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Authentication handling in wfdb.io.dl_files, error 403

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Evaluación

Dificultad
4/5
Tiempo estimado
3-5 días
Aptitud para principiantes
45/100
Tipo de issue
Nueva funcionalidad
Claridad
Bastante claro
Estado de actividad
Tranquilo
Stack tecnológico
python

Línea de trabajo

Comienza en wfdb/io/download.py, en dl_files, dl_pn_file y dl_full_file; después inspecciona RangeTransfer y _parse_headers en wfdb/io/_url.py. Reproduce la solicitud 403 contra la URL autenticada de PhysioNet y sigue el flujo de gestión del acceso; se considera terminado cuando exista una ruta de autenticación documentada y compatible que permita a dl_files obtener archivos protegidos seleccionados.

Escrito por el modelo de indexación a partir del texto del issue.

Descripción

Context

I am trying to download specific files (subsets) from credentialed databases on PhysioNet using wfdb helper functions.

What I am trying to do is downloading selected files (not the entire dataset), e.g. :

from wfdb.io import dl_files
dl_files('mimiciv','data\\tmp',['hosp/patients.csv.gz'])

Stack trace

Created local base download directory: data\tmp
Downloading files...
Traceback (most recent call last):
  File "c:\Users\pa10198\Documents\_code\zarrow\dev.py", line 12, in <module>
    dl_files('mimiciv','data\\tmp',['hosp/patients.csv.gz'])
  File "C:\Users\pa10198\Documents\_code\zarrow\.venv\Lib\site-packages\wfdb\io\download.py", line 544, in dl_files
    pool.map(dl_pn_file, dl_inputs)
  File "C:\Users\pa10198\AppData\Local\Programs\Python\Python312\Lib\multiprocessing\pool.py", line 367, in map
    return self._map_async(func, iterable, mapstar, chunksize).get()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\pa10198\AppData\Local\Programs\Python\Python312\Lib\multiprocessing\pool.py", line 774, in get
    raise self._value
  File "C:\Users\pa10198\AppData\Local\Programs\Python\Python312\Lib\multiprocessing\pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
                    ^^^^^^^^^^^^^^^^^^^
  File "C:\Users\pa10198\AppData\Local\Programs\Python\Python312\Lib\multiprocessing\pool.py", line 48, in mapstar
    return list(map(*args))
           ^^^^^^^^^^^^^^^^
  File "C:\Users\pa10198\Documents\_code\zarrow\.venv\Lib\site-packages\wfdb\io\download.py", line 450, in dl_pn_file
    dl_full_file(url, local_file)
  File "C:\Users\pa10198\Documents\_code\zarrow\.venv\Lib\site-packages\wfdb\io\download.py", line 472, in dl_full_file
    content = readfile.read()
              ^^^^^^^^^^^^^^^
  File "C:\Users\pa10198\Documents\_code\zarrow\.venv\Lib\site-packages\wfdb\io\_url.py", line 580, in read
    result = b"".join(self._read_range(start, end))
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\pa10198\Documents\_code\zarrow\.venv\Lib\site-packages\wfdb\io\_url.py", line 473, in _read_range
    with RangeTransfer(self._current_url, req_start, req_end) as xfer:
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\pa10198\Documents\_code\zarrow\.venv\Lib\site-packages\wfdb\io\_url.py", line 167, in __init__
    self._parse_headers(method, self._response)
  File "C:\Users\pa10198\Documents\_code\zarrow\.venv\Lib\site-packages\wfdb\io\_url.py", line 213, in _parse_headers
    raise cls(
wfdb.io._url.NetFilePermissionError: 403 Error: Forbidden for url: https://physionet.org/files/mimiciv/3.1/hosp/patients.csv.gz

Remarks

  • I have the credentialed physionet account and access to the databases I request.
  • The same URL works in a browser after login and the file downloads successfully.

Questions

  • Is there any supported way to pass authentification when using dl_files or related functions, e.g. through env vars, config, etc.
  • If not, are there recommended workarounds (e.g., using cookies, tokens, or another library)? Ideally not leaving python and avoiding the multiplication of libraries within projects.

Feature idea

It would be very useful if wfdb supported:

  • authentication for credentialed MIMIC-IV (and similar datasets), and
  • partial downloads (which already works on the open datasets and seem supported structurally, but fail due to auth)

This would allow to avoid downloading entire large datasets and keep workflows within a single library.

Lenguaje dominante
Jupyter Notebook
Estrellas
853
Forks
322
Métricas de merge de PR
Sin PR fusionados en 30 d

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