Add a database backend and migrations

Makefile

@@ -27,3 +27,6 @@ test:
 
 retest:
 	pytest -n 4 --lf
+
+revision:
+	cd thallium-backend && poetry run alembic revision --autogenerate -m CHANGEME

docker-compose.yml

@@ -17,11 +17,14 @@ services:
   thallium:
     build: thallium-backend
     restart: unless-stopped
-    command: ["src.app:fastapi_app", "--host", "0.0.0.0", "--port", "80", "--reload"]
+    command: ["alembic upgrade head && uvicorn src.app:fastapi_app --host 0.0.0.0 --port 8000 --reload"]
     volumes:
       - ./thallium-backend/src:/thallium/src:ro
     env_file:
       - .env
+    environment:
+      BACKEND_DATABASE_URL: postgresql+psycopg_async://thallium:thallium@postgres:5432/thallium
+      BACKEND_TOKEN: suitable-for-development-only
     ports:
       - "8000:80"
     depends_on:

pyproject.toml

@@ -54,13 +54,14 @@ ignore = [
 ]
 
 [tool.ruff.lint.isort]
-known-first-party = ["tests", "src"]
+known-first-party = ["tests", "src", "migrations"]
 order-by-type = false
 case-sensitive = true
 combine-as-imports = true
 
 [tool.ruff.lint.per-file-ignores]
-"*/tests/**" = ["D103", "S101"]
+"thallium-backend/tests/**" = ["D103", "S101"]
+"thallium-backend/migrations/*" = ["N999"]
 
 [tool.pytest.ini_options]
 # addopts = "--ignore=examples"

thallium-backend/.dockerignore

@@ -2,6 +2,8 @@
 **
 
 # Except what we need
+!alembic.ini
+!migrations
 !src
 !requirements.txt
 !LICENSE

thallium-backend/Dockerfile

@@ -1,9 +1,13 @@
-FROM --platform=linux/amd64 python:3.12-slim
+FROM python:3.12-slim
 
 # Define Git SHA build argument for sentry
 ARG git_sha="development"
 ENV GIT_SHA=$git_sha
 
+RUN apt update -y \
+  && apt install -y curl \
+  && rm -rf /var/lib/apt/lists/*
+
 # Install project dependencies
 WORKDIR /thallium
 COPY requirements.txt ./
@@ -12,5 +16,7 @@ RUN pip install -r requirements.txt
 # Copy the source code in last to optimize rebuilding the image
 COPY . .
 
-ENTRYPOINT ["uvicorn"]
-CMD ["src.app:fastapi_app", "--host", "0.0.0.0", "--port", "80"]
+HEALTHCHECK --start-period=5s --interval=30s --timeout=1s CMD curl http://localhost/heartbeat || exit 1
+
+ENTRYPOINT ["/bin/bash", "-c"]
+CMD ["alembic upgrade head && uvicorn src.app:fastapi_app --host 0.0.0.0 --port 8000"]

thallium-backend/alembic.ini

@@ -0,0 +1,53 @@
+# A generic, single database configuration.
+
+[alembic]
+script_location = migrations
+file_template = %%(epoch)s-%%(rev)s_%%(slug)s
+prepend_sys_path = .
+timezone = utc
+version_path_separator = os
+output_encoding = utf-8
+
+[post_write_hooks]
+hooks = ruff-lint, ruff-format
+ruff-lint.type = exec
+ruff-lint.executable = ruff
+ruff-lint.options = check --fix-only REVISION_SCRIPT_FILENAME
+
+ruff-format.type = exec
+ruff-format.executable = ruff
+ruff-format.options = format REVISION_SCRIPT_FILENAME
+
+[loggers]
+keys = root,sqlalchemy,alembic
+
+[handlers]
+keys = console
+
+[formatters]
+keys = generic
+
+[logger_root]
+level = WARN
+handlers = console
+qualname =
+
+[logger_sqlalchemy]
+level = WARN
+handlers =
+qualname = sqlalchemy.engine
+
+[logger_alembic]
+level = INFO
+handlers =
+qualname = alembic
+
+[handler_console]
+class = StreamHandler
+args = (sys.stderr,)
+level = NOTSET
+formatter = generic
+
+[formatter_generic]
+format = %(levelname)-5.5s [%(name)s] %(message)s
+datefmt = %H:%M:%S

thallium-backend/migrations/env.py

@@ -0,0 +1,86 @@
+import asyncio
+from logging.config import fileConfig
+
+from alembic import context
+from sqlalchemy import engine_from_config, pool
+from sqlalchemy.ext.asyncio import AsyncEngine
+from sqlalchemy.ext.asyncio.engine import AsyncConnection
+
+# This is a required step by Alembic to properly generate migrations
+import src.orm
+from src.settings import CONFIG
+
+target_metadata = src.orm.base.Base.metadata
+
+# this is the Alembic Config object, which provides
+# access to the values within the .ini file in use.
+config = context.config
+
+# Interpret the config file for Python logging.
+# This line sets up loggers basically.
+fileConfig(config.config_file_name)
+config.set_main_option("sqlalchemy.url", CONFIG.database_url.get_secret_value())
+
+
+def run_migrations_offline() -> None:
+    """
+    Run migrations in 'offline' mode.
+
+    This configures the context with just a URL
+    and not an Engine, though an Engine is acceptable
+    here as well.  By skipping the Engine creation
+    we don't even need a DBAPI to be available.
+
+    Calls to context.execute() here emit the given string to the
+    script output.
+
+    """
+    url = config.get_main_option("sqlalchemy.url")
+    context.configure(
+        url=url,
+        target_metadata=target_metadata,
+        literal_binds=True,
+        dialect_opts={"paramstyle": "named"},
+    )
+
+    with context.begin_transaction():
+        context.run_migrations()
+
+
+def do_run_migrations(connection: AsyncConnection) -> None:
+    """Run all migrations on the given connection."""
+    context.configure(
+        connection=connection,
+        target_metadata=target_metadata,
+        compare_type=True,
+        compare_server_default=True,
+    )
+
+    with context.begin_transaction():
+        context.run_migrations()
+
+
+async def run_migrations_online() -> None:
+    """
+    Run migrations in 'online' mode.
+
+    In this scenario we need to create an Engine
+    and associate a connection with the context.
+    """
+    connectable = AsyncEngine(
+        engine_from_config(
+            config.get_section(config.config_ini_section),
+            prefix="sqlalchemy.",
+            poolclass=pool.NullPool,
+            future=True,
+        ),
+    )
+
+    async with connectable.connect() as connection:
+        await connection.run_sync(do_run_migrations)
+
+
+if context.is_offline_mode():
+    run_migrations_offline()
+else:
+    asyncio.run(run_migrations_online())

thallium-backend/migrations/script.py.mako

@@ -0,0 +1,27 @@
+"""
+${message}
+
+Revision ID: ${up_revision}
+Revises: ${down_revision | comma,n}
+Create Date: ${create_date}
+"""
+import sqlalchemy as sa
+from alembic import op
+
+${imports if imports else ""}
+
+# revision identifiers, used by Alembic.
+revision = ${repr(up_revision)}
+down_revision = ${repr(down_revision)}
+branch_labels = ${repr(branch_labels)}
+depends_on = ${repr(depends_on)}
+
+
+def upgrade() -> None:
+    """Apply this migration."""
+    ${upgrades if upgrades else "pass"}
+
+
+def downgrade() -> None:
+    """Revert this migration."""
+    ${downgrades if downgrades else "pass"}

thallium-backend/src/__init__.py

@@ -1,7 +1,13 @@
+import asyncio
 import logging
+import os
 
 from src.settings import CONFIG
 
+# On Windows, the selector event loop is required for aiodns.
+if os.name == "nt":
+    asyncio.set_event_loop_policy(asyncio.WindowsSelectorEventLoopPolicy())
+
 # Console handler prints to terminal
 console_handler = logging.StreamHandler()
 level = logging.DEBUG if CONFIG.debug else logging.INFO

thallium-backend/src/orm/__init__.py

@@ -0,0 +1,12 @@
+"""Database models."""
+
+from .base import AuditBase, Base
+from .products import Product
+from .users import User
+
+__all__ = (
+    "AuditBase",
+    "Base",
+    "Product",
+    "User",
+)

thallium-backend/src/orm/base.py

@@ -0,0 +1,44 @@
+"""The base classes for ORM models."""
+
+import re
+from datetime import datetime
+from uuid import UUID, uuid4
+
+from pydantic import BaseModel
+from sqlalchemy.ext.asyncio import AsyncAttrs
+from sqlalchemy.orm import DeclarativeBase, Mapped, mapped_column
+from sqlalchemy.schema import MetaData
+from sqlalchemy.sql import func
+from sqlalchemy.types import DateTime
+
+NAMING_CONVENTIONS = {
+    "ix": "%(column_0_label)s_ix",
+    "uq": "%(table_name)s_%(column_0_name)s_uq",
+    "ck": "%(table_name)s_%(constraint_name)s_ck",
+    "fk": "%(table_name)s_%(column_0_name)s_%(referred_table_name)s_fk",
+    "pk": "%(table_name)s_pk",
+}
+table_name_regexp = re.compile("((?<=[a-z0-9])[A-Z]|(?!^)[A-Z](?=[a-z]))")
+
+
+class Base(AsyncAttrs, DeclarativeBase):
+    """Classes that inherit this class will be automatically mapped using declarative mapping."""
+
+    metadata = MetaData(naming_convention=NAMING_CONVENTIONS)
+
+    def patch_from_pydantic(self, pydantic_model: BaseModel) -> None:
+        """Patch this model using the given pydantic model, unspecified attributes remain the same."""
+        for key, value in pydantic_model.model_dump(exclude_unset=True).items():
+            setattr(self, key, value)
+
+
+class AuditBase:
+    """Base for declarative models with UUID primary keys and audit columns."""
+
+    id: Mapped[UUID] = mapped_column(default=uuid4, primary_key=True)
+    created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), server_default=func.now())
+    updated_at: Mapped[datetime] = mapped_column(
+        DateTime(timezone=True),
+        server_default=func.now(),
+        onupdate=func.now(),
+    )

thallium-backend/src/settings.py

@@ -1,9 +1,46 @@
-from pydantic_settings import BaseSettings
+import typing
+from collections.abc import AsyncGenerator
+from logging import getLogger
 
+import pydantic
+import pydantic_settings
+from fastapi import Depends
+from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker, create_async_engine
+
+log = getLogger(__name__)
+
+
+class _Config(
+    pydantic_settings.BaseSettings,
+    env_prefix="backend_",
+    env_file=".env",
+    env_file_encoding="utf-8",
+    env_nested_delimiter="__",
+    extra="ignore",
+):
+    """General configuration settings for the service."""
 
-class _CONFIG(BaseSettings, env_file=".env", env_file_encoding="utf-8"):
     debug: bool = False
     git_sha: str = "development"
 
+    database_url: pydantic.SecretStr
+    token: pydantic.SecretStr
+
+
+CONFIG = _Config()
+
+
+class Connections:
+    """How to connect to other, internal services."""
+
+    DB_ENGINE = create_async_engine(CONFIG.database_url.get_secret_value(), echo=CONFIG.debug)
+    DB_SESSION_MAKER = async_sessionmaker(DB_ENGINE)
+
+
+async def _get_db_session() -> AsyncGenerator[AsyncSession, None]:
+    """Yield a database session, for use with a FastAPI dependency."""
+    async with Connections.DB_SESSION_MAKER() as session, session.begin():
+        yield session
+
 
-CONFIG = _CONFIG()
+DBSession = typing.Annotated[AsyncSession, Depends(_get_db_session)]