biors 0.5.0

Command-line tools for bio-rs biological AI model input workflows.
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use serde_json::Value;
use std::io::Write;
use std::path::Path;
use std::process::{Command, Stdio};

#[test]
fn tokenize_multi_fasta_outputs_json_array() {
    let manifest_dir = Path::new(env!("CARGO_MANIFEST_DIR"));
    let example = manifest_dir.join("../../../examples/multi.fasta");

    let output = Command::new(env!("CARGO_BIN_EXE_biors"))
        .arg("tokenize")
        .arg(example)
        .output()
        .expect("run biors tokenize");

    assert!(
        output.status.success(),
        "stderr: {}",
        String::from_utf8_lossy(&output.stderr)
    );

    let value: Value = serde_json::from_slice(&output.stdout).expect("valid JSON output");
    let records = value.as_array().expect("multi-FASTA output is an array");

    assert_eq!(records.len(), 2);
    assert_eq!(records[0]["id"], "seq1");
    assert_eq!(records[1]["id"], "seq2");
}

#[test]
fn tokenize_stdin_outputs_json_array() {
    let output = run_with_stdin("tokenize", ">seq1\nACDE\n");
    let value: Value = serde_json::from_slice(&output).expect("valid JSON output");
    let records = value.as_array().expect("tokenize output is an array");

    assert_eq!(records.len(), 1);
    assert_eq!(records[0]["id"], "seq1");
    assert_eq!(records[0]["tokens"], serde_json::json!([0, 1, 2, 3]));
}

#[test]
fn inspect_stdin_outputs_json_summary() {
    let output = run_with_stdin("inspect", ">seq1\nACX\n>seq2\nM*\n");
    let value: Value = serde_json::from_slice(&output).expect("valid JSON output");

    assert_eq!(value["records"], 2);
    assert_eq!(value["total_length"], 5);
    assert_eq!(value["valid_records"], 0);
    assert_eq!(value["warning_count"], 1);
    assert_eq!(value["error_count"], 1);
}

fn run_with_stdin(command: &str, input: &str) -> Vec<u8> {
    let mut child = Command::new(env!("CARGO_BIN_EXE_biors"))
        .arg(command)
        .arg("-")
        .stdin(Stdio::piped())
        .stdout(Stdio::piped())
        .stderr(Stdio::piped())
        .spawn()
        .expect("spawn biors");

    child
        .stdin
        .as_mut()
        .expect("stdin pipe")
        .write_all(input.as_bytes())
        .expect("write stdin");

    let output = child.wait_with_output().expect("wait for biors");
    assert!(
        output.status.success(),
        "stderr: {}",
        String::from_utf8_lossy(&output.stderr)
    );

    output.stdout
}