#!/usr/bin/env python3

"""
Example: Advanced filtering with sample type and platform.
"""

from pathlib import Path

from tcga_downloader.manifest import (
    ManifestRecord,
    format_manifest_stats,
    get_manifest_stats,
    write_manifest,
)
from tcga_downloader.query import query_files


def main():
    project = "TCGA-BRCA"
    data_type = "Gene Expression"
    sample_type = "Primary Tumor"
    platform = "Illumina HiSeq"
    manifest_path = Path("filtered_manifest.tsv")

    print("Advanced Query Parameters:")
    print(f"  Project: {project}")
    print(f"  Data Type: {data_type}")
    print(f"  Sample Type: {sample_type}")
    print(f"  Platform: {platform}")

    hits = query_files(
        project=project,
        data_type=data_type,
        sample_type=sample_type,
        platform=platform,
    )

    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")

    stats = get_manifest_stats(records)
    print("\nManifest Statistics:")
    print(format_manifest_stats(stats))

    print(f"\nManifest written to: {manifest_path}")
    print("You can now download with:")
    print(f"  tcga-downloader download --manifest {manifest_path} --out-dir ./data")


if __name__ == "__main__":
    main()