File size: 4,290 Bytes
19ee463 | 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 | # 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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