"""Sample-sheet matrix — spec EDGE-007 (IN-001 … IN-014)."""

from __future__ import annotations

from pathlib import Path

import pytest

from simurg.core.errors import SimurgError
from simurg.formats.samplesheet import output_stem, parse_samplesheet

HEAD = "[Header]\nInvestigator Name,X\n[Manifests]\nA,foo.bpm\n[Data]\n"


def sheet(tmp_path: Path, body: str, name: str = "s.csv", raw: bytes | None = None) -> Path:
    p = tmp_path / name
    if raw is not None:
        p.write_bytes(raw)
    else:
        p.write_text(body, encoding="utf-8")
    return p


def code_of(tmp_path: Path, body: str) -> str:
    with pytest.raises(SimurgError) as e:
        parse_samplesheet(sheet(tmp_path, body))
    return e.value.code


def test_basic_sections_and_passthrough(tmp_path) -> None:  # type: ignore[no-untyped-def]
    s = parse_samplesheet(
        sheet(
            tmp_path,
            HEAD + "Sample_ID,SentrixBarcode_A,SentrixPosition_A,Gender,Tissue\na,203790110013,r04c01,Female,blood\n",
        )
    )
    assert s.rows[0].sample_id == "203790110013_R04C01"
    assert s.rows[0].reported_sex == "F"
    assert s.passthrough_columns() == ["Sample_ID", "Gender", "Tissue"]
    assert s.header == {"Investigator Name": "X"}


def test_sectionless(tmp_path) -> None:  # type: ignore[no-untyped-def]
    s = parse_samplesheet(sheet(tmp_path, "SentrixBarcode_A,SentrixPosition_A\n203790110013,R01C01\n"))
    assert len(s.rows) == 1


def test_bom_crlf_quotes(tmp_path) -> None:  # type: ignore[no-untyped-def]
    raw = ('[Data]\r\nSentrixBarcode_A,SentrixPosition_A,Note\r\n203790110013,R01C01,"a, b"\r\n').encode()
    s = parse_samplesheet(sheet(tmp_path, "", raw=raw))
    assert s.rows[0].values["Note"] == "a, b"


def test_trailing_empty_columns(tmp_path) -> None:  # type: ignore[no-untyped-def]
    s = parse_samplesheet(sheet(tmp_path, "[Data]\nSentrixBarcode_A,SentrixPosition_A,,\n203790110013,R01C01,,\n"))
    assert s.columns == ["SentrixBarcode_A", "SentrixPosition_A"]
    assert [c for c, _ in s.warnings] == ["W_SHEET_EMPTY_COLUMN"]
    assert "" not in s.rows[0].values


def test_manifests_section_with_values_ignored(tmp_path) -> None:  # type: ignore[no-untyped-def]
    body = (
        "[Header],,\nDate,1,\n[Manifests],GSA.bpm,\nA,,\n[Data],,\nSentrixBarcode_A,SentrixPosition_A,x\n"
        "203790110013,R01C01,1\n"
    )
    s = parse_samplesheet(sheet(tmp_path, body))
    assert s.header == {"Date": "1"} and len(s.rows) == 1


@pytest.mark.parametrize(
    "body,code",
    [
        ("[Data]\nSentrixBarcode_A,SentrixPosition_A,Sample_Name,sample_name\n1,2,3,4\n", "E_SHEET_DUP_COLUMN"),
        ("[Data]\nSentrixBarcode_A,SentrixPosition_A,Sex Estimate\n203790110013,R01C01,M\n", "E_SHEET_RESERVED"),
        ("[Data]\nSentrixBarcode_A,SentrixPosition_A,call_rate\n203790110013,R01C01,1\n", "E_SHEET_RESERVED"),
        ("[Data]\nSentrixBarcode_A,SentrixPosition_A,x\n203790110013,R01C01," + "a" * 501 + "\n", "E_SHEET_TOO_LONG"),
        ("[Data]\nSentrixBarcode_A,SentrixPosition_A\n2.04753E+11,R01C01\n", "E_SHEET_BARCODE_FORMAT"),
        ("[Data]\nSentrixBarcode_A,SentrixPosition_A\n203790110013,R1C1\n", "E_SHEET_BARCODE_FORMAT"),
        ("[Data]\nSentrixBarcode_A;SentrixPosition_A\n203790110013;R01C01\n", "E_SHEET_DELIMITER"),
        ('{"samples": []}', "E_SHEET_DELIMITER"),
        ("[Data]\nSample_ID,Foo\n1,2\n", "E_SHEET_NO_KEY_COLUMNS"),
        ("[Data]\nSentrixBarcode_A,SentrixPosition_A\n", "E_SHEET_EMPTY"),
        ("[Header]\nA,B\n", "E_SHEET_EMPTY"),
        (
            "[Data]\nSentrixBarcode_A,SentrixPosition_A,Sample_Name\n203790110013,R01C01,a\n203790110013,R02C01,\n",
            "E_SHEET_NAME_EMPTY",
        ),
        (
            "[Data]\nSentrixBarcode_A,SentrixPosition_A,Sample_Name\n203790110013,R01C01,203790110013_R02C01\n"
            "203790110013,R02C01,b\n",
            "E_SHEET_NAME_COLLISION",
        ),
        (
            "[Data]\nSentrixBarcode_A,SentrixPosition_A,Sample_Name\n203790110013,R01C01,a\n203790110013,R02C01,a\n",
            "E_SHEET_NAME_COLLISION",
        ),
        (
            "[Data]\nSentrixBarcode_A,SentrixPosition_A\n203790110013,R01C01\n203790110013,r01c01\n",
            "E_SHEET_DUP_SAMPLE",
        ),
    ],
)
def test_error_matrix(tmp_path, body, code) -> None:  # type: ignore[no-untyped-def]
    assert code_of(tmp_path, body) == code


def test_barcode_decimal_repaired(tmp_path) -> None:  # type: ignore[no-untyped-def]
    s = parse_samplesheet(sheet(tmp_path, "[Data]\nSentrixBarcode_A,SentrixPosition_A\n204753010023.0,R01C01\n"))
    assert s.rows[0].barcode == "204753010023"
    assert s.warnings[0][0] == "W_SHEET_BARCODE_REPAIRED"


def test_scientific_notation_hint(tmp_path) -> None:  # type: ignore[no-untyped-def]
    with pytest.raises(SimurgError) as e:
        parse_samplesheet(sheet(tmp_path, '[Data]\nSentrixBarcode_A,SentrixPosition_A\n"2,04753E+11",R01C01\n'))
    assert e.value.hint and "0 decimals" in e.value.hint


def test_alias_keys_and_rootfolder(tmp_path) -> None:  # type: ignore[no-untyped-def]
    s = parse_samplesheet(
        sheet(tmp_path, "[Header]\nRootFolder,idats\n[Data]\nbeadChipName,sampleSectionName\n203790110013,R01C01\n")
    )
    assert s.barcode_column == "beadChipName"
    assert s.root_folder == tmp_path / "idats"


def test_sex_columns(tmp_path) -> None:  # type: ignore[no-untyped-def]
    s = parse_samplesheet(
        sheet(
            tmp_path,
            "[Data]\nSentrixBarcode_A,SentrixPosition_A,Gender,Sex\n"
            "203790110013,R01C01,Male,F\n203790110013,R02C01,,\n",
        )
    )
    assert [r.reported_sex for r in s.rows] == ["F", "U"]
    assert any(c == "W_SHEET_SEX_CONFLICT" for c, _ in s.warnings)


def test_turkish_case_folding_is_locale_independent(tmp_path) -> None:  # type: ignore[no-untyped-def]  # EDGE-001
    s = parse_samplesheet(sheet(tmp_path, "[Data]\nSENTRIXBARCODE_A,SentrixPosition_A,İl\n203790110013,R01C01,x\n"))
    assert s.barcode_column == "SENTRIXBARCODE_A"


def test_ten_thousand_rows_fast(tmp_path) -> None:  # type: ignore[no-untyped-def]  # PERF-007 (parse part)
    import time

    lines = ["[Data]", "SentrixBarcode_A,SentrixPosition_A,Sample_Name"]
    for i in range(10_000):
        lines.append(f"{200000000000 + i // 24},R{(i % 24) + 1:02d}C01,s{i}")
    p = sheet(tmp_path, "\n".join(lines) + "\n")
    t = time.perf_counter()
    s = parse_samplesheet(p)
    assert len(s.rows) == 10_000
    assert time.perf_counter() - t < 2.0


def test_output_stem() -> None:
    assert output_stem("NA 12878/ü") == "NA_12878__"
    assert output_stem("..hidden") == "hidden"
    assert len(output_stem("x" * 500)) == 200