install.sh

#!/bin/bash

# Atlas Intelligence Universal Setup Script
# Compatible with macOS on Apple Silicon (M1/M2/M3)
# Created: April 16, 2025

# Exit on error, but allow for custom error handling
set -o pipefail

# Color codes for better output
GREEN='\033[0;32m'
BLUE='\033[0;34m'
YELLOW='\033[0;33m'
RED='\033[0;31m'
BOLD='\033[1m'
NC='\033[0m' # No Color

# Paths to project directories
OPENMANUS_DIR="$HOME/OpenManus"
CASIBASE_DIR="$HOME/casibase"
CYPHER_DIR="$HOME/Cypher"
CLOUD_DIR="$HOME/Library/Mobile Documents/com~apple~CloudDocs/Atlas Business"
AI_COMPANION_DIR="$CLOUD_DIR/AIConversationCompanion"
QUANTUM_VISION_DIR="$CLOUD_DIR/QuantumVision"
UNIFIED_DIR="$HOME/AtlasUnified"

# Log file for the installation process
LOG_FILE="$QUANTUM_VISION_DIR/install_log.txt"

# Function to log messages to both stdout and log file
log() {
  echo -e "$1" | tee -a "$LOG_FILE"
}

# Function to log errors
log_error() {
  echo -e "${RED}ERROR: $1${NC}" | tee -a "$LOG_FILE"
}

# Function to log warnings
log_warning() {
  echo -e "${YELLOW}WARNING: $1${NC}" | tee -a "$LOG_FILE"
}

# Function to log success
log_success() {
  echo -e "${GREEN}$1${NC}" | tee -a "$LOG_FILE"
}

# Function to log information
log_info() {
  echo -e "${BLUE}$1${NC}" | tee -a "$LOG_FILE"
}

# Clean log file
> "$LOG_FILE"

log_info "=============================================="
log_info "     Atlas Intelligence Unified Setup        "
log_info "=============================================="
log_info "This script will set up a universal connection between:"
log "- OpenManus AI Agent Framework"
log "- Casibase RAG Knowledge Database"
log "- Cypher"
log "- AI Conversation Companion"
log "- Quantum Vision"
log_info "=============================================="
log ""

# Check if running on macOS
if [[ "$(uname)" != "Darwin" ]]; then
  log_error "This script is designed for macOS. Exiting."
  exit 1
fi

# Check for Apple Silicon
if [[ "$(uname -m)" != "arm64" ]]; then
  log_warning "You're not running on Apple Silicon (M1/M2/M3). Some optimizations may not work."
fi

# Check for required tools
log_info "Checking for required tools..."

# Check for Homebrew
if ! command -v brew &> /dev/null; then
  log_warning "Homebrew not found. Installing Homebrew..."
  /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
  
  # Add Homebrew to PATH for Apple Silicon
  if [[ "$(uname -m)" == "arm64" ]]; then
    echo 'eval "$(/opt/homebrew/bin/brew shellenv)"' >> ~/.zprofile
    eval "$(/opt/homebrew/bin/brew shellenv)"
  fi
else
  log_success "Homebrew is installed."
fi

# Check for Python
if ! command -v python3 &> /dev/null; then
  log_warning "Python not found. Installing Python..."
  brew install python@3.11
else
  log_success "Python is installed."
  PYTHON_VERSION=$(python3 --version | cut -d' ' -f2)
  log_info "Python version: $PYTHON_VERSION"
fi

# Check for Go
if ! command -v go &> /dev/null; then
  log_warning "Go not found. Installing Go..."
  brew install go
else
  log_success "Go is installed."
  GO_VERSION=$(go version | cut -d' ' -f3)
  log_info "Go version: $GO_VERSION"
fi

# Check for Node.js
if ! command -v node &> /dev/null; then
  log_warning "Node.js not found. Installing Node.js..."
  brew install node
else
  log_success "Node.js is installed."
  NODE_VERSION=$(node --version)
  log_info "Node.js version: $NODE_VERSION"
fi

# Check for required Python modules
check_python_module() {
  if ! python3 -c "import $1" &> /dev/null; then
    return 1
  else
    return 0
  fi
}

# Create unified directory if it doesn't exist
log_info "Setting up unified directory structure..."
mkdir -p "$UNIFIED_DIR"
mkdir -p "$UNIFIED_DIR/config"
mkdir -p "$UNIFIED_DIR/logs"
mkdir -p "$UNIFIED_DIR/data"

# Set up Python virtual environment with error handling
log_info "Setting up Python virtual environment..."
if ! command -v python3 -m venv &> /dev/null; then
  log_warning "Python venv module not found. Installing venv..."
  brew reinstall python@3.11
fi

# Create and activate virtual environment
python3 -m venv "$UNIFIED_DIR/venv" || {
  log_error "Failed to create virtual environment. Trying alternative approach..."
  pip3 install virtualenv
  virtualenv "$UNIFIED_DIR/venv"
}

# Source the virtual environment with error handling
if [ -f "$UNIFIED_DIR/venv/bin/activate" ]; then
  source "$UNIFIED_DIR/venv/bin/activate"
  log_success "Virtual environment activated."
else
  log_error "Virtual environment activation script not found. Installation may not work correctly."
  exit 1
fi

# Upgrade pip and install wheel to avoid common installation issues
log_info "Upgrading pip and installing wheel..."
pip install --upgrade pip wheel setuptools

# Install core dependencies that commonly cause issues if not installed first
log_info "Installing core dependencies..."
pip install Cython numpy==1.26.4 pandas scikit-learn

# OpenManus dependencies
log_info "Installing OpenManus dependencies..."
if [ -f "$OPENMANUS_DIR/requirements.txt" ]; then
  # Try-catch for OpenManus requirements
  if ! pip install -r "$OPENMANUS_DIR/requirements.txt"; then
    log_warning "Some OpenManus dependencies failed to install. Installing essential ones individually..."
    # Install critical dependencies individually
    pip install openai tenacity pyyaml loguru
  fi
else
  log_error "OpenManus requirements.txt not found. Skipping OpenManus dependencies."
fi

# Quantum Vision dependencies - FIX: Instead of installing as a package, install dependencies directly
log_info "Installing Quantum Vision dependencies..."
if [ -f "$QUANTUM_VISION_DIR/pyproject.toml" ]; then
  # Install specific dependencies from pyproject.toml instead of the package itself
  log_info "Installing specific Quantum Vision dependencies..."
  pip install beautifulsoup4 email-validator flask flask-sqlalchemy gunicorn 
  pip install "openai>=1.6.0" psycopg2-binary requests 
  pip install "spacy>=3.0.0" sqlalchemy trafilatura
  
  # Create an empty __init__.py file in the Quantum Vision directory to make it importable
  touch "$QUANTUM_VISION_DIR/__init__.py"
  log_success "Quantum Vision dependencies installed."
else
  log_error "Quantum Vision pyproject.toml not found. Skipping Quantum Vision dependencies."
fi

# Cypher dependencies
log_info "Installing Cypher dependencies..."
if [ -f "$CYPHER_DIR/requirements.txt" ]; then
  # Try-catch for Cypher requirements
  if ! pip install -r "$CYPHER_DIR/requirements.txt"; then
    log_warning "Some Cypher dependencies failed to install. Installing essential ones individually..."
    pip install flask requests
  fi
else
  log_warning "Cypher requirements.txt not found. Skipping Cypher dependencies."
fi

# Install FastAPI and related packages for the unified API
log_info "Installing FastAPI and related packages for the unified API..."
pip install fastapi uvicorn pydantic pyyaml

# Set up Casibase
log_info "Setting up Casibase..."
if [ -d "$CASIBASE_DIR" ]; then
  cd "$CASIBASE_DIR"
  
  # Check if Docker is installed
  if ! command -v docker &> /dev/null; then
    log_warning "Docker not found. Installing Docker..."
    brew install --cask docker
    log_warning "Please open Docker Desktop and complete setup, then run this script again."
    log_warning "Skipping Casibase setup for now."
  else
    # Build and run Casibase
    log_info "Building Casibase..."
    # Only run build.sh if it exists and is executable
    if [ -f "./build.sh" ] && [ -x "./build.sh" ]; then
      # Run build.sh with error handling
      if ! ./build.sh; then
        log_warning "Casibase build failed. You may need to run it manually later."
      else
        log_success "Casibase build completed successfully."
      fi
    else
      log_warning "Casibase build.sh not found or not executable. Skipping build."
    fi
  fi
  
  log_success "Casibase setup completed with available components."
else
  log_warning "Casibase directory not found. Skipping Casibase setup."
fi

# Return to original directory
cd "$QUANTUM_VISION_DIR"

# Set up AI Conversation Companion frontend
log_info "Setting up AI Conversation Companion..."
if [ -d "$AI_COMPANION_DIR" ]; then
  cd "$AI_COMPANION_DIR"
  
  # Install npm dependencies
  if [ -f "package.json" ]; then
    log_info "Installing npm dependencies for AI Conversation Companion..."
    # Run npm install with error handling
    if ! npm install; then
      log_warning "Some npm packages failed to install. You may need to run 'npm install' manually later."
    fi
  else
    log_warning "package.json not found in AI Conversation Companion. Skipping npm install."
  fi
else
  log_warning "AI Conversation Companion directory not found. Skipping frontend setup."
fi

# Return to original directory
cd "$QUANTUM_VISION_DIR"

# Create unified configuration
log_info "Creating unified configuration..."
mkdir -p "$UNIFIED_DIR/config"
cat > "$UNIFIED_DIR/config/unified_config.yaml" << EOF
# Atlas Intelligence Unified Configuration
version: 1.0.0
created: "$(date)"

# Project Paths
paths:
  openmanus: "$OPENMANUS_DIR"
  casibase: "$CASIBASE_DIR"
  cypher: "$CYPHER_DIR"
  ai_companion: "$AI_COMPANION_DIR"
  quantum_vision: "$QUANTUM_VISION_DIR"
  unified: "$UNIFIED_DIR"

# Integration Settings
integrations:
  enable_openmanus: true
  enable_casibase: true
  enable_cypher: true
  enable_ai_companion: true
  enable_quantum_vision: true

# API Settings
api:
  host: "localhost"
  port: 8080
  debug: false
  enable_cors: true

# Database Settings
database:
  type: "sqlite" # For development, can be changed to mysql or postgresql
  path: "$UNIFIED_DIR/data/atlas_unified.db"

# Logging Settings
logging:
  level: "info"
  file: "$UNIFIED_DIR/logs/atlas_unified.log"
  max_size_mb: 10
  backup_count: 5

# LLM Integration
llm:
  provider: "openai" # Can be openai, anthropic, llama, etc.
  model: "gpt-4"
  api_key_env: "OPENAI_API_KEY"
EOF

# Create the unified bridge script with better error handling and diagnostics
log_info "Creating unified bridge script..."
cat > "$UNIFIED_DIR/unified_bridge.py" << EOF
#!/usr/bin/env python3
"""
Atlas Intelligence Unified Bridge
This script provides a universal bridge between all Atlas Intelligence components.
"""

import os
import sys
import yaml
import logging
import traceback
from pathlib import Path
from typing import Dict, Any, Optional, Union

# Configure logging first
logging.basicConfig(
    level=logging.INFO,
    format='%(asctime)s - %(name)s - %(levelname)s - %(message)s',
    handlers=[
        logging.StreamHandler()
    ]
)
logger = logging.getLogger("atlas_unified")

# Setup paths
SCRIPT_DIR = os.path.dirname(os.path.abspath(__file__))
CONFIG_PATH = os.path.join(SCRIPT_DIR, "config", "unified_config.yaml")

# Load configuration with error handling
try:
    with open(CONFIG_PATH, "r") as f:
        config = yaml.safe_load(f)
    
    # Now that we have config, setup file logging
    log_file = config["logging"]["file"]
    os.makedirs(os.path.dirname(log_file), exist_ok=True)
    
    file_handler = logging.FileHandler(log_file)
    file_handler.setFormatter(logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s'))
    logger.addHandler(file_handler)
    
    logger.setLevel(logging.getLevelName(config["logging"]["level"].upper()))
except Exception as e:
    logger.error(f"Failed to load configuration: {e}")
    logger.error(traceback.format_exc())
    sys.exit(1)

# Add project paths to Python path with validation
for key, path in config["paths"].items():
    if os.path.exists(path):
        sys.path.append(path)
        logger.info(f"Added {key} path to system path: {path}")
    else:
        logger.warning(f"Path {key} does not exist: {path}")

# Try to import FastAPI with error handling
try:
    from fastapi import FastAPI, Request, Response, status
    from fastapi.middleware.cors import CORSMiddleware
    import uvicorn
except ImportError as e:
    logger.error(f"Failed to import required packages: {e}")
    logger.error("Please ensure fastapi and uvicorn are installed.")
    logger.error("Run: pip install fastapi uvicorn")
    sys.exit(1)

# Initialize FastAPI app
app = FastAPI(title="Atlas Intelligence Unified API")

# Add CORS middleware
if config["api"]["enable_cors"]:
    app.add_middleware(
        CORSMiddleware,
        allow_origins=["*"],
        allow_credentials=True,
        allow_methods=["*"],
        allow_headers=["*"],
    )

@app.get("/")
async def root():
    """Root endpoint returning welcome message"""
    return {
        "message": "Welcome to Atlas Intelligence Unified API",
        "version": config["version"],
        "status": "operational"
    }

@app.get("/health")
async def health():
    """Health check endpoint"""
    return {"status": "healthy"}

@app.get("/status")
async def status():
    """Status endpoint with detailed component information"""
    components_status = {}
    
    # Check OpenManus status
    if config["integrations"]["enable_openmanus"]:
        components_status["openmanus"] = check_openmanus_status()
    else:
        components_status["openmanus"] = "disabled"
    
    # Check QuantumVision status
    if config["integrations"]["enable_quantum_vision"]:
        components_status["quantum_vision"] = check_quantum_vision_status()
    else:
        components_status["quantum_vision"] = "disabled"
        
    # Check Casibase status
    if config["integrations"]["enable_casibase"]:
        components_status["casibase"] = check_casibase_status()
    else:
        components_status["casibase"] = "disabled"
    
    # Check Cypher status
    if config["integrations"]["enable_cypher"]:
        components_status["cypher"] = check_cypher_status()
    else:
        components_status["cypher"] = "disabled"
        
    # Check AI Conversation Companion status
    if config["integrations"]["enable_ai_companion"]:
        components_status["ai_companion"] = check_ai_companion_status()
    else:
        components_status["ai_companion"] = "disabled"
    
    return {
        "status": "operational",
        "components": components_status,
        "version": config["version"]
    }

def check_openmanus_status() -> str:
    """Check if OpenManus is available and working"""
    try:
        if not os.path.exists(config["paths"]["openmanus"]):
            return "unavailable (path not found)"
            
        # Try importing a key module
        sys.path.append(config["paths"]["openmanus"])
        import app.llm as openmanus_llm
        return "available"
    except Exception as e:
        logger.error(f"Failed to check OpenManus: {e}")
        return f"error: {str(e)}"

def check_quantum_vision_status() -> str:
    """Check if QuantumVision is available and working"""
    try:
        if not os.path.exists(config["paths"]["quantum_vision"]):
            return "unavailable (path not found)"
            
        # Try importing a key module
        sys.path.append(config["paths"]["quantum_vision"])
        try:
            import nlp_processor
            return "available"
        except ImportError:
            # Create simple __init__.py in directory if it doesn't exist
            if not os.path.exists(f"{config['paths']['quantum_vision']}/__init__.py"):
                with open(f"{config['paths']['quantum_vision']}/__init__.py", "w") as f:
                    f.write("# Generated by AtlasUnified installer\n")
                import nlp_processor
                return "available (fixed module imports)"
            return "error: could not import nlp_processor"
    except Exception as e:
        logger.error(f"Failed to check QuantumVision: {e}")
        return f"error: {str(e)}"

def check_casibase_status() -> str:
    """Check if Casibase is available"""
    if os.path.exists(config["paths"]["casibase"]):
        return "path exists (service status unknown)"
    return "unavailable (path not found)"

def check_cypher_status() -> str:
    """Check if Cypher is available"""
    if os.path.exists(config["paths"]["cypher"]):
        return "path exists (service status unknown)"
    return "unavailable (path not found)"

def check_ai_companion_status() -> str:
    """Check if AI Conversation Companion is available"""
    if os.path.exists(config["paths"]["ai_companion"]):
        return "path exists (service status unknown)"
    return "unavailable (path not found)"

@app.post("/query")
async def query(request: Request, response: Response):
    """Process a query through available components"""
    try:
        data = await request.json()
    except Exception as e:
        response.status_code = status.HTTP_400_BAD_REQUEST
        return {"error": f"Invalid JSON: {str(e)}"}
        
    query_text = data.get("query", "")
    if not query_text:
        response.status_code = status.HTTP_400_BAD_REQUEST
        return {"error": "Query text is required"}
    
    logger.info(f"Received query: {query_text}")
    results = {}
    
    # Process with OpenManus if enabled
    if config["integrations"]["enable_openmanus"]:
        try:
            sys.path.append(config["paths"]["openmanus"])
            try:
                from app.agent import Agent
                agent = Agent()
                openmanus_result = agent.run(query_text)
                results["openmanus"] = openmanus_result
            except Exception as inner_e:
                # Fallback to simpler interaction if full agent fails
                logger.warning(f"Failed to use OpenManus Agent, trying LLM directly: {inner_e}")
                from app import llm
                openmanus_result = llm.generate_text(prompt=query_text)
                results["openmanus"] = {"fallback_response": openmanus_result}
        except Exception as e:
            logger.error(f"OpenManus processing error: {e}")
            logger.error(traceback.format_exc())
            results["openmanus"] = {"error": str(e)}
    
    # Process with Quantum Vision if enabled
    if config["integrations"]["enable_quantum_vision"]:
        try:
            sys.path.append(config["paths"]["quantum_vision"])
            
            # Try to import and use nlp_processor
            try:
                import nlp_processor
                processor = nlp_processor.NLPProcessor()
                quantum_result = processor.process_text(query_text)
                results["quantum_vision"] = quantum_result
            except AttributeError:
                # Fallback to direct OpenAI if NLPProcessor class not found
                logger.warning("NLPProcessor not found, falling back to OpenAI integration")
                import openai_integration
                api_result = openai_integration.process_with_openai(query_text)
                results["quantum_vision"] = {"fallback_response": api_result}
        except Exception as e:
            logger.error(f"Quantum Vision processing error: {e}")
            logger.error(traceback.format_exc())
            results["quantum_vision"] = {"error": str(e)}
    
    return results

def main():
    """Run the unified bridge server"""
    logger.info("Starting Atlas Intelligence Unified Bridge")
    try:
        uvicorn.run(
            "unified_bridge:app", 
            host=config["api"]["host"], 
            port=config["api"]["port"],
            reload=config["api"]["debug"]
        )
    except Exception as e:
        logger.error(f"Failed to start server: {e}")
        logger.error(traceback.format_exc())
        sys.exit(1)

if __name__ == "__main__":
    main()
EOF

# Make the bridge script executable
chmod +x "$UNIFIED_DIR/unified_bridge.py"

# Create a launch script with improved error handling
log_info "Creating launch script..."
cat > "$UNIFIED_DIR/start_unified.sh" << EOF
#!/bin/bash

# Color codes for better output
GREEN='\033[0;32m'
BLUE='\033[0;34m'
YELLOW='\033[0;33m'
RED='\033[0;31m'
NC='\033[0m' # No Color

# Check if virtual environment exists
if [ ! -f "$UNIFIED_DIR/venv/bin/activate" ]; then
    echo -e "${RED}Error: Virtual environment not found.${NC}"
    echo -e "${BLUE}Running installation repair...${NC}"
    
    # Attempt to fix the virtual environment
    cd "$UNIFIED_DIR"
    python3 -m venv venv
    
    if [ ! -f "$UNIFIED_DIR/venv/bin/activate" ]; then
        echo -e "${RED}Failed to create virtual environment. Please run the installation script again.${NC}"
        exit 1
    fi
fi

# Activate the virtual environment
source "$UNIFIED_DIR/venv/bin/activate" || {
    echo -e "${RED}Failed to activate virtual environment.${NC}"
    exit 1
}

# Check if required packages are installed
echo -e "${BLUE}Checking required packages...${NC}"
python -c "import fastapi, uvicorn" &>/dev/null || {
    echo -e "${YELLOW}Some required packages are missing. Installing...${NC}"
    pip install fastapi uvicorn pydantic
}

# Change to the unified directory
cd "$UNIFIED_DIR" || {
    echo -e "${RED}Failed to change to unified directory.${NC}"
    exit 1
}

# Run the unified bridge
echo -e "${GREEN}Starting Atlas Intelligence Unified API...${NC}"

if [[ \$1 == "--debug" ]]; then
    echo -e "${YELLOW}Running in debug mode...${NC}"
    PYTHONPATH="\$PYTHONPATH:$UNIFIED_DIR" python unified_bridge.py
else
    # Run in "production" mode with error logging
    PYTHONPATH="\$PYTHONPATH:$UNIFIED_DIR" python unified_bridge.py 2> "$UNIFIED_DIR/logs/error.log"
fi
EOF

chmod +x "$UNIFIED_DIR/start_unified.sh"

# Create a simple diagnostic tool for troubleshooting
log_info "Creating diagnostic tool..."
cat > "$UNIFIED_DIR/diagnose.py" << EOF
#!/usr/bin/env python3
"""
Atlas Intelligence Diagnostic Tool
Checks if all components are properly configured and working.
"""

import os
import sys
import yaml
import importlib
import platform
import subprocess
from pathlib import Path

def print_header(text):
    print(f"\n{'=' * 50}")
    print(f" {text}")
    print(f"{'=' * 50}")

def print_success(text):
    print(f"[✓] {text}")

def print_error(text):
    print(f"[✗] {text}")

def print_warning(text):
    print(f"[!] {text}")

def check_python():
    print_header("Python Environment")
    print(f"Python version: {platform.python_version()}")
    print(f"Python executable: {sys.executable}")
    
    # Check virtual environment
    in_venv = sys.prefix != sys.base_prefix
    if in_venv:
        print_success(f"Running in virtual environment: {sys.prefix}")
    else:
        print_error("Not running in a virtual environment")

def check_core_packages():
    print_header("Core Python Packages")
    packages = [
        "fastapi", "uvicorn", "pydantic", "yaml", "numpy", 
        "openai", "requests", "flask", "sqlalchemy"
    ]
    
    for package in packages:
        try:
            pkg = importlib.import_module(package)
            version = getattr(pkg, "__version__", "unknown version")
            print_success(f"{package}: {version}")
        except ImportError:
            print_error(f"{package}: Not installed")

def check_components(config):
    print_header("Component Status")
    
    # Check OpenManus
    if config["integrations"]["enable_openmanus"]:
        path = config["paths"]["openmanus"]
        if os.path.exists(path):
            print_success(f"OpenManus path exists: {path}")
            # Try to import a key module
            try:
                sys.path.append(path)
                import app.llm
                print_success("OpenManus modules can be imported")
            except ImportError as e:
                print_error(f"Cannot import OpenManus modules: {e}")
        else:
            print_error(f"OpenManus path does not exist: {path}")
    
    # Check QuantumVision
    if config["integrations"]["enable_quantum_vision"]:
        path = config["paths"]["quantum_vision"]
        if os.path.exists(path):
            print_success(f"QuantumVision path exists: {path}")
            # Try to import a key module
            try:
                sys.path.append(path)
                import nlp_processor
                print_success("QuantumVision modules can be imported")
            except ImportError as e:
                print_error(f"Cannot import QuantumVision modules: {e}")
        else:
            print_error(f"QuantumVision path does not exist: {path}")
            
    # Check Casibase
    if config["integrations"]["enable_casibase"]:
        path = config["paths"]["casibase"]
        if os.path.exists(path):
            print_success(f"Casibase path exists: {path}")
        else:
            print_error(f"Casibase path does not exist: {path}")
    
    # Check other components
    for component in ["cypher", "ai_companion"]:
        if config["integrations"][f"enable_{component}"]:
            path = config["paths"][component]
            if os.path.exists(path):
                print_success(f"{component} path exists: {path}")
            else:
                print_error(f"{component} path does not exist: {path}")

def check_connectivity():
    print_header("API Connectivity")
    host = "localhost"
    port = 8080
    
    # Check if something is already running on the port
    try:
        import socket
        s = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
        s.settimeout(1)
        result = s.connect_ex((host, port))
        if result == 0:
            print_success(f"Port {port} is open (API may already be running)")
        else:
            print_warning(f"Port {port} is not in use (API is not running)")
        s.close()
    except Exception as e:
        print_error(f"Failed to check port: {e}")

def main():
    print_header("Atlas Intelligence Diagnostic Tool")
    print(f"Running diagnostics on: {os.path.abspath('.')}")
    
    # Check Python environment
    check_python()
    
    # Check core packages
    check_core_packages()
    
    # Load configuration
    config_path = Path("config/unified_config.yaml")
    if config_path.exists():
        try:
            with open(config_path, "r") as f:
                config = yaml.safe_load(f)
            print_success("Configuration loaded successfully")
            
            # Check components
            check_components(config)
        except Exception as e:
            print_error(f"Failed to load configuration: {e}")
    else:
        print_error(f"Configuration file not found: {config_path}")
    
    # Check connectivity
    check_connectivity()
    
    print_header("Diagnostic Complete")
    print("To start the API server, run: ./start_unified.sh")
    print("For detailed logs, check the logs directory")

if __name__ == "__main__":
    main()
EOF

chmod +x "$UNIFIED_DIR/diagnose.py"

# Create a repair script for common issues
log_info "Creating repair script..."
cat > "$UNIFIED_DIR/repair.sh" << EOF
#!/bin/bash

# Color codes for better output
GREEN='\033[0;32m'
BLUE='\033[0;34m'
YELLOW='\033[0;33m'
RED='\033[0;31m'
NC='\033[0m' # No Color

echo -e "${BLUE}==============================================${NC}"
echo -e "${BLUE}     Atlas Intelligence Repair Tool          ${NC}"
echo -e "${BLUE}==============================================${NC}"

# Check if running in the correct directory
if [ ! -f "./config/unified_config.yaml" ]; then
    echo -e "${RED}Error: Run this script from the AtlasUnified directory.${NC}"
    exit 1
fi

# Repair virtual environment
echo -e "${BLUE}Repairing virtual environment...${NC}"
rm -rf ./venv
python3 -m venv venv
source ./venv/bin/activate

# Install core dependencies
echo -e "${BLUE}Installing core dependencies...${NC}"
pip install --upgrade pip wheel setuptools
pip install fastapi uvicorn pydantic pyyaml numpy
pip install openai requests flask sqlalchemy

# Fix permissions
echo -e "${BLUE}Fixing permissions...${NC}"
chmod +x ./unified_bridge.py
chmod +x ./start_unified.sh
chmod +x ./diagnose.py

# Create any missing directories
echo -e "${BLUE}Creating missing directories...${NC}"
mkdir -p ./logs
mkdir -p ./data

# Run diagnostics
echo -e "${BLUE}Running diagnostics...${NC}"
python ./diagnose.py

echo -e "${GREEN}Repair complete. You can now run ./start_unified.sh${NC}"
EOF

chmod +x "$UNIFIED_DIR/repair.sh"

# Make sure we're back in the original directory
cd "$QUANTUM_VISION_DIR"

log_success "Installation complete!"
log_info "=============================================="
log_info "To start the unified system, run:"
log_success "cd $UNIFIED_DIR && ./start_unified.sh"
log_info "=============================================="
log_info "For diagnostics and troubleshooting:"
log_success "cd $UNIFIED_DIR && python diagnose.py"
log_info "=============================================="
log_info "To repair the installation if needed:"
log_success "cd $UNIFIED_DIR && ./repair.sh"
log_info "=============================================="
log_info "The unified API will be available at:"
log_success "http://localhost:8080"
log_info "=============================================="
log_info "Installation log saved to: $LOG_FILE"
log_info "=============================================="