jonasfreimuth
commented
1 week ago Since I checked in and saw that #77 has been merged, I checked if this is fixed now, but it doesn't quite seem to be the case. Running the above example on the current version produced the following error:
Python 3.10.7 (main, Jan 1 1970, 00:00:01) [GCC 11.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import GEOparse as gp
>>> gp.get_GEO("GSE108587")
23-Aug-2024 20:01:43 DEBUG utils - Directory ./ already exists. Skipping.
23-Aug-2024 20:01:43 INFO GEOparse - Downloading ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108587/soft/GSE108587_family.soft.gz to ./GSE108587_family.soft.gz
23-Aug-2024 20:01:44 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 "/home/jonas/proj/geoparse-temp/.venv/lib/python3.10/site-packages/GEOparse/downloader.py", line 150, in _download_ftp
ftp_size = ftp.size(parsed_url.path)
File "/gnu/store/1w5v338qk5m8khcazwclprs3znqp6f7f-python-3.10.7/lib/python3.10/ftplib.py", line 630, in size
resp = self.sendcmd('SIZE ' + filename)
File "/gnu/store/1w5v338qk5m8khcazwclprs3znqp6f7f-python-3.10.7/lib/python3.10/ftplib.py", line 281, in sendcmd
return self.getresp()
File "/gnu/store/1w5v338qk5m8khcazwclprs3znqp6f7f-python-3.10.7/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
23-Aug-2024 20:01:44 DEBUG downloader - Moving /tmp/tmpw8ka7_9d to /home/jonas/proj/geoparse-temp/GSE108587_family.soft.gz
Traceback (most recent call last):
File "/home/jonas/proj/geoparse-temp/.venv/lib/python3.10/site-packages/GEOparse/utils.py", line 80, in download_from_url
fn.download(silent=silent, force=force)
File "/home/jonas/proj/geoparse-temp/.venv/lib/python3.10/site-packages/GEOparse/downloader.py", line 82, in download
_download()
File "/home/jonas/proj/geoparse-temp/.venv/lib/python3.10/site-packages/GEOparse/downloader.py", line 57, in _download
shutil.copyfile(self._temp_file_name, self.destination)
File "/gnu/store/1w5v338qk5m8khcazwclprs3znqp6f7f-python-3.10.7/lib/python3.10/shutil.py", line 254, in copyfile
with open(src, 'rb') as fsrc:
FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmpw8ka7_9d'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/jonas/proj/geoparse-temp/.venv/lib/python3.10/site-packages/GEOparse/GEOparse.py", line 96, in get_GEO
filepath, geotype = get_GEO_file(
File "/home/jonas/proj/geoparse-temp/.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 "/home/jonas/proj/geoparse-temp/.venv/lib/python3.10/site-packages/GEOparse/utils.py", line 82, in download_from_url
raise IOError(
OSError: Download failed due to '[Errno 2] No such file or directory: '/tmp/tmpw8ka7_9d''. ID could be incorrect or the data might not be public yet.It seems the Error 550 would need to explicitly be handled somethwere to properly address this. Again, this results in an error in any case, but the error message is still a bit misleading.
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
venvwith just GEOparse 2.0.3 and its dependencies installed.)I get the following output:
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!