"""PGx on the GSA v4 PGx demo (30 CEPH individuals) — definition sanity (PGX-023), array limitations (PGX-009),
determinism (PGX-029) and JSON ↔ TSV equivalence (PGX-028).

Needs the local PGx DB (``simurg pgx db build`` with the GSA v4 PGx manifest, see docs/validation/V2_pgx_star.md) and
the demo SNV + PGx CN VCFs under ``data/pgx/demo``; skipped when absent.
"""

from __future__ import annotations

import csv
import json
import sqlite3
from pathlib import Path

import pytest
from tests.conftest import ROOT
from typer.testing import CliRunner

from simurg.cli.main import app

pytestmark = pytest.mark.data
DEMO = ROOT / "data" / "pgx" / "demo"
DBDIR = ROOT / "data" / "pgx" / "dbm"
DBS = sorted(DBDIR.glob("pgx_db-*.sqlite")) if DBDIR.exists() else []
MANIFEST = "GSA-PGx-48v4-0_20079540_E2.bpm"


def _need() -> Path:
    if not DBS or not (DEMO / "vcf").exists() or not (DEMO / "call").exists():
        pytest.skip("PGx demo DB/VCFs not present")
    return DBS[-1]


def test_definition_sanity() -> None:  # PGX-023
    db = _need()
    con = sqlite3.connect(db)
    assert con.execute("SELECT COUNT(*) FROM allele_variants WHERE gene = 'CYP2A6' AND allele = '*1'").fetchone() == (
        0,
    )
    from simurg.pgx.phenotype import build_table, phenotype

    rows = con.execute("SELECT lookup_key, activity_score, phenotype FROM phenotypes WHERE gene = 'ABCG2'").fetchall()
    alle = con.execute("SELECT allele, function, activity FROM alleles WHERE gene = 'ABCG2'").fetchall()
    ref = next(a for a, *_ in alle if "reference" in a)
    assert phenotype(build_table("ABCG2", rows, alle), (ref, ref)).phenotype.startswith("Normal")


def test_known_limitations() -> None:  # PGX-009 regression oracles that hold for our definitions
    from simurg.pipeline.pgx_db import coverage_rows

    st = {(r["gene"], r["allele"]): r["status"] for r in coverage_rows(_need(), MANIFEST)}
    assert st[("CYP4F2", "*2")] == "not_covered"  # reference: CYP4F2 *2 reported as *1
    assert st[("CYP4F2", "*4")] == "equivalent_to:*3"  # reference: *4 reported as *3


def test_determinism_and_json_tsv(tmp_path: Path) -> None:  # PGX-029, PGX-028
    db = _need()
    run = CliRunner()
    outs = []
    for k in range(2):
        out = tmp_path / f"s{k}"
        r = run.invoke(app, ["pgx", "star-allele", "call", "--vcfs", str(DEMO / "vcf"), "--vcfs", str(DEMO / "call"),
                             "--db", str(db), "--out", str(out), "--gene", "CYP2D6", "--gene", "CYP2C19", "--quiet"])  # fmt: skip
        assert r.exit_code == 0, r.output
        r = run.invoke(app, ["pgx", "phenotype", "--calls", str(out), "--db", str(db), "--quiet"])
        assert r.exit_code == 0, r.output
        outs.append(out)
    for name in ("diplotype_summary.tsv", "supporting_variants.tsv", "diplotype_annotations.tsv", "pgx_calls.json"):
        assert (outs[0] / name).read_bytes() == (outs[1] / name).read_bytes(), name
    with (outs[0] / "diplotype_annotations.tsv").open() as fh:
        rows = list(csv.DictReader((ln for ln in fh if not ln.startswith("#")), delimiter="\t"))
    for r in rows:
        doc = json.loads((outs[0] / f"{r['sample_id']}.pgx.json").read_text())
        g = next(x for x in doc["genes"] if x["gene"] == r["gene"])
        assert g["genotype"] == r["genotype"] and (g["phenotype"] or "") == r["phenotype"]