Add files using upload-large-folder tool

.gitattributes

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SYNC_README.md

@@ -0,0 +1,89 @@
+# 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.

delete_old_folders.py

@@ -0,0 +1,42 @@
+"""Delete the old numeric-named documents/<#>/ folders from the HF dataset."""
+
+from __future__ import annotations
+
+from huggingface_hub import HfApi
+
+REPO = "trialdesignbench/source"
+
+
+def main() -> None:
+    api = HfApi()
+    files = api.list_repo_files(REPO, repo_type="dataset")
+
+    old = [
+        f for f in files
+        if f.startswith("documents/")
+        and len(f.split("/")) >= 2
+        and f.split("/")[1].isdigit()
+    ]
+    print(f"Found {len(old)} files under numeric folders. First 5:")
+    for p in old[:5]:
+        print(" ", p)
+
+    if not old:
+        return
+
+    confirm = input(f"Delete all {len(old)} files? [y/N] ").strip().lower()
+    if confirm != "y":
+        print("Aborted.")
+        return
+
+    api.delete_files(
+        delete_patterns=old,
+        repo_id=REPO,
+        repo_type="dataset",
+        commit_message="Remove old numeric-named document folders",
+    )
+    print("Deleted.")
+
+
+if __name__ == "__main__":
+    main()

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download_docs.py

@@ -12,6 +12,7 @@ import time
 import urllib.error
 import urllib.request
 from pathlib import Path
+from urllib.parse import urlparse
 
 CSV_PATH = Path(__file__).parent / "file.csv"
 OUT_ROOT = Path(__file__).parent / "downloads"
@@ -25,6 +26,12 @@ UA = (
 )
 
 
+def paper_link_slug(link: str) -> str:
+    path = urlparse((link or "").strip()).path.strip("/")
+    parts = [p for p in path.split("/") if p]
+    return "_".join(parts[-2:]) if len(parts) >= 2 else ""
+
+
 def download(url: str, dest: Path) -> tuple[bool, str]:
     if dest.exists() and dest.stat().st_size > 0:
         return True, "exists"
@@ -64,7 +71,12 @@ def main(start_row: int = 3) -> None:
                 print(f"[{num}] skip: no links")
                 continue
 
-            row_dir = OUT_ROOT / str(num)
+            slug = paper_link_slug(row.get("Paper Link") or "")
+            if not slug:
+                print(f"[{num}] skip: no usable Paper Link")
+                continue
+
+            row_dir = OUT_ROOT / slug
             row_dir.mkdir(exist_ok=True)
 
             if protocol:

replace_doc.py

@@ -0,0 +1,15 @@
+from huggingface_hub import HfApi
+
+api = HfApi()
+# api.delete_folder(
+#     "documents",
+#     repo_id="trialdesignbench/source",
+#     repo_type="dataset",
+# )
+api.upload_large_folder(
+    folder_path="/users/teng77/source",     # parent — preserves "documents/" prefix
+    repo_id="trialdesignbench/source",
+    repo_type="dataset",
+    allow_patterns=["documents/**"],
+    ignore_patterns=[".cache/**", "**/.cache/**"],
+)