feat: initial commit - oncology literature search platform
OncoLit: a multi-tenant oncology literature search, feed, and collaboration platform. Built with FastAPI + Vue 3 + PostgreSQL. Includes PubMed pipeline, drug approvals, AI summaries, and systematic review tools.
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34047007@qq.com
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# SciLit 生产环境 Docker Compose
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#
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# 使用方式：
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# cp .env.example .env # 填入实际值
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# docker compose -f docker-compose.prod.yml --env-file .env up -d
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#
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# HTTPS 终止建议使用上游反向代理（Caddy / Nginx / ALB），
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# 前端 Nginx 容器本身仅提供 HTTP 服务。
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version: "3.9"
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networks:
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scilit:
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driver: bridge
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services:
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postgres:
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image: pgvector/pgvector:pg16
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networks:
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- scilit
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environment:
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POSTGRES_DB: scilit
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POSTGRES_USER: scilit
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POSTGRES_PASSWORD: ${PG_PASSWORD}
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ports: []
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volumes:
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- pgdata:/var/lib/postgresql/data
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restart: unless-stopped
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healthcheck:
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test: ["CMD-SHELL", "pg_isready -U scilit"]
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interval: 10s
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timeout: 5s
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retries: 5
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logging:
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driver: "json-file"
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options:
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max-size: "10m"
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max-file: "3"
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redis:
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image: redis:7-alpine
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networks:
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- scilit
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command: redis-server --requirepass ${REDIS_PASSWORD}
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ports: []
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volumes:
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- redisdata:/data
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restart: unless-stopped
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healthcheck:
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test: ["CMD", "redis-cli", "-a", "${REDIS_PASSWORD}", "ping"]
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interval: 10s
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timeout: 5s
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retries: 5
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logging:
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driver: "json-file"
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options:
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max-size: "10m"
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max-file: "3"
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elasticsearch:
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image: elasticsearch:8.11.0
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networks:
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- scilit
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environment:
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discovery.type: single-node
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xpack.security.enabled: "false"
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"ES_JAVA_OPTS": "-Xms1g -Xmx1g"
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bootstrap.memory_lock: "true"
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ports: []
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volumes:
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- esdata:/usr/share/elasticsearch/data
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restart: unless-stopped
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ulimits:
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memlock:
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soft: -1
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hard: -1
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healthcheck:
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test: ["CMD-SHELL", "curl -s http://localhost:9200/_cluster/health | grep -qE 'green|yellow'"]
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interval: 15s
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timeout: 10s
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retries: 5
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start_period: 30s
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logging:
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driver: "json-file"
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options:
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max-size: "10m"
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max-file: "3"
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minio:
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image: minio/minio:latest
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command: server /data --console-address ":9001"
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networks:
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- scilit
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environment:
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MINIO_ROOT_USER: ${MINIO_ROOT_USER:-minioadmin}
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MINIO_ROOT_PASSWORD: ${MINIO_ROOT_PASSWORD:-minioadmin}
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ports: []
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volumes:
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- miniodata:/data
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restart: unless-stopped
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healthcheck:
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test: ["CMD-SHELL", "curl -sf http://localhost:9000/minio/health/live || exit 1"]
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interval: 15s
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timeout: 5s
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retries: 5
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start_period: 10s
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logging:
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driver: "json-file"
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options:
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max-size: "10m"
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max-file: "3"
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migrate:
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build: ./backend
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networks:
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- scilit
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command: alembic -c alembic/alembic.ini upgrade head
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environment:
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DATABASE_URL: postgresql+asyncpg://scilit:${PG_PASSWORD}@postgres:5432/scilit
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JWT_SECRET: ${JWT_SECRET}
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SPECIALTY: ${SPECIALTY:-oncology}
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DEBUG: "false"
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depends_on:
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postgres:
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condition: service_healthy
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restart: "no"
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backend:
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build: ./backend
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networks:
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- scilit
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# ENTRYPOINT 自动执行迁移，CMD 启动 uvicorn（4 workers + proxy-headers）
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# 无需额外 command
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environment:
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DATABASE_URL: postgresql+asyncpg://scilit:${PG_PASSWORD}@postgres:5432/scilit
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REDIS_URL: redis://default:${REDIS_PASSWORD}@redis:6379
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ES_URL: http://elasticsearch:9200
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S3_ENDPOINT: ${S3_ENDPOINT}
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S3_ACCESS_KEY: ${S3_ACCESS_KEY}
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S3_SECRET_KEY: ${S3_SECRET_KEY}
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S3_BUCKET: ${S3_BUCKET:-scilit-files}
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COS_SECRET_ID: ${COS_SECRET_ID:-}
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COS_SECRET_KEY: ${COS_SECRET_KEY:-}
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COS_REGION: ${COS_REGION:-ap-guangzhou}
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COS_BUCKET: ${COS_BUCKET:-scilit-files}
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JWT_SECRET: ${JWT_SECRET}
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SPECIALTY: ${SPECIALTY:-oncology}
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DEBUG: "false"
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SMTP_HOST: ${SMTP_HOST}
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SMTP_PORT: ${SMTP_PORT:-587}
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SMTP_USER: ${SMTP_USER}
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SMTP_PASSWORD: ${SMTP_PASSWORD}
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SMTP_FROM: ${SMTP_FROM}
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SENTRY_DSN: ${SENTRY_DSN}
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AI_API_KEY: ${AI_API_KEY}
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AI_BASE_URL: ${AI_BASE_URL}
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AI_MODEL: ${AI_MODEL}
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PUBMED_API_KEY: ${PUBMED_API_KEY}
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CORS_ORIGINS: ${CORS_ORIGINS}
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PUBLIC_BASE_URL: ${PUBLIC_BASE_URL}
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ports:
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- "127.0.0.1:8000:8000"
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depends_on:
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postgres:
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condition: service_healthy
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redis:
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condition: service_healthy
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elasticsearch:
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condition: service_started
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minio:
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condition: service_healthy
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migrate:
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condition: service_completed_successfully
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healthcheck:
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test: ["CMD-SHELL", "curl -sf http://localhost:8000/health || exit 1"]
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interval: 15s
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timeout: 5s
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retries: 3
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start_period: 20s
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restart: unless-stopped
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logging:
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driver: "json-file"
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options:
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max-size: "10m"
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max-file: "3"
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worker:
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build: ./backend
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networks:
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- scilit
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# 通过 CMD 覆写默认的 uvicorn 启动，改为 ARQ worker（异步任务消费）
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# 迁移由独立的 migrate 服务完成（depends_on 确保顺序）
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command: arq app.tasks.worker.WorkerSettings
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healthcheck:
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test: ["CMD-SHELL", "grep -q arq /proc/1/cmdline"]
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interval: 30s
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timeout: 5s
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start_period: 30s
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retries: 3
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environment:
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DATABASE_URL: postgresql+asyncpg://scilit:${PG_PASSWORD}@postgres:5432/scilit
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REDIS_URL: redis://default:${REDIS_PASSWORD}@redis:6379
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ES_URL: http://elasticsearch:9200
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S3_ENDPOINT: ${S3_ENDPOINT}
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S3_ACCESS_KEY: ${S3_ACCESS_KEY}
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S3_SECRET_KEY: ${S3_SECRET_KEY}
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S3_BUCKET: ${S3_BUCKET:-scilit-files}
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COS_SECRET_ID: ${COS_SECRET_ID:-}
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COS_SECRET_KEY: ${COS_SECRET_KEY:-}
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COS_REGION: ${COS_REGION:-ap-guangzhou}
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COS_BUCKET: ${COS_BUCKET:-scilit-files}
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JWT_SECRET: ${JWT_SECRET}
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SPECIALTY: ${SPECIALTY:-oncology}
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DEBUG: "false"
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SMTP_HOST: ${SMTP_HOST}
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SMTP_PORT: ${SMTP_PORT:-587}
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SMTP_USER: ${SMTP_USER}
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SMTP_PASSWORD: ${SMTP_PASSWORD}
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SMTP_FROM: ${SMTP_FROM}
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AI_API_KEY: ${AI_API_KEY}
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AI_BASE_URL: ${AI_BASE_URL}
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AI_MODEL: ${AI_MODEL}
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PUBMED_API_KEY: ${PUBMED_API_KEY}
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depends_on:
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postgres:
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condition: service_healthy
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redis:
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condition: service_healthy
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minio:
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condition: service_healthy
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migrate:
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condition: service_completed_successfully
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restart: unless-stopped
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logging:
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driver: "json-file"
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options:
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max-size: "10m"
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max-file: "3"
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frontend:
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build:
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context: ./frontend
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dockerfile: Dockerfile.prod
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networks:
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- scilit
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environment:
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VITE_API_BASE: /api/v1
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ports:
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- "80:80"
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volumes:
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- /var/log/scilit/nginx:/var/log/nginx
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depends_on:
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backend:
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condition: service_started
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restart: unless-stopped
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logging:
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driver: "json-file"
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options:
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max-size: "10m"
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max-file: "3"
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volumes:
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pgdata:
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redisdata:
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esdata:
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miniodata:
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