import json
from pathlib import Path

from apps.web import pipeline_backend


def _valid_manifest() -> dict:
    return {
        "stage": "wgs_qc", "status": "success", "prefix": "Cohort", "job_id": "qc-job",
        "wgs_sample_set_id": "wgs-samples:" + "a" * 64,
        "wgs_analysis_id": "wgs-analysis:" + "b" * 64,
        "artifacts": {
            "wgs_sample_config": {"role": "wgs_sample_config"},
            **{f"{role}.S1": {"role": role, "sample_id": "S1"}
               for role in ("clean_reads_r1", "clean_reads_r2", "fastp_html", "fastp_json")},
        },
    }


def test_wgs_manifest_validator_rejects_wrong_config_role_and_incomplete_sample_roles() -> None:
    wrong_role = _valid_manifest()
    wrong_role["artifacts"]["wgs_sample_config"]["role"] = "input_config"
    assert not pipeline_backend._valid_wgs_qc_manifest(wrong_role, job_id="qc-job", prefix="Cohort", sample_ids={"S1"})
    incomplete = _valid_manifest()
    del incomplete["artifacts"]["fastp_json.S1"]
    assert not pipeline_backend._valid_wgs_qc_manifest(incomplete, job_id="qc-job", prefix="Cohort", sample_ids={"S1"})


def test_wgs_qc_backend_maps_api_config_to_canonical_cli_and_requires_fresh_manifest(monkeypatch, tmp_path: Path) -> None:
    input_dir = tmp_path / "input"
    workspace = tmp_path / "workspace"
    input_dir.mkdir()
    (input_dir / "S1.R1.fastq").write_text("@r\nA\n+\nI\n", encoding="utf-8")
    (input_dir / "S1.R2.fastq").write_text("@r\nA\n+\nI\n", encoding="utf-8")
    config = input_dir / "wgs_samples.yaml"
    config.write_text("samples:\n  S1:\n    r1: S1.R1.fastq\n    r2: S1.R2.fastq\n", encoding="utf-8")
    final_dir = workspace / "final"
    final_dir.mkdir(parents=True)
    manifest_path = final_dir / "Cohort.wgs_qc.manifest.json"
    manifest_path.write_text(json.dumps({"stage": "wgs_qc", "status": "success", "prefix": "Cohort", "artifacts": {}}), encoding="utf-8")
    captured = {}

    def fake_run(cmd, log_file, cwd):
        captured["cmd"] = list(cmd)
        manifest_path.write_text(json.dumps({
            "stage": "wgs_qc", "status": "success", "prefix": "Cohort",
            "artifacts": {"wgs_sample_config": {"role": "wgs_sample_config", "path": "final/config.yaml"}, **{f"{role}.S1": {"role": role, "sample_id": "S1"} for role in ("clean_reads_r1", "clean_reads_r2", "fastp_html", "fastp_json")}},
            "job_id": "qc-job",
            "wgs_sample_set_id": "wgs-samples:" + "a" * 64,
            "wgs_analysis_id": "wgs-analysis:" + "a" * 64,
        }), encoding="utf-8")
        return 0

    monkeypatch.setattr(pipeline_backend, "run_cmd_logged", fake_run)
    message, returned_manifest = pipeline_backend.run_stage(
        stage="wgs_qc",
        job=pipeline_backend.JobInfo("qc-job", str(input_dir), str(workspace), str(workspace / "logs"), "now"),
        prefix="Cohort",
        wgs_sample_config=str(config),
        wgs_fastp="/opt/fastp",
        wgs_threads=3,
        wgs_max_jobs=2,
    )

    assert "completed" in message.lower()
    assert returned_manifest == manifest_path
    assert captured["cmd"][:3] == [pipeline_backend.sys.executable, "-m", "apps.cli.run_wgs_qc"]
    assert captured["cmd"][captured["cmd"].index("--wgs-samples") + 1] == str(config)
    assert captured["cmd"][captured["cmd"].index("--fastp") + 1] == "/opt/fastp"


def test_wgs_qc_backend_rejects_missing_or_multiple_sample_configs(tmp_path: Path) -> None:
    job = pipeline_backend.JobInfo("qc-job", str(tmp_path / "input"), str(tmp_path / "workspace"), str(tmp_path / "logs"), "now")
    message, _ = pipeline_backend.run_stage(stage="wgs_qc", job=job, prefix="Cohort")
    assert "wgs_samples.yaml" in message
    input_dir = Path(job.input_dir); workspace = Path(job.workspace_dir)
    input_dir.mkdir(); workspace.mkdir()
    (input_dir / "wgs_samples.yaml").write_text("samples: {}\n", encoding="utf-8")
    (workspace / "wgs_samples.yaml").write_text("samples: {}\n", encoding="utf-8")
    message, _ = pipeline_backend.run_stage(stage="wgs_qc", job=job, prefix="Cohort")
    assert "exactly one" in message


def test_wgs_qc_backend_rejects_fresh_but_identityless_manifest(monkeypatch, tmp_path: Path) -> None:
    input_dir = tmp_path / "input"; workspace = tmp_path / "workspace"; input_dir.mkdir()
    for mate in ("R1", "R2"):
        (input_dir / f"S1.{mate}.fastq").write_text("@r\nA\n+\nI\n", encoding="utf-8")
    config = input_dir / "wgs_samples.yaml"
    config.write_text("samples:\n  S1:\n    r1: S1.R1.fastq\n    r2: S1.R2.fastq\n", encoding="utf-8")
    manifest = workspace / "final" / "Cohort.wgs_qc.manifest.json"; manifest.parent.mkdir(parents=True)
    def fake_run(*_args, **_kwargs):
        manifest.write_text(json.dumps({"stage": "wgs_qc", "status": "success", "prefix": "Cohort", "job_id": "qc-job", "artifacts": {}}), encoding="utf-8")
        return 0
    monkeypatch.setattr(pipeline_backend, "run_cmd_logged", fake_run)
    message, _ = pipeline_backend.run_stage(stage="wgs_qc", job=pipeline_backend.JobInfo("qc-job", str(input_dir), str(workspace), str(workspace / "logs"), "now"), prefix="Cohort", wgs_sample_config=str(config))
    assert "failed" in message.lower()


def test_wgs_qc_backend_rejects_stale_success_manifest(monkeypatch, tmp_path: Path) -> None:
    input_dir = tmp_path / "input"; workspace = tmp_path / "workspace"; input_dir.mkdir()
    for mate in ("R1", "R2"):
        (input_dir / f"S1.{mate}.fastq").write_text("@r\nA\n+\nI\n", encoding="utf-8")
    config = input_dir / "wgs_samples.yaml"
    config.write_text("samples:\n  S1:\n    r1: S1.R1.fastq\n    r2: S1.R2.fastq\n", encoding="utf-8")
    manifest = workspace / "final" / "Cohort.wgs_qc.manifest.json"; manifest.parent.mkdir(parents=True)
    manifest.write_text(json.dumps(_valid_manifest()), encoding="utf-8")
    monkeypatch.setattr(pipeline_backend, "run_cmd_logged", lambda *_args, **_kwargs: 0)
    message, returned = pipeline_backend.run_stage(stage="wgs_qc", job=pipeline_backend.JobInfo("qc-job", str(input_dir), str(workspace), str(workspace / "logs"), "now"), prefix="Cohort", wgs_sample_config=str(config))
    assert "failed" in message.lower()
    assert returned == manifest