import sys
from pathlib import Path


ROOT = Path(__file__).resolve().parents[2]
if str(ROOT) not in sys.path:
    sys.path.insert(0, str(ROOT))


def test_rnaseq_env_bin_can_be_overridden(monkeypatch, tmp_path):
    from apps.cli import rnaseq_env

    custom_bin = tmp_path / "rnaseq" / "bin"
    monkeypatch.setenv("PLANTAI_RNASEQ_BIN", str(custom_bin))

    assert rnaseq_env.rnaseq_bin() == custom_bin
    assert rnaseq_env.rnaseq_tool("salmon") == str(custom_bin / "salmon")
    assert rnaseq_env.rnaseq_rscript() == str(custom_bin / "Rscript")


def test_rnar_rscript_uses_rnaR_environment(monkeypatch, tmp_path):
    from apps.cli import rnaseq_env

    conda_base = tmp_path / "miniconda3"
    monkeypatch.delenv("PLANTAI_RNAR_BIN", raising=False)
    monkeypatch.setenv("PLANTAI_CONDA_BASE", str(conda_base))

    assert rnaseq_env.rnar_rscript() == str(conda_base / "envs" / "rnaR" / "bin" / "Rscript")


def test_wgcna_script_caps_wgcna_and_blas_threads(tmp_path):
    from apps.cli import run_rnaseq_wgcna as wgcna

    script = tmp_path / "run_wgcna.R"
    wgcna.write_r_script(script, threads=12)
    text = script.read_text(encoding="utf-8")

    assert "wgcna_threads <- 12" in text
    assert "allowWGCNAThreads(nThreads = wgcna_threads)" in text
    assert "OMP_NUM_THREADS" in text
    assert "OPENBLAS_NUM_THREADS" in text


def test_annotation_interproscan_uses_rnaseq_path(monkeypatch, tmp_path):
    from apps.cli import run_annotation

    rnaseq_bin = tmp_path / "miniconda3" / "envs" / "rnaseq" / "bin"
    monkeypatch.setenv("PLANTAI_RNASEQ_BIN", str(rnaseq_bin))
    captured = {}

    class Result:
        returncode = 0
        stdout = ""
        stderr = ""

    def fake_run(cmd, **kwargs):
        captured["cmd"] = cmd
        captured["env"] = kwargs.get("env")
        return Result()

    monkeypatch.setattr(run_annotation.subprocess, "run", fake_run)

    run_annotation.run_interproscan(
        tmp_path / "proteins.fa",
        tmp_path / "out",
        tmp_path / "interproscan.sh",
        4,
        "Pfam",
        tmp_path / "tmp",
    )

    assert captured["env"] is not None
    assert str(rnaseq_bin) in captured["env"]["PATH"].split(":")