Merge pull request #10 from bento-platform/chore/tests

chore: tests

.github/workflows/test.yml

@@ -0,0 +1,57 @@
+name: Test
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [ "3.10", "3.12" ]
+    services:
+      postgres:
+        image: postgres:16
+        env:
+          POSTGRES_DB: postgres
+          POSTGRES_PASSWORD: postgres
+          POSTGRES_USER: postgres
+        ports:
+          - 5432:5432
+        options: >-
+          --health-cmd pg_isready 
+          --health-interval 10s 
+          --health-timeout 5s 
+          --health-retries 5
+    steps:
+      - name: Tweak Postgres
+        run: |
+          docker exec ${{ job.services.postgres.id }} sh -c 'echo "max_connections=200" >> /var/lib/postgresql/data/postgresql.conf'
+          docker kill --signal=SIGHUP ${{ job.services.postgres.id }}
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        name: Set up Python
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install poetry
+        run: pip install poetry
+      - name: Install dependencies
+        run: poetry install
+      - name: Setup authz plugin
+        run: |
+          mkdir lib
+          cp authz_plugins/api_key/authz.module.py lib/
+          cp authz_plugins/api_key/example.env lib/.env
+      - name: Test
+        run: |
+          export DATABASE_URI="postgres://postgres:postgres@localhost:5432/postgres"
+          poetry run pytest -svv --cov=transcriptomics_data_service --cov-branch --cov-report xml
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+          verbose: true

authz_plugins/api_key/authz.module.py

@@ -1,6 +1,6 @@
 from logging import Logger
 from typing import Annotated, Any, Awaitable, Callable, Coroutine, Sequence
-from fastapi import Depends, FastAPI, HTTPException, Header, Request, Response
+from fastapi import Depends, HTTPException, Header, Request, Response
 from fastapi.responses import JSONResponse
 
 from transcriptomics_data_service.authz.middleware_base import BaseAuthzMiddleware
@@ -40,9 +40,6 @@ def __init__(self, config: Config, logger: Logger) -> None:
 
     # Middleware lifecycle
 
-    def attach(self, app: FastAPI):
-        app.middleware("http")(self.dispatch)
-
     async def dispatch(
         self, request: Request, call_next: Callable[[Request], Awaitable[Response]]
     ) -> Coroutine[Any, Any, Response]:

docker-compose.test.yaml

@@ -0,0 +1,33 @@
+# Standalone docker-compose file to run local tests using the PG database
+
+services:
+  tds:
+    build:
+      context: .
+      dockerfile: ./dev.Dockerfile
+    container_name: tds
+    depends_on:
+      - tds-db
+    environment:
+      - BENTO_UID=${UID}
+      - DATABASE_URI=postgres://tds_user:tds_password@tds-db:5432/tds_db
+      - CORS_ORIGINS="*"
+      - BENTO_AUTHZ_SERVICE_URL=""
+    volumes:
+      # Mounts local repository
+      - $PWD:/tds
+      # Use API key plugin for authz testing
+      - $PWD/authz_plugins/api_key:/tds/lib
+      - $PWD/authz_plugins/api_key/example.env:/tds/lib/.env # map example.env to .env
+    ports:
+      - "5000:5000"
+
+  tds-db:
+    image: postgres:16
+    container_name: tds-db
+    environment:
+      - POSTGRES_USER=tds_user
+      - POSTGRES_PASSWORD=tds_password
+      - POSTGRES_DB=tds_db
+    expose:
+      - 5432

test-docker.bash

@@ -0,0 +1,16 @@
+#!/usr/bin/env bash
+export UID=$(id -u)
+
+docker compose -f docker-compose.test.yaml down
+docker compose -f docker-compose.test.yaml up  -d --build --wait
+
+docker exec tds /bin/bash -c "
+    cd /tds &&
+    /poetry_user_install_dev.bash &&
+    pytest -svv --cov=transcriptomics_data_service --cov-branch &&
+    coverage html
+    "
+
+docker compose -f docker-compose.test.yaml down
+
+docker rmi transcriptomics_data_service-tds:latest

tests/conftest.py

@@ -0,0 +1,75 @@
+from typing import AsyncGenerator
+import asyncpg
+from fastapi.testclient import TestClient
+import pytest
+import os
+import pytest_asyncio
+from httpx._types import HeaderTypes
+
+from tests.test_db import TEST_EXPERIMENT_RESULT
+from transcriptomics_data_service.db import Database, get_db
+from transcriptomics_data_service.logger import get_logger
+
+os.environ["BENTO_DEBUG"] = "true"
+os.environ["BENTO_VALIDATE_SSL"] = "false"
+os.environ["CORS_ORIGINS"] = "*"
+os.environ["BENTO_AUTHZ_SERVICE_URL"] = "https://authz.local"
+
+from transcriptomics_data_service.config import Config, get_config
+from transcriptomics_data_service.main import app
+
+
+@pytest.fixture
+def config() -> Config:
+    return get_config()
+
+
+async def get_test_db() -> AsyncGenerator[Database, None]:
+    config = get_config()
+    db = Database(config, get_logger(config))
+    await db.initialize(pool_size=1)
+    yield db
+
+
+db_fixture = pytest_asyncio.fixture(get_test_db, name="db")
+
+
+@pytest_asyncio.fixture
+async def db_cleanup(db: Database):
+    yield
+    conn: asyncpg.Connection
+    async with db.connect() as conn:
+        await conn.execute(
+            """
+            DROP TABLE IF EXISTS gene_expressions;
+            DROP TABLE IF EXISTS experiment_results;
+            
+            DROP INDEX IF EXISTS idx_gene_code;
+            DROP INDEX IF EXISTS idx_sample_id;
+            DROP INDEX IF EXISTS idx_experiment_result_id;
+            """
+        )
+    await db.close()
+
+
+@pytest_asyncio.fixture
+async def db_with_experiment(db: Database):
+    await db.create_experiment_result(TEST_EXPERIMENT_RESULT)
+
+
+@pytest.fixture
+def test_client(db: Database):
+    with TestClient(app) as client:
+        app.dependency_overrides[get_db] = get_test_db
+        yield client
+
+
+@pytest.fixture
+def authz_headers(config) -> HeaderTypes:
+    api_key = config.model_extra.get("api_key")
+    return {"x-api-key": api_key}
+
+
+@pytest.fixture
+def authz_headers_bad() -> HeaderTypes:
+    return {"x-api-key": "bad key"}