"""Smoke tests for data_pipeline.build. No network."""

from __future__ import annotations

import math
from pathlib import Path

import pytest

from data_pipeline import build, schema


def test_label_msi_thresholds():
    # >= 10  -> MSI-H
    assert build.label_msi(10.0) == "MSI-H"
    assert build.label_msi(42.3) == "MSI-H"
    # < 4    -> MSS
    assert build.label_msi(0.0) == "MSS"
    assert build.label_msi(3.99) == "MSS"
    # in between -> Indeterminate
    assert build.label_msi(4.0) == "MSI-Indeterminate"
    assert build.label_msi(9.99) == "MSI-Indeterminate"
    # missing
    assert build.label_msi(float("nan")) == "NA"
    assert build.label_msi(None) == "NA"  # type: ignore[arg-type]


def test_normalise_stage():
    assert build.normalise_stage("STAGE IIIB") == "III"
    assert build.normalise_stage("Stage iv") == "IV"
    assert build.normalise_stage("STAGE I") == "I"
    assert build.normalise_stage("STAGE IIA") == "II"
    assert build.normalise_stage("[Not Available]") == "NA"
    assert build.normalise_stage(None) == "NA"
    assert build.normalise_stage(float("nan")) == "NA"


def test_parse_os_status():
    assert build.parse_os_status("0:LIVING") == 0.0
    assert build.parse_os_status("1:DECEASED") == 1.0
    assert math.isnan(build.parse_os_status(""))
    assert math.isnan(build.parse_os_status(None))


def _write_fake_clinical(tmp_path: Path, columns: list[str], rows: list[list[str]]) -> Path:
    """Write a cBioPortal-shaped TSV: 4 leading '#'-prefixed metadata lines, header, rows."""
    p = tmp_path / "data_clinical_sample.txt"
    lines = [
        "#" + "\t".join(columns),                      # display names
        "#" + "\t".join("desc" for _ in columns),       # descriptions
        "#" + "\t".join("STRING" for _ in columns),     # types
        "#" + "\t".join("1" for _ in columns),          # priorities
        "\t".join(columns),
        *["\t".join(r) for r in rows],
    ]
    p.write_text("\n".join(lines) + "\n")
    return p


def test_read_clinical_missing_column_raises_loudly(tmp_path):
    cols = ["PATIENT_ID", "SAMPLE_ID", "ONCOTREE_CODE"]   # missing MSI_SENSOR_SCORE, TMB_NONSYNONYMOUS
    path = _write_fake_clinical(tmp_path, cols, [["P1", "P1-01", "COAD"]])
    with pytest.raises(KeyError) as exc:
        build.read_clinical(path, schema.REQUIRED_SAMPLE_COLS)
    msg = str(exc.value)
    assert "MSI_SENSOR_SCORE" in msg
    assert "TMB_NONSYNONYMOUS" in msg
    # Must surface what *is* present so a human can debug.
    assert "ONCOTREE_CODE" in msg


def test_read_clinical_happy_path(tmp_path):
    cols = schema.REQUIRED_SAMPLE_COLS
    path = _write_fake_clinical(
        tmp_path,
        cols,
        [
            ["P1", "P1-01", "COAD", "12.3", "5.4"],
            ["P2", "P2-01", "READ", "0.5", "1.2"],
        ],
    )
    df = build.read_clinical(path, schema.REQUIRED_SAMPLE_COLS)
    assert len(df) == 2
    assert list(df.columns)[: len(cols)] == cols
    assert df.iloc[0]["PATIENT_ID"] == "P1"