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Dockerfile

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+# Hugging Face Spaces - ResearchOS MVP Deployment
+# Compatible with HF Spaces Docker SDK
+
+FROM python:3.11-slim
+
+WORKDIR /app
+
+# Install system dependencies
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    nodejs npm curl \
+    gcc libpq-dev \
+    && rm -rf /var/lib/apt/lists/*
+
+# Install Python dependencies for all services
+COPY services/api-gateway/requirements.txt /tmp/req-gateway.txt
+COPY services/project-service/requirements.txt /tmp/req-project.txt
+COPY services/analysis-service/requirements.txt /tmp/req-analysis.txt
+COPY services/auth-service/requirements.txt /tmp/req-auth.txt
+COPY services/manuscript-service/requirements.txt /tmp/req-manuscript.txt
+COPY services/verification-service/requirements.txt /tmp/req-verification.txt
+COPY services/agent-service/requirements.txt /tmp/req-agent.txt
+
+RUN pip install --no-cache-dir \
+    -r /tmp/req-gateway.txt \
+    -r /tmp/req-project.txt \
+    -r /tmp/req-analysis.txt \
+    -r /tmp/req-auth.txt \
+    -r /tmp/req-manuscript.txt \
+    -r /tmp/req-verification.txt \
+    -r /tmp/req-agent.txt \
+    gradio==4.0.0
+
+# Copy all source code
+COPY services/ /app/services/
+COPY agents/ /app/agents/
+COPY packages/ /app/packages/
+COPY apps/web/ /app/apps/web/
+COPY docs/ /app/docs/
+COPY scripts/ /app/scripts/
+
+# Build Next.js frontend
+RUN cd /app/apps/web && npm install && npm run build
+
+# Copy HF-specific files
+COPY infrastructure/huggingface/start.sh /app/start.sh
+COPY infrastructure/huggingface/app.py /app/app.py
+RUN chmod +x /app/start.sh
+
+# Environment setup for HF Spaces
+ENV PYTHONPATH=/app
+ENV NODE_ENV=production
+ENV DATABASE_URL=sqlite:///app/researchos.db
+ENV JWT_SECRET=hf-spaces-secret-change-me
+ENV API_GATEWAY_URL=http://localhost:8000
+ENV WEBSOCKET_URL=ws://localhost:8003
+
+# HF Spaces exposes 7860
+EXPOSE 7860
+ENV PORT=7860
+
+# Use start.sh for Docker SDK, app.py for Gradio SDK fallback
+CMD ["/app/start.sh"]

README.md

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+---
+title: ResearchOS
+colorFrom: blue
+colorTo: indigo
+sdk: docker
+app_port: 7860
+---
+
+# ResearchOS on Hugging Face Spaces
+
+AI-Powered Research Operating System MVP deployed on Hugging Face Spaces.
+
+## What's Included
+
+- **Frontend**: Next.js 14 app with project dashboard, manuscript editor, literature search, analysis upload, and peer review
+- **API Gateway**: FastAPI router with JWT authentication
+- **Auth Service**: User registration/login with bcrypt + JWT
+- **Project Service**: Project CRUD with PostgreSQL/SQLite
+- **Manuscript Service**: Document storage with versioning
+- **Analysis Service**: Statistical engine with schema detection and APA output
+- **Agent Service**: Literature search, writing generation, peer review simulation
+- **Verification Service**: Cryptographic receipts + 3-probe verification
+- **Collaboration Service**: WebSocket + Yjs real-time editing
+
+## Environment Variables
+
+Set these in your Space Settings:
+
+| Variable | Required | Description |
+|----------|----------|-------------|
+| `JWT_SECRET` | Yes | Secret key for JWT tokens |
+| `OPENAI_API_KEY` | No | For AI generation (falls back to HF API) |
+| `HUGGINGFACE_API_TOKEN` | No | For HF Inference API fallback |
+
+## Architecture on HF Spaces
+
+Since HF Spaces is ephemeral:
+- Uses **SQLite** instead of PostgreSQL (data resets on restart)
+- File uploads stored in container (ephemeral)
+- All services run in single container (simplified for MVP)
+
+## Usage
+
+1. Open the Space URL
+2. Register a new account
+3. Create a research project
+4. Use Literature tab to search papers
+5. Upload data in Analysis tab
+6. Write manuscript in Writing tab
+7. Run peer review simulation
+
+## Limitations
+
+- No persistent database (use external DB for production)
+- Docker sandbox limited (analysis runs in-process)
+- WebSockets may need polling fallback behind HF proxy
+- File storage is ephemeral
+
+## GitHub
+
+Full source: [your-repo/researchos](https://github.com/your-repo/researchos)

app.py

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+"""
+Hugging Face Spaces Entry Point for ResearchOS
+This serves as the main entry point when using Gradio SDK fallback,
+or as a health-check wrapper when using Docker SDK.
+"""
+
+import gradio as gr
+import os
+import subprocess
+import threading
+import time
+
+# Start all backend services in background thread
+def start_services():
+    print("[HF Spaces] Starting ResearchOS services...")
+
+    # Set SQLite fallback for HF Spaces
+    os.environ.setdefault('DATABASE_URL', 'sqlite:///app/researchos.db')
+    os.environ.setdefault('JWT_SECRET', os.getenv('JWT_SECRET', 'hf-spaces-secret'))
+
+    services = [
+        ("auth", "python services/auth-service/src/main.py"),
+        ("project", "python services/project-service/src/main.py"),
+        ("manuscript", "python services/manuscript-service/src/main.py"),
+        ("analysis", "python services/analysis-service/src/main.py"),
+        ("agent", "python services/agent-service/src/main.py"),
+        ("verification", "python services/verification-service/src/main.py"),
+    ]
+
+    for name, cmd in services:
+        try:
+            subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+            print(f"[HF Spaces] Started {name} service")
+            time.sleep(1)
+        except Exception as e:
+            print(f"[HF Spaces] Failed to start {name}: {e}")
+
+    # Start API Gateway
+    time.sleep(2)
+    try:
+        subprocess.Popen("python services/api-gateway/src/main.py", shell=True)
+        print("[HF Spaces] Started API Gateway")
+    except Exception as e:
+        print(f"[HF Spaces] Failed to start API Gateway: {e}")
+
+    # Start Next.js frontend
+    time.sleep(2)
+    try:
+        subprocess.Popen("cd apps/web && PORT=7860 node server.js", shell=True)
+        print("[HF Spaces] Started Web Frontend on port 7860")
+    except Exception as e:
+        print(f"[HF Spaces] Failed to start frontend: {e}")
+
+# Start services in background
+threading.Thread(target=start_services, daemon=True).start()
+
+# Gradio interface as fallback/wrapper
+def health_check():
+    import urllib.request
+    try:
+        req = urllib.request.Request('http://localhost:8000/health', method='GET')
+        with urllib.request.urlopen(req, timeout=5) as resp:
+            return resp.read().decode()
+    except Exception as e:
+        return f"Services starting... ({str(e)})"
+
+with gr.Blocks(title="ResearchOS") as demo:
+    gr.Markdown("# ResearchOS - AI Research Platform")
+    gr.Markdown("The full Next.js application is running in the background.")
+
+    with gr.Row():
+        with gr.Column():
+            gr.Markdown("### System Status")
+            status_btn = gr.Button("Check Health")
+            status_output = gr.Textbox(label="Status", value="Starting...")
+            status_btn.click(health_check, outputs=status_output)
+
+        with gr.Column():
+            gr.Markdown("### Quick Links")
+            gr.Markdown("- [Open Full App](/)")
+            gr.Markdown("- API Gateway: `http://localhost:8000`")
+
+    gr.Markdown("---")
+    gr.Markdown("If the full app doesn't load, wait 30 seconds for services to boot, then refresh.")
+
+# Launch Gradio (this is required for HF Spaces Gradio SDK)
+# But if using Docker SDK, this file is ignored and start.sh is used instead
+demo.launch(server_name="0.0.0.0", server_port=7860, share=False)

start.sh

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+#!/bin/bash
+set -e
+
+echo "=========================================="
+echo "  ResearchOS MVP - Hugging Face Spaces"
+echo "=========================================="
+
+# Initialize SQLite database
+echo "[1/9] Initializing SQLite database..."
+python3 << 'PYEOF'
+import os
+from sqlalchemy import create_engine
+
+# Import all model bases
+import sys
+sys.path.insert(0, '/app')
+
+# Create engine
+engine = create_engine('sqlite:///app/researchos.db', echo=False)
+
+# Create tables by importing main modules
+from services.auth_service.src.main import Base as AuthBase
+from services.project_service.src.main import Base as ProjectBase
+from services.manuscript_service.src.main import Base as ManuscriptBase
+from services.verification_service.src.main import Base as VerificationBase
+
+AuthBase.metadata.create_all(engine)
+ProjectBase.metadata.create_all(engine)
+ManuscriptBase.metadata.create_all(engine)
+VerificationBase.metadata.create_all(engine)
+
+print("Database initialized successfully")
+PYEOF
+
+# Function to start a service
+start_service() {
+    local name=$1
+    local port=$2
+    local cmd=$3
+    echo "[START] $name on port $port..."
+    eval "$cmd > /tmp/$name.log 2>&1 &"
+    echo $! > /tmp/$name.pid
+}
+
+# Start all backend services
+start_service "auth-service" "8005" "python3 services/auth-service/src/main.py"
+start_service "project-service" "8002" "python3 services/project-service/src/main.py"
+start_service "manuscript-service" "8007" "python3 services/manuscript-service/src/main.py"
+start_service "analysis-service" "8001" "python3 services/analysis-service/src/main.py"
+start_service "agent-service" "8004" "python3 services/agent-service/src/main.py"
+start_service "verification-service" "8006" "python3 services/verification-service/src/main.py"
+
+# Wait for services to be ready
+echo "[2/9] Waiting for services to boot..."
+sleep 5
+
+# Start API Gateway
+start_service "api-gateway" "8000" "python3 services/api-gateway/src/main.py"
+
+sleep 3
+
+# Start Next.js frontend on port 7860 (HF Spaces requirement)
+echo "[3/9] Starting Next.js frontend on port 7860..."
+cd /app/apps/web && PORT=7860 node server.js > /tmp/web.log 2>&1 &
+echo $! > /tmp/web.pid
+
+echo ""
+echo "=========================================="
+echo "  ResearchOS is starting up!"
+echo "=========================================="
+echo ""
+echo "Services:"
+echo "  - Auth:        http://localhost:8005"
+echo "  - Projects:    http://localhost:8002"
+echo "  - Manuscripts: http://localhost:8007"
+echo "  - Analysis:    http://localhost:8001"
+echo "  - Agents:      http://localhost:8004"
+echo "  - Verification:http://localhost:8006"
+echo "  - API Gateway: http://localhost:8000"
+echo "  - Web App:     http://localhost:7860"
+echo ""
+echo "Logs available in /tmp/*.log"
+echo ""
+
+# Health check loop
+for i in {1..30}; do
+    if curl -s http://localhost:8000/health > /dev/null 2>&1; then
+        echo "[✓] API Gateway is ready!"
+        break
+    fi
+    echo "[...] Waiting for API Gateway ($i/30)..."
+    sleep 2
+done
+
+echo ""
+echo "=========================================="
+echo "  ResearchOS is LIVE!"
+echo "=========================================="
+
+# Keep container alive and stream logs
+tail -f /tmp/web.log /tmp/api-gateway.log 2>/dev/null || wait