#!/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.paper_metadata_enricher_v16_1_2 import (
    PaperMetadataEnricherV16,
)


def main() -> int:
    parser = argparse.ArgumentParser(
        description="Add canonical DOI/PMID/PMCID and citation metadata to a V16 result.json."
    )
    parser.add_argument("--result-json", required=True, type=Path)
    parser.add_argument("--pdf", type=Path)
    parser.add_argument("--doi", default="")
    parser.add_argument("--pmid", default="")
    parser.add_argument("--pmcid", default="")
    parser.add_argument("--output", type=Path)
    parser.add_argument("--in-place", action="store_true")
    args = parser.parse_args()

    source = args.result_json.resolve()
    if not source.exists():
        raise SystemExit(f"Missing result JSON: {source}")
    if not args.in_place and not args.output:
        raise SystemExit("Use --in-place or provide --output.")
    destination = source if args.in_place else args.output.resolve()

    data = json.loads(source.read_text(encoding="utf-8"))
    enricher = PaperMetadataEnricherV16()
    paper = enricher.resolve(
        pdf_path=args.pdf.resolve() if args.pdf else None,
        doi=args.doi,
        pmid=args.pmid,
        pmcid=args.pmcid,
    )
    enricher.enrich_output(data, paper)
    destination.parent.mkdir(parents=True, exist_ok=True)
    destination.write_text(
        json.dumps(data, ensure_ascii=False, indent=2),
        encoding="utf-8",
    )
    audit_path = destination.parent / "paper_metadata_enrichment_audit.json"
    enricher.save_audit(audit_path, paper)
    print(
        json.dumps(
            {
                "result_json": str(destination),
                "audit": str(audit_path),
                "paper": paper,
                "relations": len(data.get("relations", [])),
            },
            ensure_ascii=False,
            indent=2,
        )
    )
    return 0


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