from __future__ import annotations

from pathlib import Path
import inspect

from apps.web import pipeline_backend
from apps.web.vue3.main import ExecuteRequest
from gfa_core.project_paths import (
    get_conda_env_bin,
    get_conda_env_rscript,
    get_configured_path,
)
from gfa_core import project_paths


ROOT = Path(__file__).resolve().parents[2]
SCOPED_FILES = (
    ROOT / "gfa_core/mas/tools/stage_tools.py",
    ROOT / "apps/web/pipeline_backend.py",
    ROOT / "apps/web/vue3/main.py",
    ROOT / "apps/web/vue3/index.html",
)
FORBIDDEN_TOOL_PATHS = (
    "/data/miniconda3/envs/ASAW",
    "/home/xzq/miniconda3/envs/ASAW",
    "/home/xia-lab/miniconda3/envs/ASAW",
    "/usr/bin/emmax",
)


def test_asaw_paths_follow_bbav5_conda_base(monkeypatch, tmp_path: Path) -> None:
    conda_base = tmp_path / "conda"
    monkeypatch.setenv("BBAV5_CONDA_BASE", str(conda_base))

    assert get_conda_env_bin("ASAW") == conda_base / "envs/ASAW/bin"
    assert get_conda_env_rscript("ASAW") == conda_base / "envs/ASAW/bin/Rscript"


def test_configured_tool_path_comes_from_environment(monkeypatch) -> None:
    monkeypatch.setenv("GWAS_EMMAX_BIN", "/configured/emmax")

    assert get_configured_path("GWAS_EMMAX_BIN", "emmax") == "/configured/emmax"
    assert get_configured_path("UNSET_TOOL", "fallback") == "fallback"


def test_wgs_tool_defaults_are_resolved_server_side() -> None:
    request = ExecuteRequest(stage="wgs_qc")
    asaw_bin = get_conda_env_bin("ASAW")
    parameters = inspect.signature(pipeline_backend.run_stage).parameters

    assert request.wgsFastp == ""
    assert request.wgsSamtools == ""
    assert request.wgsBwaMem2 == ""
    assert request.wgsGatk == ""
    assert request.wgsBcftools == ""
    assert request.wgsJava == ""
    assert parameters["wgs_fastp"].default == str(asaw_bin / "fastp")
    assert parameters["wgs_samtools"].default == str(asaw_bin / "samtools")
    assert parameters["wgs_bwa_mem2"].default == str(asaw_bin / "bwa-mem2")
    assert parameters["wgs_gatk"].default == str(asaw_bin / "gatk")
    assert hasattr(project_paths, "get_wgs_bcftools")
    assert parameters["wgs_bcftools"].default == project_paths.get_wgs_bcftools()
    assert hasattr(project_paths, "get_wgs_java")
    assert parameters["wgs_java"].default == project_paths.get_wgs_java()


def test_wgs_java_uses_environment_then_test4py311(
    monkeypatch, tmp_path: Path
) -> None:
    assert hasattr(project_paths, "get_wgs_java")
    get_wgs_java = project_paths.get_wgs_java
    monkeypatch.setenv("WGS_JAVA", "/configured/java")
    assert get_wgs_java() == "/configured/java"
    assert get_wgs_java("/requested/java") == "/requested/java"

    monkeypatch.delenv("WGS_JAVA")
    monkeypatch.setenv("BBAV5_CONDA_BASE", str(tmp_path / "conda"))
    assert get_wgs_java() == str(
        tmp_path / "conda/envs/test4py311/bin/java"
    )


def test_wgs_bcftools_uses_environment_then_compatible_default(
    monkeypatch,
) -> None:
    assert hasattr(project_paths, "get_wgs_bcftools")
    get_wgs_bcftools = project_paths.get_wgs_bcftools
    monkeypatch.setenv("WGS_BCFTOOLS", "/configured/bcftools")
    assert get_wgs_bcftools() == "/configured/bcftools"
    assert get_wgs_bcftools("/requested/bcftools") == "/requested/bcftools"


def test_gwas_population_wgs_defaults_have_no_machine_tool_paths() -> None:
    violations = []
    for path in SCOPED_FILES:
        text = path.read_text(encoding="utf-8")
        for forbidden in FORBIDDEN_TOOL_PATHS:
            if forbidden in text:
                violations.append(f"{path.relative_to(ROOT)}: {forbidden}")

    assert violations == []