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Sync Dataset

sync_dataset.py pulls the latest rows from the master Google Sheet, downloads the protocol/SAP PDFs for any new rows, and pushes everything to the Hugging Face dataset at trialdesignbench/source.

What it does

  1. Downloads the Google Sheet as CSV, converts to Parquet → overwrites data/tdr.parquet.
  2. Diffs against the previous tdr.parquet by the # column to find new rows.
  3. For each new row, downloads:
    • Study Protocol Link → documents/<#>/protocol.pdf
    • Protocol+SAP / SAP Link → documents/<#>/sap.pdf
    • Skips empty links. Skips files already on disk. Writes a *.error.txt on failure.
  4. Uploads the updated tdr.parquet and any new PDFs to Hugging Face.

One-time setup 

# 1. Python deps
pip install -U "huggingface_hub[cli]" pandas pyarrow openpyxl
# pandas + pyarrow are required for the Parquet read/write.
# openpyxl is only needed if the source file is an uploaded .xlsx
# (htmlview URL) rather than a native Google Sheet.

# 2. Authenticate to Hugging Face (write token from https://huggingface.co/settings/tokens)
hf auth login

# 3. Make sure the Google Sheet is shared as "Anyone with the link: Viewer"
#    Sheet URL: https://docs.google.com/spreadsheets/d/1Vb6U9Jzigtg5hLcn4R_5REW_G84cNVk6

Usage

Run from the source/ directory:

cd /Users/tengjun2/Desktop/clinical/tdb/source

# Preview new rows without changing anything
python3 sync_dataset.py --dry-run

# Download new PDFs and update tdr.parquet locally, but don't upload
python3 sync_dataset.py --no-upload

# Full sync: fetch sheet, download new PDFs, upload to Hugging Face
python3 sync_dataset.py

Output layout 

source/
├── data/
│   └── tdr.parquet               # latest sheet content (snappy-compressed)
├── documents/
│   └── <row_#>/
│       ├── protocol.pdf
│       ├── sap.pdf
│       ├── protocol.error.txt    # only present on download failure
│       └── sap.error.txt
└── sync_dataset.py

Configuration

Edit constants at the top of sync_dataset.py if any of these change:

Variable Default Meaning
SHEET_ID 1Vb6U9Jzigtg5hLcn4R_5REW_G84cNVk6 Google Sheet document ID
SHEET_GID 0 Sheet tab GID (find it in the sheet URL)
HF_REPO trialdesignbench/source Hugging Face dataset repo
PARQUET_PATH data/tdr.parquet Local Parquet path
DOCS_DIR documents/ PDF output root

Troubleshooting

"Google Sheet is not publicly shared" — Open the sheet → Share → General access → "Anyone with the link" → Viewer.

A PDF row writes *.error.txt — The source server rejected the request (often HTTP 403 on paywalled publisher links like NEJM). The row stays in tdr.parquet; only the PDF is missing. Re-running won't retry automatically — delete the .error.txt and the partial file, then re-run, if you want to retry.

Upload is slow — Throughput is bounded by your upstream bandwidth. For small incremental syncs (a handful of new files) hf upload is used per file. For > 200 new files the script falls back to hf upload-large-folder which parallelizes and is resumable.

Diff missed a row whose # was reused — The script keys on the # column. If a row's content changed without # changing, it won't be detected as new. Inspect manually in that case.

Notes

  • The script only adds new rows. Rows deleted from the sheet are kept in the local Parquet file and on Hugging Face — clean those up by hand if needed.
  • tdr.parquet is always overwritten with the latest sheet content, so edits in the sheet (typo fixes, etc.) propagate.
  • PDFs are never re-downloaded if already present. Force a re-download by deleting the file.