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;
}
}
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");
if desktop_candidate.join("config.yaml").exists()
|| desktop_candidate.join("env").exists()
|| desktop_candidate.join("data").exists()
{
Some(desktop_candidate)
} else {
None
}
}
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> {
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> {
if let Some(dir) = TEST_SYFTBOX_DATA_DIR.with(|p| p.borrow().clone()) {
return Ok(dir);
}
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> {
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> {
if let Some(cfg) = TEST_CONFIG.with(|c| c.borrow().clone()) {
return Ok(cfg);
}
match Config::load() {
Ok(config) => Ok(config),
Err(e) => Err(anyhow::anyhow!("{}", e)),
}
}
pub fn get_biovault_home() -> anyhow::Result<PathBuf> {
if let Some(home) = TEST_BIOVAULT_HOME.with(|h| h.borrow().clone()) {
fs::create_dir_all(&home).with_context(|| {
format!(
"Failed to create test biovault directory: {}",
home.display()
)
})?;
return Ok(home);
}
if let Some(test_home) = get_env_var("BIOVAULT_TEST_HOME") {
let path = PathBuf::from(test_home);
fs::create_dir_all(&path).with_context(|| {
format!(
"Failed to create test biovault directory: {}",
path.display()
)
})?;
return Ok(path);
}
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);
}
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);
}
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);
}
let desktop_dir = resolve_desktop_dir(&home_dir);
let desktop_path = desktop_dir.join("BioVault");
if desktop_path.exists() {
fs::create_dir_all(&desktop_path).with_context(|| {
format!(
"Failed to create biovault directory: {}",
desktop_path.display()
)
})?;
persist_home_pointer(&desktop_path);
return Ok(desktop_path);
}
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,
}
}
}
fs::create_dir_all(&desktop_path).with_context(|| {
format!(
"Failed to create biovault directory: {}",
desktop_path.display()
)
})?;
persist_home_pointer(&desktop_path);
Ok(desktop_path)
}
pub fn get_cache_dir() -> anyhow::Result<PathBuf> {
if let Ok(cache_dir) = env::var("BIOVAULT_CACHE_DIR") {
return Ok(PathBuf::from(cache_dir));
}
Ok(get_biovault_home()?.join("data").join("cache"))
}
pub fn is_syftbox_env() -> bool {
env::var("SYFTBOX_DATA_DIR").is_ok() || env::var("SYFTBOX_EMAIL").is_ok()
}
pub fn get_syftbox_binary() -> Option<String> {
env::var("SYFTBOX_BINARY").ok()
}
pub fn get_syftbox_version() -> Option<String> {
env::var("SYFTBOX_VERSION").ok()
}
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);
}
}