MIT-LCP / MIT-LCP/wfdb-python

wfdb.io._url.NetFileNotFoundError: 404 Error: Not Found for url: https://physionet.org/files/ecg-arrhythmia/1.0.0/WFDBRecords/01/010/.hea

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Description

import os
import wfdb

for db in wfdb.get_dbs():
    print(db)

def download_dataset_from_physionet(dataset_name: str):
    # https://wfdb.readthedocs.io/en/latest/io.html#module-1
    print(f"Downloading {dataset_name} dataset from PhysioNet...")
    if not os.path.exists("physionet"):
        os.makedirs("physionet")
    if not os.path.exists("physionet/" + dataset_name):
        os.makedirs("physionet/" + dataset_name)
    
    wfdb.dl_database(db_dir=dataset_name,
                     dl_dir=os.path.join(os.getcwd(), "physionet", dataset_name),
                     records='all',
                     annotators='all',
                     keep_subdirs=True,
                     overwrite=False)
    print(f"Downloaded {dataset_name} dataset from PhysioNet!")

# Download the MIT-BIH dataset
download_dataset_from_physionet("mitdb") # This one downloads

# Download the ECG arrhythmia dataset
download_dataset_from_physionet("ecg-arrhythmia") # This one doesn't, see traceback below

...
['ecg-arrhythmia', 'A large scale 12-lead electrocardiogram database for arrhythmia study']
.....

Downloading mitdb dataset from PhysioNet...
Downloading ecg-arrhythmia dataset from PhysioNet...
Generating list of all files for: WFDBRecords/01/010/
Traceback (most recent call last):
  File "I:\nasty\Python_Projects\Healthcare\ECG_Classification_Scholarship_Project\main.py", line 27, in <module>
    download_dataset_from_physionet("ecg-arrhythmia")
  File "I:\nasty\Python_Projects\Healthcare\ECG_Classification_Scholarship_Project\main.py", line 15, in download_dataset_from_physionet
    wfdb.dl_database(db_dir=dataset_name,
  File "C:\Users\chalu\AppData\Local\Programs\Python\Python311\Lib\site-packages\wfdb\io\record.py", line 3065, in dl_database  
    record = rdheader(
             ^^^^^^^^^
  File "C:\Users\chalu\AppData\Local\Programs\Python\Python311\Lib\site-packages\wfdb\io\record.py", line 1847, in rdheader     
    header_content = download._stream_header(file_name, pn_dir)
                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\chalu\AppData\Local\Programs\Python\Python311\Lib\site-packages\wfdb\io\download.py", line 109, in _stream_header
    content = f.read()
              ^^^^^^^^
  File "C:\Users\chalu\AppData\Local\Programs\Python\Python311\Lib\site-packages\wfdb\io\_url.py", line 581, in read
    result = b"".join(self._read_range(start, end))
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\chalu\AppData\Local\Programs\Python\Python311\Lib\site-packages\wfdb\io\_url.py", line 474, in _read_range     
    with RangeTransfer(self._current_url, req_start, req_end) as xfer:
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\chalu\AppData\Local\Programs\Python\Python311\Lib\site-packages\wfdb\io\_url.py", line 168, in __init__        
    self._parse_headers(method, self._response)
  File "C:\Users\chalu\AppData\Local\Programs\Python\Python311\Lib\site-packages\wfdb\io\_url.py", line 214, in _parse_headers  
    raise cls(
wfdb.io._url.NetFileNotFoundError: 404 Error: Not Found for url: https://physionet.org/files/ecg-arrhythmia/1.0.0/WFDBRecords/01/010/.hea

Seems to be trying to find a filename that doesn't exist? When you navigate to https://physionet.org/files/ecg-arrhythmia/1.0.0/WFDBRecords/01/010 there are files in there, but the code is looking for .hea which doesn't exist?

Contributor guide

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start at wfdb.dl_database in wfdb/io/record.py and trace the download through wfdb/io/download.py and wfdb/io/_url.py. Reproduce the request for the ecg-arrhythmia dataset and inspect how WFDBRecords/01/010/ is interpreted. Done means the dataset can be downloaded without requesting the missing .hea path.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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