_for_next_step=use,
-                mol=parse_obj_as(schemas.Molecule, metabolite.mol),
+                mol=schemas.Molecule.model_validate(metabolite.mol),
             )
             for (_, use, metabolite) in index_group
         ]
@@ -1007,6 +1006,13 @@ def get_session(database: Session, session_id: int) -> LoginSession | None:
     return database.execute(qry).scalar_one_or_none()
 
 
+def get_session_by_token(database: Session, token: str) -> LoginSession | None:
+    """Fetch a login session by its token."""
+    qry = select(LoginSession).where(LoginSession.token == token)
+
+    return database.execute(qry).scalar_one_or_none()
+
+
 def delete_all_sessions(database: Session, user_id: int) -> None:
     """Delete all login sessions for a user."""
     qry = delete(LoginSession).where(LoginSession.user_id == user_id)