Add files using upload-large-folder tool

.gitattributes

@@ -58,3 +58,48 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 # Video files - compressed
 *.mp4 filter=lfs diff=lfs merge=lfs -text
 *.webm filter=lfs diff=lfs merge=lfs -text
+documents/959/protocol.pdf filter=lfs diff=lfs merge=lfs -text
+documents/959/sap.pdf filter=lfs diff=lfs merge=lfs -text
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README.md

@@ -1,20 +1,13 @@
 ---
-pretty_name: "TrialDesignBench Source"
-license: other
-license_name: "mixed"
-license_link: LICENSE
-tags:
-  - clinical-trials
-  - statistical-analysis-plan
-  - protocols
-  - benchmark
-  - source-corpus
+license: cc-by-4.0
+pretty_name: TrialDesignBench Source
+configs:
+- config_name: default
+  data_files:
+  - split: train
+    path: data/tdr.csv
 ---
 
-## License
+# TrialDesignBench Source
 
-This repository is a mixed-rights source corpus.
-
-- The curated trial metadata, manifests, and dataset annotations created by the TrialDesignBench maintainers are released under the Creative Commons Attribution 4.0 International License (CC BY 4.0).
-- Downloaded Statistical Analysis Plans, protocols, and other source PDFs are third-party documents. They are provided with provenance metadata for research transparency and reproducibility. The TrialDesignBench maintainers do not claim copyright ownership over these documents and do not grant additional rights beyond those available from the original sources.
-- Users are responsible for complying with the terms, rights, and restrictions associated with the original source documents.
+CSV index of clinical trials with linked protocol and SAP PDFs under `documents/<row_id>/`.

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download_docs.py

@@ -0,0 +1,91 @@
+"""Download Protocol and SAP PDFs for each row of file.csv.
+
+Outputs go to source/downloads/row_<#>/{protocol,sap}.pdf.
+Skips rows with empty links and rows already downloaded.
+"""
+
+from __future__ import annotations
+
+import csv
+import sys
+import time
+import urllib.error
+import urllib.request
+from pathlib import Path
+
+CSV_PATH = Path(__file__).parent / "file.csv"
+OUT_ROOT = Path(__file__).parent / "downloads"
+TIMEOUT = 60
+RETRIES = 2
+SLEEP_BETWEEN = 0.3
+
+UA = (
+    "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) "
+    "AppleWebKit/537.36 (KHTML, like Gecko) Chrome/120.0.0.0 Safari/537.36"
+)
+
+
+def download(url: str, dest: Path) -> tuple[bool, str]:
+    if dest.exists() and dest.stat().st_size > 0:
+        return True, "exists"
+    req = urllib.request.Request(url, headers={"User-Agent": UA})
+    last_err = ""
+    for attempt in range(RETRIES + 1):
+        try:
+            with urllib.request.urlopen(req, timeout=TIMEOUT) as resp:
+                data = resp.read()
+            dest.write_bytes(data)
+            return True, f"ok ({len(data)} bytes)"
+        except urllib.error.HTTPError as e:
+            last_err = f"HTTP {e.code}"
+        except (urllib.error.URLError, TimeoutError) as e:
+            last_err = f"network: {e}"
+        except Exception as e:  # noqa: BLE001
+            last_err = f"error: {e}"
+        time.sleep(1 + attempt)
+    return False, last_err
+
+
+def main(start_row: int = 3) -> None:
+    OUT_ROOT.mkdir(exist_ok=True)
+    with CSV_PATH.open(newline="", encoding="utf-8") as fh:
+        reader = csv.DictReader(fh)
+        for row in reader:
+            num_str = (row.get("#") or "").strip()
+            if not num_str.isdigit():
+                continue
+            num = int(num_str)
+            if num < start_row:
+                continue
+
+            protocol = (row.get("Study Protocol Link") or "").strip()
+            sap = (row.get("Protocol+SAP / SAP Link") or "").strip()
+            if not protocol and not sap:
+                print(f"[{num}] skip: no links")
+                continue
+
+            row_dir = OUT_ROOT / str(num)
+            row_dir.mkdir(exist_ok=True)
+
+            if protocol:
+                ok, msg = download(protocol, row_dir / "protocol.pdf")
+                print(f"[{num}] protocol: {msg}")
+                if not ok:
+                    (row_dir / "protocol.error.txt").write_text(
+                        f"{protocol}\n{msg}\n", encoding="utf-8"
+                    )
+                time.sleep(SLEEP_BETWEEN)
+
+            if sap:
+                ok, msg = download(sap, row_dir / "sap.pdf")
+                print(f"[{num}] sap: {msg}")
+                if not ok:
+                    (row_dir / "sap.error.txt").write_text(
+                        f"{sap}\n{msg}\n", encoding="utf-8"
+                    )
+                time.sleep(SLEEP_BETWEEN)
+
+
+if __name__ == "__main__":
+    start = int(sys.argv[1]) if len(sys.argv) > 1 else 3
+    main(start_row=start)