"""Shared test configuration.

Tests marked ``data`` need files fetched by ``scripts/fetch_data.sh p0``; tests marked ``oracle`` need
reference repositories under ``refs/`` (``scripts/bootstrap_refs.sh``). Both are skipped when absent.
"""

from __future__ import annotations

import sys
from pathlib import Path

import pytest

ROOT = Path(__file__).resolve().parents[1]
DATA = ROOT / "data" / "p0"
REFS = ROOT / "refs"

GSA = DATA / "gsa_v4_pgx"
GSA_BPM = GSA / "GSA-PGx-48v4-0_20079540_E2_bpm" / "GSA-PGx-48v4-0_20079540_E2.bpm"
GSA_CSV = GSA / "GSA-PGx-48v4-0_20079540_E2_csv" / "GSA-PGx-48v4-0_20079540_E2.csv"
GSA_EGT = GSA / "GSA-PGx-48v4-0_20079540_E2_ClusterFile" / "GSA-PGx-48v4-0_20079540_E2_ClusterFile.egt"
GSA_IDATS = GSA / "idats_Demo_36" / "idats_Demo_36"
GDA_EGT = DATA / "gda_v1" / "infinium-global-diversity-array-8-v1-0-D1-cluster-file" / "GDA-8v1-0_D1_ClusterFile.egt"
GDA_BPM = DATA / "gda_v1" / "infinium-global-diversity-array-8-v1-0-D1-manifest-file-bpm" / "GDA-8v1-0_D1.bpm"
GDA_SHEET = DATA / "gda_v1" / "infinium-global-diversity-array-8-v1-0_D1_SampleSheet_Demo_36.csv"
BIOC_IDATS = DATA / "bioc" / "IlluminaDataTestFiles_1.50.0" / "IlluminaDataTestFiles" / "inst" / "extdata" / "idat"
ORACLE_GTCS = DATA / "oracle" / "gsa_gtc_gtc2vcf"


def need(*paths: Path) -> None:
    missing = [p for p in paths if not p.exists()]
    if missing:
        pytest.skip(f"missing test data: {missing[0]} (run scripts/fetch_data.sh p0)")


@pytest.fixture(scope="session")
def beadarrayfiles():  # type: ignore[no-untyped-def]
    """Illumina BeadArrayFiles (BSD-2) as an oracle."""
    path = REFS / "BeadArrayFiles"
    if not (path / "module").is_dir():
        pytest.skip("refs/BeadArrayFiles not present (run scripts/bootstrap_refs.sh)")
    sys.path.insert(0, str(path))
    import module  # type: ignore[import-not-found]

    return module