use ruv_fann::security::{SecurityLayer, SecurityConfig};

// Configure multi-layer security
let security_config = SecurityConfig::builder()
    .add_layer(SecurityLayer::NetworkIsolation)
    .add_layer(SecurityLayer::Authentication)
    .add_layer(SecurityLayer::Authorization)
    .add_layer(SecurityLayer::Encryption)
    .add_layer(SecurityLayer::AuditLogging)
    .add_layer(SecurityLayer::IntrusionDetection)
    .build()?;

// Apply to neural network system
let secure_system = NeuralSystem::new()
    .with_security(security_config)
    .build()?;

use jsonwebtoken::{encode, decode, Header, Validation, EncodingKey, DecodingKey};
use serde::{Serialize, Deserialize};

#[derive(Debug, Serialize, Deserialize)]
struct Claims {
    sub: String,           // Subject (user ID)
    exp: usize,           // Expiration time
    iat: usize,           // Issued at
    roles: Vec<String>,   // User roles
    permissions: Vec<String>, // Specific permissions
}

// Authentication service
pub struct AuthService {
    encoding_key: EncodingKey,
    decoding_key: DecodingKey,
    validation: Validation,
}

impl AuthService {
    pub fn new(secret: &[u8]) -> Self {
        Self {
            encoding_key: EncodingKey::from_secret(secret),
            decoding_key: DecodingKey::from_secret(secret),
            validation: Validation::default(),
        }
    }
    
    pub fn generate_token(&self, user_id: &str, roles: Vec<String>) -> Result<String> {
        let expiration = Utc::now()
            .checked_add_signed(chrono::Duration::hours(24))
            .expect("valid timestamp")
            .timestamp();
        
        let claims = Claims {
            sub: user_id.to_string(),
            exp: expiration as usize,
            iat: Utc::now().timestamp() as usize,
            roles,
            permissions: self.derive_permissions(&roles),
        };
        
        encode(&Header::default(), &claims, &self.encoding_key)
            .map_err(|e| Error::TokenGeneration(e.to_string()))
    }
    
    pub fn verify_token(&self, token: &str) -> Result<Claims> {
        decode::<Claims>(token, &self.decoding_key, &self.validation)
            .map(|data| data.claims)
            .map_err(|e| Error::TokenValidation(e.to_string()))
    }
}

use ruv_fann::security::rbac::{Role, Permission, Resource};

// Define roles and permissions
#[derive(Debug, Clone)]
enum SystemRole {
    Admin,
    DataScientist,
    MLEngineer,
    Viewer,
}

#[derive(Debug, Clone)]
enum SystemPermission {
    TrainModel,
    DeployModel,
    ViewMetrics,
    ManageData,
    ConfigureSystem,
}

// RBAC implementation
pub struct RBACManager {
    role_permissions: HashMap<SystemRole, HashSet<SystemPermission>>,
    user_roles: HashMap<String, HashSet<SystemRole>>,
}

impl RBACManager {
    pub fn new() -> Self {
        let mut role_permissions = HashMap::new();
        
        // Admin has all permissions
        role_permissions.insert(SystemRole::Admin, 
            vec![
                SystemPermission::TrainModel,
                SystemPermission::DeployModel,
                SystemPermission::ViewMetrics,
                SystemPermission::ManageData,
                SystemPermission::ConfigureSystem,
            ].into_iter().collect()
        );
        
        // Data Scientist permissions
        role_permissions.insert(SystemRole::DataScientist,
            vec![
                SystemPermission::TrainModel,
                SystemPermission::ViewMetrics,
                SystemPermission::ManageData,
            ].into_iter().collect()
        );
        
        // ML Engineer permissions
        role_permissions.insert(SystemRole::MLEngineer,
            vec![
                SystemPermission::DeployModel,
                SystemPermission::ViewMetrics,
                SystemPermission::ConfigureSystem,
            ].into_iter().collect()
        );
        
        // Viewer permissions
        role_permissions.insert(SystemRole::Viewer,
            vec![SystemPermission::ViewMetrics].into_iter().collect()
        );
        
        Self {
            role_permissions,
            user_roles: HashMap::new(),
        }
    }
    
    pub fn check_permission(
        &self,
        user_id: &str,
        permission: SystemPermission,
    ) -> bool {
        self.user_roles
            .get(user_id)
            .map(|roles| {
                roles.iter().any(|role| {
                    self.role_permissions
                        .get(role)
                        .map(|perms| perms.contains(&permission))
                        .unwrap_or(false)
                })
            })
            .unwrap_or(false)
    }
}

// Authorization middleware
pub async fn require_permission(
    permission: SystemPermission,
) -> impl Filter<Extract = (), Error = Rejection> + Clone {
    warp::header::<String>("authorization")
        .and_then(move |token: String| {
            let permission = permission.clone();
            async move {
                let claims = AUTH_SERVICE.verify_token(&token)
                    .map_err(|_| warp::reject::unauthorized())?;
                
                if RBAC_MANAGER.check_permission(&claims.sub, permission) {
                    Ok(())
                } else {
                    Err(warp::reject::forbidden())
                }
            }
        })
        .untuple_one()
}

use oauth2::{
    AuthorizationCode, AuthUrl, ClientId, ClientSecret,
    CsrfToken, PkceCodeChallenge, RedirectUrl, Scope,
    TokenResponse, TokenUrl,
};

// OAuth2 client configuration
pub struct OAuth2Config {
    client_id: ClientId,
    client_secret: ClientSecret,
    auth_url: AuthUrl,
    token_url: TokenUrl,
    redirect_url: RedirectUrl,
}

impl OAuth2Config {
    pub fn github() -> Self {
        Self {
            client_id: ClientId::new(env::var("GITHUB_CLIENT_ID").unwrap()),
            client_secret: ClientSecret::new(env::var("GITHUB_CLIENT_SECRET").unwrap()),
            auth_url: AuthUrl::new("https://github.com/login/oauth/authorize".to_string()).unwrap(),
            token_url: TokenUrl::new("https://github.com/login/oauth/access_token".to_string()).unwrap(),
            redirect_url: RedirectUrl::new("http://localhost:8080/auth/callback".to_string()).unwrap(),
        }
    }
}

use aes_gcm::{Aes256Gcm, Key, Nonce};
use aes_gcm::aead::{Aead, NewAead};

pub struct DataEncryption {
    cipher: Aes256Gcm,
}

impl DataEncryption {
    pub fn new(key: &[u8; 32]) -> Self {
        let key = Key::from_slice(key);
        let cipher = Aes256Gcm::new(key);
        Self { cipher }
    }
    
    pub fn encrypt_model(&self, model: &NeuralNetwork) -> Result<Vec<u8>> {
        let serialized = bincode::serialize(model)?;
        let nonce = Nonce::from_slice(b"unique nonce"); // Use random nonce in production
        
        self.cipher
            .encrypt(nonce, serialized.as_ref())
            .map_err(|e| Error::Encryption(e.to_string()))
    }
    
    pub fn decrypt_model(&self, encrypted: &[u8]) -> Result<NeuralNetwork> {
        let nonce = Nonce::from_slice(b"unique nonce");
        
        let decrypted = self.cipher
            .decrypt(nonce, encrypted)
            .map_err(|e| Error::Decryption(e.to_string()))?;
        
        bincode::deserialize(&decrypted)
            .map_err(|e| Error::Deserialization(e.to_string()))
    }
}

// Encrypted model storage
pub struct SecureModelStore {
    encryption: DataEncryption,
    storage: Box<dyn Storage>,
}

impl SecureModelStore {
    pub async fn save_model(
        &self,
        model_id: &str,
        model: &NeuralNetwork,
    ) -> Result<()> {
        let encrypted = self.encryption.encrypt_model(model)?;
        
        // Add metadata
        let metadata = ModelMetadata {
            id: model_id.to_string(),
            created_at: Utc::now(),
            encrypted: true,
            algorithm: "AES-256-GCM",
        };
        
        self.storage.put(
            &format!("models/{}", model_id),
            &encrypted,
            Some(serde_json::to_vec(&metadata)?),
        ).await
    }
}

use rustls::{ServerConfig, Certificate, PrivateKey};
use tokio_rustls::TlsAcceptor;

// TLS configuration
pub fn configure_tls() -> Result<ServerConfig> {
    let cert_file = std::fs::File::open("cert.pem")?;
    let key_file = std::fs::File::open("key.pem")?;
    
    let cert_chain = rustls_pemfile::certs(&mut BufReader::new(cert_file))?
        .into_iter()
        .map(Certificate)
        .collect();
    
    let mut keys = rustls_pemfile::pkcs8_private_keys(&mut BufReader::new(key_file))?;
    let key = PrivateKey(keys.remove(0));
    
    let config = ServerConfig::builder()
        .with_safe_defaults()
        .with_no_client_auth()
        .with_single_cert(cert_chain, key)?;
    
    Ok(config)
}

// Secure gRPC server
pub async fn start_secure_grpc_server() -> Result<()> {
    let addr = "[::1]:50051".parse()?;
    let tls_config = configure_tls()?;
    
    let neural_service = NeuralServiceImpl::new();
    
    Server::builder()
        .tls_config(tls_config)?
        .add_service(NeuralServiceServer::new(neural_service))
        .serve(addr)
        .await?;
    
    Ok(())
}

use tfhe::prelude::*;

// Homomorphic neural network inference
pub struct HomomorphicNN {
    parameters: ServerKey,
    weights: Vec<Vec<LweBootstrappingKey>>,
}

impl HomomorphicNN {
    pub fn encrypted_inference(
        &self,
        encrypted_input: &[Ciphertext],
    ) -> Result<Vec<Ciphertext>> {
        let mut activation = encrypted_input.to_vec();
        
        for (layer_idx, layer_weights) in self.weights.iter().enumerate() {
            let mut next_activation = Vec::new();
            
            for neuron_weights in layer_weights {
                let mut sum = self.parameters.create_trivial(0);
                
                // Homomorphic matrix multiplication
                for (w, a) in neuron_weights.iter().zip(&activation) {
                    let product = self.parameters.mul(w, a);
                    sum = self.parameters.add(&sum, &product);
                }
                
                // Homomorphic activation (approximated ReLU)
                let activated = self.homomorphic_relu(&sum);
                next_activation.push(activated);
            }
            
            activation = next_activation;
        }
        
        Ok(activation)
    }
}

use governor::{Quota, RateLimiter};
use std::num::NonZeroU32;

// Rate limiter implementation
pub struct DDoSProtection {
    inference_limiter: RateLimiter<String, DefaultKeyedStateStore<String>>,
    training_limiter: RateLimiter<String, DefaultKeyedStateStore<String>>,
}

impl DDoSProtection {
    pub fn new() -> Self {
        Self {
            inference_limiter: RateLimiter::keyed(
                Quota::per_second(NonZeroU32::new(100).unwrap())
            ),
            training_limiter: RateLimiter::keyed(
                Quota::per_minute(NonZeroU32::new(10).unwrap())
            ),
        }
    }
    
    pub async fn check_inference_limit(&self, client_id: &str) -> Result<()> {
        self.inference_limiter
            .check_key(&client_id.to_string())
            .map_err(|_| Error::RateLimitExceeded)?;
        Ok(())
    }
}

// Circuit breaker for downstream services
use circuit_breaker::{CircuitBreaker, Config};

pub struct ServiceProtection {
    breaker: CircuitBreaker,
}

impl ServiceProtection {
    pub fn new() -> Self {
        let config = Config::new()
            .failure_rate_threshold(0.5)
            .slow_call_rate_threshold(0.5)
            .wait_duration_in_open_state(Duration::from_secs(30))
            .slow_call_duration_threshold(Duration::from_secs(1))
            .permitted_calls_in_half_open_state(10)
            .sliding_window_size(100);
        
        Self {
            breaker: CircuitBreaker::new(config),
        }
    }
    
    pub async fn call_service<F, T>(&self, f: F) -> Result<T>
    where
        F: Future<Output = Result<T>>,
    {
        self.breaker.call(f).await
    }
}

use seccomp::{Context, Action, Arch, Syscall};

// Seccomp security profile
pub fn apply_seccomp_profile() -> Result<()> {
    let mut ctx = Context::new(Action::Errno(libc::EPERM))?;
    
    // Allow only required syscalls
    let allowed_syscalls = vec![
        Syscall::read,
        Syscall::write,
        Syscall::open,
        Syscall::close,
        Syscall::mmap,
        Syscall::munmap,
        Syscall::brk,
        Syscall::rt_sigaction,
        Syscall::rt_sigprocmask,
        Syscall::ioctl,
        Syscall::nanosleep,
        Syscall::exit,
        Syscall::exit_group,
    ];
    
    for syscall in allowed_syscalls {
        ctx.add_rule(Action::Allow, syscall)?;
    }
    
    ctx.load()?;
    Ok(())
}

// AppArmor profile
const APPARMOR_PROFILE: &str = r#"
#include <tunables/global>

profile ruv-fann flags=(attach_disconnected,mediate_deleted) {
  #include <abstractions/base>
  
  # Application binary
  /usr/local/bin/ruv-fann ix,
  
  # Read access to models
  /models/** r,
  
  # Write access to logs
  /var/log/ruv-fann/** w,
  
  # Network access
  network tcp,
  network udp,
  
  # Deny everything else
  deny /** wklx,
  deny @{PROC}/** wklx,
  deny /sys/** wklx,
}
"#;

#[cfg(test)]
mod security_tests {
    use super::*;
    
    #[test]
    fn test_sql_injection_prevention() {
        let malicious_input = "'; DROP TABLE models; --";
        let result = sanitize_input(malicious_input);
        assert!(!result.contains("DROP"));
    }
    
    #[test]
    fn test_xss_prevention() {
        let xss_attempt = "<script>alert('XSS')</script>";
        let sanitized = html_escape(xss_attempt);
        assert_eq!(sanitized, "&lt;script&gt;alert('XSS')&lt;/script&gt;");
    }
    
    #[test]
    fn test_path_traversal_prevention() {
        let malicious_path = "../../../etc/passwd";
        let result = validate_file_path(malicious_path);
        assert!(result.is_err());
    }
    
    #[test]
    fn test_command_injection_prevention() {
        let malicious_cmd = "echo test; rm -rf /";
        let result = execute_safe_command(malicious_cmd);
        assert!(result.is_err());
    }
}

// Fuzzing tests
#[cfg(test)]
mod fuzz_tests {
    use arbitrary::{Arbitrary, Unstructured};
    
    #[test]
    fn fuzz_input_validation() {
        let data = vec![0u8; 1024];
        let mut u = Unstructured::new(&data);
        
        for _ in 0..1000 {
            if let Ok(input) = String::arbitrary(&mut u) {
                let _ = validate_neural_input(&input);
                // Should not panic
            }
        }
    }
}

use serde_json::json;
use chrono::Utc;

// Security event logging
#[derive(Debug, Serialize)]
pub struct SecurityEvent {
    timestamp: DateTime<Utc>,
    event_type: SecurityEventType,
    severity: Severity,
    source_ip: Option<String>,
    user_id: Option<String>,
    details: serde_json::Value,
}

#[derive(Debug, Serialize)]
pub enum SecurityEventType {
    AuthenticationFailure,
    AuthorizationFailure,
    RateLimitExceeded,
    AnomalousActivity,
    DataExfiltrationAttempt,
    ModelExtractionAttempt,
}

pub struct SecurityMonitor {
    event_sender: mpsc::Sender<SecurityEvent>,
}

impl SecurityMonitor {
    pub async fn log_event(&self, event: SecurityEvent) {
        // Send to SIEM
        if let Err(e) = self.event_sender.send(event).await {
            eprintln!("Failed to log security event: {}", e);
        }
    }
    
    pub async fn detect_anomalies(&self, request: &Request) -> Option<SecurityEvent> {
        // Check for unusual patterns
        if self.is_model_extraction_attempt(request) {
            return Some(SecurityEvent {
                timestamp: Utc::now(),
                event_type: SecurityEventType::ModelExtractionAttempt,
                severity: Severity::High,
                source_ip: request.remote_addr().map(|a| a.to_string()),
                user_id: request.user_id().cloned(),
                details: json!({
                    "endpoint": request.uri().to_string(),
                    "query_count": request.query_count(),
                }),
            });
        }
        
        None
    }
}

use ml_ids::{AnomalyDetector, NetworkFlow};

pub struct NeuralIDS {
    detector: AnomalyDetector,
    baseline: NetworkBaseline,
}

impl NeuralIDS {
    pub async fn analyze_traffic(&mut self, flow: NetworkFlow) -> Option<Alert> {
        // Extract features
        let features = self.extract_features(&flow);
        
        // Check against baseline
        let anomaly_score = self.detector.predict(&features);
        
        if anomaly_score > self.baseline.threshold {
            return Some(Alert {
                severity: self.calculate_severity(anomaly_score),
                description: format!("Anomalous network traffic detected: score {:.2}", anomaly_score),
                source: flow.source_ip,
                destination: flow.dest_ip,
                timestamp: Utc::now(),
            });
        }
        
        // Update baseline
        self.baseline.update(&features);
        
        None
    }
}

pub struct IncidentResponder {
    isolation_controller: NetworkIsolation,
    evidence_collector: ForensicsCollector,
    notification_service: NotificationService,
}

impl IncidentResponder {
    pub async fn handle_security_incident(&mut self, incident: SecurityIncident) -> Result<()> {
        match incident.severity {
            Severity::Critical => {
                // Immediate automated response
                self.isolation_controller.isolate_system(&incident.affected_system).await?;
                self.evidence_collector.start_collection(&incident).await?;
                self.notification_service.alert_security_team(&incident).await?;
                
                // Initiate emergency procedures
                self.initiate_emergency_response(&incident).await?;
            }
            Severity::High => {
                // Partial automation with human verification
                self.evidence_collector.start_collection(&incident).await?;
                self.notification_service.request_approval(&incident).await?;
            }
            _ => {
                // Log and monitor
                self.log_incident(&incident).await?;
            }
        }
        
        Ok(())
    }
}

// Data privacy implementation
pub struct PrivacyManager {
    encryption: DataEncryption,
    anonymizer: DataAnonymizer,
}

impl PrivacyManager {
    pub fn handle_data_request(&self, request: DataRequest) -> Result<DataResponse> {
        match request {
            DataRequest::Access { user_id } => {
                let data = self.get_user_data(&user_id)?;
                Ok(DataResponse::UserData(self.anonymize_pii(data)))
            }
            DataRequest::Deletion { user_id } => {
                self.delete_user_data(&user_id)?;
                Ok(DataResponse::Deleted)
            }
            DataRequest::Portability { user_id } => {
                let data = self.export_user_data(&user_id)?;
                Ok(DataResponse::Export(data))
            }
        }
    }
    
    fn anonymize_pii(&self, data: UserData) -> UserData {
        UserData {
            id: self.hash_identifier(&data.id),
            email: self.anonymizer.anonymize_email(&data.email),
            name: self.anonymizer.anonymize_name(&data.name),
            ..data
        }
    }
}

#[derive(Debug, Serialize)]
pub struct AuditLog {
    timestamp: DateTime<Utc>,
    user_id: String,
    action: String,
    resource: String,
    result: ActionResult,
    metadata: HashMap<String, String>,
}

pub struct AuditLogger {
    storage: SecureStorage,
    signer: MessageSigner,
}

impl AuditLogger {
    pub async fn log_action(&self, log: AuditLog) -> Result<()> {
        // Sign log entry for tamper detection
        let serialized = serde_json::to_string(&log)?;
        let signature = self.signer.sign(&serialized)?;
        
        let signed_log = SignedAuditLog {
            log,
            signature,
        };
        
        // Store immutably
        self.storage.append_only_write(&signed_log).await?;
        
        Ok(())
    }
}

// Security checks in CI/CD
#[cfg(test)]
mod security_ci {
    #[test]
    fn check_no_hardcoded_secrets() {
        let files = glob::glob("**/*.rs").unwrap();
        for file in files {
            let content = std::fs::read_to_string(file.unwrap()).unwrap();
            assert!(!content.contains("password ="));
            assert!(!content.contains("api_key ="));
            assert!(!content.contains("secret ="));
        }
    }
}

// Configuration validation
pub struct SecureConfig {
    inner: Config,
}

impl SecureConfig {
    pub fn load() -> Result<Self> {
        let config = Config::builder()
            .add_source(config::File::with_name("config"))
            .add_source(config::Environment::with_prefix("RUVFANN"))
            .build()?;
        
        // Validate security settings
        Self::validate_tls_config(&config)?;
        Self::validate_auth_config(&config)?;
        Self::validate_encryption_config(&config)?;
        
        Ok(Self { inner: config })
    }
}

// Security middleware
pub fn security_headers() -> impl Filter<Extract = (), Error = Rejection> + Clone {
    warp::reply::with::headers(vec![
        ("X-Content-Type-Options", "nosniff"),
        ("X-Frame-Options", "DENY"),
        ("X-XSS-Protection", "1; mode=block"),
        ("Strict-Transport-Security", "max-age=31536000; includeSubDomains"),
        ("Content-Security-Policy", "default-src 'self'"),
        ("Referrer-Policy", "strict-origin-when-cross-origin"),
        ("Permissions-Policy", "geolocation=(), microphone=(), camera=()"),
    ])
}

use validator::{Validate, ValidationError};

#[derive(Debug, Validate)]
pub struct ModelInput {
    #[validate(length(min = 1, max = 1000))]
    #[validate(custom = "validate_no_injection")]
    name: String,
    
    #[validate(range(min = 0.0, max = 1.0))]
    learning_rate: f32,
    
    #[validate(range(min = 1, max = 1000000))]
    epochs: u32,
}

fn validate_no_injection(value: &str) -> Result<(), ValidationError> {
    let forbidden = ["<script>", "DROP", "DELETE", "../", "\\x00"];
    
    for pattern in forbidden {
        if value.contains(pattern) {
            return Err(ValidationError::new("injection_attempt"));
        }
    }
    
    Ok(())
}

impl Default for SecurityConfig {
    fn default() -> Self {
        Self {
            require_https: true,
            min_tls_version: TlsVersion::V1_2,
            enable_rate_limiting: true,
            max_requests_per_minute: 100,
            enable_audit_logging: true,
            require_authentication: true,
            session_timeout: Duration::from_hours(1),
            max_login_attempts: 5,
            password_min_length: 12,
            require_mfa: true,
        }
    }
}