labarchive-integration
Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/REDCap, for programmatic ELN workflows.
architecture-patterns
Implement proven backend architecture patterns including Clean Architecture, Hexagonal Architecture, and Domain-Driven Design. Use when architecting complex backend systems or refactoring existing applications for better maintainability.
Full skill instructions
Master proven backend architecture patterns including Clean Architecture, Hexagonal Architecture, and Domain-Driven Design to build maintainable, testable, and scalable systems.
Layers (dependency flows inward):
Key Principles:
Components:
Benefits:
Strategic Patterns:
Tactical Patterns:
app/
├── domain/ # Entities & business rules
│ ├── entities/
│ │ ├── user.py
│ │ └── order.py
│ ├── value_objects/
│ │ ├── email.py
│ │ └── money.py
│ └── interfaces/ # Abstract interfaces
│ ├── user_repository.py
│ └── payment_gateway.py
├── use_cases/ # Application business rules
│ ├── create_user.py
│ ├── process_order.py
│ └── send_notification.py
├── adapters/ # Interface implementations
│ ├── repositories/
│ │ ├── postgres_user_repository.py
│ │ └── redis_cache_repository.py
│ ├── controllers/
│ │ └── user_controller.py
│ └── gateways/
│ ├── stripe_payment_gateway.py
│ └── sendgrid_email_gateway.py
└── infrastructure/ # Framework & external concerns
├── database.py
├── config.py
└── logging.py
# domain/entities/user.py
from dataclasses import dataclass
from datetime import datetime
from typing import Optional
@dataclass
class User:
"""Core user entity - no framework dependencies."""
id: str
email: str
name: str
created_at: datetime
is_active: bool = True
def deactivate(self):
"""Business rule: deactivating user."""
self.is_active = False
def can_place_order(self) -> bool:
"""Business rule: active users can order."""
return self.is_active
# domain/interfaces/user_repository.py
from abc import ABC, abstractmethod
from typing import Optional, List
from domain.entities.user import User
class IUserRepository(ABC):
"""Port: defines contract, no implementation."""
@abstractmethod
async def find_by_id(self, user_id: str) -> Optional[User]:
pass
@abstractmethod
async def find_by_email(self, email: str) -> Optional[User]:
pass
@abstractmethod
async def save(self, user: User) -> User:
pass
@abstractmethod
async def delete(self, user_id: str) -> bool:
pass
# use_cases/create_user.py
from domain.entities.user import User
from domain.interfaces.user_repository import IUserRepository
from dataclasses import dataclass
from datetime import datetime
import uuid
@dataclass
class CreateUserRequest:
email: str
name: str
@dataclass
class CreateUserResponse:
user: User
success: bool
error: Optional[str] = None
class CreateUserUseCase:
"""Use case: orchestrates business logic."""
def __init__(self, user_repository: IUserRepository):
self.user_repository = user_repository
async def execute(self, request: CreateUserRequest) -> CreateUserResponse:
# Business validation
existing = await self.user_repository.find_by_email(request.email)
if existing:
return CreateUserResponse(
user=None,
success=False,
error="Email already exists"
)
# Create entity
user = User(
id=str(uuid.uuid4()),
email=request.email,
name=request.name,
created_at=datetime.now(),
is_active=True
)
# Persist
saved_user = await self.user_repository.save(user)
return CreateUserResponse(
user=saved_user,
success=True
)
# adapters/repositories/postgres_user_repository.py
from domain.interfaces.user_repository import IUserRepository
from domain.entities.user import User
from typing import Optional
import asyncpg
class PostgresUserRepository(IUserRepository):
"""Adapter: PostgreSQL implementation."""
def __init__(self, pool: asyncpg.Pool):
self.pool = pool
async def find_by_id(self, user_id: str) -> Optional[User]:
async with self.pool.acquire() as conn:
row = await conn.fetchrow(
"SELECT * FROM users WHERE id = $1", user_id
)
return self._to_entity(row) if row else None
async def find_by_email(self, email: str) -> Optional[User]:
async with self.pool.acquire() as conn:
row = await conn.fetchrow(
"SELECT * FROM users WHERE email = $1", email
)
return self._to_entity(row) if row else None
async def save(self, user: User) -> User:
async with self.pool.acquire() as conn:
await conn.execute(
"""
INSERT INTO users (id, email, name, created_at, is_active)
VALUES ($1, $2, $3, $4, $5)
ON CONFLICT (id) DO UPDATE
SET email = $2, name = $3, is_active = $5
""",
user.id, user.email, user.name, user.created_at, user.is_active
)
return user
async def delete(self, user_id: str) -> bool:
async with self.pool.acquire() as conn:
result = await conn.execute(
"DELETE FROM users WHERE id = $1", user_id
)
return result == "DELETE 1"
def _to_entity(self, row) -> User:
"""Map database row to entity."""
return User(
id=row["id"],
email=row["email"],
name=row["name"],
created_at=row["created_at"],
is_active=row["is_active"]
)
# adapters/controllers/user_controller.py
from fastapi import APIRouter, Depends, HTTPException
from use_cases.create_user import CreateUserUseCase, CreateUserRequest
from pydantic import BaseModel
router = APIRouter()
class CreateUserDTO(BaseModel):
email: str
name: str
@router.post("/users")
async def create_user(
dto: CreateUserDTO,
use_case: CreateUserUseCase = Depends(get_create_user_use_case)
):
"""Controller: handles HTTP concerns only."""
request = CreateUserRequest(email=dto.email, name=dto.name)
response = await use_case.execute(request)
if not response.success:
raise HTTPException(status_code=400, detail=response.error)
return {"user": response.user}
# Core domain (hexagon center)
class OrderService:
"""Domain service - no infrastructure dependencies."""
def __init__(
self,
order_repository: OrderRepositoryPort,
payment_gateway: PaymentGatewayPort,
notification_service: NotificationPort
):
self.orders = order_repository
self.payments = payment_gateway
self.notifications = notification_service
async def place_order(self, order: Order) -> OrderResult:
# Business logic
if not order.is_valid():
return OrderResult(success=False, error="Invalid order")
# Use ports (interfaces)
payment = await self.payments.charge(
amount=order.total,
customer=order.customer_id
)
if not payment.success:
return OrderResult(success=False, error="Payment failed")
order.mark_as_paid()
saved_order = await self.orders.save(order)
await self.notifications.send(
to=order.customer_email,
subject="Order confirmed",
body=f"Order {order.id} confirmed"
)
return OrderResult(success=True, order=saved_order)
# Ports (interfaces)
class OrderRepositoryPort(ABC):
@abstractmethod
async def save(self, order: Order) -> Order:
pass
class PaymentGatewayPort(ABC):
@abstractmethod
async def charge(self, amount: Money, customer: str) -> PaymentResult:
pass
class NotificationPort(ABC):
@abstractmethod
async def send(self, to: str, subject: str, body: str):
pass
# Adapters (implementations)
class StripePaymentAdapter(PaymentGatewayPort):
"""Primary adapter: connects to Stripe API."""
def __init__(self, api_key: str):
self.stripe = stripe
self.stripe.api_key = api_key
async def charge(self, amount: Money, customer: str) -> PaymentResult:
try:
charge = self.stripe.Charge.create(
amount=amount.cents,
currency=amount.currency,
customer=customer
)
return PaymentResult(success=True, transaction_id=charge.id)
except stripe.error.CardError as e:
return PaymentResult(success=False, error=str(e))
class MockPaymentAdapter(PaymentGatewayPort):
"""Test adapter: no external dependencies."""
async def charge(self, amount: Money, customer: str) -> PaymentResult:
return PaymentResult(success=True, transaction_id="mock-123")
# Value Objects (immutable)
from dataclasses import dataclass
from typing import Optional
@dataclass(frozen=True)
class Email:
"""Value object: validated email."""
value: str
def __post_init__(self):
if "@" not in self.value:
raise ValueError("Invalid email")
@dataclass(frozen=True)
class Money:
"""Value object: amount with currency."""
amount: int # cents
currency: str
def add(self, other: "Money") -> "Money":
if self.currency != other.currency:
raise ValueError("Currency mismatch")
return Money(self.amount + other.amount, self.currency)
# Entities (with identity)
class Order:
"""Entity: has identity, mutable state."""
def __init__(self, id: str, customer: Customer):
self.id = id
self.customer = customer
self.items: List[OrderItem] = []
self.status = OrderStatus.PENDING
self._events: List[DomainEvent] = []
def add_item(self, product: Product, quantity: int):
"""Business logic in entity."""
item = OrderItem(product, quantity)
self.items.append(item)
self._events.append(ItemAddedEvent(self.id, item))
def total(self) -> Money:
"""Calculated property."""
return sum(item.subtotal() for item in self.items)
def submit(self):
"""State transition with business rules."""
if not self.items:
raise ValueError("Cannot submit empty order")
if self.status != OrderStatus.PENDING:
raise ValueError("Order already submitted")
self.status = OrderStatus.SUBMITTED
self._events.append(OrderSubmittedEvent(self.id))
# Aggregates (consistency boundary)
class Customer:
"""Aggregate root: controls access to entities."""
def __init__(self, id: str, email: Email):
self.id = id
self.email = email
self._addresses: List[Address] = []
self._orders: List[str] = [] # Order IDs, not full objects
def add_address(self, address: Address):
"""Aggregate enforces invariants."""
if len(self._addresses) >= 5:
raise ValueError("Maximum 5 addresses allowed")
self._addresses.append(address)
@property
def primary_address(self) -> Optional[Address]:
return next((a for a in self._addresses if a.is_primary), None)
# Domain Events
@dataclass
class OrderSubmittedEvent:
order_id: str
occurred_at: datetime = field(default_factory=datetime.now)
# Repository (aggregate persistence)
class OrderRepository:
"""Repository: persist/retrieve aggregates."""
async def find_by_id(self, order_id: str) -> Optional[Order]:
"""Reconstitute aggregate from storage."""
pass
async def save(self, order: Order):
"""Persist aggregate and publish events."""
await self._persist(order)
await self._publish_events(order._events)
order._events.clear()
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