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.
2026-07-27 07:59:18 +08:00
commit a6cd99a4ca
473 changed files with 151472 additions and 0 deletions
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+version: "3.9"
+
+services:
+  postgres:
+    image: pgvector/pgvector:pg16
+    environment:
+      POSTGRES_DB: scilit
+      POSTGRES_USER: scilit
+      POSTGRES_PASSWORD: scilit_dev
+    ports:
+      - "5432:5432"
+    volumes:
+      - pgdata:/var/lib/postgresql/data
+    healthcheck:
+      test: ["CMD-SHELL", "pg_isready -U scilit"]
+      interval: 5s
+      timeout: 5s
+      retries: 5
+
+  redis:
+    image: redis:7-alpine
+    ports:
+      - "6379:6379"
+    healthcheck:
+      test: ["CMD", "redis-cli", "ping"]
+      interval: 5s
+      timeout: 5s
+      retries: 5
+
+  elasticsearch:
+    image: elasticsearch:8.11.0
+    environment:
+      discovery.type: single-node
+      xpack.security.enabled: "false"
+      "ES_JAVA_OPTS": "-Xms512m -Xmx512m"
+    ports:
+      - "9200:9200"
+    volumes:
+      - esdata:/usr/share/elasticsearch/data
+    healthcheck:
+      test: ["CMD-SHELL", "curl -s http://localhost:9200/_cluster/health | grep -q green"]
+      interval: 10s
+      timeout: 5s
+      retries: 5
+
+  minio:
+    image: minio/minio
+    command: server /data --console-address ":9001"
+    environment:
+      MINIO_ROOT_USER: minioadmin
+      MINIO_ROOT_PASSWORD: minioadmin
+    ports:
+      - "9000:9000"
+      - "9001:9001"
+    volumes:
+      - miniodata:/data
+
+  migrate:
+    build: ./backend
+    command: alembic -c alembic/alembic.ini upgrade head
+    volumes:
+      - ./backend:/app
+    depends_on:
+      postgres:
+        condition: service_healthy
+
+  backend:
+    build: ./backend
+    depends_on:
+      postgres:
+        condition: service_healthy
+      redis:
+        condition: service_healthy
+      migrate:
+        condition: service_completed_successfully
+    command: uvicorn app.main:app --host 0.0.0.0 --port 8000 --reload --log-level debug
+    volumes:
+      - ./backend:/app
+    ports:
+      - "8000:8000"
+    healthcheck:
+      test: ["CMD-SHELL", "curl -sf http://localhost:8000/health || exit 1"]
+      interval: 15s
+      timeout: 5s
+      retries: 3
+      start_period: 10s
+    environment:
+      DATABASE_URL: postgresql+asyncpg://scilit:scilit_dev@postgres:5432/scilit
+      REDIS_URL: redis://redis:6379
+      ES_URL: http://elasticsearch:9200
+      S3_ENDPOINT: http://minio:9000
+      S3_ACCESS_KEY: minioadmin
+      S3_SECRET_KEY: minioadmin
+      S3_BUCKET: scilit-files
+      COS_SECRET_ID: ${COS_SECRET_ID:-}
+      COS_SECRET_KEY: ${COS_SECRET_KEY:-}
+      COS_REGION: ${COS_REGION:-ap-guangzhou}
+      COS_BUCKET: ${COS_BUCKET:-scilit-files}
+      JWT_SECRET: dev-secret-change-in-production
+      SPECIALTY: oncology
+
+  worker:
+    build: ./backend
+    command: arq app.tasks.worker.WorkerSettings
+    volumes:
+      - ./backend:/app
+    environment:
+      DATABASE_URL: postgresql+asyncpg://scilit:scilit_dev@postgres:5432/scilit
+      REDIS_URL: redis://redis:6379
+      ES_URL: http://elasticsearch:9200
+      S3_ENDPOINT: http://minio:9000
+      S3_ACCESS_KEY: minioadmin
+      S3_SECRET_KEY: minioadmin
+      S3_BUCKET: scilit-files
+      COS_SECRET_ID: ${COS_SECRET_ID:-}
+      COS_SECRET_KEY: ${COS_SECRET_KEY:-}
+      COS_REGION: ${COS_REGION:-ap-guangzhou}
+      COS_BUCKET: ${COS_BUCKET:-scilit-files}
+      JWT_SECRET: dev-secret-change-in-production
+      SPECIALTY: oncology
+    depends_on:
+      postgres:
+        condition: service_healthy
+      redis:
+        condition: service_healthy
+
+  frontend:
+    build: ./frontend
+    command: npm run dev -- --host 0.0.0.0
+    volumes:
+      - ./frontend:/app
+      - /app/node_modules
+    ports:
+      - "5173:5173"
+    environment:
+      VITE_API_BASE: http://localhost:8000/api/v1
+    healthcheck:
+      test: ["CMD-SHELL", "curl -sf http://localhost:5173 || exit 1"]
+      interval: 15s
+      timeout: 5s
+      retries: 3
+      start_period: 30s
+
+volumes:
+  pgdata:
+  esdata:
+  miniodata: