#!/usr/bin/env python3

"""
Basic example: Query TCGA data and download files.
"""

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 main():
    query_project = "TCGA-BRCA"
    data_type = "Gene Expression"
    manifest_path = Path("manifest.tsv")
    data_dir = Path("data")

    print(f"Querying {query_project} for {data_type}...")
    hits = query_files(query_project, data_type)

    print(f"Found {len(hits)} files")
    print(f"Writing manifest to {manifest_path}...")

    records = [
        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"],
        )
        for h in hits
    ]

    write_manifest(records, manifest_path, fmt="tsv")

    print(f"Downloading files to {data_dir}...")
    data_dir.mkdir(exist_ok=True)
    run_gdc_download(manifest_path, data_dir, processes=4, retries=3)

    print("Download complete!")


if __name__ == "__main__":
    main()