"""Download BindingDB full dataset (TSV in ZIP archive). Source: https://www.bindingdb.org/bind/downloads/ File: BindingDB_All_*.tsv (~525 MB zip -> ~2 GB TSV) """ import zipfile from pathlib import Path import requests from tqdm import tqdm from negbiodb.download import ( check_disk_space, load_config, verify_file_exists, ) def download_bindingdb_zip(servlet_url: str, file_url: str, dest: Path) -> None: """Download BindingDB ZIP using session-based two-step approach. BindingDB requires visiting a servlet page first to prepare the file, then downloading from the direct URL with the same session. """ if dest.exists() and dest.stat().st_size > 0: print(f"Already exists: {dest}") return dest.parent.mkdir(parents=True, exist_ok=True) session = requests.Session() # Step 1: Hit the servlet to prepare the file and get session cookie print("Requesting file preparation from BindingDB servlet...") prep = session.get(servlet_url, timeout=60) prep.raise_for_status() # Step 2: Download the actual file with the session print("Downloading ZIP file...") resp = session.get(file_url, stream=True, timeout=300) resp.raise_for_status() total = int(resp.headers.get("content-length", 0)) try: with ( open(dest, "wb") as f, tqdm(total=total or None, unit="B", unit_scale=True, desc="BindingDB ZIP") as pbar, ): for chunk in resp.iter_content(chunk_size=8192): f.write(chunk) pbar.update(len(chunk)) except Exception: if dest.exists(): dest.unlink() raise print(f"Downloaded: {dest} ({dest.stat().st_size / (1024**2):.1f} MB)") def main(): cfg = load_config() dl = cfg["downloads"]["bindingdb"] servlet_url = dl["servlet_url"] file_url = dl["file_url"] dest_dir = Path(dl["dest_dir"]) min_bytes = dl["min_size_bytes"] dest_dir.mkdir(parents=True, exist_ok=True) zip_path = dest_dir / "bindingdb_all.zip" print("=== BindingDB Download ===") print(f"Servlet: {servlet_url}") print(f"File: {file_url}") print(f"Dest: {dest_dir}") check_disk_space(dest_dir, required_gb=3.0) try: download_bindingdb_zip(servlet_url, file_url, zip_path) except (requests.RequestException, OSError) as e: print(f"\nERROR: Download failed: {e}") print( "BindingDB uses a servlet-based URL that may require manual download." ) print(f"Please download manually from: https://www.bindingdb.org/bind/downloads/") print(f"Save the ZIP file as: {zip_path}") return # Extract TSV from ZIP print("Extracting TSV from ZIP...") tsv_path = None with zipfile.ZipFile(zip_path) as zf: for name in zf.namelist(): if name.endswith(".tsv"): zf.extract(name, dest_dir) extracted = dest_dir / name tsv_path = dest_dir / "BindingDB_All.tsv" if extracted != tsv_path: extracted.rename(tsv_path) break if tsv_path is None: print("WARNING: No TSV file found in ZIP archive") return # Remove ZIP to save space zip_path.unlink() print(f"Removed ZIP: {zip_path}") if not verify_file_exists(tsv_path, min_bytes=min_bytes): print(f"WARNING: TSV smaller than expected ({min_bytes / 1e6:.0f} MB)") print(f"Extracted: {tsv_path} ({tsv_path.stat().st_size / (1024**2):.1f} MB)") print("\nBindingDB download complete.") if __name__ == "__main__": main()