biovault 0.1.6

A bioinformatics data vault CLI tool
Documentation 
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use crate::error::Error;
use crate::Result;
use anyhow::Context;
use serde::{Deserialize, Serialize};
use std::fs;
use std::path::{Path, PathBuf};

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

#[derive(Debug, Clone, Serialize, Deserialize)]
pub struct SyftBoxConfig {
    pub data_dir: 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();
        let yaml_content = serde_yaml::to_string(&self)?;
        fs::write(path, yaml_content)
            .with_context(|| format!("Failed to write config file: {}", path.display()))?;
        Ok(())
    }

    pub fn get_syftbox_data_dir(&self) -> crate::error::Result<PathBuf> {
        let syftbox_config_path = if let Some(ref path) = self.syftbox_config {
            PathBuf::from(path)
        } else {
            let home_dir = dirs::home_dir()
                .ok_or_else(|| anyhow::anyhow!("Could not determine home directory"))?;
            home_dir.join(".syftbox").join("config.json")
        };

        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> {
        let home_dir = if let Ok(test_home) = std::env::var("BIOVAULT_TEST_HOME") {
            PathBuf::from(test_home)
        } else {
            dirs::home_dir().ok_or_else(|| anyhow::anyhow!("Could not determine home directory"))?
        };
        Ok(home_dir.join(".biovault").join("config.yaml"))
    }

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