#!/usr/bin/env python3
"""Build BindingDB source records and an exact-Kd gold file from pinned zips.

Reads the publisher-verified BindingDB curated-articles export (main TSV),
the Reactant_set_id -> ENTRYID_ASSAYID mapping, and the Assays export from
their ZIP archives, verifies every archive's SHA-256 against the pinned
config, and writes:

- ``source_records.jsonl``: one versioned JSON envelope per valid
  single-chain record/measurement (all measurement types and relations),
- ``gold_exact_kd.jsonl``: only exact '=' Kd records with one chain, a
  sequence, a canonicalizable SMILES, a positive nM value, and an assay join,
- ``bindingdb_audit.json``: deterministic audit of counts, coverage, and
  every rejection reason.

Nothing is aggregated across rows or assays, and Ki/IC50/EC50 values are
never relabeled as Kd.
"""

from __future__ import annotations

import argparse
import json
from pathlib import Path

from mitointeract_recovery import bindingdb_adapter

DEFAULT_CONFIG = Path(__file__).resolve().parents[1] / "config-bindingdb.json"


def load_config(path: Path) -> dict:
    config = json.loads(path.read_text())
    files = config.get("files")
    if not isinstance(files, dict):
        raise ValueError(f"{path}: config must contain a 'files' object")
    for key in bindingdb_adapter.INPUT_KEYS:
        entry = files.get(key)
        if not isinstance(entry, dict):
            raise ValueError(f"{path}: config files entry {key!r} missing")
        for field in ("url", "member", "sha256"):
            if not entry.get(field):
                raise ValueError(f"{path}: config files[{key!r}] missing {field!r}")
    return config


def main() -> None:
    parser = argparse.ArgumentParser(description=__doc__)
    parser.add_argument(
        "--main-zip", type=Path, required=True, help="main articles TSV zip"
    )
    parser.add_argument(
        "--mapping-zip",
        type=Path,
        required=True,
        help="rsid -> ENTRYID_ASSAYID map zip",
    )
    parser.add_argument(
        "--assays-zip", type=Path, required=True, help="assay names/descriptions zip"
    )
    parser.add_argument(
        "--config",
        type=Path,
        default=DEFAULT_CONFIG,
        help="pinned release config (URLs, members, SHA-256 checksums)",
    )
    parser.add_argument("--output-dir", type=Path, required=True)
    parser.add_argument(
        "--max-source-rows",
        type=int,
        default=None,
        help="process at most this many main-TSV data rows (for smoke runs)",
    )
    args = parser.parse_args()

    if args.max_source_rows is not None and args.max_source_rows < 1:
        parser.error("--max-source-rows must be a positive integer")

    config = load_config(args.config)
    bindingdb_adapter.run_pipeline(
        main_zip=args.main_zip,
        mapping_zip=args.mapping_zip,
        assays_zip=args.assays_zip,
        config=config,
        output_dir=args.output_dir,
        max_source_rows=args.max_source_rows,
    )


if __name__ == "__main__":
    main()