biors 0.47.9

Command-line tools for bio-rs biological AI model input workflows.
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use serde_json::Value;
use std::path::Path;
use std::process::Command;

mod common;

#[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["data"]
        .as_array()
        .expect("multi-FASTA output is an array");

    assert_eq!(value["ok"], true);
    assert_eq!(value["biors_version"], env!("CARGO_PKG_VERSION"));
    assert!(value["input_hash"]
        .as_str()
        .expect("input hash")
        .starts_with("fnv1a64:"));
    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 = common::run_biors_stdin(&["tokenize", "-"], ">seq1\nACDE\n").stdout;
    let value: Value = serde_json::from_slice(&output).expect("valid JSON output");
    let records = value["data"]
        .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 tokenize_preserves_unknown_token_positions() {
    let output = common::run_biors_stdin(&["tokenize", "-"], ">seq1\nAX*\n").stdout;
    let value: Value = serde_json::from_slice(&output).expect("valid JSON output");
    let record = &value["data"][0];

    assert_eq!(record["length"], 3);
    assert_eq!(record["tokens"], serde_json::json!([0, 20, 20]));
    assert_eq!(record["warnings"].as_array().expect("warnings").len(), 1);
    assert_eq!(record["errors"].as_array().expect("errors").len(), 1);
}

#[test]
fn tokenize_accepts_dna_and_rna_profiles() {
    let dna_output = common::run_biors_stdin(
        &["tokenize", "--profile", "dna-iupac", "-"],
        ">dna\nACGTN\n",
    )
    .stdout;
    let dna: Value = serde_json::from_slice(&dna_output).expect("valid DNA JSON output");
    assert_eq!(dna["data"][0]["alphabet"], "dna-iupac");
    assert_eq!(dna["data"][0]["tokens"], serde_json::json!([0, 1, 2, 3, 4]));
    assert_eq!(
        dna["data"][0]["warnings"]
            .as_array()
            .expect("warnings")
            .len(),
        1
    );

    let rna_output = common::run_biors_stdin(
        &["tokenize", "--profile", "rna-iupac-special", "-"],
        ">rna\nACGUN\n",
    )
    .stdout;
    let rna: Value = serde_json::from_slice(&rna_output).expect("valid RNA JSON output");
    assert_eq!(rna["data"][0]["alphabet"], "rna-iupac-special");
    assert_eq!(
        rna["data"][0]["tokens"],
        serde_json::json!([6, 0, 1, 2, 3, 4, 7])
    );
    assert_eq!(
        rna["data"][0]["warnings"]
            .as_array()
            .expect("warnings")
            .len(),
        1
    );
}

#[test]
fn public_behavior_snapshot_for_tokenize_stdout() {
    let output = common::run_biors_stdin(&["tokenize", "-"], ">seq1\nACDE\n").stdout;
    let value: Value = serde_json::from_slice(&output).expect("valid JSON output");

    assert_eq!(
        value["data"],
        serde_json::json!([
            {
                "id": "seq1",
                "length": 4,
                "alphabet": "protein-20",
                "valid": true,
                "tokens": [0, 1, 2, 3],
                "warnings": [],
                "errors": []
            }
        ])
    );
}