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cokelaer / bioservices

Access to Biological Web Services from Python.
http://bioservices.readthedocs.io
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Error in bioservices/uniprot.py #254

Open chagas98 opened 1 year ago

chagas98 commented 1 year ago

I got an error from bioservices when it was running the cazy_webscraper application. I opened an issue there. 

File "/usr/local/lib/python3.10/dist-packages/bioservices/uniprot.py", line 744, in search
    batch = batch.split("\n")[1:]
AttributeError: 'int' object has no attribute 'split'`

The error arose when I tried to get some data from UniProt. It seems that batch = self.services.http_get(link, frmt="txt") returns an integer instead of a string. When I forced the process with str(batch), I got a warning message, but I could have access to the data. 

 WARNING [bioservices.UniProt:596]:  status is not ok with Forbidden

However, it was not a good practice, which led me to come and check this issue. Any thoughts?

Thanks in advance.

cokelaer commented 1 year ago

If an integer is returned, it may be the error code from the web service itself (e.g. 404). I should add a try/except but meanwhile, I believe, you may do it in your code instead of str(batch) since str(batch) will work (if your output is the error code 404). Maybe the service was down when you try, or you request is wrong. Could you provide a working exmaple ? thanks