from __future__ import annotations

import pytest

from gfa_core.wgs_samples import WgsSample, load_wgs_samples


def test_load_wgs_samples_resolves_paths_from_yaml_parent(tmp_path):
    reads = tmp_path / "reads"
    reads.mkdir()
    for name in ("S1_R1.fastq.gz", "S1_R2.fastq.gz"):
        (reads / name).write_bytes(b"reads")
    config = tmp_path / "wgs_samples.yaml"
    config.write_text(
        "samples:\n  S1:\n    r1: reads/S1_R1.fastq.gz\n    r2: reads/S1_R2.fastq.gz\n",
        encoding="utf-8",
    )
    assert load_wgs_samples(config) == (
        WgsSample("S1", reads / "S1_R1.fastq.gz", reads / "S1_R2.fastq.gz"),
    )


def test_load_wgs_samples_rejects_include(tmp_path):
    r1 = tmp_path / "r1.fastq.gz"
    r2 = tmp_path / "r2.fastq.gz"
    r1.write_bytes(b"r1")
    r2.write_bytes(b"r2")
    path = tmp_path / "wgs_samples.yaml"
    path.write_text(
        f"samples:\n  S1: {{r1: {r1}, r2: {r2}, include: false}}\n",
        encoding="utf-8",
    )
    with pytest.raises(ValueError, match="include"):
        load_wgs_samples(path)


def test_load_wgs_samples_sorts_ids_and_rejects_identical_mates(tmp_path):
    for name in ("a_R1.fastq", "a_R2.fastq", "z_R1.fastq", "z_R2.fastq"):
        (tmp_path / name).write_bytes(b"reads")
    config = tmp_path / "wgs_samples.yaml"
    config.write_text(
        "samples:\n"
        "  Z: {r1: z_R1.fastq, r2: z_R2.fastq}\n"
        "  A: {r1: a_R1.fastq, r2: a_R2.fastq}\n",
        encoding="utf-8",
    )
    assert [sample.sample_id for sample in load_wgs_samples(config)] == ["A", "Z"]
    config.write_text("samples:\n  A: {r1: a_R1.fastq, r2: a_R1.fastq}\n", encoding="utf-8")
    with pytest.raises(ValueError, match="different"):
        load_wgs_samples(config)


def test_load_wgs_samples_rejects_duplicate_sample_id(tmp_path):
    for name in ("S1_R1.fastq", "S1_R2.fastq"):
        (tmp_path / name).write_bytes(b"reads")
    config = tmp_path / "wgs_samples.yaml"
    config.write_text(
        "samples:\n"
        "  S1: {r1: S1_R1.fastq, r2: S1_R2.fastq}\n"
        "  S1: {r1: S1_R1.fastq, r2: S1_R2.fastq}\n",
        encoding="utf-8",
    )
    with pytest.raises(ValueError, match="duplicate key"):
        load_wgs_samples(config)