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guma44 / GEOparse

Python library to access Gene Expression Omnibus Database (GEO)
BSD 3-Clause "New" or "Revised" License
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Missing File Error when GEO is Down #51

Open Miserlou opened 5 years ago

Miserlou commented 5 years ago

When NCBI/GEO is down, I'd expect a custom exception or some kind of graceful handling, instead you get:

  File "/home/user/data_refinery_foreman/surveyor/geo.py", line 222, in create_experiment_and_samples_from_api
    gse = GEOparse.get_GEO(experiment_accession_code, destdir=self.get_temp_path(), how="brief", silent=True)
  File "/usr/local/lib/python3.5/dist-packages/GEOparse/GEOparse.py", line 84, in get_GEO
    return parse_GSE(filepath)
  File "/usr/local/lib/python3.5/dist-packages/GEOparse/GEOparse.py", line 502, in parse_GSE
    with utils.smart_open(filepath) as soft:
  File "/usr/lib/python3.5/contextlib.py", line 59, in __enter__
    return next(self.gen)
  File "/usr/local/lib/python3.5/dist-packages/GEOparse/utils.py", line 156, in smart_open
    fh = fopen(filepath, mode, errors="ignore")
  File "/usr/lib/python3.5/gzip.py", line 53, in open
    binary_file = GzipFile(filename, gz_mode, compresslevel)
  File "/usr/lib/python3.5/gzip.py", line 163, in __init__
    fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/tmp/1/GSE11915_family.soft.gz'

which looks like it's a local disk error, which it isn't, it's a GEO-is-down-error.

guma44 commented 5 years ago

Hi, thanks for pointing this out. I never had this issue but you are right. It should be checked for timeout or any other http error and the exception should tell it.