from __future__ import annotations

import json
import subprocess
import sys
from pathlib import Path

ROOT = Path(__file__).resolve().parents[2]


def test_subfamily_confirm_inherits_scope_from_source_prediction_manifest(tmp_path):
    workspace = tmp_path / "job_scope_confirm"
    final_dir = workspace / "final"
    input_dir = tmp_path / "input" / "job_scope_confirm"
    final_dir.mkdir(parents=True)
    input_dir.mkdir(parents=True)

    edited = final_dir / "Lc.SPL.confirmed_subfamily.edited.tsv"
    edited.write_text(
        "gene_id\tspecies\tpredicted_subfamily\tconfirmed_subfamily\tconfidence\tnote\n"
        "LcGene1\tLc\tI\tI\thigh\tkept\n"
        "LcGene2\tLc\tII\tIII\tmedium\tmanual\n",
        encoding="utf-8",
    )

    source_manifest = final_dir / "Target.SPL.target-Lc.ref-At.subfamily_prediction.reference_classification.manifest.json"
    source_manifest.write_text(
        json.dumps(
            {
                "manifest_version": "1.0",
                "stage": "reference_classification",
                "status": "success",
                "prefix": "Lc.SPL",
                "output_prefix": "Target.SPL.target-Lc.ref-At.subfamily_prediction",
                "scope_id": "SPL.target-Lc.ref-At.target_plus_reference",
                "scope_mode": "target_plus_reference",
                "target_species": ["Lc"],
                "reference_species": ["At"],
                "comparative_species": [],
                "selected_species": ["Lc", "At"],
                "analysis_route": "subfamily_prediction",
            }
        ),
        encoding="utf-8",
    )

    proc = subprocess.run(
        [
            sys.executable,
            str(ROOT / "apps/cli/run_subfamily_confirm.py"),
            "--workspace",
            str(workspace),
            "--input-dir",
            str(input_dir),
            "--prefix",
            "Lc.SPL",
            "--edited-subfamily",
            str(edited),
            "--source-prediction-manifest",
            str(source_manifest),
        ],
        cwd=str(ROOT),
        capture_output=True,
        text=True,
        check=False,
    )

    assert proc.returncode == 0, proc.stderr or proc.stdout
    manifest_path = final_dir / "Lc.SPL.subfamily_confirm.manifest.json"
    assert manifest_path.exists()
    manifest = json.loads(manifest_path.read_text(encoding="utf-8"))

    assert manifest["output_prefix"] == "Lc.SPL"
    assert manifest["scope_id"] == "SPL.target-Lc.ref-At.target_plus_reference"
    assert manifest["target_species"] == ["Lc"]
    assert manifest["reference_species"] == ["At"]
    assert manifest["parameters"]["source_prediction_manifest"] == str(source_manifest)
    assert manifest["parameters"]["source_prediction_prefix"] == "Target.SPL.target-Lc.ref-At.subfamily_prediction"
    assert (final_dir / "Lc.SPL.confirmed_subfamily.tsv").exists()
    assert not (final_dir / "Lc.SPL.confirmed_subfamily.subfamily_confirm.manifest.json").exists()


def test_subfamily_confirm_promotes_curated_members_to_final_members(tmp_path):
    workspace = tmp_path / "job_confirm_members"
    final_dir = workspace / "final"
    input_dir = tmp_path / "input" / "job_confirm_members"
    final_dir.mkdir(parents=True)
    input_dir.mkdir(parents=True)

    (final_dir / "Ft.SPL.final_members.id").write_text("FtGene1\nFtGene2\nFtGene3\n", encoding="utf-8")
    (final_dir / "Ft.SPL.final_members.pep.fa").write_text(
        ">FtGene1\nMA\n>FtGene2\nMT\n>FtGene3\nMG\n",
        encoding="utf-8",
    )
    (final_dir / "Ft.SPL.curated_members.id").write_text("FtGene1\nFtGene3\n", encoding="utf-8")
    (final_dir / "Ft.SPL.curated_members.pep.fa").write_text(
        ">FtGene1\nMA\n>FtGene3\nMG\n",
        encoding="utf-8",
    )
    edited = final_dir / "Ft.SPL.confirmed_subfamily.edited.tsv"
    edited.write_text(
        "gene_id\tconfirmed_subfamily\n"
        "FtGene1\tI\n"
        "FtGene3\tII\n",
        encoding="utf-8",
    )

    proc = subprocess.run(
        [
            sys.executable,
            str(ROOT / "apps/cli/run_subfamily_confirm.py"),
            "--workspace",
            str(workspace),
            "--input-dir",
            str(input_dir),
            "--prefix",
            "Ft.SPL",
            "--edited-subfamily",
            str(edited),
        ],
        cwd=str(ROOT),
        capture_output=True,
        text=True,
        check=False,
    )

    assert proc.returncode == 0, proc.stderr or proc.stdout
    assert (final_dir / "Ft.SPL.final_members.id").read_text(encoding="utf-8") == "FtGene1\nFtGene3\n"
    assert (final_dir / "Ft.SPL.final_members.pep.fa").read_text(encoding="utf-8") == ">FtGene1\nMA\n>FtGene3\nMG\n"
    manifest = json.loads((final_dir / "Ft.SPL.subfamily_confirm.manifest.json").read_text(encoding="utf-8"))
    assert manifest["metrics"]["final_members_count"] == 2
    assert manifest["parameters"]["final_members_source_stage"] == "subfamily_confirm"
    assert manifest["artifacts"]["final_members_id"]["path"] == "final/Ft.SPL.final_members.id"