| # 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`](https://huggingface.co/datasets/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 |
|
|
| ```bash |
| # 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: |
|
|
| ```bash |
| 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. |
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|
