from __future__ import annotations

import json
from pathlib import Path
from typing import Dict, Iterable, List, Set


def merge_mappings(inputs: Iterable[Path], output: Path, version: str = "merged", sources: List[str] | None = None) -> Path:
    """
    Merge multiple phenotype→gene mapping JSON files into one.
    Input schema: {"phenotype_to_genes": {"HP:xxxx": ["GENE1", ...]}, "version": "...", "source": "..."}
    """
    merged: Dict[str, Set[str]] = {}
    source_list: List[str] = sources or []
    for path in inputs:
        data = json.loads(Path(path).read_text())
        phenos = data.get("phenotype_to_genes", {})
        for pid, genes in phenos.items():
            merged.setdefault(pid, set()).update(genes)
        src_label = data.get("source") or path.name
        source_list.append(src_label)

    out = {
        "version": version,
        "source": ",".join(source_list),
        "phenotype_to_genes": {pid: sorted(list(genes)) for pid, genes in merged.items()},
        "metadata": {"merged_from": [str(p) for p in inputs]},
    }
    output.parent.mkdir(parents=True, exist_ok=True)
    output.write_text(json.dumps(out, indent=2))
    return output