#!/usr/bin/env python3
from __future__ import annotations

import argparse
import json
import sys
from pathlib import Path

PROJECT_ROOT = Path(__file__).resolve().parents[1]
if str(PROJECT_ROOT) not in sys.path:
    sys.path.insert(0, str(PROJECT_ROOT))

from src.rag.extractors.v16_1_2.v16_extractor import V16Extractor


def parse_args() -> argparse.Namespace:
    parser = argparse.ArgumentParser(
        description="Run the formal V16.1.2 plant-science SRT extraction pipeline."
    )
    parser.add_argument("--pdf", required=True, type=Path)
    parser.add_argument("--output-dir", required=True, type=Path)
    parser.add_argument("--pmid", default="")
    parser.add_argument("--doi", default="")
    parser.add_argument("--disable-llm", action="store_true")
    parser.add_argument("--use-pc-data", action="store_true")
    return parser.parse_args()


def main() -> int:
    args = parse_args()
    pdf = args.pdf.resolve()
    output_dir = args.output_dir.resolve()
    if not pdf.exists():
        raise SystemExit(f"PDF does not exist: {pdf}")
    output_dir.mkdir(parents=True, exist_ok=True)
    extractor = V16Extractor(
        output_dir=output_dir,
        use_mineru=True,
        use_llm_relations=not args.disable_llm,
        use_rule_relation_fallback=False,
        use_vlm=False,
        use_neo4j=False,
        use_unified_storage=False,
        use_llm_definitions=False,
        use_pc_data=args.use_pc_data,
        use_disambiguation=args.use_pc_data,
    )
    result = extractor.extract(
        pdf,
        pmid=args.pmid or None,
        doi=args.doi or None,
    )
    summary = {
        "version": result.get("metadata", {}).get("version"),
        "pdf": str(pdf),
        "output_dir": str(output_dir),
        "entities": len(result.get("entities", [])),
        "relations": len(result.get("relations", [])),
        "relation_units": len(result.get("chunks", [])),
        "result_json": str(output_dir / "result.json"),
    }
    print(json.dumps(summary, ensure_ascii=False, indent=2))
    return 0


if __name__ == "__main__":
    raise SystemExit(main())