LabFlow

A reliable distributed job platform for reproducible scientific computing.

LabFlow is a portfolio project for laboratory teams that need to submit, run, observe, and compare scientific computing jobs. The system accepts validated molecular inputs and versioned PySCF configurations, dispatches work to Python workers, streams execution logs, and preserves enough provenance to explain and reproduce every result.

The central engineering problem is reliability rather than raw job volume. LabFlow is designed around RabbitMQ's at-least-once delivery: a job may be executed more than once after a failure, but leases, attempt tokens, and a database uniqueness constraint ensure that only one valid final result is accepted.

Why LabFlow?

Scientific jobs are long-running and failure-prone. A worker can disappear after accepting a message, a broker can redeliver an event, and a client can retry the same submission. Treating these as normal system behavior leads to several explicit design goals:

Idempotent submission — concurrent requests with the same Idempotency-Key create one job.
Recoverable execution — heartbeats and leases allow an abandoned job to be claimed by another worker.
Fenced results — a stale worker cannot overwrite the result of a newer attempt.
Reproducibility — each job records immutable input, configuration, code, image, and runtime metadata.
Observable behavior — job events, attempts, live logs, retry reasons, and recovery time remain inspectable.

LabFlow does not claim strict exactly-once execution. Its intended guarantee is:

Work may run more than once, but only one authorized final result can be committed for a job.

Target architecture

flowchart LR
    UI[React + TypeScript] -->|User API / SSE| API[Spring Boot API]
    API -->|State, metadata, outbox| DB[(PostgreSQL)]
    API -->|Publish job signal| MQ[(RabbitMQ)]
    MQ -->|At-least-once delivery| WORKER[Python Worker]
    WORKER -->|Claim, heartbeat, logs, result| API
    API --> ARTIFACTS[(Artifact volume)]
    WORKER --> ARTIFACTS

PostgreSQL is the source of truth for job state. RabbitMQ carries only execution signals. Workers do not write job state directly to the database; they use protected internal APIs so state transitions, authorization, lease checks, and result fencing remain centralized in the backend.

The intended execution flow is:

The API creates a job, an idempotency record, and an outbox event in one database transaction.
The outbox publisher sends the job ID to RabbitMQ.
A worker consumes the message and atomically claims a new job attempt.
The worker uploads ordered log chunks and runs a whitelisted task in an isolated subprocess.
The backend accepts the result only when the attempt token is still active.
A later recovery stage will expire abandoned leases, mark attempts LOST, and queue another attempt.

Planned reliability model

Job and attempt separation

A Job represents the computation requested by a user. An Attempt represents one worker's execution of that job. A worker failure creates another attempt for the same job rather than a duplicate job, preserving both the user's intent and the complete failure history.

Transactional outbox

Creating a job and recording its pending message happens in the same PostgreSQL transaction. This prevents a committed QUEUED job from being silently lost if RabbitMQ is unavailable between the database write and message publication. A scheduled publisher claims available rows with FOR UPDATE SKIP LOCKED, sends persistent messages, waits for correlated publisher confirms, and only then records published_at. Failed sends remain unpublished and use capped exponential backoff. A crash after broker confirmation but before the database update can publish a duplicate, which is intentional under the system's at-least-once contract.

The version 1 broker message is deliberately small:

{"jobId": 42, "eventId": 87, "schemaVersion": 1}

RabbitMQ declares a durable direct exchange, a durable quorum work queue, 15/60/300-second TTL retry queues, and a durable DLQ. Workers consume manually with prefetch one, claim jobs through the protected backend API, and acknowledge messages only after the backend confirms a terminal result.

Lease and fencing token

Each claimed attempt receives a lease and a unique fencing token. Every log and terminal result write must present that token, and writes from a non-active attempt are rejected as STALE_ATTEMPT. Lease renewal and automatic abandoned-attempt recovery are the next reliability stage.

Unique final result

The job_results table has a primary key on job_id and a unique attempt constraint. Combined with transactional token validation, it is the final safeguard against duplicate or late result commits.

Implemented API

Authentication

Registering creates the account and returns a one-hour Bearer token:

POST /api/auth/register
Content-Type: application/json

{
  "email": "scientist@example.com",
  "password": "strong-password",
  "displayName": "Ada Lovelace"
}

POST /api/auth/login
Content-Type: application/json

{
  "email": "scientist@example.com",
  "password": "strong-password"
}

Validate a token and load the current account:

GET /api/auth/me
Authorization: Bearer <access-token>

Passwords are stored only as BCrypt hashes. Email addresses are trimmed and normalized to lowercase. Missing, expired, malformed, or incorrectly signed tokens receive the same non-leaking JSON 401 structure; authenticated authorization failures use the corresponding JSON 403 structure.

For non-local environments, provide a random AUTH_JWT_SECRET containing at least 32 UTF-8 bytes. AUTH_JWT_ISSUER and the ISO-8601 duration AUTH_JWT_TTL are also configurable.

System information

GET /api/system/info

Example response:

{
  "service": "labflow-api",
  "version": "0.1.0",
  "status": "UP"
}

Actuator health

GET /actuator/health

The Actuator response includes PostgreSQL and RabbitMQ health. RabbitMQ also has its own Docker healthcheck.

Versioned experiment configurations

Project contributors create an immutable configuration version with:

POST /api/projects/{projectId}/configs
Authorization: Bearer <access-token>
Content-Type: application/json

{
  "name": "Baseline",
  "spec": {
    "schemaVersion": 1,
    "taskType": "pyscf.single_point",
    "method": "RHF",
    "basis": "sto-3g",
    "charge": 0,
    "spin": 0,
    "maxMemoryMb": 1024,
    "timeoutSeconds": 300
  }
}

Posting the same name again creates the next version; it never updates an existing row. Project members can inspect every version with GET /api/projects/{projectId}/configs or fetch one through GET /api/projects/{projectId}/configs/{configId}. The version 1 contract is published at backend/src/main/resources/schemas/experiment-config-v1.schema.json.

Idempotent job submission

Project owners, maintainers, and members can submit a job using an input and configuration from the same project:

POST /api/jobs
Authorization: Bearer <access-token>
Idempotency-Key: <client-generated-unique-key>
Content-Type: application/json

{
  "projectId": 1,
  "molecularInputId": 2,
  "experimentConfigId": 3
}

The first request creates a QUEUED job, an idempotency record, a pending outbox event, and a job audit event in one transaction. The response is 201 Created with Location: /api/jobs/{id}. Reusing the key in the same user/project scope with the same semantic request returns the original 201 response; reusing it with different IDs returns 409 IDEMPOTENCY_KEY_REUSED. JSON property order and whitespace do not affect the request hash, and unsupported fields are rejected. A job submission stores an immutable snapshot of the input and configuration. The outbox publisher reliably delivers its execution signal to RabbitMQ, where a registered worker claims and executes it.

Worker execution and observation

Workers authenticate to /internal/** with a dedicated service token, register their image digest and explicit capabilities, then atomically claim a fenced job attempt. They never execute broker-provided commands: the broker carries only IDs, and task dispatch is limited to the demo.sleep_hash and pyscf.single_point registry entries. Tasks run without a shell in a separate process group with a reduced environment, a wall-clock timeout, CPU limits, and a Linux address-space limit.

pyscf.single_point validates the immutable input checksum, parses XYZ coordinates, executes the configured SCF calculation, and records energy, convergence, timing, PySCF/Python/platform versions, image identity, spec hash, and artifact metadata. Ordered stdout/stderr/system chunks are persisted idempotently and exposed through both the job detail response and resumable SSE:

GET /api/projects/{projectId}/jobs
GET /api/jobs/{jobId}
GET /api/jobs/{jobId}/events
Authorization: Bearer <access-token>
Last-Event-ID: <last-seen-log-id>

Set WORKER_SERVICE_TOKEN to the same random value of at least 32 bytes for the backend and workers outside local development.

Web workspace

The React workspace provides registration and login, visible-project selection, owner-only membership management, validated XYZ upload, immutable configuration creation, and a job view with status, attempt, live-polled logs, result energy, failures, and reproducibility manifest. Controls reflect the current project role, while the backend remains the authorization boundary.

For frontend development, start the backend on port 8080, then run:

cd frontend
npm run dev

Vite proxies /api to the backend. The production Nginx image uses the same paths inside Docker Compose.

Run the local stack

Prerequisites

Docker Engine or Docker Desktop with Docker Compose

The Compose file includes development defaults. Copy .env.example to .env first if you want to customize credentials or host ports.

git clone <https://github.com/xyydcoldcold/LabFlow>
cd LabFlow
docker compose up --build --wait

The local services are available at:

Frontend: http://localhost:3000
Backend API: http://localhost:8080
Backend health: http://localhost:8080/actuator/health
RabbitMQ Management: http://localhost:15672
PostgreSQL: localhost:5432

Stop the stack without deleting persistent database or broker volumes:

docker compose down

Run the current checks with:

cd backend
./gradlew test
cd ../frontend
npm ci
npm run typecheck
cd ../worker
python3 -m pytest

Technology stack

Implemented

Java 21
Spring Boot 4.1
Spring Web MVC
Spring Security
OAuth2 Resource Server JWT validation
Spring Boot Actuator
Gradle Kotlin DSL
JUnit 5
PostgreSQL 17 and Flyway
RabbitMQ 4, Spring AMQP, publisher confirms, retry queues, and DLQ topology
Python 3.12+ worker package, PySCF, Pika, and pytest
Server-Sent Events (SSE) log streaming
React 19, TypeScript, and Vite
Docker Compose
Testcontainers
GitHub Actions

Selected for upcoming stages

Lease renewal and abandoned-attempt recovery
Fault injection and retry orchestration

Repository layout

LabFlow/
├── backend/                 # Spring Boot API and Flyway migrations
├── worker/                  # Python RabbitMQ consumer and scientific task runtime
├── frontend/                # React/Vite scaffold served by Nginx
├── infra/                   # Reserved for broker and operational assets
├── tests/
│   ├── fault-injection/     # Worker and dependency failure scenarios
│   └── performance/         # Repeatable performance scenarios and results
├── docs/adr/                # Architecture decision records
├── .github/workflows/ci.yml # Backend, frontend, worker, and image checks
├── docker-compose.yml       # Six-service local development stack
└── README.md

License

No license has been selected yet. Until a license is added, all rights are reserved.

FilesExpand file tree

README.md

Latest commit

History