import json
import stat
from pathlib import Path

from apps.web import pipeline_backend
from gfa_core.mas.stage_capabilities import CAPABILITIES
from gfa_core.mas.stage_catalog import EXECUTABLE_STAGES, STAGE_DEPENDENCIES
from gfa_core.mas.tools.stage_identity import resolve_stage_identity
from gfa_core.mas.tools.stage_status import get_stage_status


def _manifest() -> dict:
    components = (".0123", ".amb", ".ann", ".bwt.2bit.64", ".pac")
    artifacts = {
        "reference_fasta": {"role": "reference_fasta", "sha256": "a" * 64},
        "reference_fai": {"role": "reference_fai", "sha256": "b" * 64},
        "reference_dict": {"role": "reference_dict", "sha256": "c" * 64},
    }
    artifacts.update({f"bwa_mem2_index_component.{part}": {"role": "bwa_mem2_index_component", "component": part, "sha256": "d" * 64} for part in components})
    return {"stage": "wgs_index", "status": "success", "prefix": "Cohort", "job_id": "index-job", "wgs_reference_id": "wgs-reference:" + "e" * 64, "wgs_analysis_id": "wgs-analysis:" + "f" * 64, "artifacts": artifacts}


def test_wgs_index_backend_requires_exact_roles_and_fresh_manifest(monkeypatch, tmp_path: Path) -> None:
    reference = tmp_path / "input" / "reference.fasta"; reference.parent.mkdir(parents=True)
    reference.write_text(">chr1\nACGT\n", encoding="utf-8")
    workspace = tmp_path / "workspace"; final = workspace / "final"; final.mkdir(parents=True)
    manifest_path = final / "Cohort.wgs_index.manifest.json"
    manifest_path.write_text(json.dumps({"status": "success"}), encoding="utf-8")
    captured = {}
    def fake_run(command, *_args, **_kwargs):
        captured["command"] = list(command)
        manifest_path.write_text(json.dumps(_manifest()), encoding="utf-8")
        return 0
    monkeypatch.setattr(pipeline_backend, "run_cmd_logged", fake_run)
    message, returned = pipeline_backend.run_stage(
        stage="wgs_index", job=pipeline_backend.JobInfo("index-job", str(reference.parent), str(workspace), str(workspace / "logs"), "now"),
        prefix="Cohort", wgs_reference_fasta=str(reference), wgs_samtools="sam", wgs_bwa_mem2="bwa", wgs_gatk="gatk", wgs_threads=3,
    )
    assert "completed" in message.lower() and returned == manifest_path
    assert captured["command"][:3] == [pipeline_backend.sys.executable, "-m", "apps.cli.run_wgs_index"]
    assert captured["command"][captured["command"].index("--reference-fasta") + 1] == str(reference)
    assert not pipeline_backend._valid_wgs_index_manifest({**_manifest(), "artifacts": {}}, job_id="index-job", prefix="Cohort")
    identityless = _manifest(); identityless.pop("wgs_reference_id")
    assert not pipeline_backend._valid_wgs_index_manifest(identityless, job_id="index-job", prefix="Cohort")


def test_wgs_index_is_a_registered_root_with_exact_reference_identity_and_preflight(tmp_path: Path) -> None:
    assert STAGE_DEPENDENCIES["wgs_index"] == [] and "wgs_index" in EXECUTABLE_STAGES
    assert {item.role for item in CAPABILITIES["wgs_index"].provides} == {"reference_fasta", "reference_fai", "reference_dict", "bwa_mem2_index_component"}
    identity = resolve_stage_identity("wgs_index", "Cohort", {"wgsReferenceId": "ref", "wgsAnalysisId": "analysis"})
    assert identity.wgs_reference_id == "ref" and identity.wgs_analysis_id == "analysis"
    missing = get_stage_status("index-job", "Cohort", "wgs_index", workspace_root=tmp_path)
    assert "wgs_reference_id" in missing.errors[0]
    try:
        pipeline_backend._resolve_wgs_reference_fasta(tmp_path, "")
    except ValueError as exc:
        assert "explicit" in str(exc)
    else:
        raise AssertionError("missing root reference must fail preflight")


def _backend_tool(path: Path, kind: str) -> Path:
    path.write_text(
        "#!/usr/bin/env python3\n"
        "import sys\n"
        f"KIND = {kind!r}\n"
        "args = sys.argv[1:]\n"
        "if '--version' in args or args == ['version']:\n"
        " print(KIND + ' 1.0'); raise SystemExit(0)\n"
        "if KIND == 'samtools':\n"
        " ref = args[args.index('faidx') + 1]; open(ref + '.fai', 'w').write('chr1\\t8\\t6\\t8\\t9\\n')\n"
        "elif KIND == 'gatk':\n"
        " out = args[args.index('-O') + 1]; open(out, 'w').write('@HD\\tVN:1.6\\n@SQ\\tSN:chr1\\tLN:8\\n')\n"
        "else:\n"
        " ref = args[-1]\n"
        " for suffix in ('.0123', '.amb', '.ann', '.bwt.2bit.64', '.pac'):\n"
        "  open(ref + suffix, 'w').write(suffix + '\\n')\n",
        encoding="utf-8",
    )
    path.chmod(path.stat().st_mode | stat.S_IXUSR)
    return path


def test_wgs_index_backend_accepts_valid_cli_reuse_with_same_run_id(tmp_path: Path) -> None:
    reference = tmp_path / "input" / "reference.fasta"
    reference.parent.mkdir(parents=True)
    reference.write_text(">chr1\nACGTACGT\n", encoding="utf-8")
    tools = {
        "samtools": _backend_tool(tmp_path / "samtools", "samtools"),
        "bwa_mem2": _backend_tool(tmp_path / "bwa-mem2", "bwa-mem2"),
        "gatk": _backend_tool(tmp_path / "gatk", "gatk"),
    }
    workspace = tmp_path / "workspace"
    job = pipeline_backend.JobInfo(
        "index-job", str(reference.parent), str(workspace), str(workspace / "logs"), "now",
    )
    params = {
        "stage": "wgs_index", "job": job, "prefix": "Cohort",
        "wgs_reference_fasta": str(reference), "wgs_samtools": str(tools["samtools"]),
        "wgs_bwa_mem2": str(tools["bwa_mem2"]), "wgs_gatk": str(tools["gatk"]),
        "wgs_threads": 2,
    }

    first_message, manifest_path = pipeline_backend.run_stage(**params)
    assert "completed" in first_message.lower() and manifest_path is not None
    first = json.loads(manifest_path.read_text(encoding="utf-8"))
    second_message, second_path = pipeline_backend.run_stage(**params)
    assert "completed" in second_message.lower() and second_path == manifest_path
    second = json.loads(second_path.read_text(encoding="utf-8"))
    assert second["run_id"] == first["run_id"]
    assert second["wgs_reference_id"] == first["wgs_reference_id"]
    assert second["wgs_analysis_id"] == first["wgs_analysis_id"]
    assert second.get("reuse", {}).get("count") == 1