biovault 0.1.89

use crate::error::Error;
use crate::Result;
use anyhow::Context;
use serde::{Deserialize, Serialize};
use std::cell::RefCell;
use std::env;
use std::fs;
use std::io::ErrorKind;
use std::path::{Path, PathBuf};

#[cfg(test)]
use std::collections::HashMap;

thread_local! {
    static TEST_CONFIG: RefCell<Option<Config>> = const { RefCell::new(None) };
    static TEST_SYFTBOX_DATA_DIR: RefCell<Option<PathBuf>> = const { RefCell::new(None) };
    static TEST_BIOVAULT_HOME: RefCell<Option<PathBuf>> = const { RefCell::new(None) };
    static TEST_POINTER_FILE: RefCell<Option<PathBuf>> = const { RefCell::new(None) };
}

#[cfg(test)]
thread_local! {
    static TEST_ENV_OVERRIDES: RefCell<HashMap<String, Vec<Option<String>>>> =
        RefCell::new(HashMap::new());
}

const BIOVAULT_POINTER_DIR: &str = "BioVault";
const BIOVAULT_POINTER_FILE: &str = "home_path";
const BIOVAULT_POINTER_OVERRIDE: &str = "BIOVAULT_POINTER_PATH";

fn should_persist_home_pointer() -> bool {
    get_env_var("BIOVAULT_HOME").is_none() && get_env_var("SYFTBOX_DATA_DIR").is_none()
}

fn pointer_file_path() -> Option<PathBuf> {
    if let Some(test_path) = TEST_POINTER_FILE.with(|p| p.borrow().clone()) {
        return Some(test_path);
    }
    if let Ok(path) = env::var(BIOVAULT_POINTER_OVERRIDE) {
        return Some(PathBuf::from(path));
    }
    dirs::config_dir().map(|dir| dir.join(BIOVAULT_POINTER_DIR).join(BIOVAULT_POINTER_FILE))
}

fn get_env_var(key: &str) -> Option<String> {
    #[cfg(test)]
    {
        if let Some(value) = TEST_ENV_OVERRIDES.with(|map| {
            map.borrow()
                .get(key)
                .and_then(|stack| stack.last().cloned())
        }) {
            return value;
        }
    }

    env::var(key).ok()
}

fn read_persisted_home() -> Option<PathBuf> {
    let pointer_path = pointer_file_path()?;
    let contents = match fs::read_to_string(pointer_path) {
        Ok(val) => val,
        Err(err) => match err.kind() {
            ErrorKind::NotFound => return None,
            _ => return None,
        },
    };

    let trimmed = contents.trim();
    if trimmed.is_empty() {
        None
    } else {
        Some(PathBuf::from(trimmed))
    }
}

fn persist_home_pointer(path: &Path) {
    if !should_persist_home_pointer() {
        return;
    }

    if let Some(pointer_path) = pointer_file_path() {
        if let Some(parent) = pointer_path.parent() {
            if fs::create_dir_all(parent).is_err() {
                return;
            }
        }

        // Best effort persistence; ignore failures here
        let path_str = path.to_string_lossy().into_owned();
        let _ = fs::write(pointer_path, path_str);
    }
}

fn detect_existing_home(home_dir: &Path) -> Option<PathBuf> {
    let desktop_root = resolve_desktop_dir(home_dir);
    let desktop_candidate = desktop_root.join("BioVault");
    let legacy_candidate = home_dir.join(".biovault");

    [desktop_candidate, legacy_candidate]
        .into_iter()
        .find(|candidate| {
            candidate.join("config.yaml").exists()
                || candidate.join("env").exists()
                || candidate.join("data").exists()
        })
}

fn resolve_desktop_dir(home_dir: &Path) -> PathBuf {
    if let Some(desktop_dir) = dirs::desktop_dir() {
        if desktop_dir.starts_with(home_dir) {
            return desktop_dir;
        }
    }
    home_dir.join("Desktop")
}

pub fn set_persisted_biovault_home<P: AsRef<Path>>(path: P) {
    persist_home_pointer(path.as_ref());
}

#[derive(Debug, Clone, Serialize, Deserialize)]
pub struct Config {
    pub email: String,
    #[serde(skip_serializing_if = "Option::is_none")]
    pub syftbox_config: Option<String>,
    #[serde(skip_serializing_if = "Option::is_none")]
    pub version: Option<String>,
    #[serde(skip_serializing_if = "Option::is_none")]
    pub binary_paths: Option<BinaryPaths>,
    #[serde(skip_serializing_if = "Option::is_none")]
    pub syftbox_credentials: Option<SyftboxCredentials>,
}

#[derive(Debug, Clone, Serialize, Deserialize, Default)]
pub struct BinaryPaths {
    #[serde(skip_serializing_if = "Option::is_none")]
    pub java: Option<String>,
    #[serde(skip_serializing_if = "Option::is_none")]
    pub docker: Option<String>,
    #[serde(skip_serializing_if = "Option::is_none")]
    pub nextflow: Option<String>,
    #[serde(skip_serializing_if = "Option::is_none")]
    pub syftbox: Option<String>,
    #[serde(skip_serializing_if = "Option::is_none")]
    pub uv: Option<String>,
}

#[derive(Debug, Clone, Serialize, Deserialize)]
pub struct SyftBoxConfig {
    pub data_dir: String,
}

#[derive(Debug, Clone, Serialize, Deserialize, Default)]
pub struct SyftboxCredentials {
    #[serde(skip_serializing_if = "Option::is_none")]
    pub refresh_token: Option<String>,
    #[serde(skip_serializing_if = "Option::is_none")]
    pub access_token: Option<String>,
    #[serde(skip_serializing_if = "Option::is_none")]
    pub server_url: Option<String>,
    #[serde(skip_serializing_if = "Option::is_none")]
    pub client_url: Option<String>,
    #[serde(skip_serializing_if = "Option::is_none")]
    pub data_dir: Option<String>,
    #[serde(skip_serializing_if = "Option::is_none")]
    pub email: Option<String>,
}

impl Config {
    pub fn from_file<P: AsRef<Path>>(path: P) -> Result<Self> {
        let path = path.as_ref();
        let content = fs::read_to_string(path)
            .with_context(|| format!("Failed to read config file: {}", path.display()))?;

        let config: Config = serde_yaml::from_str(&content)
            .with_context(|| format!("Failed to parse config file: {}", path.display()))?;

        Ok(config)
    }

    pub fn save<P: AsRef<Path>>(&self, path: P) -> crate::error::Result<()> {
        let path = path.as_ref();
        if let Some(parent) = path.parent() {
            fs::create_dir_all(parent).with_context(|| {
                format!("Failed to create config directory: {}", parent.display())
            })?;
        }
        let yaml_content = serde_yaml::to_string(&self)?;

        if let Some(dir) = path.parent() {
            fs::create_dir_all(dir)
                .with_context(|| format!("Failed to create config directory: {}", dir.display()))?;
        }

        fs::write(path, yaml_content)
            .with_context(|| format!("Failed to write config file: {}", path.display()))?;
        Ok(())
    }

    pub fn new(email: String) -> Self {
        Self {
            email,
            syftbox_config: None,
            version: None,
            binary_paths: None,
            syftbox_credentials: None,
        }
    }

    pub fn load_or_new(default_email: &str) -> crate::error::Result<Self> {
        match Self::load() {
            Ok(config) => Ok(config),
            Err(Error::NotInitialized) => Ok(Self::new(default_email.to_string())),
            Err(err) => Err(err),
        }
    }

    pub fn set_binary_path(
        &mut self,
        name: &str,
        path: Option<String>,
    ) -> crate::error::Result<()> {
        let paths = self.binary_paths.get_or_insert_with(BinaryPaths::default);

        match name {
            "java" => paths.java = path,
            "docker" => paths.docker = path,
            "nextflow" => paths.nextflow = path,
            "syftbox" => paths.syftbox = path,
            "uv" => paths.uv = path,
            _ => return Err(anyhow::anyhow!("Unknown dependency: {}", name).into()),
        }

        Ok(())
    }

    pub fn get_binary_path(&self, name: &str) -> Option<String> {
        self.binary_paths.as_ref().and_then(|paths| match name {
            "java" => paths.java.clone(),
            "docker" => paths.docker.clone(),
            "nextflow" => paths.nextflow.clone(),
            "syftbox" => paths.syftbox.clone(),
            "uv" => paths.uv.clone(),
            _ => None,
        })
    }

    pub fn save_binary_path(name: &str, path: Option<String>) -> crate::error::Result<Self> {
        // Try to load existing config, but preserve the email if it exists
        let mut config = match Self::load() {
            Ok(existing) => existing,
            Err(_) => Self::new("setup@pending".to_string()),
        };

        let normalized = path.and_then(|p| {
            let trimmed = p.trim();
            if trimmed.is_empty() {
                None
            } else {
                Some(trimmed.to_string())
            }
        });

        config.set_binary_path(name, normalized)?;
        let config_path = Self::get_config_path()?;
        config.save(&config_path)?;
        Ok(config)
    }

    pub fn get_syftbox_data_dir(&self) -> crate::error::Result<PathBuf> {
        // Thread-local test override takes highest priority
        if let Some(dir) = TEST_SYFTBOX_DATA_DIR.with(|p| p.borrow().clone()) {
            return Ok(dir);
        }

        // Check for SYFTBOX_DATA_DIR environment variable first
        if let Ok(data_dir) = env::var("SYFTBOX_DATA_DIR") {
            return Ok(PathBuf::from(data_dir));
        }

        let syftbox_config_path = self.get_syftbox_config_path()?;

        if !syftbox_config_path.exists() {
            return Err(Error::SyftBoxConfigMissing(
                syftbox_config_path.display().to_string(),
            ));
        }

        let content = fs::read_to_string(&syftbox_config_path).with_context(|| {
            format!(
                "Failed to read SyftBox config: {}",
                syftbox_config_path.display()
            )
        })?;

        let syftbox_config: SyftBoxConfig = serde_json::from_str(&content).with_context(|| {
            format!(
                "Failed to parse SyftBox config: {}",
                syftbox_config_path.display()
            )
        })?;

        Ok(PathBuf::from(syftbox_config.data_dir))
    }

    pub fn get_config_path() -> crate::error::Result<PathBuf> {
        Ok(get_biovault_home()?.join("config.yaml"))
    }

    pub fn get_syftbox_config_path(&self) -> crate::error::Result<PathBuf> {
        // Priority order:
        // 1. SYFTBOX_CONFIG_PATH env var
        // 2. Config specified in BioVault config
        // 3. ~/.syftbox/config.json (default)

        if let Ok(config_path) = env::var("SYFTBOX_CONFIG_PATH") {
            return Ok(PathBuf::from(config_path));
        }

        if let Some(ref path) = self.syftbox_config {
            return Ok(PathBuf::from(path));
        }

        let home_dir = dirs::home_dir()
            .ok_or_else(|| anyhow::anyhow!("Could not determine home directory"))?;
        Ok(home_dir.join(".syftbox").join("config.json"))
    }

    pub fn load() -> crate::error::Result<Self> {
        let config_path = Self::get_config_path()?;
        if !config_path.exists() {
            return Err(Error::NotInitialized);
        }
        let config = Self::from_file(config_path)?;
        Ok(config)
    }

    pub fn get_biovault_dir(&self) -> crate::error::Result<PathBuf> {
        Ok(get_biovault_home()?)
    }

    pub fn get_datasite_path(&self) -> crate::error::Result<PathBuf> {
        let data_dir = self.get_syftbox_data_dir()?;
        Ok(data_dir.join("datasites").join(&self.email))
    }

    pub fn get_shared_submissions_path(&self) -> crate::error::Result<PathBuf> {
        let datasite_path = self.get_datasite_path()?;
        Ok(datasite_path
            .join("shared")
            .join("biovault")
            .join("submissions"))
    }
}

pub fn get_config() -> anyhow::Result<Config> {
    // Thread-local test override first
    if let Some(cfg) = TEST_CONFIG.with(|c| c.borrow().clone()) {
        return Ok(cfg);
    }

    // Use the Config method which respects BIOVAULT_TEST_HOME
    match Config::load() {
        Ok(config) => Ok(config),
        Err(e) => Err(anyhow::anyhow!("{}", e)),
    }
}

/// Get the BioVault home directory
/// Priority order:
/// 1. Thread-local test override (internal)
/// 2. BIOVAULT_TEST_HOME (for tests)
/// 3. BIOVAULT_HOME env var
/// 4. SYFTBOX_DATA_DIR/.biovault (if in virtualenv)
/// 5. Walk up from cwd looking for .biovault/config.yaml (for sbenv)
/// 6. ~/Desktop/BioVault (default for desktop users)
///
/// Creates the directory if it doesn't exist.
pub fn get_biovault_home() -> anyhow::Result<PathBuf> {
    // Thread-local test override first
    if let Some(home) = TEST_BIOVAULT_HOME.with(|h| h.borrow().clone()) {
        // Ensure test directory exists
        fs::create_dir_all(&home).with_context(|| {
            format!(
                "Failed to create test biovault directory: {}",
                home.display()
            )
        })?;
        return Ok(home);
    }

    // Check for test environment (must be before directory walk to prevent finding global config)
    if let Some(test_home) = get_env_var("BIOVAULT_TEST_HOME") {
        let path = PathBuf::from(test_home).join(".biovault");
        fs::create_dir_all(&path).with_context(|| {
            format!(
                "Failed to create test biovault directory: {}",
                path.display()
            )
        })?;
        return Ok(path);
    }

    // Check for explicit BIOVAULT_HOME
    if let Some(biovault_home) = get_env_var("BIOVAULT_HOME") {
        let path = PathBuf::from(biovault_home);
        fs::create_dir_all(&path)
            .with_context(|| format!("Failed to create biovault directory: {}", path.display()))?;
        return Ok(path);
    }

    // Check for SyftBox virtualenv
    if let Some(syftbox_data_dir) = get_env_var("SYFTBOX_DATA_DIR") {
        let path = PathBuf::from(syftbox_data_dir).join(".biovault");
        fs::create_dir_all(&path)
            .with_context(|| format!("Failed to create biovault directory: {}", path.display()))?;
        return Ok(path);
    }

    let home_dir =
        dirs::home_dir().ok_or_else(|| anyhow::anyhow!("Could not determine home directory"))?;

    if let Some(persisted) = read_persisted_home() {
        fs::create_dir_all(&persisted).with_context(|| {
            format!(
                "Failed to create persisted biovault directory: {}",
                persisted.display()
            )
        })?;
        return Ok(persisted);
    }

    // Walk up from current directory looking for .biovault/config.yaml (for sbenv)
    if let Ok(current_dir) = env::current_dir() {
        let mut dir = current_dir.as_path();
        loop {
            let biovault_dir = dir.join(".biovault");
            let config_file = biovault_dir.join("config.yaml");
            if config_file.exists() {
                return Ok(biovault_dir);
            }

            match dir.parent() {
                Some(parent) => dir = parent,
                None => break,
            }
        }
    }

    if let Some(existing) = detect_existing_home(&home_dir) {
        fs::create_dir_all(&existing).with_context(|| {
            format!(
                "Failed to create biovault directory: {}",
                existing.display()
            )
        })?;
        persist_home_pointer(&existing);
        return Ok(existing);
    }

    // Default to Desktop/BioVault (user-friendly, visible location)
    let desktop_dir = resolve_desktop_dir(&home_dir);
    let default_path = desktop_dir.join("BioVault");

    // Create the default directory if it doesn't exist
    fs::create_dir_all(&default_path).with_context(|| {
        format!(
            "Failed to create biovault directory: {}",
            default_path.display()
        )
    })?;

    persist_home_pointer(&default_path);

    Ok(default_path)
}

/// Get the shared cache directory
/// Priority order:
/// 1. BIOVAULT_CACHE_DIR env var
/// 2. ~/.biovault/data/cache (default shared)
pub fn get_cache_dir() -> anyhow::Result<PathBuf> {
    // Check for explicit cache directory
    if let Ok(cache_dir) = env::var("BIOVAULT_CACHE_DIR") {
        return Ok(PathBuf::from(cache_dir));
    }

    // Always use the shared cache within the BioVault home directory
    Ok(get_biovault_home()?.join("data").join("cache"))
}

/// Check if running in a SyftBox virtualenv
pub fn is_syftbox_env() -> bool {
    env::var("SYFTBOX_DATA_DIR").is_ok() || env::var("SYFTBOX_EMAIL").is_ok()
}

/// Get the SyftBox binary path from environment
pub fn get_syftbox_binary() -> Option<String> {
    env::var("SYFTBOX_BINARY").ok()
}

/// Get the SyftBox version from environment
pub fn get_syftbox_version() -> Option<String> {
    env::var("SYFTBOX_VERSION").ok()
}

// Test utilities to isolate config and paths per test thread.
// Safe to call from tests; no-ops in normal usage if unset.
pub fn set_test_config(config: Config) {
    TEST_CONFIG.with(|c| {
        *c.borrow_mut() = Some(config);
    });
}

pub fn clear_test_config() {
    TEST_CONFIG.with(|c| {
        *c.borrow_mut() = None;
    });
}

pub fn set_test_syftbox_data_dir<P: Into<PathBuf>>(path: P) {
    TEST_SYFTBOX_DATA_DIR.with(|p| {
        *p.borrow_mut() = Some(path.into());
    });
}

pub fn clear_test_syftbox_data_dir() {
    TEST_SYFTBOX_DATA_DIR.with(|p| {
        *p.borrow_mut() = None;
    });
}

pub fn set_test_biovault_home<P: Into<PathBuf>>(path: P) {
    TEST_BIOVAULT_HOME.with(|h| {
        *h.borrow_mut() = Some(path.into());
    });
}

pub fn clear_test_biovault_home() {
    TEST_BIOVAULT_HOME.with(|h| {
        *h.borrow_mut() = None;
    });
}

#[cfg(test)]
pub fn set_test_pointer_file<P: Into<PathBuf>>(path: P) {
    TEST_POINTER_FILE.with(|p| {
        *p.borrow_mut() = Some(path.into());
    });
}

#[cfg(test)]
pub fn clear_test_pointer_file() {
    TEST_POINTER_FILE.with(|p| {
        *p.borrow_mut() = None;
    });
}

#[cfg(test)]
pub fn set_test_env_override(key: &str, value: Option<&str>) {
    TEST_ENV_OVERRIDES.with(|overrides| {
        overrides
            .borrow_mut()
            .entry(key.to_string())
            .or_default()
            .push(value.map(|v| v.to_string()));
    });
}

#[cfg(test)]
pub fn clear_test_env_override(key: &str) {
    TEST_ENV_OVERRIDES.with(|overrides| {
        let mut map = overrides.borrow_mut();
        if let Some(stack) = map.get_mut(key) {
            stack.pop();
            if stack.is_empty() {
                map.remove(key);
            }
        }
    });
}

#[cfg(test)]
mod tests {
    use super::*;
    use std::fs;
    use tempfile::TempDir;

    struct EnvGuard {
        key: String,
        previous: Option<String>,
    }

    impl EnvGuard {
        fn set(key: &str, value: &str) -> Self {
            let previous = env::var(key).ok();
            env::set_var(key, value);
            set_test_env_override(key, Some(value));
            Self {
                key: key.to_string(),
                previous,
            }
        }

        fn unset(key: &str) -> Self {
            let previous = env::var(key).ok();
            env::remove_var(key);
            set_test_env_override(key, None);
            Self {
                key: key.to_string(),
                previous,
            }
        }
    }

    impl Drop for EnvGuard {
        fn drop(&mut self) {
            if let Some(ref value) = self.previous {
                env::set_var(&self.key, value);
            } else {
                env::remove_var(&self.key);
            }
            clear_test_env_override(&self.key);
        }
    }

    #[test]
    fn config_save_and_load_round_trip() {
        let tmp = TempDir::new().unwrap();
        let path = tmp.path().join("config.yaml");
        let cfg = Config {
            email: "user@example.com".into(),
            syftbox_config: None,
            version: Some("1.0.0".into()),
            binary_paths: None,
            syftbox_credentials: None,
        };
        cfg.save(&path).unwrap();
        let loaded = Config::from_file(&path).unwrap();
        assert_eq!(loaded.email, "user@example.com");
        assert_eq!(loaded.version.as_deref(), Some("1.0.0"));
    }

    #[test]
    fn config_syftbox_dir_from_json_and_paths() {
        let tmp = TempDir::new().unwrap();
        let data_dir = tmp.path().join("syftbox_data");
        fs::create_dir_all(&data_dir).unwrap();

        let syft_cfg = SyftBoxConfig {
            data_dir: data_dir.to_string_lossy().to_string(),
        };
        let syft_cfg_path = tmp.path().join("syftbox_config.json");
        fs::write(&syft_cfg_path, serde_json::to_string(&syft_cfg).unwrap()).unwrap();

        let cfg = Config {
            email: "user@example.com".into(),
            syftbox_config: Some(syft_cfg_path.to_string_lossy().to_string()),
            version: None,
            binary_paths: None,
            syftbox_credentials: None,
        };

        let dir = cfg.get_syftbox_data_dir().unwrap();
        assert!(dir.ends_with("syftbox_data"));

        let fake = tmp.path().join("override");
        fs::create_dir_all(&fake).unwrap();
        set_test_syftbox_data_dir(&fake);
        let dir2 = cfg.get_syftbox_data_dir().unwrap();
        assert_eq!(dir2, fake);
        clear_test_syftbox_data_dir();

        let datasite = cfg.get_datasite_path().unwrap();
        assert!(datasite.ends_with(PathBuf::from("datasites/user@example.com")));
        let shared = cfg.get_shared_submissions_path().unwrap();
        assert!(shared.ends_with(PathBuf::from(
            "datasites/user@example.com/shared/biovault/submissions"
        )));
    }

    #[test]
    fn config_biovault_home_threadlocal_override() {
        let tmp = TempDir::new().unwrap();
        let home = tmp.path().join("home");
        fs::create_dir_all(&home).unwrap();
        set_test_biovault_home(&home);
        let got = get_biovault_home().unwrap();
        assert_eq!(got, home);
        clear_test_biovault_home();
    }

    #[test]
    fn config_get_config_path_uses_biovault_home() {
        let tmp = TempDir::new().unwrap();
        let home = tmp.path().join("bv_home");
        fs::create_dir_all(&home).unwrap();
        set_test_biovault_home(&home);
        let p = Config::get_config_path().unwrap();
        assert!(p.ends_with("config.yaml"));
        assert!(p.starts_with(&home));
        clear_test_biovault_home();
    }

    #[test]
    #[serial_test::serial]
    fn persisted_home_pointer_is_respected() {
        let tmp = TempDir::new().unwrap();
        let home_dir = tmp.path().join("home");
        let config_dir = tmp.path().join("config");
        fs::create_dir_all(&home_dir).unwrap();
        fs::create_dir_all(&config_dir).unwrap();
        fs::create_dir_all(home_dir.join("Desktop")).unwrap();

        let home_guard = EnvGuard::set("HOME", home_dir.to_string_lossy().as_ref());
        let config_guard = EnvGuard::set("XDG_CONFIG_HOME", config_dir.to_string_lossy().as_ref());
        let pointer_path = config_dir.join("pointer.txt");
        set_test_pointer_file(&pointer_path);
        let _unset_biovault_home = EnvGuard::unset("BIOVAULT_HOME");
        let _unset_syftbox_dir = EnvGuard::unset("SYFTBOX_DATA_DIR");
        let _unset_test_home = EnvGuard::unset("BIOVAULT_TEST_HOME");

        clear_test_biovault_home();

        let _ = fs::remove_file(&pointer_path);

        let default_home = home_dir.join("Desktop").join("BioVault");
        fs::create_dir_all(&default_home).unwrap();
        set_test_biovault_home(&default_home);
        let initial = get_biovault_home().unwrap();
        assert_eq!(initial, default_home);
        clear_test_biovault_home();

        let custom_home = home_dir.join("custom_location");
        set_persisted_biovault_home(&custom_home);
        assert_eq!(
            fs::read_to_string(&pointer_path).unwrap().trim(),
            custom_home.to_string_lossy()
        );
        let resolved_home = get_biovault_home().unwrap();
        assert_eq!(resolved_home, custom_home);
        assert!(resolved_home.exists());

        set_persisted_biovault_home(&default_home);
        let resolved_again = get_biovault_home().unwrap();
        assert_eq!(resolved_again, default_home);

        clear_test_pointer_file();
        drop(config_guard);
        drop(home_guard);
    }
}