Datasets:
Formats:
parquet
Languages:
English
Size:
10M - 100M
Tags:
biology
chemistry
drug-discovery
clinical-trials
protein-protein-interaction
gene-essentiality
License:
File size: 3,660 Bytes
6d1bbc7 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 | """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()
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