from __future__ import annotations

import json
import subprocess
import sys
from pathlib import Path

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


def test_msa_region_plot_inherits_scope_from_source_manifest(tmp_path):
    workspace = tmp_path / "job_msa_scope"
    final_dir = workspace / "final"
    final_dir.mkdir(parents=True)
    prefix = "Target.SPL.target-Lc.ref-At.subfamily_prediction"

    msa = final_dir / f"{prefix}.pep.msa.fa"
    msa.write_text(
        ">LcGene1\nACDEFGHIKL\n"
        ">LcGene2\nACDEYGHIKL\n"
        ">AtGene1\nACDEFGHIKL\n",
        encoding="utf-8",
    )

    source_manifest = final_dir / f"{prefix}.phylogeny.manifest.json"
    source_manifest.write_text(
        json.dumps({
            "manifest_version": "1.0",
            "stage": "phylogeny",
            "status": "success",
            "prefix": "Lc.SPL",
            "output_prefix": prefix,
            "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",
            "member_set_id": "SPL.target-Lc.ref-At.target_plus_reference:subfamily_prediction:all_members",
            "artifacts": {"msa": {"full_path": str(msa), "type": "fasta"}},
        }),
        encoding="utf-8",
    )

    fake_r = tmp_path / "fake_msa_plot.sh"
    fake_r.write_text(
        "#!/usr/bin/env bash\n"
        "outbase=\"$2\"\n"
        "printf fake > \"${outbase}_msa.png\"\n"
        "printf fake > \"${outbase}_msa.pdf\"\n",
        encoding="utf-8",
    )
    fake_r.chmod(0o755)

    proc = subprocess.run(
        [
            sys.executable,
            str(ROOT / "apps/cli/run_msa_region_plot.py"),
            "--workspace", str(workspace),
            "--prefix", prefix,
            "--msa-file", str(msa),
            "--auto-conserved",
            "--window-len", "4",
            "--min-nongap", "0",
            "--source-manifest", str(source_manifest),
            "--rscript", "/bin/bash",
            "--r-script", str(fake_r),
            "--force",
        ],
        cwd=str(ROOT),
        capture_output=True,
        text=True,
        check=False,
    )

    assert proc.returncode == 0, proc.stderr or proc.stdout
    manifests = list(final_dir.glob(f"{prefix}.msa_conserved_region_*.manifest.json"))
    assert len(manifests) == 1
    manifest = json.loads(manifests[0].read_text(encoding="utf-8"))

    assert manifest["scope_id"] == "SPL.target-Lc.ref-At.target_plus_reference"
    assert manifest["target_species"] == ["Lc"]
    assert manifest["reference_species"] == ["At"]
    assert manifest["analysis_route"] == "subfamily_prediction"
    assert manifest["member_set_id"] == "SPL.target-Lc.ref-At.target_plus_reference:subfamily_prediction:all_members"
    assert manifest["stage_context"]["scope_id"] == "SPL.target-Lc.ref-At.target_plus_reference"
    assert manifest["parameters"]["source_manifest"] == str(source_manifest.resolve())
    assert manifest["source_manifest"] == str(source_manifest.resolve())
    assert any(path.endswith("_msa.png") for path in manifest["artifacts"]["output_files"])