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
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+#!/bin/bash
+# SciLit Oncology — 一键部署脚本
+# Usage: bash setup.sh [dev|prod]
+
+set -e
+
+MODE=${1:-dev}
+PROJECT_DIR=$(cd "$(dirname "$0")/.." && pwd)
+
+echo "========================================="
+echo "  SciLit Oncology — Setup ($MODE)"
+echo "========================================="
+
+# Check dependencies
+check_cmd() {
+    if ! command -v "$1" &>/dev/null; then
+        echo "ERROR: $1 is required but not installed."
+        exit 1
+    fi
+}
+
+check_cmd docker
+check_cmd python3
+
+if [ "$MODE" = "prod" ]; then
+    echo ""
+    echo ">>> Production deployment <<<"
+    echo ""
+
+    # Check env file
+    if [ ! -f "$PROJECT_DIR/.env" ]; then
+        echo "Creating .env from example..."
+        cp "$PROJECT_DIR/backend/.env.example" "$PROJECT_DIR/.env"
+        echo "⚠️  Please edit $PROJECT_DIR/.env with your production secrets!"
+        echo "    Required: DB_PASSWORD, JWT_SECRET, S3_ACCESS_KEY, S3_SECRET_KEY"
+        echo "    Optional: SMTP_HOST, SMTP_USER, SMTP_PASSWORD"
+        exit 1
+    fi
+
+    echo "Starting production services..."
+    docker compose -f "$PROJECT_DIR/docker-compose.prod.yml" up -d
+
+    echo ""
+    echo "Running database migrations..."
+    docker compose -f "$PROJECT_DIR/docker-compose.prod.yml" exec backend alembic upgrade head
+
+    echo ""
+    echo "Loading seed data..."
+    docker compose -f "$PROJECT_DIR/docker-compose.prod.yml" exec backend python scripts/seed_data.py
+
+    echo ""
+    echo "========================================="
+    echo "  Production deployment complete!"
+    echo "  Frontend: http://localhost"
+    echo "  API Docs: http://localhost:8000/docs"
+    echo ""
+    echo "  Admin: admin@scilit.cn / admin123"
+    echo "  Demo:  demo@test.cn / 123456"
+    echo "========================================="
+
+elif [ "$MODE" = "dev" ]; then
+    echo ""
+    echo ">>> Development setup <<<"
+    echo ""
+
+    # Backend
+    echo "Setting up backend..."
+    cd "$PROJECT_DIR/backend"
+    python3 -m venv venv 2>/dev/null || true
+    source venv/bin/activate 2>/dev/null || source venv/Scripts/activate 2>/dev/null || true
+    pip install -e ".[dev]" 2>/dev/null || pip install fastapi uvicorn sqlalchemy aiosqlite asyncpg pydantic pydantic-settings python-jose passlib bcrypt==4.0.1 python-multipart httpx lxml structlog pyyaml email-validator
+
+    # Initialize DB + seed data
+    echo "Initializing database..."
+    python scripts/seed_data.py
+
+    echo ""
+    echo "Starting backend (dev mode)..."
+    uvicorn app.main:app --host 0.0.0.0 --port 8000 --reload &
+    BACKEND_PID=$!
+    echo "Backend PID: $BACKEND_PID"
+
+    # Frontend
+    echo ""
+    echo "Setting up frontend..."
+    cd "$PROJECT_DIR/frontend"
+    npm install
+
+    echo ""
+    echo "Starting frontend (dev mode)..."
+    npm run dev &
+    FRONTEND_PID=$!
+    echo "Frontend PID: $FRONTEND_PID"
+
+    echo ""
+    echo "========================================="
+    echo "  Dev environment ready!"
+    echo "  Frontend: http://localhost:5173"
+    echo "  Backend:  http://localhost:8000/docs"
+    echo "  Admin: admin@scilit.cn / admin123"
+    echo "  Demo:  demo@test.cn / 123456"
+    echo ""
+    echo "  Press Ctrl+C to stop both services"
+    echo "========================================="
+
+    trap "kill $BACKEND_PID $FRONTEND_PID 2>/dev/null" EXIT
+    wait
+
+elif [ "$MODE" = "import-pubmed" ]; then
+    echo ">>> PubMed Baseline Import <<<"
+    BASELINE_DIR="$2"
+    if [ -z "$BASELINE_DIR" ]; then
+        echo "Usage: bash setup.sh import-pubmed /path/to/pubmed/baseline/"
+        echo ""
+        echo "Download baseline from: ftp.ncbi.nlm.nih.gov/pubmed/baseline/"
+        exit 1
+    fi
+    cd "$PROJECT_DIR/backend"
+    python scripts/pubmed_baseline.py --dir "$BASELINE_DIR" --demo
+
+else
+    echo "Usage: bash setup.sh [dev|prod|import-pubmed <dir>]"
+    exit 1
+fi