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pull_structures.py
----------------------------
Pulls all glycan structure files from GlycoShape API and uploads
to HuggingFace as a Parquet dataset.
Requirements:
pip install requests huggingface_hub pyarrow tqdm
Usage:
python pull_structures.py --repo your-username/GlycoShape
"""
import argparse, io, json, os, time, zipfile, requests
from pathlib import Path
import pyarrow as pa
import pyarrow.parquet as pq
from tqdm import tqdm
from huggingface_hub import HfApi
# ── Config ─────────────────────────────────────────────────────────────────────
BASE_URL = "https://glycoshape.org/api"
BATCH_SIZE = 50 # write to parquet every N glycans (memory control)
SLEEP_SEC = 0.3 # polite delay between requests
TIMEOUT = 30 # seconds per request
# ── Fetch the full list of GlyTouCan IDs ───────────────────────────────
def fetch_available_ids() -> list[str]:
print("Fetching GlyTouCan ID list from /api/available …")
r = requests.get(f"{BASE_URL}/available", timeout=TIMEOUT)
r.raise_for_status()
ids = r.json()
print(f" → {len(ids)} glycans found")
return ids
# ── Download ZIP and extract PDB files for a glycan ──────────────────
def download_structures(glycan_id: str) -> list[dict]:
"""
Returns a list of records, one per PDB file inside the ZIP:
{
glytoucan_id : str – GlyTouCan accession (e.g. "G00028MO")
filename : str – original filename inside the ZIP
file_type : str – extension: "pdb", "mol2", etc.
cluster : str – cluster label parsed from filename (if present)
pdb_content : str – full text content of the file
}
"""
url = f"{BASE_URL}/download/{glycan_id}"
try:
r = requests.get(url, timeout=60)
r.raise_for_status()
except requests.HTTPError as e:
print(f" HTTP error for {glycan_id}: {e}")
return []
except requests.RequestException as e:
print(f" Network error for {glycan_id}: {e}")
return []
records = []
try:
with zipfile.ZipFile(io.BytesIO(r.content)) as zf:
for name in zf.namelist():
ext = Path(name).suffix.lstrip(".").lower()
if ext not in {"pdb", "mol2", "cif", "xyz"}:
continue # skip non-structure files (logs, etc.)
raw = zf.read(name)
try:
content = raw.decode("utf-8")
except UnicodeDecodeError:
content = raw.decode("latin-1")
# Parse cluster label from filename, e.g. "cluster_1.pdb" → "1"
stem = Path(name).stem
cluster = ""
for part in stem.replace("-", "_").split("_"):
if part.isdigit():
cluster = part
break
records.append({
"glytoucan_id": glycan_id,
"filename": name,
"file_type": ext,
"cluster": cluster,
"pdb_content": content,
})
except zipfile.BadZipFile:
print(f" Bad ZIP for {glycan_id}")
return records
# ── Write a batch of records to a Parquet shard ─────────────────────────
def write_parquet(records: list[dict], out_dir: Path, shard_idx: int) -> Path:
schema = pa.schema([
pa.field("glytoucan_id", pa.string()),
pa.field("filename", pa.string()),
pa.field("file_type", pa.string()),
pa.field("cluster", pa.string()),
pa.field("pdb_content", pa.large_string()),
])
table = pa.Table.from_pylist(records, schema=schema)
out_path = out_dir / f"shard-{shard_idx:05d}.parquet"
pq.write_table(table, out_path, compression="zstd")
print(f" → wrote {out_path.name} ({len(records)} structure files)")
return out_path
# ── Main ───────────────────────────────────────────────────────────────────────
def main():
parser = argparse.ArgumentParser()
parser.add_argument("--out-dir", default="../data/structure_parquets/", help="Output dir for parquet shards (default: ../data/structure_parquets/)")
parser.add_argument("--limit", type=int, default=None, help="Only process first N glycans (for testing)")
parser.add_argument("--retry-failed", action="store_true", help="Retry only the IDs listed in failed_ids.json")
args = parser.parse_args()
out_dir = Path(args.out_dir)
out_dir.mkdir(parents=True, exist_ok=True)
# 1. Get IDs — either from failed_ids.json or the full API list
if args.retry_failed:
fail_path = out_dir / "failed_ids.json"
if not fail_path.exists():
print(f"No failed_ids.json found in {out_dir}")
return
all_ids = json.loads(fail_path.read_text())
print(f"Retrying {len(all_ids)} previously failed glycans …")
else:
all_ids = fetch_available_ids()
if args.limit:
all_ids = all_ids[: args.limit]
print(f" (limited to first {args.limit} for testing)")
# 2. Download + write in batches
# Use a high shard_idx start when retrying so we don't overwrite existing shards
batch: list[dict] = []
shard_idx: int = len(list(out_dir.glob("shard-*.parquet")))
failed: list[str] = []
for glycan_id in tqdm(all_ids, desc="Downloading"):
records = download_structures(glycan_id)
if records:
batch.extend(records)
else:
failed.append(glycan_id)
if len(batch) >= BATCH_SIZE * 10:
write_parquet(batch, out_dir, shard_idx)
shard_idx += 1
batch = []
time.sleep(SLEEP_SEC)
# flush remainder
if batch:
write_parquet(batch, out_dir, shard_idx)
if failed:
fail_path = out_dir / "failed_ids.json"
fail_path.write_text(json.dumps(failed, indent=2))
print(f"\n⚠ {len(failed)} glycans failed — saved to {fail_path}")
elif args.retry_failed:
# clean up failed_ids.json if everything succeeded this time
(out_dir / "failed_ids.json").unlink(missing_ok=True)
print("\n✓ All previously failed glycans downloaded successfully")
if __name__ == "__main__":
main() |