| """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 |
| from urllib.parse import urlparse |
|
|
| 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 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" |
| 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: |
| 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 |
|
|
| 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: |
| 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) |
|
|
