UnboundLocalError when GSE non-existent

[jonasfreimuth]

Hello,

when trying to download a non-exising (because deleted) GEO Series I get an UnboundLocalError.

Minimal example, that particular GSE is what raised this issue for me. According to its GEO page it has been deleted in 2019:

(This was run using Python 3.10.12 in a venv with just GEOparse 2.0.3 and its dependencies installed.)

import GEOparse as gp
gp.get_GEO("GSE108587")

I get the following output:

26-Sep-2023 17:07:29 DEBUG utils - Directory ./ already exists. Skipping.
26-Sep-2023 17:07:29 INFO GEOparse - Downloading ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108587/soft/GSE108587_family.soft.gz to ./GSE108587_family.soft.gz
26-Sep-2023 17:07:30 ERROR downloader - Error when trying to retreive ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108587/soft/GSE108587_family.soft.gz.
Traceback (most recent call last):
  File "/tmp/tmp.BcsQuqwIqU/.venv/lib/python3.10/site-packages/GEOparse/downloader.py", line 149, in _download_ftp
    total_size = ftp.size(parsed_url.path)
  File "/gnu/store/a547z6gpzimk68vdv8afmjsmgblnal9w-profile/lib/python3.10/ftplib.py", line 630, in size
    resp = self.sendcmd('SIZE ' + filename)
  File "/gnu/store/a547z6gpzimk68vdv8afmjsmgblnal9w-profile/lib/python3.10/ftplib.py", line 281, in sendcmd
    return self.getresp()
  File "/gnu/store/a547z6gpzimk68vdv8afmjsmgblnal9w-profile/lib/python3.10/ftplib.py", line 254, in getresp
    raise error_perm(resp)
ftplib.error_perm: 550 /geo/series/GSE108nnn/GSE108587/soft/GSE108587_family.soft.gz: No such file or directory
Traceback (most recent call last):
  File "/tmp/tmp.BcsQuqwIqU/.venv/lib/python3.10/site-packages/GEOparse/utils.py", line 80, in download_from_url
    fn.download(silent=silent, force=force)
  File "/tmp/tmp.BcsQuqwIqU/.venv/lib/python3.10/site-packages/GEOparse/downloader.py", line 82, in download
    _download()
  File "/tmp/tmp.BcsQuqwIqU/.venv/lib/python3.10/site-packages/GEOparse/downloader.py", line 53, in _download
    self._download_ftp(silent=silent)
  File "/tmp/tmp.BcsQuqwIqU/.venv/lib/python3.10/site-packages/GEOparse/downloader.py", line 187, in _download_ftp
    if total_size != 0:
UnboundLocalError: local variable 'total_size' referenced before assignment

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/tmp/tmp.BcsQuqwIqU/.venv/lib/python3.10/site-packages/GEOparse/GEOparse.py", line 96, in get_GEO
    filepath, geotype = get_GEO_file(
  File "/tmp/tmp.BcsQuqwIqU/.venv/lib/python3.10/site-packages/GEOparse/GEOparse.py", line 263, in get_GEO_file
    utils.download_from_url(url, filepath, silent=silent, aspera=aspera)
  File "/tmp/tmp.BcsQuqwIqU/.venv/lib/python3.10/site-packages/GEOparse/utils.py", line 82, in download_from_url
    raise IOError(
OSError: Download failed due to 'local variable 'total_size' referenced before assignment'. ID could be incorrect or the data might not be public yet.

While this get's "caught" and repackaged with a hint that there's something wrong with the ID, seeing the text "Download failed due to 'local variable 'total_size' referenced before assignment" won't let you think that there was something wrong with the GSE itself.

I just noticed that #77 ought to fix this.

Anyways nice package, thank you very much for creating it! I hope to see it get further improvements in the future!