from __future__ import annotations

from pathlib import Path

from openpyxl import Workbook

from apps.web.vue3 import main


def _write_config(input_dir: Path, pep: Path, cds: Path) -> None:
    workbook = Workbook()
    sheet = workbook.active
    sheet.title = "config"
    sheet.append(
        [
            "Species_Code",
            "Species_Role",
            "File_Type",
            "Original_File_Name",
            "Ref",
        ]
    )
    sheet.append(["At", "reference", "pep", pep.name, True])
    sheet.append(["At", "reference", "cds", cds.name, True])
    workbook.save(input_dir / "config.xlsx")


def test_execute_validation_accepts_config_resolved_reference_pep_and_cds(
    tmp_path: Path,
    monkeypatch,
) -> None:
    input_root = tmp_path / "input"
    job_input = input_root / "job_at"
    external = tmp_path / "external"
    job_input.mkdir(parents=True)
    external.mkdir()
    pep = external / "Arabidopsis_thaliana.TAIR10.pep.all.fa"
    cds = external / "Arabidopsis_thaliana.TAIR10.cds.all.fa"
    pep.write_text(">AT1G01010\nMA\n", encoding="utf-8")
    cds.write_text(">AT1G01010\nATGGCT\n", encoding="utf-8")
    _write_config(job_input, pep, cds)
    monkeypatch.setattr(main, "INPUT_ROOT", input_root)
    monkeypatch.setenv("PLANTAI_REF_DATA_ROOT", str(external))

    available, source = main._reference_bundle_species_available(
        "job_at",
        "At",
        require_cds=True,
    )

    assert available is True
    assert source == str(job_input)


def test_execute_validation_keeps_accepting_downloaded_reference_bundle(
    tmp_path: Path,
    monkeypatch,
) -> None:
    input_root = tmp_path / "input"
    species_dir = input_root / "job_spinach" / "string_taxon_3562"
    species_dir.mkdir(parents=True)
    (species_dir / "string_taxon_3562.pep.fasta").write_text(">S1\nMA\n", encoding="utf-8")
    (species_dir / "string_taxon_3562.cds.fasta").write_text(">S1\nATGGCT\n", encoding="utf-8")
    monkeypatch.setattr(main, "INPUT_ROOT", input_root)

    available, source = main._reference_bundle_species_available(
        "job_spinach",
        "string_taxon_3562",
        require_cds=True,
    )

    assert available is True
    assert source == str(species_dir)


def test_execute_validation_still_rejects_a_truly_incomplete_reference(
    tmp_path: Path,
    monkeypatch,
) -> None:
    input_root = tmp_path / "input"
    species_dir = input_root / "job_incomplete" / "At"
    species_dir.mkdir(parents=True)
    (species_dir / "At.pep.fasta").write_text(">AT1G01010\nMA\n", encoding="utf-8")
    monkeypatch.setattr(main, "INPUT_ROOT", input_root)

    available, reason = main._reference_bundle_species_available(
        "job_incomplete",
        "At",
        require_cds=True,
    )

    assert available is False
    assert "missing CDS" in reason