"""Maintenance tools in scripts/jev: everything except the API calls."""

from __future__ import annotations

import gzip
import importlib.util
import json
import sys
from pathlib import Path
from types import ModuleType

ROOT = Path(__file__).resolve().parents[2]
JEV = ROOT / "scripts" / "jev"


def _load(name: str) -> ModuleType:
    if str(JEV) not in sys.path:
        sys.path.insert(0, str(JEV))
    spec = importlib.util.spec_from_file_location(name, JEV / f"{name}.py")
    assert spec is not None and spec.loader is not None
    mod = importlib.util.module_from_spec(spec)
    sys.modules[name] = mod
    spec.loader.exec_module(mod)
    return mod


client = _load("client")
cov = _load("spec_coverage")
voice = _load("voice_check")
tri = _load("nightly_triage")


def test_client_builders() -> None:
    assert client.noul("x?", true="a", false="b") == {"type": "noul", "instructions": "x?",
                                                      "criteria": {"true": "a", "false": "b"}}  # fmt: skip
    assert client.choice("pick", {"a": "A"})["type"] == "choice"
    assert client.score("how", ["low", "high"])["criteria"] == ["low", "high"]


def test_spec_parsing_skips_open_questions() -> None:
    text = (
        "## 14 CLI\n- **CLI-005** `§14 · P1` **Option precedence.**\nCLI flags beat config files.\n"
        "- **OQ-001** `§20` Is this needed?\n## 15 Outputs\n- **OUT-031** `§9 · P6` VCF records are sorted.\n"
    )
    items = cov.parse_spec(text)
    assert [i.id for i in items] == ["CLI-005", "OUT-031"]
    assert items[0].tag == "§14 · P1" and "config files" in items[0].text


def test_bm25_prefers_matching_test() -> None:
    bm = cov.Bm25(["def test_vcf_sorted(): records sorted by position", "def test_idat_header(): magic bytes"])
    assert bm.top("VCF records are sorted by position", 1) == [0]


def test_voice_rules() -> None:
    paras = voice.paragraphs(Path("x.md"), "# H\n\nA seamless — revolutionary tool.\n\n```\nnot prose\n```\n")
    assert len(paras) == 1 and paras[0].heading == "H"
    issues = voice.mechanical(paras[0])
    assert "em or en dash in prose" in issues and any("seamless" in i for i in issues)
    quoted = voice.Para("x.md", 1, "", 'Never write "revolutionary" or "seamless".')
    assert voice.mechanical(quoted) == []


def test_known_findings_and_evidence(tmp_path: Path) -> None:
    kf = tri.known_findings("| K-014 | 2026-09-28 | NaN sign | NaNs take the platform's sign. | resolved |\n")
    assert kf == {"K-014": "NaN sign: NaNs take the platform's sign."}
    (tmp_path / "s" / "compare").mkdir(parents=True)
    (tmp_path / "s" / "compare" / "summary.json").write_text(
        json.dumps({"fields": {"GT": {"tolerance": "exact", "discrepancies": 2}, "X": {"discrepancies": 0}}})
    )
    with gzip.open(tmp_path / "s" / "compare" / "discrepancies.tsv.gz", "wt") as fh:
        fh.write("pair\tfield\n1\tGT\n")
    (tmp_path / "run.log").write_text("pi_run: MemAvailable 500 MiB < 800 MiB -- stopping the job\n")
    ev = tri.evidence(tmp_path, "s", {"verdict": "FAIL", "report": "s/compare/dashboard.html"})
    assert ev["differing_fields"] == {"GT": {"tolerance": "exact", "discrepancies": 2}}
    assert ev["first_rows"][1] == "1\tGT" and "log" not in ev  # another step's log line must not leak in
    ev2 = tri.evidence(tmp_path, "t", {"verdict": "ERROR", "error": "exit 137"})
    assert ev2["log"] == ["pi_run: MemAvailable 500 MiB < 800 MiB -- stopping the job"]


issue = _load("issue_triage")
lit = _load("literature_watch")


def test_issue_missing_info_and_comment() -> None:
    body = "### SimurgArray version\n\n_No response_\n\n### Command\n\n```shell\nsimurg genotype\n```\n"
    assert issue.missing_info(body, "bug") == ["the SimurgArray version"]
    assert issue.missing_info(body.replace("_No response_", "2.0.0"), "bug") == []
    assert issue.missing_info("no template at all", "feature") == []
    d = {"kind": "security", "labels": ["kind/security"], "privacy": ["credentials"], "clinical": True,
         "missing": []}  # fmt: skip
    text = issue.comment_text(d)
    assert "support@yaylali.uk" in text and "credentials" in text and "research tool" in text


def test_literature_prefilter() -> None:
    p = lit.Paper
    papers = [
        p("bioRxiv", "Fast genotype calling for Infinium arrays", "We call genotypes from IDAT files.", "u1", "d"),
        p("PubMed", "Fast genotype calling for Infinium arrays!", "Duplicate title.", "u2", "d"),
        p("bioRxiv", "Protein folding at scale", "Nothing about arrays here.", "u3", "d"),
        p("bioRxiv", "No abstract", "", "u4", "d"),
    ]
    assert [x.url for x in lit.prefilter(papers)] == ["u1"]