XCaliburMethodReader/test_reader.py at master · mmmddd98/XCaliburMethodReader · GitHub

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from pathlib import Path

from XCaliburMethodReader import main
from xcalibur_method_reader import XCaliburMethod, extract_gradients, plot_gradient

TEST_FILE = Path("data/test.meth")


def test_parser_accepts_file(capsys):
    main((str(TEST_FILE),))
    captured = capsys.readouterr()
    assert "Proxeon" in captured.out
    assert "Thermo Exactive" in captured.out


def test_stream_text_output(capsys):
    main((str(TEST_FILE), "-s", "Thermo Exactive"))
    captured = capsys.readouterr()
    assert "Method" in captured.out

    main((str(TEST_FILE), "-s", "Proxeon_EASY-nLC", "--to", "text"))
    captured = capsys.readouterr()
    assert "Sample" in captured.out


def test_stream_machine_readable_output(capsys):
    main((str(TEST_FILE), "-s", "Thermo Exactive", "--to", "json"))
    captured = capsys.readouterr()
    assert captured.out[0] == "{"
    assert captured.out.strip()[-1] == "}"

    main((str(TEST_FILE), "-s", "Thermo Exactive", "--to", "xml"))
    captured = capsys.readouterr()
    assert captured.out[:5] == "<?xml"
    assert captured.out.strip()[-1] == ">"


def test_reader_api_lists_and_reads_streams():
    method = XCaliburMethod(TEST_FILE)

    assert method.stream_names() == ["AuditData", "LCQ Header", "Proxeon_EASY-nLC", "Thermo Exactive"]
    assert "InstrumentSetupMethod" in method.read_dict("Thermo Exactive")
    assert method.readable_xml_streams() == ["Proxeon_EASY-nLC", "Thermo Exactive"]


def test_extract_gradients_from_easy_nlc_xml():
    gradient = extract_gradients(TEST_FILE)

    assert list(gradient["percent_b"]) == [5, 30, 60, 95, 95, 5, 5]
    assert list(gradient["time_min"]) == [0, 95, 100, 105, 110, 115, 120]
    assert set(gradient["pump"]) == {"LC"}


def test_cli_prints_gradients(capsys):
    main((str(TEST_FILE), "--gradients"))
    captured = capsys.readouterr()

    assert "time_min,pump,percent_b" in captured.out
    assert "95.0,LC,30" in captured.out


def test_plot_gradient_writes_png(tmp_path):
    output = tmp_path / "gradient.png"

    ax = plot_gradient(TEST_FILE, output=output)

    assert output.exists()
    assert output.stat().st_size > 0
    assert ax.get_xlabel() == "Time [min]"