from __future__ import annotations

import argparse
from pathlib import Path

from tcga_downloader.download import run_gdc_download
from tcga_downloader.manifest import ManifestRecord, write_manifest
from tcga_downloader.query import query_files


def build_parser() -> argparse.ArgumentParser:
    parser = argparse.ArgumentParser(prog="tcga-downloader")
    sub = parser.add_subparsers(dest="command", required=True)

    q = sub.add_parser("query")
    q.add_argument("--project", required=True)
    q.add_argument("--data-type", required=True)
    q.add_argument("--out", required=True)
    q.add_argument("--format", choices=["tsv", "json"], default="tsv")

    d = sub.add_parser("download")
    d.add_argument("--manifest", required=True)
    d.add_argument("--out-dir", required=True)
    d.add_argument("--processes", type=int, default=4)
    d.add_argument("--retries", type=int, default=3)

    r = sub.add_parser("run")
    r.add_argument("--project", required=True)
    r.add_argument("--data-type", required=True)
    r.add_argument("--out", required=True)
    r.add_argument("--format", choices=["tsv", "json"], default="tsv")
    r.add_argument("--out-dir", required=True)
    r.add_argument("--processes", type=int, default=4)
    r.add_argument("--retries", type=int, default=3)

    return parser


def _records_from_hits(hits: list[dict]) -> list[ManifestRecord]:
    records = []
    for h in hits:
        records.append(
            ManifestRecord(
                file_id=h["file_id"],
                file_name=h["file_name"],
                data_type=h["data_type"],
                data_format=h["data_format"],
                size=int(h["file_size"]),
                md5=h["md5sum"],
            )
        )
    return records


def main() -> None:
    parser = build_parser()
    args = parser.parse_args()

    if args.command in {"query", "run"}:
        hits = query_files(args.project, args.data_type)
        records = _records_from_hits(hits)
        write_manifest(records, Path(args.out), fmt=args.format)

    if args.command in {"download", "run"}:
        manifest_path = Path(args.manifest if args.command == "download" else args.out)
        run_gdc_download(manifest_path, Path(args.out_dir), args.processes, args.retries)