from __future__ import annotations

import hashlib
import json
from pathlib import Path

import pytest

from gfa_core.gwas_legacy_lineage import LegacyLineageError, validate_legacy_lineage


def _sha(path: Path) -> str:
    return hashlib.sha256(path.read_bytes()).hexdigest()


def _write_fixture(tmp_path: Path) -> Path:
    parent = tmp_path / "parent.vcf"
    parent.write_text(
        "##fileformat=VCFv4.2\n"
        "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tS1\tS2\n"
        "1\t10\t.\tA\tG\t.\tPASS\t.\tGT\t0/0\t0/1\n",
        encoding="utf-8",
    )
    fam = tmp_path / "cohort.fam"
    fam.write_text("F1 S1 0 0 0 -9\nF2 S2 0 0 0 -9\n", encoding="utf-8")
    q = tmp_path / "cohort.2.Q"
    q.write_text("0.6 0.4\n0.2 0.8\n", encoding="utf-8")
    script = tmp_path / "pop_structure.sh"
    script.write_text("plink --indep-pairwise 50 10 0.2\n", encoding="utf-8")
    log = tmp_path / "structure.log"
    log.write_text("PLINK v1.90b6.21\nADMIXTURE Version 1.3.0\n", encoding="utf-8")
    ordered_ids = "S1\nS2\n".encode()
    manifest = {
        "schema_version": "legacy_lineage.v1",
        "stage": "pop_struct",
        "status": "success",
        "audited_at": "2026-07-21T00:00:00Z",
        "source_genotype_sha256": _sha(parent),
        "parent_genotype": {
            "path": str(parent.resolve()),
            "sha256": _sha(parent),
            "sample_count": 2,
            "variant_count": 1,
        },
        "sample_identity": {
            "fam_id_column": "IID",
            "count": 2,
            "ordered_iid_sha256": hashlib.sha256(ordered_ids).hexdigest(),
        },
        "method": {
            "ld_pruning": {"window_variants": 50, "step_variants": 10, "r2": 0.2},
            "plink_version": "1.90b6.21",
            "admixture_version": "1.3.0",
            "admixture_k": 2,
        },
        "artifacts": {
            "sample_fam": {"path": str(fam.resolve()), "sha256": _sha(fam)},
            "admixture_q": {"path": str(q.resolve()), "sha256": _sha(q)},
            "source_script": {"path": str(script.resolve()), "sha256": _sha(script)},
            "execution_log": {"path": str(log.resolve()), "sha256": _sha(log)},
        },
    }
    path = tmp_path / "legacy_lineage.manifest.json"
    path.write_text(json.dumps(manifest), encoding="utf-8")
    return path


def test_valid_legacy_lineage_proves_parent_samples_and_q(tmp_path: Path) -> None:
    result = validate_legacy_lineage(_write_fixture(tmp_path), expected_genotype_sha256=None)
    assert result["source_genotype_sha256"] == result["parent_genotype"]["sha256"]
    assert result["sample_identity"]["count"] == 2


def test_legacy_lineage_allows_additional_audit_evidence(tmp_path: Path) -> None:
    path = _write_fixture(tmp_path)
    data = json.loads(path.read_text())
    data["method"]["ld_pruning"]["retained_variants"] = 1
    path.write_text(json.dumps(data), encoding="utf-8")
    assert validate_legacy_lineage(path)["method"]["ld_pruning"]["retained_variants"] == 1


def test_legacy_lineage_rejects_artifact_hash_drift(tmp_path: Path) -> None:
    path = _write_fixture(tmp_path)
    data = json.loads(path.read_text())
    Path(data["artifacts"]["admixture_q"]["path"]).write_text("0.5 0.5\n", encoding="utf-8")
    with pytest.raises(LegacyLineageError, match="sha256 mismatch"):
        validate_legacy_lineage(path)


def test_legacy_lineage_rejects_q_fam_row_mismatch(tmp_path: Path) -> None:
    path = _write_fixture(tmp_path)
    data = json.loads(path.read_text())
    q_path = Path(data["artifacts"]["admixture_q"]["path"])
    q_path.write_text("0.6 0.4\n", encoding="utf-8")
    data["artifacts"]["admixture_q"]["sha256"] = _sha(q_path)
    path.write_text(json.dumps(data), encoding="utf-8")
    with pytest.raises(LegacyLineageError, match="Q/FAM row count mismatch"):
        validate_legacy_lineage(path)


def test_legacy_lineage_rejects_wrong_expected_parent(tmp_path: Path) -> None:
    path = _write_fixture(tmp_path)
    with pytest.raises(LegacyLineageError, match="expected genotype"):
        validate_legacy_lineage(path, expected_genotype_sha256="0" * 64)