import json
import sys
from pathlib import Path

import pytest


def test_domain_scope_records_protein_count_before_manifest(tmp_path, monkeypatch):
    from apps.cli import run_domain

    ws = tmp_path / "job_scope_domain"
    final_dir = ws / "final"
    analysis_dir = ws / "domain" / "analysis"
    phylogeny_dir = ws / "phylogeny" / "analysis"
    final_dir.mkdir(parents=True)
    analysis_dir.mkdir(parents=True)
    phylogeny_dir.mkdir(parents=True)

    scope_id = "SPL.target-Ft.ref-At.target_plus_reference"
    scope_file = final_dir / "Ft.SPL.scope.json"
    scope_file.write_text(
        json.dumps(
            {
                "family": "SPL",
                "prefix": "Ft.SPL",
                "scope_id": scope_id,
                "scope_mode": "target_plus_reference",
                "target_species": ["Ft"],
                "reference_species": ["At"],
                "comparative_species": [],
                "selected_species": ["Ft", "At"],
            }
        ),
        encoding="utf-8",
    )

    protein_file = phylogeny_dir / "scope.pep.fa"
    protein_file.write_text(">Ft_gene1\nMAAA\n>At_gene1\nMCCC\n", encoding="utf-8")
    tree_file = final_dir / "Target.SPL.target-Ft.ref-At.subfamily_evidence.tree.nwk"
    tree_file.write_text("(Ft_gene1,At_gene1);\n", encoding="utf-8")

    phylogeny_manifest = final_dir / f"Ft.SPL.{run_domain.sanitize_token(scope_id)}.phylogeny.manifest.json"
    phylogeny_manifest.write_text(
        json.dumps(
            {
                "stage": "phylogeny",
                "status": "success",
                "prefix": "Ft.SPL",
                "parameters": {"scope_input_fasta": str(protein_file)},
                "artifacts": {"tree": {"path": str(tree_file.relative_to(ws))}},
            }
        ),
        encoding="utf-8",
    )

    pfam_hmm = tmp_path / "Pfam-A.hmm"
    pfam_hmm.write_text("HMMER3/f\n", encoding="utf-8")
    domtblout = analysis_dir / "scope.domtblout"
    tblout = analysis_dir / "scope.tblout"
    plot_png = final_dir / "Target.SPL.target-Ft.ref-At.subfamily_evidence.domain.png"
    plot_pdf = final_dir / "Target.SPL.target-Ft.ref-At.subfamily_evidence.domain.pdf"

    def fake_run_hmmscan(*args, **kwargs):
        domtblout.write_text("# empty domtblout\n", encoding="utf-8")
        tblout.write_text("# empty tblout\n", encoding="utf-8")
        return True, {"elapsed_sec": 0.01, "domtblout": domtblout, "tblout": tblout}

    def fake_run_r_plotting(*args, **kwargs):
        plot_png.write_text("png", encoding="utf-8")
        plot_pdf.write_text("pdf", encoding="utf-8")
        return {"success": True, "output_files": [str(plot_png), str(plot_pdf)]}

    monkeypatch.setattr(run_domain, "prepare_pfam_database", lambda *args, **kwargs: (pfam_hmm, True, ""))
    monkeypatch.setattr(run_domain, "run_hmmscan", fake_run_hmmscan)
    monkeypatch.setattr(
        run_domain,
        "parse_domtblout",
        lambda *args, **kwargs: (
            [],
            {"total_hits": 0, "significant_hits": 0, "unique_proteins": 0, "unique_domains": 0},
        ),
    )
    monkeypatch.setattr(run_domain, "run_r_plotting", fake_run_r_plotting)
    monkeypatch.setattr(run_domain, "get_tool_versions", lambda: {})
    monkeypatch.setattr(
        sys,
        "argv",
        [
            "run_domain.py",
            "--prefix",
            "Ft.SPL",
            "--workspace",
            str(ws),
            "--scope-file",
            str(scope_file),
            "--analysis-route",
            "subfamily_evidence",
            "--member-set-id",
            f"{scope_id}:subfamily_evidence:domain_refined",
            "--tree",
            str(tree_file),
            "--subfamily",
            "NONE",
        ],
    )

    with pytest.raises(SystemExit) as exit_info:
        run_domain.main()

    assert exit_info.value.code == 0
    manifest_file = final_dir / "Target.SPL.target-Ft.ref-At.subfamily_evidence.domain.manifest.json"
    assert manifest_file.exists()
    manifest = json.loads(manifest_file.read_text(encoding="utf-8"))
    assert manifest["parameters"]["protein_record_count"] == 2
    assert manifest["metrics"]["protein_record_count"] == 2