biovault 0.1.51

use assert_cmd::Command;
use predicates::prelude::*;
use std::fs;
use std::sync::Mutex;
use tempfile::TempDir;

// Use a mutex to ensure HOME modification tests don't run in parallel
static HOME_MUTEX: Mutex<()> = Mutex::new(());

#[test]
fn test_cli_version() {
    // Read version from Cargo.toml to avoid hardcoding
    let cargo_toml = include_str!("../Cargo.toml");
    let version = cargo_toml
        .lines()
        .find(|line| line.starts_with("version = "))
        .and_then(|line| line.split('"').nth(1))
        .expect("Version not found in Cargo.toml");

    let mut cmd = Command::cargo_bin("bv").unwrap();
    cmd.arg("--version")
        .assert()
        .success()
        .stdout(predicate::str::contains(version));
}

#[test]
fn test_cli_help() {
    let mut cmd = Command::cargo_bin("bv").unwrap();
    cmd.arg("--help")
        .assert()
        .success()
        .stdout(predicate::str::contains("BioVault"))
        .stdout(predicate::str::contains("init"))
        .stdout(predicate::str::contains("info"))
        .stdout(predicate::str::contains("check"));
}

#[test]
fn test_init_command() {
    let _guard = HOME_MUTEX
        .lock()
        .unwrap_or_else(|poisoned| poisoned.into_inner());

    let temp_dir = TempDir::new().unwrap();
    let config_dir = temp_dir.path().join(".biovault");

    // Save original HOME/USERPROFILE and set temporary one
    let original_home = if cfg!(windows) {
        // On Windows, dirs::home_dir() may use multiple env vars
        let original_profile = std::env::var("USERPROFILE").ok();
        std::env::set_var("USERPROFILE", temp_dir.path());
        original_profile
    } else {
        let original_home = std::env::var("HOME").ok();
        std::env::set_var("HOME", temp_dir.path());
        original_home
    };

    let mut cmd = Command::cargo_bin("bv").unwrap();
    // Use our test-specific env var that the init command will respect
    cmd.env("BIOVAULT_TEST_HOME", temp_dir.path());
    // Also set platform-specific home for other commands that might use dirs::home_dir()
    if cfg!(windows) {
        cmd.env("USERPROFILE", temp_dir.path());
        // Clear other Windows home-related env vars to prevent interference
        cmd.env_remove("HOMEDRIVE");
        cmd.env_remove("HOMEPATH");
    } else {
        cmd.env("HOME", temp_dir.path());
    }
    cmd.arg("init")
        .arg("test@example.com")
        .assert()
        .success()
        .stdout(predicate::str::contains(
            "BioVault initialized successfully",
        ));

    // Check that config file was created
    let config_file = config_dir.join("config.yaml");
    assert!(
        config_file.exists(),
        "Config file should exist at: {}",
        config_file.display()
    );

    // Check config file contents
    let contents = fs::read_to_string(&config_file).unwrap();
    assert!(contents.contains("email: test@example.com"));

    // Restore original HOME/USERPROFILE
    if cfg!(windows) {
        if let Some(home) = original_home {
            std::env::set_var("USERPROFILE", home);
        } else {
            std::env::remove_var("USERPROFILE");
        }
    } else if let Some(home) = original_home {
        std::env::set_var("HOME", home);
    } else {
        std::env::remove_var("HOME");
    }
}

#[test]
fn test_init_command_existing_config() {
    let _guard = HOME_MUTEX
        .lock()
        .unwrap_or_else(|poisoned| poisoned.into_inner());

    let temp_dir = TempDir::new().unwrap();
    let config_dir = temp_dir.path().join(".biovault");
    fs::create_dir_all(&config_dir).unwrap();

    // Create existing config
    let config_file = config_dir.join("config.yaml");
    fs::write(&config_file, "email: existing@example.com\n").unwrap();

    // Save original HOME/USERPROFILE and set temporary one
    let original_home = if cfg!(windows) {
        // On Windows, dirs::home_dir() may use multiple env vars
        let original_profile = std::env::var("USERPROFILE").ok();
        std::env::set_var("USERPROFILE", temp_dir.path());
        original_profile
    } else {
        let original_home = std::env::var("HOME").ok();
        std::env::set_var("HOME", temp_dir.path());
        original_home
    };

    let mut cmd = Command::cargo_bin("bv").unwrap();
    // Use our test-specific env var that the init command will respect
    cmd.env("BIOVAULT_TEST_HOME", temp_dir.path());
    // Also set platform-specific home for other commands that might use dirs::home_dir()
    if cfg!(windows) {
        cmd.env("USERPROFILE", temp_dir.path());
        // Clear other Windows home-related env vars to prevent interference
        cmd.env_remove("HOMEDRIVE");
        cmd.env_remove("HOMEPATH");
    } else {
        cmd.env("HOME", temp_dir.path());
    }
    cmd.arg("init")
        .arg("new@example.com")
        .assert()
        .success()
        .stdout(predicate::str::contains("already exists"));

    // Check that original config is unchanged
    let contents = fs::read_to_string(&config_file).unwrap();
    assert!(contents.contains("email: existing@example.com"));
    assert!(!contents.contains("email: new@example.com"));

    // Restore original HOME/USERPROFILE
    if cfg!(windows) {
        if let Some(home) = original_home {
            std::env::set_var("USERPROFILE", home);
        } else {
            std::env::remove_var("USERPROFILE");
        }
    } else if let Some(home) = original_home {
        std::env::set_var("HOME", home);
    } else {
        std::env::remove_var("HOME");
    }
}

#[test]
fn test_info_command() {
    let mut cmd = Command::cargo_bin("bv").unwrap();
    cmd.arg("info")
        .assert()
        .success()
        .stdout(predicate::str::contains("System Information"))
        .stdout(predicate::str::contains("OS:"))
        .stdout(predicate::str::contains("CPU Arch:"))
        .stdout(predicate::str::contains("CPUs:"))
        .stdout(predicate::str::contains("RAM:"))
        .stdout(predicate::str::contains("DISK FREE:"));
}

#[test]
fn test_project_examples_cli() {
    let mut cmd = Command::cargo_bin("bv").unwrap();
    cmd.arg("project")
        .arg("examples")
        .assert()
        .success()
        .stdout(predicate::str::contains("Available example templates"));
}

#[test]
fn test_sample_data_list_cli() {
    let mut cmd = Command::cargo_bin("bv").unwrap();
    cmd.arg("sample-data")
        .arg("list")
        .assert()
        .success()
        .stdout(predicate::str::contains("Available sample data"));
}

#[test]
fn test_run_dry_run_cli() {
    let tmp = TempDir::new().unwrap();
    // Set explicit BIOVAULT_HOME for templates
    let bv_home = tmp.path().join(".bvhome");
    fs::create_dir_all(bv_home.join("env/test_tpl")).unwrap();
    fs::write(bv_home.join("env/test_tpl/template.nf"), "// template").unwrap();
    fs::write(bv_home.join("env/test_tpl/nextflow.config"), "// config").unwrap();

    // Prepare minimal project
    let proj = tmp.path().join("proj");
    fs::create_dir_all(&proj).unwrap();
    fs::write(
        proj.join("project.yaml"),
        "name: p\nauthor: a\nworkflow: main.nf\ntemplate: test_tpl\n",
    )
    .unwrap();
    fs::write(proj.join("workflow.nf"), "// wf").unwrap();
    fs::write(
        proj.join("participants.yaml"),
        "participants:\n  X:\n    ref_version: GRCh38\n",
    )
    .unwrap();

    let mut cmd = Command::cargo_bin("bv").unwrap();
    cmd.env("BIOVAULT_HOME", &bv_home)
        .arg("run")
        .arg(proj.to_string_lossy().to_string())
        .arg(
            proj.join("participants.yaml#participants.X")
                .to_string_lossy()
                .to_string(),
        )
        .arg("--dry-run")
        .arg("--template=test_tpl")
        .assert()
        .success()
        .stdout(predicate::str::contains("Nextflow command:"));
}

// Removed test_check_command: behavior is covered by OS/nightly installation tests.

#[test]
fn test_invalid_command() {
    let mut cmd = Command::cargo_bin("bv").unwrap();
    cmd.arg("invalid-command")
        .assert()
        .failure()
        .stderr(predicate::str::contains("unrecognized subcommand"));
}

#[test]
fn test_init_missing_email() {
    let mut cmd = Command::cargo_bin("bv").unwrap();
    cmd.arg("init")
        .assert()
        .failure()
        .stderr(predicate::str::contains("required"));
}