from __future__ import annotations

import hashlib
import json
from pathlib import Path

from apps.web import pipeline_backend as backend
from apps.web.vue3 import main as api
from gfa_core.mas.tools.stage_status import get_stage_status


def _upstream(workspace: Path) -> tuple[Path, str]:
    final = workspace / "final"
    final.mkdir(parents=True)
    vcf = final / "cohort.gwas_fmt.sorted.vcf.gz"
    vcf.write_bytes(b"sorted")
    sha = hashlib.sha256(vcf.read_bytes()).hexdigest()
    scope = "genotype:" + "a" * 64
    manifest = {
        "manifest_version": "1.0",
        "stage": "gwas_fmt",
        "status": "success",
        "prefix": "cohort",
        "genotype_scope_id": scope,
        "artifacts": {
            "sorted_vcf": {
                "role": "sorted_vcf",
                "path": str(vcf.relative_to(workspace)),
                "full_path": str(vcf.resolve()),
                "size": vcf.stat().st_size,
                "sha256": sha,
            }
        },
    }
    (final / "cohort.gwas_fmt.manifest.json").write_text(json.dumps(manifest), encoding="utf-8")
    return vcf, scope


def test_backend_resolves_stage19_only_from_gwas_fmt_manifest(tmp_path: Path) -> None:
    workspace = tmp_path / "workspace" / "job"
    vcf, scope = _upstream(workspace)
    decision = backend._resolve_gwas_kinship_input(workspace=workspace, prefix="cohort")
    assert decision["path"] == str(vcf.resolve())
    assert decision["genotype_scope_id"] == scope


def test_backend_builds_only_canonical_stage19_runner_command(tmp_path: Path) -> None:
    command = backend._gwas_kinship_cli_command(
        workspace=tmp_path,
        job_id="job",
        prefix="cohort",
        sorted_vcf=tmp_path / "sorted.vcf.gz",
        genotype_scope_id="genotype:" + "a" * 64,
        tassel_pipeline="/opt/tassel/run_pipeline.pl",
        xmx="10g",
        log_file=tmp_path / "logs" / "gwas_kinship.log",
    )
    joined = " ".join(command)
    assert "-m apps.cli.run_gwas_kinship" in joined
    assert "--genotype-scope-id genotype:" in joined
    assert "-ck" not in command
    assert command.count("apps.cli.run_gwas_kinship") == 1


def test_api_preflight_short_circuits_gene_family_resolution(
    tmp_path: Path, monkeypatch
) -> None:
    workspace_root = tmp_path / "workspace"
    _upstream(workspace_root / "job")
    monkeypatch.setattr(api, "WORKSPACE_ROOT", workspace_root)
    result = api._api_semantic_preflight("job", "gwas_kinship", "cohort", {})
    assert result["valid"] is True
    assert result["issues"] == []
    assert result["decisions"]["sorted_vcf"]["producer_stage"] == "gwas_fmt"


def test_status_finds_stage_then_identity_manifest_filename(tmp_path: Path) -> None:
    workspace_root = tmp_path / "workspace"
    final = workspace_root / "job" / "final"
    final.mkdir(parents=True)
    manifest_path = final / "cohort.gwas_kinship.123456789abc.manifest.json"
    manifest_path.write_text(json.dumps({
        "stage": "gwas_kinship",
        "prefix": "cohort",
        "status": "success",
        "genotype_scope_id": "genotype:" + "a" * 64,
        "analysis_scope_id": "gwas-analysis:" + "1" * 64,
        "artifacts": {},
    }), encoding="utf-8")
    report = get_stage_status(
        job_id="job",
        prefix="cohort",
        stage="gwas_kinship",
        workspace_root=workspace_root,
        require_artifacts=False,
        strict_identity=True,
        genotype_scope_id="genotype:" + "a" * 64,
    )
    assert report.manifest_path == manifest_path
    assert report.completed is True